Web-based decision support and visualization tools for water quality management in the Chesapeake Bay watershed

USGS Publications Warehouse

Mullinix, C.; Hearn, P.; Zhang, H.; Aguinaldo, J.

2009-01-01

Federal, State, and local water quality managers charged with restoring the Chesapeake Bay ecosystem require tools to maximize the impact of their limited resources. To address this need, the U.S. Geological Survey (USGS) and the Environmental Protection Agency's Chesapeake Bay Program (CBP) are developing a suite of Web-based tools called the Chesapeake Online Assessment Support Toolkit (COAST). The goal of COAST is to help CBP partners identify geographic areas where restoration activities would have the greatest effect, select the appropriate management strategies, and improve coordination and prioritization among partners. As part of the COAST suite of tools focused on environmental restoration, a water quality management visualization component called the Nutrient Yields Mapper (NYM) tool is being developed by USGS. The NYM tool is a web application that uses watershed yield estimates from USGS SPAtially Referenced Regressions On Watershed (SPARROW) attributes model (Schwarz et al., 2006) [6] to allow water quality managers to identify important sources of nitrogen and phosphorous within the Chesapeake Bay watershed. The NYM tool utilizes new open source technologies that have become popular in geospatial web development, including components such as OpenLayers and GeoServer. This paper presents examples of water quality data analysis based on nutrient type, source, yield, and area of interest using the NYM tool for the Chesapeake Bay watershed. In addition, we describe examples of map-based techniques for identifying high and low nutrient yield areas; web map engines; and data visualization and data management techniques.

A web platform for integrated surface water - groundwater modeling and data management

NASA Astrophysics Data System (ADS)

Fatkhutdinov, Aybulat; Stefan, Catalin; Junghanns, Ralf

2016-04-01

Model-based decision support systems are considered to be reliable and time-efficient tools for resources management in various hydrology related fields. However, searching and acquisition of the required data, preparation of the data sets for simulations as well as post-processing, visualization and publishing of the simulations results often requires significantly more work and time than performing the modeling itself. The purpose of the developed software is to combine data storage facilities, data processing instruments and modeling tools in a single platform which potentially can reduce time required for performing simulations, hence decision making. The system is developed within the INOWAS (Innovative Web Based Decision Support System for Water Sustainability under a Changing Climate) project. The platform integrates spatially distributed catchment scale rainfall - runoff, infiltration and groundwater flow models with data storage, processing and visualization tools. The concept is implemented in a form of a web-GIS application and is build based on free and open source components, including the PostgreSQL database management system, Python programming language for modeling purposes, Mapserver for visualization and publishing the data, Openlayers for building the user interface and others. Configuration of the system allows performing data input, storage, pre- and post-processing and visualization in a single not disturbed workflow. In addition, realization of the decision support system in the form of a web service provides an opportunity to easily retrieve and share data sets as well as results of simulations over the internet, which gives significant advantages for collaborative work on the projects and is able to significantly increase usability of the decision support system.

Design and implementation of a risk assessment module in a spatial decision support system

NASA Astrophysics Data System (ADS)

Zhang, Kaixi; van Westen, Cees; Bakker, Wim

2014-05-01

The spatial decision support system named 'Changes SDSS' is currently under development. The goal of this system is to analyze changing hydro-meteorological hazards and the effect of risk reduction alternatives to support decision makers in choosing the best alternatives. The risk assessment module within the system is to assess the current risk, analyze the risk after implementations of risk reduction alternatives, and analyze the risk in different future years when considering scenarios such as climate change, land use change and population growth. The objective of this work is to present the detailed design and implementation plan of the risk assessment module. The main challenges faced consist of how to shift the risk assessment from traditional desktop software to an open source web-based platform, the availability of input data and the inclusion of uncertainties in the risk analysis. The risk assessment module is developed using Ext JS library for the implementation of user interface on the client side, using Python for scripting, as well as PostGIS spatial functions for complex computations on the server side. The comprehensive consideration of the underlying uncertainties in input data can lead to a better quantification of risk assessment and a more reliable Changes SDSS, since the outputs of risk assessment module are the basis for decision making module within the system. The implementation of this module will contribute to the development of open source web-based modules for multi-hazard risk assessment in the future. This work is part of the "CHANGES SDSS" project, funded by the European Community's 7th Framework Program.

A Lifecycle Approach to Brokered Data Management for Hydrologic Modeling Data Using Open Standards.

NASA Astrophysics Data System (ADS)

Blodgett, D. L.; Booth, N.; Kunicki, T.; Walker, J.

2012-12-01

The U.S. Geological Survey Center for Integrated Data Analytics has formalized an information management-architecture to facilitate hydrologic modeling and subsequent decision support throughout a project's lifecycle. The architecture is based on open standards and open source software to decrease the adoption barrier and to build on existing, community supported software. The components of this system have been developed and evaluated to support data management activities of the interagency Great Lakes Restoration Initiative, Department of Interior's Climate Science Centers and WaterSmart National Water Census. Much of the research and development of this system has been in cooperation with international interoperability experiments conducted within the Open Geospatial Consortium. Community-developed standards and software, implemented to meet the unique requirements of specific disciplines, are used as a system of interoperable, discipline specific, data types and interfaces. This approach has allowed adoption of existing software that satisfies the majority of system requirements. Four major features of the system include: 1) assistance in model parameter and forcing creation from large enterprise data sources; 2) conversion of model results and calibrated parameters to standard formats, making them available via standard web services; 3) tracking a model's processes, inputs, and outputs as a cohesive metadata record, allowing provenance tracking via reference to web services; and 4) generalized decision support tools which rely on a suite of standard data types and interfaces, rather than particular manually curated model-derived datasets. Recent progress made in data and web service standards related to sensor and/or model derived station time series, dynamic web processing, and metadata management are central to this system's function and will be presented briefly along with a functional overview of the applications that make up the system. As the separate pieces of this system progress, they will be combined and generalized to form a sort of social network for nationally consistent hydrologic modeling.

Web-based GIS for spatial pattern detection: application to malaria incidence in Vietnam.

PubMed

Bui, Thanh Quang; Pham, Hai Minh

2016-01-01

There is a great concern on how to build up an interoperable health information system of public health and health information technology within the development of public information and health surveillance programme. Technically, some major issues remain regarding to health data visualization, spatial processing of health data, health information dissemination, data sharing and the access of local communities to health information. In combination with GIS, we propose a technical framework for web-based health data visualization and spatial analysis. Data was collected from open map-servers and geocoded by open data kit package and data geocoding tools. The Web-based system is designed based on Open-source frameworks and libraries. The system provides Web-based analyst tool for pattern detection through three spatial tests: Nearest neighbour, K function, and Spatial Autocorrelation. The result is a web-based GIS, through which end users can detect disease patterns via selecting area, spatial test parameters and contribute to managers and decision makers. The end users can be health practitioners, educators, local communities, health sector authorities and decision makers. This web-based system allows for the improvement of health related services to public sector users as well as citizens in a secure manner. The combination of spatial statistics and web-based GIS can be a solution that helps empower health practitioners in direct and specific intersectional actions, thus provide for better analysis, control and decision-making.

Design and Implementation WebGIS for Improving the Quality of Exploration Decisions at Sin-Quyen Copper Mine, Northern Vietnam

NASA Astrophysics Data System (ADS)

Quang Truong, Xuan; Luan Truong, Xuan; Nguyen, Tuan Anh; Nguyen, Dinh Tuan; Cong Nguyen, Chi

2017-12-01

The objective of this study is to design and implement a WebGIS Decision Support System (WDSS) for reducing uncertainty and supporting to improve the quality of exploration decisions in the Sin-Quyen copper mine, northern Vietnam. The main distinctive feature of the Sin-Quyen deposit is an unusual composition of ores. Computer and software applied to the exploration problem have had a significant impact on the exploration process over the past 25 years, but up until now, no online system has been undertaken. The system was completely built on open source technology and the Open Geospatial Consortium Web Services (OWS). The input data includes remote sensing (RS), Geographical Information System (GIS) and data from drillhole explorations, the drillhole exploration data sets were designed as a geodatabase and stored in PostgreSQL. The WDSS must be able to processed exploration data and support users to access 2-dimensional (2D) or 3-dimensional (3D) cross-sections and map of boreholles exploration data and drill holes. The interface was designed in order to interact with based maps (e.g., Digital Elevation Model, Google Map, OpenStreetMap) and thematic maps (e.g., land use and land cover, administrative map, drillholes exploration map), and to provide GIS functions (such as creating a new map, updating an existing map, querying and statistical charts). In addition, the system provides geological cross-sections of ore bodies based on Inverse Distance Weighting (IDW), nearest neighbour interpolation and Kriging methods (e.g., Simple Kriging, Ordinary Kriging, Indicator Kriging and CoKriging). The results based on data available indicate that the best estimation method (of 23 borehole exploration data sets) for estimating geological cross-sections of ore bodies in Sin-Quyen copper mine is Ordinary Kriging. The WDSS could provide useful information to improve drilling efficiency in mineral exploration and for management decision making.

Managing multicentre clinical trials with open source.

PubMed

Raptis, Dimitri Aristotle; Mettler, Tobias; Fischer, Michael Alexander; Patak, Michael; Lesurtel, Mickael; Eshmuminov, Dilmurodjon; de Rougemont, Olivier; Graf, Rolf; Clavien, Pierre-Alain; Breitenstein, Stefan

2014-03-01

Multicentre clinical trials are challenged by high administrative burden, data management pitfalls and costs. This leads to a reduced enthusiasm and commitment of the physicians involved and thus to a reluctance in conducting multicentre clinical trials. The purpose of this study was to develop a web-based open source platform to support a multi-centre clinical trial. We developed on Drupal, an open source software distributed under the terms of the General Public License, a web-based, multi-centre clinical trial management system with the design science research approach. This system was evaluated by user-testing and well supported several completed and on-going clinical trials and is available for free download. Open source clinical trial management systems are capable in supporting multi-centre clinical trials by enhancing efficiency, quality of data management and collaboration.

Weather forecasting with open source software

NASA Astrophysics Data System (ADS)

Rautenhaus, Marc; Dörnbrack, Andreas

2013-04-01

To forecast the weather situation during aircraft-based atmospheric field campaigns, we employ a tool chain of existing and self-developed open source software tools and open standards. Of particular value are the Python programming language with its extension libraries NumPy, SciPy, PyQt4, Matplotlib and the basemap toolkit, the NetCDF standard with the Climate and Forecast (CF) Metadata conventions, and the Open Geospatial Consortium Web Map Service standard. These open source libraries and open standards helped to implement the "Mission Support System", a Web Map Service based tool to support weather forecasting and flight planning during field campaigns. The tool has been implemented in Python and has also been released as open source (Rautenhaus et al., Geosci. Model Dev., 5, 55-71, 2012). In this presentation we discuss the usage of free and open source software for weather forecasting in the context of research flight planning, and highlight how the field campaign work benefits from using open source tools and open standards.

A Web-Based Earth-Systems Knowledge Portal and Collaboration Platform

NASA Astrophysics Data System (ADS)

D'Agnese, F. A.; Turner, A. K.

2010-12-01

In support of complex water-resource sustainability projects in the Great Basin region of the United States, Earth Knowledge, Inc. has developed several web-based data management and analysis platforms that have been used by its scientists, clients, and public to facilitate information exchanges, collaborations, and decision making. These platforms support accurate water-resource decision-making by combining second-generation internet (Web 2.0) technologies with traditional 2D GIS and web-based 2D and 3D mapping systems such as Google Maps, and Google Earth. Most data management and analysis systems use traditional software systems to address the data needs and usage behavior of the scientific community. In contrast, these platforms employ more accessible open-source and “off-the-shelf” consumer-oriented, hosted web-services. They exploit familiar software tools using industry standard protocols, formats, and APIs to discover, process, fuse, and visualize earth, engineering, and social science datasets. Thus, they respond to the information needs and web-interface expectations of both subject-matter experts and the public. Because the platforms continue to gather and store all the contributions of their broad-spectrum of users, each new assessment leverages the data, information, and expertise derived from previous investigations. In the last year, Earth Knowledge completed a conceptual system design and feasibility study for a platform, which has a Knowledge Portal providing access to users wishing to retrieve information or knowledge developed by the science enterprise and a Collaboration Environment Module, a framework that links the user-access functions to a Technical Core supporting technical and scientific analyses including Data Management, Analysis and Modeling, and Decision Management, and to essential system administrative functions within an Administrative Module. The over-riding technical challenge is the design and development of a single technical platform that is accessed through a flexible series of knowledge portal and collaboration environment styles reflecting the information needs and user expectations of a diverse community of users. Recent investigations have defined the information needs and expectations of the major end-users and also have reviewed and assessed a wide variety of modern web-based technologies. Combining these efforts produced design specifications and recommendations for the selection and integration of web- and client-based tools. When fully developed, the resulting platform will: -Support new, advanced information systems and decision environments that take full advantage of multiple data sources and platforms; -Provide a distribution network tailored to the timely delivery of products to a broad range of users that are needed to support applications in disaster management, resource management, energy, and urban sustainability; -Establish new integrated multiple-user requirements and knowledge databases that support researchers and promote infusion of successful technologies into existing processes; and -Develop new decision support strategies and presentation methodologies for applied earth science applications to reduce risk, cost, and time.

Tethys: A Platform for Water Resources Modeling and Decision Support Apps

NASA Astrophysics Data System (ADS)

Nelson, J.; Swain, N. R.

2015-12-01

The interactive nature of web applications or "web apps" makes it an excellent medium for conveying complex scientific concepts to lay audiences and creating decision support tools that harness cutting edge modeling techniques. However, the technical expertise required to develop web apps represents a barrier for would-be developers. This barrier can be characterized by the following hurdles that developers must overcome: (1) identify, select, and install software that meet the spatial and computational capabilities commonly required for water resources modeling; (2) orchestrate the use of multiple free and open source (FOSS) projects and navigate their differing application programming interfaces; (3) learn the multi-language programming skills required for modern web development; and (4) develop a web-secure and fully featured web portal to host the app. Tethys Platform has been developed to lower the technical barrier and minimize the initial development investment that prohibits many scientists and engineers from making use of the web app medium. It includes (1) a suite of FOSS that address the unique data and computational needs common to water resources web app development, (2) a Python software development kit that streamlines development, and (3) a customizable web portal that is used to deploy the completed web apps. Tethys synthesizes several software projects including PostGIS, 52°North WPS, GeoServer, Google Maps™, OpenLayers, and Highcharts. It has been used to develop a broad array of web apps for water resources modeling and decision support for several projects including CI-WATER, HydroShare, and the National Flood Interoperability Experiment. The presentation will include live demos of some of the apps that have been developed using Tethys to demonstrate its capabilities.

Urban Climate Resilience - Connecting climate models with decision support cyberinfrastructure using open standards

NASA Astrophysics Data System (ADS)

Bermudez, L. E.; Percivall, G.; Idol, T. A.

2015-12-01

Experts in climate modeling, remote sensing of the Earth, and cyber infrastructure must work together in order to make climate predictions available to decision makers. Such experts and decision makers worked together in the Open Geospatial Consortium's (OGC) Testbed 11 to address a scenario of population displacement by coastal inundation due to the predicted sea level rise. In a Policy Fact Sheet "Harnessing Climate Data to Boost Ecosystem & Water Resilience", issued by White House Office of Science and Technology (OSTP) in December 2014, OGC committed to increase access to climate change information using open standards. In July 2015, the OGC Testbed 11 Urban Climate Resilience activity delivered on that commitment with open standards based support for climate-change preparedness. Using open standards such as the OGC Web Coverage Service and Web Processing Service and the NetCDF and GMLJP2 encoding standards, Testbed 11 deployed an interoperable high-resolution flood model to bring climate model outputs together with global change assessment models and other remote sensing data for decision support. Methods to confirm model predictions and to allow "what-if-scenarios" included in-situ sensor webs and crowdsourcing. A scenario was in two locations: San Francisco Bay Area and Mozambique. The scenarios demonstrated interoperation and capabilities of open geospatial specifications in supporting data services and processing services. The resultant High Resolution Flood Information System addressed access and control of simulation models and high-resolution data in an open, worldwide, collaborative Web environment. The scenarios examined the feasibility and capability of existing OGC geospatial Web service specifications in supporting the on-demand, dynamic serving of flood information from models with forecasting capacity. Results of this testbed included identification of standards and best practices that help researchers and cities deal with climate-related issues. Results of the testbeds will now be deployed in pilot applications. The testbed also identified areas of additional development needed to help identify scientific investments and cyberinfrastructure approaches needed to improve the application of climate science research results to urban climate resilence.

Development of a spatial decision support system for flood risk management in Brazil that combines volunteered geographic information with wireless sensor networks

NASA Astrophysics Data System (ADS)

Horita, Flávio E. A.; Albuquerque, João Porto de; Degrossi, Lívia C.; Mendiondo, Eduardo M.; Ueyama, Jó

2015-07-01

Effective flood risk management requires updated information to ensure that the correct decisions can be made. This can be provided by Wireless Sensor Networks (WSN) which are a low-cost means of collecting updated information about rivers. Another valuable resource is Volunteered Geographic Information (VGI) which is a comparatively new means of improving the coverage of monitored areas because it is able to supply supplementary information to the WSN and thus support decision-making in flood risk management. However, there still remains the problem of how to combine WSN data with VGI. In this paper, an attempt is made to investigate AGORA-DS, which is a Spatial Decision Support System (SDSS) that is able to make flood risk management more effective by combining these data sources, i.e. WSN with VGI. This approach is built over a conceptual model that complies with the interoperable standards laid down by the Open Geospatial Consortium (OGC) - e.g. Sensor Observation Service (SOS) and Web Feature Service (WFS) - and seeks to combine and present unified information in a web-based decision support tool. This work was deployed in a real scenario of flood risk management in the town of São Carlos in Brazil. The evidence obtained from this deployment confirmed that interoperable standards can support the integration of data from distinct data sources. In addition, they also show that VGI is able to provide information about areas of the river basin which lack data since there is no appropriate station in the area. Hence it provides a valuable support for the WSN data. It can thus be concluded that AGORA-DS is able to combine information provided by WSN and VGI, and provide useful information for supporting flood risk management.

Building Geospatial Web Services for Ecological Monitoring and Forecasting

NASA Astrophysics Data System (ADS)

Hiatt, S. H.; Hashimoto, H.; Melton, F. S.; Michaelis, A. R.; Milesi, C.; Nemani, R. R.; Wang, W.

2008-12-01

The Terrestrial Observation and Prediction System (TOPS) at NASA Ames Research Center is a modeling system that generates a suite of gridded data products in near real-time that are designed to enhance management decisions related to floods, droughts, forest fires, human health, as well as crop, range, and forest production. While these data products introduce great possibilities for assisting management decisions and informing further research, realization of their full potential is complicated by their shear volume and by the need for a necessary infrastructure for remotely browsing, visualizing, and analyzing the data. In order to address these difficulties we have built an OGC-compliant WMS and WCS server based on an open source software stack that provides standardized access to our archive of data. This server is built using the open source Java library GeoTools which achieves efficient I/O and image rendering through Java Advanced Imaging. We developed spatio-temporal raster management capabilities using the PostGrid raster indexation engine. We provide visualization and browsing capabilities through a customized Ajax web interface derived from the kaMap project. This interface allows resource managers to quickly assess ecosystem conditions and identify significant trends and anomalies from within their web browser without the need to download source data or install special software. Our standardized web services also expose TOPS data to a range of potential clients, from web mapping applications to virtual globes and desktop GIS packages. However, support for managing the temporal dimension of our data is currently limited in existing software systems. Future work will attempt to overcome this shortcoming by building time-series visualization and analysis tools that can be integrated with existing geospatial software.

OpenFlyData: an exemplar data web integrating gene expression data on the fruit fly Drosophila melanogaster.

PubMed

Miles, Alistair; Zhao, Jun; Klyne, Graham; White-Cooper, Helen; Shotton, David

2010-10-01

Integrating heterogeneous data across distributed sources is a major requirement for in silico bioinformatics supporting translational research. For example, genome-scale data on patterns of gene expression in the fruit fly Drosophila melanogaster are widely used in functional genomic studies in many organisms to inform candidate gene selection and validate experimental results. However, current data integration solutions tend to be heavy weight, and require significant initial and ongoing investment of effort. Development of a common Web-based data integration infrastructure (a.k.a. data web), using Semantic Web standards, promises to alleviate these difficulties, but little is known about the feasibility, costs, risks or practical means of migrating to such an infrastructure. We describe the development of OpenFlyData, a proof-of-concept system integrating gene expression data on D. melanogaster, combining Semantic Web standards with light-weight approaches to Web programming based on Web 2.0 design patterns. To support researchers designing and validating functional genomic studies, OpenFlyData includes user-facing search applications providing intuitive access to and comparison of gene expression data from FlyAtlas, the BDGP in situ database, and FlyTED, using data from FlyBase to expand and disambiguate gene names. OpenFlyData's services are also openly accessible, and are available for reuse by other bioinformaticians and application developers. Semi-automated methods and tools were developed to support labour- and knowledge-intensive tasks involved in deploying SPARQL services. These include methods for generating ontologies and relational-to-RDF mappings for relational databases, which we illustrate using the FlyBase Chado database schema; and methods for mapping gene identifiers between databases. The advantages of using Semantic Web standards for biomedical data integration are discussed, as are open issues. In particular, although the performance of open source SPARQL implementations is sufficient to query gene expression data directly from user-facing applications such as Web-based data fusions (a.k.a. mashups), we found open SPARQL endpoints to be vulnerable to denial-of-service-type problems, which must be mitigated to ensure reliability of services based on this standard. These results are relevant to data integration activities in translational bioinformatics. The gene expression search applications and SPARQL endpoints developed for OpenFlyData are deployed at http://openflydata.org. FlyUI, a library of JavaScript widgets providing re-usable user-interface components for Drosophila gene expression data, is available at http://flyui.googlecode.com. Software and ontologies to support transformation of data from FlyBase, FlyAtlas, BDGP and FlyTED to RDF are available at http://openflydata.googlecode.com. SPARQLite, an implementation of the SPARQL protocol, is available at http://sparqlite.googlecode.com. All software is provided under the GPL version 3 open source license.

Implementation of Open-Source Web Mapping Technologies to Support Monitoring of Governmental Schemes

NASA Astrophysics Data System (ADS)

Pulsani, B. R.

2015-10-01

Several schemes are undertaken by the government to uplift social and economic condition of people. The monitoring of these schemes is done through information technology where involvement of Geographic Information System (GIS) is lacking. To demonstrate the benefits of thematic mapping as a tool for assisting the officials in making decisions, a web mapping application for three government programs such as Mother and Child Tracking system (MCTS), Telangana State Housing Corporation Limited (TSHCL) and Ground Water Quality Mapping (GWQM) has been built. Indeed the three applications depicted the distribution of various parameters thematically and helped in identifying the areas with higher and weaker distributions. Based on the three applications, the study tends to find similarities of many government schemes reflecting the nature of thematic mapping and hence deduces to implement this kind of approach for other schemes as well. These applications have been developed using SharpMap Csharp library which is a free and open source mapping library for developing geospatial applications. The study highlights upon the cost benefits of SharpMap and brings out the advantage of this library over proprietary vendors and further discusses its advantages over other open source libraries as well.

ISTIMES Integrated System for Transport Infrastructures Surveillance and Monitoring by Electromagnetic Sensing

NASA Astrophysics Data System (ADS)

Argenti, M.; Giannini, V.; Averty, R.; Bigagli, L.; Dumoulin, J.

2012-04-01

The EC FP7 ISTIMES project has the goal of realizing an ICT-based system exploiting distributed and local sensors for non destructive electromagnetic monitoring in order to make critical transport infrastructures more reliable and safe. Higher situation awareness thanks to real time and detailed information and images of the controlled infrastructure status allows improving decision capabilities for emergency management stakeholders. Web-enabled sensors and a service-oriented approach are used as core of the architecture providing a sys-tem that adopts open standards (e.g. OGC SWE, OGC CSW etc.) and makes efforts to achieve full interoperability with other GMES and European Spatial Data Infrastructure initiatives as well as compliance with INSPIRE. The system exploits an open easily scalable network architecture to accommodate a wide range of sensors integrated with a set of tools for handling, analyzing and processing large data volumes from different organizations with different data models. Situation Awareness tools are also integrated in the system. Definition of sensor observations and services follows a metadata model based on the ISO 19115 Core set of metadata elements and the O&M model of OGC SWE. The ISTIMES infrastructure is based on an e-Infrastructure for geospatial data sharing, with a Data Cata-log that implements the discovery services for sensor data retrieval, acting as a broker through static connections based on standard SOS and WNS interfaces; a Decision Support component which helps decision makers providing support for data fusion and inference and generation of situation indexes; a Presentation component which implements system-users interaction services for information publication and rendering, by means of a WEB Portal using SOA design principles; A security framework using Shibboleth open source middleware based on the Security Assertion Markup Language supporting Single Sign On (SSO). ACKNOWLEDGEMENT - The research leading to these results has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under Grant Agreement n° 225663

Open Source and Open Standard based decision support system: the example of lake Verbano floods management.

NASA Astrophysics Data System (ADS)

Cannata, Massimiliano; Antonovic, Milan; Pozzoni, Maurizio; Graf, Andrea

2015-04-01

The Locarno area (Switzerland, Canton Ticino) is exposed to lacual floods with a return period of about 7-8 years. The risk is of particular concern because the area is located in a floodplain that registered in the last decades a great increase in settlement and values of the real estates. Moreover small differences in lake altitude may produce a significant increase in flooded area due to the very low average slope of the terrain. While fatalities are not generally registered, several important economic costs are associated, e.g.: damages to real estates, interruption of activities, evacuation and relocation and environmental damages. While important events were registered in 1978, 1993, 2000, 2002 and 2014 the local stakeholder invested time and money in the set-up of an up-to-date decision support system that allows for the reduction of risks. Thanks to impressive technological advances the visionary concept of the Digital Earth (Gore 1992, 1998) is being realizing: geospatial coverages and monitoring systems data are increasingly available on the Web, and more importantly, in a standard format. As a result, today is possible to develop innovative decision support systems (Molinari et al. 2013) which mesh-up several information sources and offers special features for risk scenarios evaluation. In agreement with the exposed view, the authors have recently developed a new Web system whose design is based on the Service Oriented Architecture pattern. Open source software (e.g.: Geoserver, PostGIS, OpenLayers) has been used throughout the whole system and geospatial Open Standards (e.g.: SOS, WMS, WFS) are the pillars it rely on. SITGAP 2.0, implemented in collaboration with the Civil protection of Locarno e Vallemaggia, combines a number of data sources such as the Federal Register of Buildings and Dwellings, the Cantonal Register of residents, the Cadastral Surveying, the Cantonal Hydro-meteorological monitoring observations, the Meteoswiss weather forecasts, and others. As a result of this orchestration of data, SITGAP 2.0 serves features that allows, for example, to be informed on active alarms, to visualize lake level forecasts and associated flooding areas, to evaluate and map exposed elements and people, to plan and manage evacuation by searching for people living in particular areas or buildings, by registering evacuation actions and by searching for evacuated people. System architecture and functionalities, and consideration on the integration and accessibility of the beneath information together with the lesson learnt during the usage of the system during the last floods of November 2014, provides interesting discussion points for the identification of current and future needs.

Evaluating the Effectiveness of Web-based Climate Resilience Decision Support Tools: Insights from Coastal New Jersey

NASA Astrophysics Data System (ADS)

Brady, M.; Lathrop, R.; Auermuller, L. M.; Leichenko, R.

2016-12-01

Despite the recent surge of Web-based decision support tools designed to promote resiliency in U.S. coastal communities, to-date there has been no systematic study of their effectiveness. This study demonstrates a method to evaluate important aspects of effectiveness of four Web map tools designed to promote consideration of climate risk information in local decision-making and planning used in coastal New Jersey. In summer 2015, the research team conducted in-depth phone interviews with users of one regulatory and three non-regulatory Web map tools using a semi-structured questionnaire. The interview and analysis design drew from a combination of effectiveness evaluation approaches developed in software and information usability, program evaluation, and management information system (MIS) research. Effectiveness assessment results were further analyzed and discussed in terms of conceptual hierarchy of system objectives defined by respective tool developer and user organizations represented in the study. Insights from the interviews suggest that users rely on Web tools as a supplement to desktop and analog map sources because they provide relevant and up-to-date information in a highly accessible and mobile format. The users also reported relying on multiple information sources and comparison between digital and analog sources for decision support. However, with respect to this decision support benefit, users were constrained by accessibility factors such as lack of awareness and training with some tools, lack of salient information such as planning time horizons associated with future flood scenarios, and environmental factors such as mandates restricting some users to regulatory tools. Perceptions of Web tool credibility seem favorable overall, but factors including system design imperfections and inconsistencies in data and information across platforms limited trust, highlighting a need for better coordination between tools. Contributions of the study include user feedback on web-tool system designs consistent with collaborative methods for enhancing usability and a systematic look at effectiveness that includes both user perspectives and consideration of developer and organizational objectives.

Integrating Socioeconomic and Earth Science Data Using Geobrowsers and Web Services: A Demonstration

NASA Astrophysics Data System (ADS)

Schumacher, J. A.; Yetman, G. G.

2007-12-01

The societal benefit areas identified as the focus for the Global Earth Observing System of Systems (GEOSS) 10- year implementation plan are an indicator of the importance of integrating socioeconomic data with earth science data to support decision makers. To aid this integration, CIESIN is delivering its global and U.S. demographic data to commercial and open source Geobrowsers and providing open standards based services for data access. Currently, data on population distribution, poverty, and detailed census data for the U.S. are available for visualization and access in Google Earth, NASA World Wind, and a browser-based 2-dimensional mapping client. The mapping client allows for the creation of web map documents that pull together layers from distributed servers and can be saved and shared. Visualization tools with Geobrowsers, user-driven map creation and sharing via browser-based clients, and a prototype for characterizing populations at risk to predicted precipitation deficits will be demonstrated.

Development of a web application for water resources based on open source software

NASA Astrophysics Data System (ADS)

Delipetrev, Blagoj; Jonoski, Andreja; Solomatine, Dimitri P.

2014-01-01

This article presents research and development of a prototype web application for water resources using latest advancements in Information and Communication Technologies (ICT), open source software and web GIS. The web application has three web services for: (1) managing, presenting and storing of geospatial data, (2) support of water resources modeling and (3) water resources optimization. The web application is developed using several programming languages (PhP, Ajax, JavaScript, Java), libraries (OpenLayers, JQuery) and open source software components (GeoServer, PostgreSQL, PostGIS). The presented web application has several main advantages: it is available all the time, it is accessible from everywhere, it creates a real time multi-user collaboration platform, the programing languages code and components are interoperable and designed to work in a distributed computer environment, it is flexible for adding additional components and services and, it is scalable depending on the workload. The application was successfully tested on a case study with concurrent multi-users access.

A Walk through TRIDEC's intermediate Tsunami Early Warning System

NASA Astrophysics Data System (ADS)

Hammitzsch, M.; Reißland, S.; Lendholt, M.

2012-04-01

The management of natural crises is an important application field of the technology developed in the project Collaborative, Complex, and Critical Decision-Support in Evolving Crises (TRIDEC), co-funded by the European Commission in its Seventh Framework Programme. TRIDEC is based on the development of the German Indonesian Tsunami Early Warning System (GITEWS) and the Distant Early Warning System (DEWS) providing a service platform for both sensor integration and warning dissemination. In TRIDEC new developments in Information and Communication Technology (ICT) are used to extend the existing platform realising a component-based technology framework for building distributed tsunami warning systems for deployment, e.g. in the North-eastern Atlantic, the Mediterranean and Connected Seas (NEAM) region. The TRIDEC system will be implemented in three phases, each with a demonstrator. Successively, the demonstrators are addressing challenges, such as the design and implementation of a robust and scalable service infrastructure supporting the integration and utilisation of existing resources with accelerated generation of large volumes of data. These include sensor systems, geo-information repositories, simulation tools and data fusion tools. In addition to conventional sensors also unconventional sensors and sensor networks play an important role in TRIDEC. The system version presented is based on service-oriented architecture (SOA) concepts and on relevant standards of the Open Geospatial Consortium (OGC), the World Wide Web Consortium (W3C) and the Organization for the Advancement of Structured Information Standards (OASIS). In this way the system continuously gathers, processes and displays events and data coming from open sensor platforms to enable operators to quickly decide whether an early warning is necessary and to send personalized warning messages to the authorities and the population at large through a wide range of communication channels. The system integrates OGC Sensor Web Enablement (SWE) compliant sensor systems for the rapid detection of hazardous events, like earthquakes, sea level anomalies, ocean floor occurrences, and ground displacements. Using OGC Web Map Service (WMS) and Web Feature Service (WFS) spatial data are utilized to depict the situation picture. The integration of a simulation system to identify affected areas is considered using the OGC Web Processing Service (WPS). Warning messages are compiled and transmitted in the OASIS Common Alerting Protocol (CAP) together with addressing information defined via the OASIS Emergency Data Exchange Language - Distribution Element (EDXL-DE). The first system demonstrator has been designed and implemented to support plausible scenarios demonstrating the treatment of simulated tsunami threats with an essential subset of a National Tsunami Warning Centre (NTWC). The feasibility and the potentials of the implemented approach are demonstrated covering standard operations as well as tsunami detection and alerting functions. The demonstrator presented addresses information management and decision-support processes in a hypothetical natural crisis situation caused by a tsunami in the Eastern Mediterranean. Developments of the system are based to the largest extent on free and open source software (FOSS) components and industry standards. Emphasis has been and will be made on leveraging open source technologies that support mature system architecture models wherever appropriate. All open source software produced is foreseen to be published on a publicly available software repository thus allowing others to reuse results achieved and enabling further development and collaboration with a wide community including scientists, developers, users and stakeholders. This live demonstration is linked with the talk "TRIDEC Natural Crisis Management Demonstrator for Tsunamis" (EGU2012-7275) given in the session "Architecture of Future Tsunami Warning Systems" (NH5.7/ESSI1.7).

WebProtégé: a collaborative Web-based platform for editing biomedical ontologies.

PubMed

Horridge, Matthew; Tudorache, Tania; Nuylas, Csongor; Vendetti, Jennifer; Noy, Natalya F; Musen, Mark A

2014-08-15

WebProtégé is an open-source Web application for editing OWL 2 ontologies. It contains several features to aid collaboration, including support for the discussion of issues, change notification and revision-based change tracking. WebProtégé also features a simple user interface, which is geared towards editing the kinds of class descriptions and annotations that are prevalent throughout biomedical ontologies. Moreover, it is possible to configure the user interface using views that are optimized for editing Open Biomedical Ontology (OBO) class descriptions and metadata. Some of these views are shown in the Supplementary Material and can be seen in WebProtégé itself by configuring the project as an OBO project. WebProtégé is freely available for use on the Web at http://webprotege.stanford.edu. It is implemented in Java and JavaScript using the OWL API and the Google Web Toolkit. All major browsers are supported. For users who do not wish to host their ontologies on the Stanford servers, WebProtégé is available as a Web app that can be run locally using a Servlet container such as Tomcat. Binaries, source code and documentation are available under an open-source license at http://protegewiki.stanford.edu/wiki/WebProtege. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

WEB-GIS Decision Support System for CO2 storage

NASA Astrophysics Data System (ADS)

Gaitanaru, Dragos; Leonard, Anghel; Radu Gogu, Constantin; Le Guen, Yvi; Scradeanu, Daniel; Pagnejer, Mihaela

2013-04-01

Environmental decision support systems (DSS) paradigm evolves and changes as more knowledge and technology become available to the environmental community. Geographic Information Systems (GIS) can be used to extract, assess and disseminate some types of information, which are otherwise difficult to access by traditional methods. In the same time, with the help of the Internet and accompanying tools, creating and publishing online interactive maps has become easier and rich with options. The Decision Support System (MDSS) developed for the MUSTANG (A MUltiple Space and Time scale Approach for the quaNtification of deep saline formations for CO2 storaGe) project is a user friendly web based application that uses the GIS capabilities. MDSS can be exploited by the experts for CO2 injection and storage in deep saline aquifers. The main objective of the MDSS is to help the experts to take decisions based large structured types of data and information. In order to achieve this objective the MDSS has a geospatial objected-orientated database structure for a wide variety of data and information. The entire application is based on several principles leading to a series of capabilities and specific characteristics: (i) Open-Source - the entire platform (MDSS) is based on open-source technologies - (1) database engine, (2) application server, (3) geospatial server, (4) user interfaces, (5) add-ons, etc. (ii) Multiple database connections - MDSS is capable to connect to different databases that are located on different server machines. (iii)Desktop user experience - MDSS architecture and design follows the structure of a desktop software. (iv)Communication - the server side and the desktop are bound together by series functions that allows the user to upload, use, modify and download data within the application. The architecture of the system involves one database and a modular application composed by: (1) a visualization module, (2) an analysis module, (3) a guidelines module, and (4) a risk assessment module. The Database component is build by using the PostgreSQL and PostGIS open source technology. The visualization module allows the user to view data of CO2 injection sites in different ways: (1) geospatial visualization, (2) table view, (3) 3D visualization. The analysis module will allow the user to perform certain analysis like Injectivity, Containment and Capacity analysis. The Risk Assessment module focus on the site risk matrix approach. The Guidelines module contains the methodologies of CO2 injection and storage into deep saline aquifers guidelines.

Web-based Discussion Forums on Pregnancy Complaints and Maternal Health Literacy in Norway: A Qualitative Study.

PubMed

Fredriksen, Eva Haukeland; Harris, Janet; Moland, Karen Marie

2016-05-26

The Internet is one of the fastest growing information sources for pregnant women and seems to be used across social and economic strata. However, we still lack knowledge on how interaction in Web-based discussion forums influence maternal health literacy, in terms of how pregnant women access, appraise, and apply information to promote and maintain good health. The aim of this study was to understand how Web-based discussion forums influence maternal health literacy; hence, we explored the role of interactions in Web-based discussion forums among women who experienced health problems during pregnancy. More specifically, we explored why media-literate women experiencing the medically unexplained condition, pelvic girdle pain (PGP), during pregnancy participated in Web-based discussion forums and how they appraised and applied the information and advice that they gained from the Web-based interaction with other women. Women were invited to participate in the study via postings on 3 different open websites for pregnant women and mothers. The sample included 11 Norwegian women who participated in open Web-based discussion forums when experiencing PGP in pregnancy. The data were collected using synchronous qualitative email interviews and were analyzed using thematic analysis. In our study sample, interaction in Web-based discussion forums influenced maternal health literacy in terms of increased health-related knowledge and competencies, increased awareness of health promotion and health protection, and increased system navigation. The women appraised and selectively applied information and advice that resonated with their own experiences. For many, the information provided online by other women in the same situation was valued more highly than advice from health professionals. Women reported that they used their knowledge and competency in encounters with health professionals but hesitated to disclose the origin of their knowledge. Those with a high level of education in medicine-related fields raised a concern about the Internet as a source of horror stories and erroneous information and were actively engaged in trying to minimize potential negative effects, by providing biomedical information. The popularity of Web-based discussion forums among pregnant women suggests that this group needs additional sources of information and support to complement traditional consultations with the health professionals. The professionals need to recognize that pregnant women access Web-based discussion forums for support and information to increase their ability to take better health decisions for themselves. This is a potential resource that health professionals may find useful in consultations with pregnant women.

Web-based Discussion Forums on Pregnancy Complaints and Maternal Health Literacy in Norway: A Qualitative Study

PubMed Central

2016-01-01

Background The Internet is one of the fastest growing information sources for pregnant women and seems to be used across social and economic strata. However, we still lack knowledge on how interaction in Web-based discussion forums influence maternal health literacy, in terms of how pregnant women access, appraise, and apply information to promote and maintain good health. Objective The aim of this study was to understand how Web-based discussion forums influence maternal health literacy; hence, we explored the role of interactions in Web-based discussion forums among women who experienced health problems during pregnancy. More specifically, we explored why media-literate women experiencing the medically unexplained condition, pelvic girdle pain (PGP), during pregnancy participated in Web-based discussion forums and how they appraised and applied the information and advice that they gained from the Web-based interaction with other women. Methods Women were invited to participate in the study via postings on 3 different open websites for pregnant women and mothers. The sample included 11 Norwegian women who participated in open Web-based discussion forums when experiencing PGP in pregnancy. The data were collected using synchronous qualitative email interviews and were analyzed using thematic analysis. Results In our study sample, interaction in Web-based discussion forums influenced maternal health literacy in terms of increased health-related knowledge and competencies, increased awareness of health promotion and health protection, and increased system navigation. The women appraised and selectively applied information and advice that resonated with their own experiences. For many, the information provided online by other women in the same situation was valued more highly than advice from health professionals. Women reported that they used their knowledge and competency in encounters with health professionals but hesitated to disclose the origin of their knowledge. Those with a high level of education in medicine-related fields raised a concern about the Internet as a source of horror stories and erroneous information and were actively engaged in trying to minimize potential negative effects, by providing biomedical information. Conclusions The popularity of Web-based discussion forums among pregnant women suggests that this group needs additional sources of information and support to complement traditional consultations with the health professionals. The professionals need to recognize that pregnant women access Web-based discussion forums for support and information to increase their ability to take better health decisions for themselves. This is a potential resource that health professionals may find useful in consultations with pregnant women. PMID:27230094

SuML: A Survey Markup Language for Generalized Survey Encoding

PubMed Central

Barclay, MW; Lober, WB; Karras, BT

2002-01-01

There is a need in clinical and research settings for a sophisticated, generalized, web based survey tool that supports complex logic, separation of content and presentation, and computable guidelines. There are many commercial and open source survey packages available that provide simple logic; few provide sophistication beyond “goto” statements; none support the use of guidelines. These tools are driven by databases, static web pages, and structured documents using markup languages such as eXtensible Markup Language (XML). We propose a generalized, guideline aware language and an implementation architecture using open source standards.

A Web-Based Decision Support System for Assessing Regional Water-Quality Conditions and Management Actions

NASA Astrophysics Data System (ADS)

Booth, N. L.; Everman, E.; Kuo, I.; Sprague, L.; Murphy, L.

2011-12-01

A new web-based decision support system has been developed as part of the U.S. Geological Survey (USGS) National Water Quality Assessment Program's (NAWQA) effort to provide ready access to Spatially Referenced Regressions On Watershed attributes (SPARROW) results of stream water-quality conditions and to offer sophisticated scenario testing capabilities for research and water-quality planning via an intuitive graphical user interface with a map-based display. The SPARROW Decision Support System (DSS) is delivered through a web browser over an Internet connection, making it widely accessible to the public in a format that allows users to easily display water-quality conditions, distribution of nutrient sources, nutrient delivery to downstream waterbodies, and simulations of altered nutrient inputs including atmospheric and agricultural sources. The DSS offers other features for analysis including various background map layers, model output exports, and the ability to save and share prediction scenarios. SPARROW models currently supported by the DSS are based on the modified digital versions of the 1:500,000-scale River Reach File (RF1) and 1:100,000-scale National Hydrography Dataset (medium-resolution, NHDPlus) stream networks. The underlying modeling framework and server infrastructure illustrate innovations in the information technology and geosciences fields for delivering SPARROW model predictions over the web by performing intensive model computations and map visualizations of the predicted conditions within the stream network.

Model My Watershed: A high-performance cloud application for public engagement, watershed modeling and conservation decision support

NASA Astrophysics Data System (ADS)

Aufdenkampe, A. K.; Tarboton, D. G.; Horsburgh, J. S.; Mayorga, E.; McFarland, M.; Robbins, A.; Haag, S.; Shokoufandeh, A.; Evans, B. M.; Arscott, D. B.

2017-12-01

The Model My Watershed Web app (https://app.wikiwatershed.org/) and the BiG-CZ Data Portal (http://portal.bigcz.org/) and are web applications that share a common codebase and a common goal to deliver high-performance discovery, visualization and analysis of geospatial data in an intuitive user interface in web browser. Model My Watershed (MMW) was designed as a decision support system for watershed conservation implementation. BiG CZ Data Portal was designed to provide context and background data for research sites. Users begin by creating an Area of Interest, via an automated watershed delineation tool, a free draw tool, selection of a predefined area such as a county or USGS Hydrological Unit (HUC), or uploading a custom polygon. Both Web apps visualize and provide summary statistics of land use, soil groups, streams, climate and other geospatial information. MMW then allows users to run a watershed model to simulate different scenarios of human impacts on stormwater runoff and water-quality. BiG CZ Data Portal allows users to search for scientific and monitoring data within the Area of Interest, which also serves as a prototype for the upcoming Monitor My Watershed web app. Both systems integrate with CUAHSI cyberinfrastructure, including visualizing observational data from CUAHSI Water Data Center and storing user data via CUAHSI HydroShare. Both systems also integrate with the new EnviroDIY Water Quality Data Portal (http://data.envirodiy.org/), a system for crowd-sourcing environmental monitoring data using open-source sensor stations (http://envirodiy.org/mayfly/) and based on the Observations Data Model v2.

Distributed GIS Systems, Open Specifications and Interoperability: How do They Relate to the Sustainable Management of Natural Resources?

Treesearch

Rafael Moreno-Sanchez

2006-01-01

The aim of this is paper is to provide a conceptual framework for the session: “The role of web-based Geographic Information Systems in supporting sustainable management.” The concepts of sustainability, sustainable forest management, Web Services, Distributed Geographic Information Systems, interoperability, Open Specifications, and Open Source Software are defined...

A Web Portal-Based Time-Aware KML Animation Tool for Exploring Spatiotemporal Dynamics of Hydrological Events

NASA Astrophysics Data System (ADS)

Bao, X.; Cai, X.; Liu, Y.

2009-12-01

Understanding spatiotemporal dynamics of hydrological events such as storms and droughts is highly valuable for decision making on disaster mitigation and recovery. Virtual Globe-based technologies such as Google Earth and Open Geospatial Consortium KML standards show great promises for collaborative exploration of such events using visual analytical approaches. However, currently there are two barriers for wider usage of such approaches. First, there lacks an easy way to use open source tools to convert legacy or existing data formats such as shapefiles, geotiff, or web services-based data sources to KML and to produce time-aware KML files. Second, an integrated web portal-based time-aware animation tool is currently not available. Thus users usually share their files in the portal but have no means to visually explore them without leaving the portal environment which the users are familiar with. We develop a web portal-based time-aware KML animation tool for viewing extreme hydrologic events. The tool is based on Google Earth JavaScript API and Java Portlet standard 2.0 JSR-286, and it is currently deployable in one of the most popular open source portal frameworks, namely Liferay. We have also developed an open source toolkit kml-soc-ncsa (http://code.google.com/p/kml-soc-ncsa/) to facilitate the conversion of multiple formats into KML and the creation of time-aware KML files. We illustrate our tool using some example cases, in which drought and storm events with both time and space dimension can be explored in this web-based KML animation portlet. The tool provides an easy-to-use web browser-based portal environment for multiple users to collaboratively share and explore their time-aware KML files as well as improving the understanding of the spatiotemporal dynamics of the hydrological events.

A Web-based Tool for Transparent, Collaborative Urban Water System Planning for Monterrey, Mexico

NASA Astrophysics Data System (ADS)

Rheinheimer, D. E.; Medellin-Azuara, J.; Garza Díaz, L. E.; Ramírez, A. I.

2017-12-01

Recent rapid advances in web technologies and cloud computing show great promise for facilitating collaboration and transparency in water planning efforts. Water resources planning is increasingly in the context of a rapidly urbanizing world, particularly in developing countries. In such countries with democratic traditions, the degree of transparency and collaboration in water planning can mean the difference between success and failure of water planning efforts. This is exemplified in the city of Monterrey, Mexico, where an effort to build a new long-distance aqueduct to increase water supply to the city dramatically failed due to lack of transparency and top-down planning. To help address, we used a new, web-based water system modeling platform, called OpenAgua, to develop a prototype decision support system for water planning in Monterrey. OpenAgua is designed to promote transparency and collaboration, as well as provide strong, cloud-based, water system modeling capabilities. We developed and assessed five water management options intended to increase water supply yield and/or reliability, a dominant water management concern in Latin America generally: 1) a new long-distance source (the previously-rejected project), 2) a new nearby reservoir, 3) expansion/re-operation of an existing major canal, 4) desalination, and 5) industrial water reuse. Using the integrated modeling and analytic capabilities of OpenAgua, and some customization, we assessed the performance of these options for water supply yield and reliability to help identify the most promising ones. In presenting this assessment, we demonstrate the viability of using online, cloud-based modeling systems for improving transparency and collaboration in decision making, reducing the gap between citizens, policy makers and water managers, and future directions.

A digital library of radiology images.

PubMed

Kahn, Charles E

2006-01-01

A web-based virtual library of peer-reviewed radiological images was created for use in education and clinical decision support. Images were obtained from open-access content of five online radiology journals and one e-learning web site. Figure captions were indexed by Medical Subject Heading (MeSH) codes, imaging modality, and patient age and sex. This digital library provides a new, valuable online resource.

Link Correlated Military Data for Better Decision Support

DTIC Science & Technology

2011-06-01

automatically translated into URI based links, thus can greatly reduce man power cost on software development. 3 Linked Data Technique Tim Berners - Lee ...Linked Data - while Linked Data is usually considered as part of Semantic Web, or “the Semantic Web done right” as described by Tim himself - has been...Required data of automatic link construction mechanism on more kinds of correlations. References [1] B. L. Tim , “The next Web of open, linked data

MCSDSS: A Multi-Criteria Decision Support System for Merging Geoscience Information with Natural User Interfaces, Preference Ranking, and Interactive Data Utilities

NASA Astrophysics Data System (ADS)

Pierce, S. A.; Gentle, J.

2015-12-01

The multi-criteria decision support system (MCSDSS) is a newly completed application for touch-enabled group decision support that uses D3 data visualization tools, a geojson conversion utility that we developed, and Paralelex to create an interactive tool. The MCSDSS is a prototype system intended to demonstrate the potential capabilities of a single page application (SPA) running atop a web and cloud based architecture utilizing open source technologies. The application is implemented on current web standards while supporting human interface design that targets both traditional mouse/keyboard interactions and modern touch/gesture enabled interactions. The technology stack for MCSDSS was selected with the goal of creating a robust and dynamic modular codebase that can be adjusted to fit many use cases and scale to support usage loads that range between simple data display to complex scientific simulation-based modelling and analytics. The application integrates current frameworks for highly performant agile development with unit testing, statistical analysis, data visualization, mapping technologies, geographic data manipulation, and cloud infrastructure while retaining support for traditional HTML5/CSS3 web standards. The software lifecylcle for MCSDSS has following best practices to develop, share, and document the codebase and application. Code is documented and shared via an online repository with the option for programmers to see, contribute, or fork the codebase. Example data files and tutorial documentation have been shared with clear descriptions and data object identifiers. And the metadata about the application has been incorporated into an OntoSoft entry to ensure that MCSDSS is searchable and clearly described. MCSDSS is a flexible platform that allows for data fusion and inclusion of large datasets in an interactive front-end application capable of connecting with other science-based applications and advanced computing resources. In addition, MCSDSS offers functionality that enables communication with non-technical users for policy, education, or engagement with groups around scientific topics with societal relevance.

Web-services-based spatial decision support system to facilitate nuclear waste siting

NASA Astrophysics Data System (ADS)

Huang, L. Xinglai; Sheng, Grant

2006-10-01

The availability of spatial web services enables data sharing among managers, decision and policy makers and other stakeholders in much simpler ways than before and subsequently has created completely new opportunities in the process of spatial decision making. Though generally designed for a certain problem domain, web-services-based spatial decision support systems (WSDSS) can provide a flexible problem-solving environment to explore the decision problem, understand and refine problem definition, and generate and evaluate multiple alternatives for decision. This paper presents a new framework for the development of a web-services-based spatial decision support system. The WSDSS is comprised of distributed web services that either have their own functions or provide different geospatial data and may reside in different computers and locations. WSDSS includes six key components, namely: database management system, catalog, analysis functions and models, GIS viewers and editors, report generators, and graphical user interfaces. In this study, the architecture of a web-services-based spatial decision support system to facilitate nuclear waste siting is described as an example. The theoretical, conceptual and methodological challenges and issues associated with developing web services-based spatial decision support system are described.

Development and implementation of an Integrated Water Resources Management System (IWRMS)

NASA Astrophysics Data System (ADS)

Flügel, W.-A.; Busch, C.

2011-04-01

One of the innovative objectives in the EC project BRAHMATWINN was the development of a stakeholder oriented Integrated Water Resources Management System (IWRMS). The toolset integrates the findings of the project and presents it in a user friendly way for decision support in sustainable integrated water resources management (IWRM) in river basins. IWRMS is a framework, which integrates different types of basin information and which supports the development of IWRM options for climate change mitigation. It is based on the River Basin Information System (RBIS) data models and delivers a graphical user interface for stakeholders. A special interface was developed for the integration of the enhanced DANUBIA model input and the NetSyMod model with its Mulino decision support system (mulino mDss) component. The web based IWRMS contains and combines different types of data and methods to provide river basin data and information for decision support. IWRMS is based on a three tier software framework which uses (i) html/javascript at the client tier, (ii) PHP programming language to realize the application tier, and (iii) a postgresql/postgis database tier to manage and storage all data, except the DANUBIA modelling raw data, which are file based and registered in the database tier. All three tiers can reside on one or different computers and are adapted to the local hardware infrastructure. IWRMS as well as RBIS are based on Open Source Software (OSS) components and flexible and time saving access to that database is guaranteed by web-based interfaces for data visualization and retrieval. The IWRMS is accessible via the BRAHMATWINN homepage: http://www.brahmatwinn.uni-jena.de and a user manual for the RBIS is available for download as well.

Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools.

PubMed

Ham, Timothy S; Dmytriv, Zinovii; Plahar, Hector; Chen, Joanna; Hillson, Nathan J; Keasling, Jay D

2012-10-01

The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about 'legacy' parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects.

Ondex Web: web-based visualization and exploration of heterogeneous biological networks.

PubMed

Taubert, Jan; Hassani-Pak, Keywan; Castells-Brooke, Nathalie; Rawlings, Christopher J

2014-04-01

Ondex Web is a new web-based implementation of the network visualization and exploration tools from the Ondex data integration platform. New features such as context-sensitive menus and annotation tools provide users with intuitive ways to explore and manipulate the appearance of heterogeneous biological networks. Ondex Web is open source, written in Java and can be easily embedded into Web sites as an applet. Ondex Web supports loading data from a variety of network formats, such as XGMML, NWB, Pajek and OXL. http://ondex.rothamsted.ac.uk/OndexWeb.

WImpiBLAST: web interface for mpiBLAST to help biologists perform large-scale annotation using high performance computing.

PubMed

Sharma, Parichit; Mantri, Shrikant S

2014-01-01

The function of a newly sequenced gene can be discovered by determining its sequence homology with known proteins. BLAST is the most extensively used sequence analysis program for sequence similarity search in large databases of sequences. With the advent of next generation sequencing technologies it has now become possible to study genes and their expression at a genome-wide scale through RNA-seq and metagenome sequencing experiments. Functional annotation of all the genes is done by sequence similarity search against multiple protein databases. This annotation task is computationally very intensive and can take days to obtain complete results. The program mpiBLAST, an open-source parallelization of BLAST that achieves superlinear speedup, can be used to accelerate large-scale annotation by using supercomputers and high performance computing (HPC) clusters. Although many parallel bioinformatics applications using the Message Passing Interface (MPI) are available in the public domain, researchers are reluctant to use them due to lack of expertise in the Linux command line and relevant programming experience. With these limitations, it becomes difficult for biologists to use mpiBLAST for accelerating annotation. No web interface is available in the open-source domain for mpiBLAST. We have developed WImpiBLAST, a user-friendly open-source web interface for parallel BLAST searches. It is implemented in Struts 1.3 using a Java backbone and runs atop the open-source Apache Tomcat Server. WImpiBLAST supports script creation and job submission features and also provides a robust job management interface for system administrators. It combines script creation and modification features with job monitoring and management through the Torque resource manager on a Linux-based HPC cluster. Use case information highlights the acceleration of annotation analysis achieved by using WImpiBLAST. Here, we describe the WImpiBLAST web interface features and architecture, explain design decisions, describe workflows and provide a detailed analysis.

WImpiBLAST: Web Interface for mpiBLAST to Help Biologists Perform Large-Scale Annotation Using High Performance Computing

PubMed Central

Sharma, Parichit; Mantri, Shrikant S.

2014-01-01

The function of a newly sequenced gene can be discovered by determining its sequence homology with known proteins. BLAST is the most extensively used sequence analysis program for sequence similarity search in large databases of sequences. With the advent of next generation sequencing technologies it has now become possible to study genes and their expression at a genome-wide scale through RNA-seq and metagenome sequencing experiments. Functional annotation of all the genes is done by sequence similarity search against multiple protein databases. This annotation task is computationally very intensive and can take days to obtain complete results. The program mpiBLAST, an open-source parallelization of BLAST that achieves superlinear speedup, can be used to accelerate large-scale annotation by using supercomputers and high performance computing (HPC) clusters. Although many parallel bioinformatics applications using the Message Passing Interface (MPI) are available in the public domain, researchers are reluctant to use them due to lack of expertise in the Linux command line and relevant programming experience. With these limitations, it becomes difficult for biologists to use mpiBLAST for accelerating annotation. No web interface is available in the open-source domain for mpiBLAST. We have developed WImpiBLAST, a user-friendly open-source web interface for parallel BLAST searches. It is implemented in Struts 1.3 using a Java backbone and runs atop the open-source Apache Tomcat Server. WImpiBLAST supports script creation and job submission features and also provides a robust job management interface for system administrators. It combines script creation and modification features with job monitoring and management through the Torque resource manager on a Linux-based HPC cluster. Use case information highlights the acceleration of annotation analysis achieved by using WImpiBLAST. Here, we describe the WImpiBLAST web interface features and architecture, explain design decisions, describe workflows and provide a detailed analysis. PMID:24979410

Tethys: A Platform for Water Resources Modeling and Decision Support Apps

NASA Astrophysics Data System (ADS)

Swain, N. R.; Christensen, S. D.; Jones, N.; Nelson, E. J.

2014-12-01

Cloud-based applications or apps are a promising medium through which water resources models and data can be conveyed in a user-friendly environment—making them more accessible to decision-makers and stakeholders. In the context of this work, a water resources web app is a web application that exposes limited modeling functionality for a scenario exploration activity in a structured workflow (e.g.: land use change runoff analysis, snowmelt runoff prediction, and flood potential analysis). The technical expertise required to develop water resources web apps can be a barrier to many potential developers of water resources apps. One challenge that developers face is in providing spatial storage, analysis, and visualization for the spatial data that is inherent to water resources models. The software projects that provide this functionality are non-standard to web development and there are a large number of free and open source software (FOSS) projects to choose from. In addition, it is often required to synthesize several software projects to provide all of the needed functionality. Another challenge for the developer will be orchestrating the use of several software components. Consequently, the initial software development investment required to deploy an effective water resources cloud-based application can be substantial. The Tethys Platform has been developed to lower the technical barrier and minimize the initial development investment that prohibits many scientists and engineers from making use of the web app medium. Tethys synthesizes several software projects including PostGIS for spatial storage, 52°North WPS for spatial analysis, GeoServer for spatial publishing, Google Earth™, Google Maps™ and OpenLayers for spatial visualization, and Highcharts for plotting tabular data. The software selection came after a literature review of software projects being used to create existing earth sciences web apps. All of the software is linked via a Python-powered software development kit (SDK). Tethys developers use the SDK to build their apps and incorporate the needed functionality from the software suite. The presentation will include several apps that have been developed using Tethys to demonstrate its capabilities. Based upon work supported by the National Science Foundation under Grant No. 1135483.

Geospatial Data Fusion and Multigroup Decision Support for Surface Water Quality Management

NASA Astrophysics Data System (ADS)

Sun, A. Y.; Osidele, O.; Green, R. T.; Xie, H.

2010-12-01

Social networking and social media have gained significant popularity and brought fundamental changes to many facets of our everyday life. With the ever-increasing adoption of GPS-enabled gadgets and technology, location-based content is likely to play a central role in social networking sites. While location-based content is not new to the geoscience community, where geographic information systems (GIS) are extensively used, the delivery of useful geospatial data to targeted user groups for decision support is new. Decision makers and modelers ought to make more effective use of the new web-based tools to expand the scope of environmental awareness education, public outreach, and stakeholder interaction. Environmental decision processes are often rife with uncertainty and controversy, requiring integration of multiple sources of information and compromises between diverse interests. Fusing of multisource, multiscale environmental data for multigroup decision support is a challenging task. Toward this goal, a multigroup decision support platform should strive to achieve transparency, impartiality, and timely synthesis of information. The latter criterion often constitutes a major technical bottleneck to traditional GIS-based media, featuring large file or image sizes and requiring special processing before web deployment. Many tools and design patterns have appeared in recent years to ease the situation somewhat. In this project, we explore the use of Web 2.0 technologies for “pushing” location-based content to multigroups involved in surface water quality management and decision making. In particular, our granular bottom-up approach facilitates effective delivery of information to most relevant user groups. Our location-based content includes in-situ and remotely sensed data disseminated by NASA and other national and local agencies. Our project is demonstrated for managing the total maximum daily load (TMDL) program in the Arroyo Colorado coastal river basin in Texas. The overall design focuses on assigning spatial information to decision support elements and on efficiently using Web 2.0 technologies to relay scientific information to the nonscientific community. We conclude that (i) social networking, if appropriately used, has great potential for mitigating difficulty associated with multigroup decision making; (ii) all potential stakeholder groups should be involved in creating a useful decision support system; and (iii) environmental decision support systems should be considered a must-have, instead of an optional component of TMDL decision support projects. Acknowledgment: This project was supported by NASA grant NNX09AR63G.

Web Map Services (WMS) Global Mosaic

NASA Technical Reports Server (NTRS)

Percivall, George; Plesea, Lucian

2003-01-01

The WMS Global Mosaic provides access to imagery of the global landmass using an open standard for web mapping. The seamless image is a mosaic of Landsat 7 scenes; geographically-accurate with 30 and 15 meter resolutions. By using the OpenGIS Web Map Service (WMS) interface, any organization can use the global mosaic as a layer in their geospatial applications. Based on a trade study, an implementation approach was chosen that extends a previously developed WMS hosting a Landsat 5 CONUS mosaic developed by JPL. The WMS Global Mosaic supports the NASA Geospatial Interoperability Office goal of providing an integrated digital representation of the Earth, widely accessible for humanity's critical decisions.

Open-Source web-based geographical information system for health exposure assessment

PubMed Central

2012-01-01

This paper presents the design and development of an open source web-based Geographical Information System allowing users to visualise, customise and interact with spatial data within their web browser. The developed application shows that by using solely Open Source software it was possible to develop a customisable web based GIS application that provides functions necessary to convey health and environmental data to experts and non-experts alike without the requirement of proprietary software. PMID:22233606

Use of volunteers' information to support proactive inspection of hydraulic structures

NASA Astrophysics Data System (ADS)

Cortes Arevalo, Juliette; Sterlacchini, Simone; Bogaard, Thom; Frigerio, Simone; Junier, Sandra; Schenato, Luca; van den Giesen, Nick

2016-04-01

Proactive management is particularly important to deal with the increasing occurrence of hydro-meteorological hazards in mountain areas were threats are often caused by multiple and sudden onset hazards such as debris flows. Citizen volunteers can be involved in supporting technicians on inspecting the structures' functional status. Such collaborative effort between managing organizations and local volunteers becomes more important under limited resources. To consider volunteers' information in support of proactive inspection of hydraulic structures, we developed a methodology applicable in day-to-day risk management. At first, in collaboration with technicians-in-charge, a data collection approach was developed for first level or pre-screening visual inspections that can be performed by volunteers. Methods comprise of a data collection exercise, an inspection forms and a learning session based on existent procedures in the FVG region and neighbouring regions. To systematically evaluate the individual inspection reports, we designed a support method by means of a multi-criteria method with fuzzy terms. The method allows the technicians-in-charge to categorize the reports in one of three levels, each corresponding with a course of action. To facilitate the evaluation of inspection reports, we transformed the decision support method into a prototype Web-GIS application. The design process of the Web-GIS framework followed a user-centred approach. The conceptual design incorporates four modules for managing the inspection reports: 1) Registered users, 2) Inspection planning; 3) Available reports and 4) Evaluation of reports. The development of the prototype focused on the evaluation module and was implemented based on standard and interoperable open source tools. Finally, we organized a workshop with technicians in the study area to test the decision support method and get insights about the usefulness of the Web-GIS framework. Participants that took part of the workshop included technicians that were not involved in previous research activities. The involvement of new technicians was important due to their fresh perspectives. We looked at the effect of the quality of the input reports on the output of the decision support method. In addition, we compared the differences in the participants' advice during the inspection and the output from the decision support method. Participants' feedback led to a set of suggested improvements in the decision support method and the web-GIS application. We hope that the knowledge, theory and concept behind this decision support method can be developed into a full-scale web-GIS application. The advantage of using this decision support method is that it allows inspections to be carried out by either skilled volunteers or technicians while ensuring technicians-in-charge that they can systematically evaluate the collected reports. Volunteers can become skilled inspectors by teaming up with technicians for the inspection of hydraulic structures. Technicians can become more aware about local impacts and changes in the structures' status by teaming up with volunteers.

Leveraging Web Services in Providing Efficient Discovery, Retrieval, and Integration of NASA-Sponsored Observations and Predictions

NASA Astrophysics Data System (ADS)

Bambacus, M.; Alameh, N.; Cole, M.

2006-12-01

The Applied Sciences Program at NASA focuses on extending the results of NASA's Earth-Sun system science research beyond the science and research communities to contribute to national priority applications with societal benefits. By employing a systems engineering approach, supporting interoperable data discovery and access, and developing partnerships with federal agencies and national organizations, the Applied Sciences Program facilitates the transition from research to operations in national applications. In particular, the Applied Sciences Program identifies twelve national applications, listed at http://science.hq.nasa.gov/earth-sun/applications/, which can be best served by the results of NASA aerospace research and development of science and technologies. The ability to use and integrate NASA data and science results into these national applications results in enhanced decision support and significant socio-economic benefits for each of the applications. This paper focuses on leveraging the power of interoperability and specifically open standard interfaces in providing efficient discovery, retrieval, and integration of NASA's science research results. Interoperability (the ability to access multiple, heterogeneous geoprocessing environments, either local or remote by means of open and standard software interfaces) can significantly increase the value of NASA-related data by increasing the opportunities to discover, access and integrate that data in the twelve identified national applications (particularly in non-traditional settings). Furthermore, access to data, observations, and analytical models from diverse sources can facilitate interdisciplinary and exploratory research and analysis. To streamline this process, the NASA GeoSciences Interoperability Office (GIO) is developing the NASA Earth-Sun System Gateway (ESG) to enable access to remote geospatial data, imagery, models, and visualizations through open, standard web protocols. The gateway (online at http://esg.gsfc.nasa.gov) acts as a flexible and searchable registry of NASA-related resources (files, services, models, etc) and allows scientists, decision makers and others to discover and retrieve a wide variety of observations and predictions of natural and human phenomena related to Earth Science from NASA and other sources. To support the goals of the Applied Sciences national applications, GIO staff is also working with the national applications communities to identify opportunities where open standards-based discovery and access to NASA data can enhance the decision support process of the national applications. This paper describes the work performed to-date on that front, and summarizes key findings in terms of identified data sources and benefiting national applications. The paper also highlights the challenges encountered in making NASA-related data accessible in a cross-cutting fashion and identifies areas where interoperable approaches can be leveraged.

OnEarth: An Open Source Solution for Efficiently Serving High-Resolution Mapped Image Products

NASA Astrophysics Data System (ADS)

Thompson, C. K.; Plesea, L.; Hall, J. R.; Roberts, J. T.; Cechini, M. F.; Schmaltz, J. E.; Alarcon, C.; Huang, T.; McGann, J. M.; Chang, G.; Boller, R. A.; Ilavajhala, S.; Murphy, K. J.; Bingham, A. W.

2013-12-01

This presentation introduces OnEarth, a server side software package originally developed at the Jet Propulsion Laboratory (JPL), that facilitates network-based, minimum-latency geolocated image access independent of image size or spatial resolution. The key component in this package is the Meta Raster Format (MRF), a specialized raster file extension to the Geospatial Data Abstraction Library (GDAL) consisting of an internal indexed pyramid of image tiles. Imagery to be served is converted to the MRF format and made accessible online via an expandable set of server modules handling requests in several common protocols, including the Open Geospatial Consortium (OGC) compliant Web Map Tile Service (WMTS) as well as Tiled WMS and Keyhole Markup Language (KML). OnEarth has recently transitioned to open source status and is maintained and actively developed as part of GIBS (Global Imagery Browse Services), a collaborative project between JPL and Goddard Space Flight Center (GSFC). The primary function of GIBS is to enhance and streamline the data discovery process and to support near real-time (NRT) applications via the expeditious ingestion and serving of full-resolution imagery representing science products from across the NASA Earth Science spectrum. Open source software solutions are leveraged where possible in order to utilize existing available technologies, reduce development time, and enlist wider community participation. We will discuss some of the factors and decision points in transitioning OnEarth to a suitable open source paradigm, including repository and licensing agreement decision points, institutional hurdles, and perceived benefits. We will also provide examples illustrating how OnEarth is integrated within GIBS and other applications.

Interoperable Data Access Services for NOAA IOOS

NASA Astrophysics Data System (ADS)

de La Beaujardiere, J.

2008-12-01

The Integrated Ocean Observing System (IOOS) is intended to enhance our ability to collect, deliver, and use ocean information. The goal is to support research and decision-making by providing data on our open oceans, coastal waters, and Great Lakes in the formats, rates, and scales required by scientists, managers, businesses, governments, and the public. The US National Oceanic and Atmospheric Administration (NOAA) is the lead agency for IOOS. NOAA's IOOS office supports the development of regional coastal observing capability and promotes data management efforts to increase data accessibility. Geospatial web services have been established at NOAA data providers including the National Data Buoy Center (NDBC), the Center for Operational Oceanographic Products and Services (CO-OPS), and CoastWatch, and at regional data provider sites. Services established include Open-source Project for a Network Data Access Protocol (OpenDAP), Open Geospatial Consortium (OGC) Sensor Observation Service (SOS), and OGC Web Coverage Service (WCS). These services provide integrated access to data holdings that have been aggregated at each center from multiple sources. We wish to collaborate with other groups to improve our service offerings to maximize interoperability and enhance cross-provider data integration, and to share common service components such as registries, catalogs, data conversion, and gateways. This paper will discuss the current status of NOAA's IOOS efforts and possible next steps.

Research on web-based decision support system for sports competitions

NASA Astrophysics Data System (ADS)

Huo, Hanqiang

2010-07-01

This paper describes the system architecture and implementation technology of the decision support system for sports competitions, discusses the design of decision-making modules, management modules and security of the system, and proposes the development idea of building a web-based decision support system for sports competitions.

A Cloud-based, Open-Source, Command-and-Control Software Paradigm for Space Situational Awareness (SSA)

NASA Astrophysics Data System (ADS)

Melton, R.; Thomas, J.

With the rapid growth in the number of space actors, there has been a marked increase in the complexity and diversity of software systems utilized to support SSA target tracking, indication, warning, and collision avoidance. Historically, most SSA software has been constructed with "closed" proprietary code, which limits interoperability, inhibits the code transparency that some SSA customers need to develop domain expertise, and prevents the rapid injection of innovative concepts into these systems. Open-source aerospace software, a rapidly emerging, alternative trend in code development, is based on open collaboration, which has the potential to bring greater transparency, interoperability, flexibility, and reduced development costs. Open-source software is easily adaptable, geared to rapidly changing mission needs, and can generally be delivered at lower costs to meet mission requirements. This paper outlines Ball's COSMOS C2 system, a fully open-source, web-enabled, command-and-control software architecture which provides several unique capabilities to move the current legacy SSA software paradigm to an open source model that effectively enables pre- and post-launch asset command and control. Among the unique characteristics of COSMOS is the ease with which it can integrate with diverse hardware. This characteristic enables COSMOS to serve as the command-and-control platform for the full life-cycle development of SSA assets, from board test, to box test, to system integration and test, to on-orbit operations. The use of a modern scripting language, Ruby, also permits automated procedures to provide highly complex decision making for the tasking of SSA assets based on both telemetry data and data received from outside sources. Detailed logging enables quick anomaly detection and resolution. Integrated real-time and offline data graphing renders the visualization of the both ground and on-orbit assets simple and straightforward.

Web GIS in practice IV: publishing your health maps and connecting to remote WMS sources using the Open Source UMN MapServer and DM Solutions MapLab

PubMed Central

Boulos, Maged N Kamel; Honda, Kiyoshi

2006-01-01

Open Source Web GIS software systems have reached a stage of maturity, sophistication, robustness and stability, and usability and user friendliness rivalling that of commercial, proprietary GIS and Web GIS server products. The Open Source Web GIS community is also actively embracing OGC (Open Geospatial Consortium) standards, including WMS (Web Map Service). WMS enables the creation of Web maps that have layers coming from multiple different remote servers/sources. In this article we present one easy to implement Web GIS server solution that is based on the Open Source University of Minnesota (UMN) MapServer. By following the accompanying step-by-step tutorial instructions, interested readers running mainstream Microsoft® Windows machines and with no prior technical experience in Web GIS or Internet map servers will be able to publish their own health maps on the Web and add to those maps additional layers retrieved from remote WMS servers. The 'digital Asia' and 2004 Indian Ocean tsunami experiences in using free Open Source Web GIS software are also briefly described. PMID:16420699

Branch: an interactive, web-based tool for testing hypotheses and developing predictive models.

PubMed

Gangavarapu, Karthik; Babji, Vyshakh; Meißner, Tobias; Su, Andrew I; Good, Benjamin M

2016-07-01

Branch is a web application that provides users with the ability to interact directly with large biomedical datasets. The interaction is mediated through a collaborative graphical user interface for building and evaluating decision trees. These trees can be used to compose and test sophisticated hypotheses and to develop predictive models. Decision trees are built and evaluated based on a library of imported datasets and can be stored in a collective area for sharing and re-use. Branch is hosted at http://biobranch.org/ and the open source code is available at http://bitbucket.org/sulab/biobranch/ asu@scripps.edu or bgood@scripps.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Launching a virtual decision lab: development and field-testing of a web-based patient decision support research platform.

PubMed

Hoffman, Aubri S; Llewellyn-Thomas, Hilary A; Tosteson, Anna N A; O'Connor, Annette M; Volk, Robert J; Tomek, Ivan M; Andrews, Steven B; Bartels, Stephen J

2014-12-12

Over 100 trials show that patient decision aids effectively improve patients' information comprehension and values-based decision making. However, gaps remain in our understanding of several fundamental and applied questions, particularly related to the design of interactive, personalized decision aids. This paper describes an interdisciplinary development process for, and early field testing of, a web-based patient decision support research platform, or virtual decision lab, to address these questions. An interdisciplinary stakeholder panel designed the web-based research platform with three components: a) an introduction to shared decision making, b) a web-based patient decision aid, and c) interactive data collection items. Iterative focus groups provided feedback on paper drafts and online prototypes. A field test assessed a) feasibility for using the research platform, in terms of recruitment, usage, and acceptability; and b) feasibility of using the web-based decision aid component, compared to performance of a videobooklet decision aid in clinical care. This interdisciplinary, theory-based, patient-centered design approach produced a prototype for field-testing in six months. Participants (n = 126) reported that: the decision aid component was easy to use (98%), information was clear (90%), the length was appropriate (100%), it was appropriately detailed (90%), and it held their interest (97%). They spent a mean of 36 minutes using the decision aid and 100% preferred using their home/library computer. Participants scored a mean of 75% correct on the Decision Quality, Knowledge Subscale, and 74 out of 100 on the Preparation for Decision Making Scale. Completing the web-based decision aid reduced mean Decisional Conflict scores from 31.1 to 19.5 (p < 0.01). Combining decision science and health informatics approaches facilitated rapid development of a web-based patient decision support research platform that was feasible for use in research studies in terms of recruitment, acceptability, and usage. Within this platform, the web-based decision aid component performed comparably with the videobooklet decision aid used in clinical practice. Future studies may use this interactive research platform to study patients' decision making processes in real-time, explore interdisciplinary approaches to designing web-based decision aids, and test strategies for tailoring decision support to meet patients' needs and preferences.

Designing Crop Simulation Web Service with Service Oriented Architecture Principle

NASA Astrophysics Data System (ADS)

Chinnachodteeranun, R.; Hung, N. D.; Honda, K.

2015-12-01

Crop simulation models are efficient tools for simulating crop growth processes and yield. Running crop models requires data from various sources as well as time-consuming data processing, such as data quality checking and data formatting, before those data can be inputted to the model. It makes the use of crop modeling limited only to crop modelers. We aim to make running crop models convenient for various users so that the utilization of crop models will be expanded, which will directly improve agricultural applications. As the first step, we had developed a prototype that runs DSSAT on Web called as Tomorrow's Rice (v. 1). It predicts rice yields based on a planting date, rice's variety and soil characteristics using DSSAT crop model. A user only needs to select a planting location on the Web GUI then the system queried historical weather data from available sources and expected yield is returned. Currently, we are working on weather data connection via Sensor Observation Service (SOS) interface defined by Open Geospatial Consortium (OGC). Weather data can be automatically connected to a weather generator for generating weather scenarios for running the crop model. In order to expand these services further, we are designing a web service framework consisting of layers of web services to support compositions and executions for running crop simulations. This framework allows a third party application to call and cascade each service as it needs for data preparation and running DSSAT model using a dynamic web service mechanism. The framework has a module to manage data format conversion, which means users do not need to spend their time curating the data inputs. Dynamic linking of data sources and services are implemented using the Service Component Architecture (SCA). This agriculture web service platform demonstrates interoperability of weather data using SOS interface, convenient connections between weather data sources and weather generator, and connecting various services for running crop models for decision support.

Development of an open-source web-based intervention for Brazilian smokers - Viva sem Tabaco.

PubMed

Gomide, H P; Bernardino, H S; Richter, K; Martins, L F; Ronzani, T M

2016-08-02

Web-based interventions for smoking cessation available in Portuguese do not adhere to evidence-based treatment guidelines. Besides, all existing web-based interventions are built on proprietary platforms that developing countries often cannot afford. We aimed to describe the development of "Viva sem Tabaco", an open-source web-based intervention. The development of the intervention included the selection of content from evidence-based guidelines for smoking cessation, the design of the first layout, conduction of 2 focus groups to identify potential features, refinement of the layout based on focus groups and correction of content based on feedback provided by specialists on smoking cessation. At the end, we released the source-code and intervention on the Internet and translated it into Spanish and English. The intervention developed fills gaps in the information available in Portuguese and the lack of open-source interventions for smoking cessation. The open-source licensing format and its translation system may help researchers from different countries deploying evidence-based interventions for smoking cessation.

Digital roadway interactive visualization and evaluation network applications to WSDOT operational data usage.

DOT National Transportation Integrated Search

2016-12-01

DRIVE Net is a region-wide, Web-based transportation decision support system that adopts digital roadway maps as : the base, and provides data layers for integrating and analyzing a variety of data sources (e.g., traffic sensors, incident : records)....

A web-based tool to support shared decision making for people with a psychotic disorder: randomized controlled trial and process evaluation.

PubMed

van der Krieke, Lian; Emerencia, Ando C; Boonstra, Nynke; Wunderink, Lex; de Jonge, Peter; Sytema, Sjoerd

2013-10-07

Mental health policy makers encourage the development of electronic decision aids to increase patient participation in medical decision making. Evidence is needed to determine whether these decision aids are helpful in clinical practice and whether they lead to increased patient involvement and better outcomes. This study reports the outcome of a randomized controlled trial and process evaluation of a Web-based intervention to facilitate shared decision making for people with psychotic disorders. The study was carried out in a Dutch mental health institution. Patients were recruited from 2 outpatient teams for patients with psychosis (N=250). Patients in the intervention condition (n=124) were provided an account to access a Web-based information and decision tool aimed to support patients in acquiring an overview of their needs and appropriate treatment options provided by their mental health care organization. Patients were given the opportunity to use the Web-based tool either on their own (at their home computer or at a computer of the service) or with the support of an assistant. Patients in the control group received care as usual (n=126). Half of the patients in the sample were patients experiencing a first episode of psychosis; the other half were patients with a chronic psychosis. Primary outcome was patient-perceived involvement in medical decision making, measured with the Combined Outcome Measure for Risk Communication and Treatment Decision-making Effectiveness (COMRADE). Process evaluation consisted of questionnaire-based surveys, open interviews, and researcher observation. In all, 73 patients completed the follow-up measurement and were included in the final analysis (response rate 29.2%). More than one-third (48/124, 38.7%) of the patients who were provided access to the Web-based decision aid used it, and most used its full functionality. No differences were found between the intervention and control conditions on perceived involvement in medical decision making (COMRADE satisfaction with communication: F1,68=0.422, P=.52; COMRADE confidence in decision: F1,67=0.086, P=.77). In addition, results of the process evaluation suggest that the intervention did not optimally fit in with routine practice of the participating teams. The development of electronic decision aids to facilitate shared medical decision making is encouraged and many people with a psychotic disorder can work with them. This holds for both first-episode patients and long-term care patients, although the latter group might need more assistance. However, results of this paper could not support the assumption that the use of electronic decision aids increases patient involvement in medical decision making. This may be because of weak implementation of the study protocol and a low response rate.

SANDS: a service-oriented architecture for clinical decision support in a National Health Information Network.

PubMed

Wright, Adam; Sittig, Dean F

2008-12-01

In this paper, we describe and evaluate a new distributed architecture for clinical decision support called SANDS (Service-oriented Architecture for NHIN Decision Support), which leverages current health information exchange efforts and is based on the principles of a service-oriented architecture. The architecture allows disparate clinical information systems and clinical decision support systems to be seamlessly integrated over a network according to a set of interfaces and protocols described in this paper. The architecture described is fully defined and developed, and six use cases have been developed and tested using a prototype electronic health record which links to one of the existing prototype National Health Information Networks (NHIN): drug interaction checking, syndromic surveillance, diagnostic decision support, inappropriate prescribing in older adults, information at the point of care and a simple personal health record. Some of these use cases utilize existing decision support systems, which are either commercially or freely available at present, and developed outside of the SANDS project, while other use cases are based on decision support systems developed specifically for the project. Open source code for many of these components is available, and an open source reference parser is also available for comparison and testing of other clinical information systems and clinical decision support systems that wish to implement the SANDS architecture. The SANDS architecture for decision support has several significant advantages over other architectures for clinical decision support. The most salient of these are:

A Web-Based Tool to Support Shared Decision Making for People With a Psychotic Disorder: Randomized Controlled Trial and Process Evaluation

PubMed Central

Emerencia, Ando C; Boonstra, Nynke; Wunderink, Lex; de Jonge, Peter; Sytema, Sjoerd

2013-01-01

Background Mental health policy makers encourage the development of electronic decision aids to increase patient participation in medical decision making. Evidence is needed to determine whether these decision aids are helpful in clinical practice and whether they lead to increased patient involvement and better outcomes. Objective This study reports the outcome of a randomized controlled trial and process evaluation of a Web-based intervention to facilitate shared decision making for people with psychotic disorders. Methods The study was carried out in a Dutch mental health institution. Patients were recruited from 2 outpatient teams for patients with psychosis (N=250). Patients in the intervention condition (n=124) were provided an account to access a Web-based information and decision tool aimed to support patients in acquiring an overview of their needs and appropriate treatment options provided by their mental health care organization. Patients were given the opportunity to use the Web-based tool either on their own (at their home computer or at a computer of the service) or with the support of an assistant. Patients in the control group received care as usual (n=126). Half of the patients in the sample were patients experiencing a first episode of psychosis; the other half were patients with a chronic psychosis. Primary outcome was patient-perceived involvement in medical decision making, measured with the Combined Outcome Measure for Risk Communication and Treatment Decision-making Effectiveness (COMRADE). Process evaluation consisted of questionnaire-based surveys, open interviews, and researcher observation. Results In all, 73 patients completed the follow-up measurement and were included in the final analysis (response rate 29.2%). More than one-third (48/124, 38.7%) of the patients who were provided access to the Web-based decision aid used it, and most used its full functionality. No differences were found between the intervention and control conditions on perceived involvement in medical decision making (COMRADE satisfaction with communication: F1,68=0.422, P=.52; COMRADE confidence in decision: F1,67=0.086, P=.77). In addition, results of the process evaluation suggest that the intervention did not optimally fit in with routine practice of the participating teams. Conclusions The development of electronic decision aids to facilitate shared medical decision making is encouraged and many people with a psychotic disorder can work with them. This holds for both first-episode patients and long-term care patients, although the latter group might need more assistance. However, results of this paper could not support the assumption that the use of electronic decision aids increases patient involvement in medical decision making. This may be because of weak implementation of the study protocol and a low response rate. Trial Registration Dutch Trial Register (NTR) trial number: 10340; http://www.trialregister.nl/trialreg/admin/rctsearch.asp?Term=10340 (Archived by WebCite at http://www.webcitation.org/6Jj5umAeS). PMID:24100091

An overview of emerging technologies in contemporary decision support system development

NASA Astrophysics Data System (ADS)

Nursal, Ahmad Taufik; Omar, Mohd Faizal; Nawi, Mohd Nasrun Mohd

2014-12-01

The rapid development of Web technology has opened a new approach to Decision Support System (DSS) development. For instance, Social Media is one of the Web 2.0 digital platforms that allow the creation and exchanges of user-generate content through an interactive interface, high user control and mass participation. The concept and characteristics of Web 2.0 such as remote, platform-independent, context-rich and easy to use, which is fulfill the concept and purpose of DSS. This paper outlines some of the elementary concepts of Web 2.0 and social media technology which can be potentially integrated within DSS to enhance the decision-making process. Our initial investigation indicates that there is limited study attempt to embed Web 2.0 into DSS. Thus, this paper highlights the importance of Web 2.0 technology in order to foster the betterment of DSS development and its usability.

SANDS: A Service-Oriented Architecture for Clinical Decision Support in a National Health Information Network

PubMed Central

Wright, Adam; Sittig, Dean F.

2008-01-01

In this paper we describe and evaluate a new distributed architecture for clinical decision support called SANDS (Service-oriented Architecture for NHIN Decision Support), which leverages current health information exchange efforts and is based on the principles of a service-oriented architecture. The architecture allows disparate clinical information systems and clinical decision support systems to be seamlessly integrated over a network according to a set of interfaces and protocols described in this paper. The architecture described is fully defined and developed, and six use cases have been developed and tested using a prototype electronic health record which links to one of the existing prototype National Health Information Networks (NHIN): drug interaction checking, syndromic surveillance, diagnostic decision support, inappropriate prescribing in older adults, information at the point of care and a simple personal health record. Some of these use cases utilize existing decision support systems, which are either commercially or freely available at present, and developed outside of the SANDS project, while other use cases are based on decision support systems developed specifically for the project. Open source code for many of these components is available, and an open source reference parser is also available for comparison and testing of other clinical information systems and clinical decision support systems that wish to implement the SANDS architecture. PMID:18434256

A Web-Based Tool to Support Data-Based Early Intervention Decision Making

ERIC Educational Resources Information Center

Buzhardt, Jay; Greenwood, Charles; Walker, Dale; Carta, Judith; Terry, Barbara; Garrett, Matthew

2010-01-01

Progress monitoring and data-based intervention decision making have become key components of providing evidence-based early childhood special education services. Unfortunately, there is a lack of tools to support early childhood service providers' decision-making efforts. The authors describe a Web-based system that guides service providers…

Cloud-Based Tools to Support High-Resolution Modeling (Invited)

NASA Astrophysics Data System (ADS)

Jones, N.; Nelson, J.; Swain, N.; Christensen, S.

2013-12-01

The majority of watershed models developed to support decision-making by water management agencies are simple, lumped-parameter models. Maturity in research codes and advances in the computational power from multi-core processors on desktop machines, commercial cloud-computing resources, and supercomputers with thousands of cores have created new opportunities for employing more accurate, high-resolution distributed models for routine use in decision support. The barriers for using such models on a more routine basis include massive amounts of spatial data that must be processed for each new scenario and lack of efficient visualization tools. In this presentation we will review a current NSF-funded project called CI-WATER that is intended to overcome many of these roadblocks associated with high-resolution modeling. We are developing a suite of tools that will make it possible to deploy customized web-based apps for running custom scenarios for high-resolution models with minimal effort. These tools are based on a software stack that includes 52 North, MapServer, PostGIS, HT Condor, CKAN, and Python. This open source stack provides a simple scripting environment for quickly configuring new custom applications for running high-resolution models as geoprocessing workflows. The HT Condor component facilitates simple access to local distributed computers or commercial cloud resources when necessary for stochastic simulations. The CKAN framework provides a powerful suite of tools for hosting such workflows in a web-based environment that includes visualization tools and storage of model simulations in a database to archival, querying, and sharing of model results. Prototype applications including land use change, snow melt, and burned area analysis will be presented. This material is based upon work supported by the National Science Foundation under Grant No. 1135482

Sharing clinical decisions for multimorbidity case management using social network and open-source tools.

PubMed

Martínez-García, Alicia; Moreno-Conde, Alberto; Jódar-Sánchez, Francisco; Leal, Sandra; Parra, Carlos

2013-12-01

Social networks applied through Web 2.0 tools have gained importance in health domain, because they produce improvements on the communication and coordination capabilities among health professionals. This is highly relevant for multimorbidity patients care because there is a large number of health professionals in charge of patient care, and this requires to obtain clinical consensus in their decisions. Our objective is to develop a tool for collaborative work among health professionals for multimorbidity patient care. We describe the architecture to incorporate decision support functionalities in a social network tool to enable the adoption of shared decisions among health professionals from different care levels. As part of the first stage of the project, this paper describes the results obtained in a pilot study about acceptance and use of the social network component in our healthcare setting. At Virgen del Rocío University Hospital we have designed and developed the Shared Care Platform (SCP) to provide support in the continuity of care for multimorbidity patients. The SCP has two consecutively developed components: social network component, called Clinical Wall, and Clinical Decision Support (CDS) system. The Clinical Wall contains a record where health professionals are able to debate and define shared decisions. We conducted a pilot study to assess the use and acceptance of the SCP by healthcare professionals through questionnaire based on the theory of the Technology Acceptance Model. In March 2012 we released and deployed the SCP, but only with the social network component. The pilot project lasted 6 months in the hospital and 2 primary care centers. From March to September 2012 we created 16 records in the Clinical Wall, all with a high priority. A total of 10 professionals took part in the exchange of messages: 3 internists and 7 general practitioners generated 33 messages. 12 of the 16 record (75%) were answered by the destination health professionals. The professionals valued positively all the items in the questionnaire. As part of the SCP, opensource tools for CDS will be incorporated to provide recommendations for medication and problem interactions, as well as to calculate indexes or scales from validated questionnaires. They will receive the patient summary information provided by the regional Electronic Health Record system through a web service with the information defined according to the virtual Medical Record specification. Clinical Wall has been developed to allow communication and coordination between the healthcare professionals involved in multimorbidity patient care. Agreed decisions were about coordination for appointment changing, patient conditions, diagnosis tests, and prescription changes and renewal. The application of interoperability standards and open source software can bridge the gap between knowledge and clinical practice, while enabling interoperability and scalability. Open source with the social network encourages adoption and facilitates collaboration. Although the results obtained for use indicators are still not as high as it was expected, based on the promising results obtained in the acceptance questionnaire of SMP, we expect that the new CDS tools will increase the use by the health professionals. Copyright © 2013 Elsevier Inc. All rights reserved.

Informatics and Decisions support in Galway Bay (SmartBay) using ERDDAP, OGC Technologies and Third Party Data Sources to Provide Services to the Marine Community.

NASA Astrophysics Data System (ADS)

Delaney, Conor; Gaughan, Paul; Smyth, Damian

2013-04-01

The global marine sector generates and consumes vast quantities of operational and forecast data on a daily basis. One of the key challenges facing the sector relates to the management and transformation of that data into knowledge. The Irish Marine Institute (MI) generates oceanographic and environmental data on a regular and frequent basis. This data comes from operational ocean models run on the MI's high performance computer (HPC) and various environmental observation sensors systems. Some of the data published by the Marine Institute is brokered by the Environmental Research Division's Data Access Program (ERDDAP) data broker, which is a broker technology that uses technology based on OPeNDAP and Open Geospatial Consortium (OGC) standards. The broker provides a consistent web service interface to the data services of the Marine Institute; these services include wave, tide and weather sensors and numerical model output. An ERDDAP server publishes data in a number of standard and developer friendly ways, including some OGC formats. The data on the MI ERDDAP (http://erddap.marine.ie) server is published as OpenData. The marine work package of the FP7 funded ENVIROFI project (http://www.envirofi.eu/) has used the ERDDAP data broker as a core resource in the development of its Marine Asset management decision Support Tool (MAST) portal and phone App. Communication between MAST and ERDDAP is via a Uniform Resource Identifier (Linked Data). A key objective of the MAST prototype is to demonstrate the potential of next-generation dynamic web-based products and services and how they can be harnessed to facilitate growth of both the marine and IT sectors. The use case driving the project is the management of ocean energy assets in the marine environment. In particular the provision of information that aid in the decision making process surrounding maintenance at sea. This question is common to any offshore industry and solution proposed here is applicable to other users of Galway Bay, Ireland. The architecture of the MAST is based on the concepts of Representational State Transfer (REST), Resource Orientated Architecture (ROA), Service Orientated Architecture (SOA), OpenData and MASHUPS. In this paper we demonstrate the architecture of the MAST system and discuss the potential of ERDDAP technology to serve complex data in formats that are accessible to the general developer community. We also discuss of the potential of next generation web technologies and OpenData to encourage the use of valuable marine data resources.

Your Personal Analysis Toolkit - An Open Source Solution

NASA Astrophysics Data System (ADS)

Mitchell, T.

2009-12-01

Open source software is commonly known for its web browsers, word processors and programming languages. However, there is a vast array of open source software focused on geographic information management and geospatial application building in general. As geo-professionals, having easy access to tools for our jobs is crucial. Open source software provides the opportunity to add a tool to your tool belt and carry it with you for your entire career - with no license fees, a supportive community and the opportunity to test, adopt and upgrade at your own pace. OSGeo is a US registered non-profit representing more than a dozen mature geospatial data management applications and programming resources. Tools cover areas such as desktop GIS, web-based mapping frameworks, metadata cataloging, spatial database analysis, image processing and more. Learn about some of these tools as they apply to AGU members, as well as how you can join OSGeo and its members in getting the job done with powerful open source tools. If you haven't heard of OSSIM, MapServer, OpenLayers, PostGIS, GRASS GIS or the many other projects under our umbrella - then you need to hear this talk. Invest in yourself - use open source!

Stable isotopes to trace food web stressors: Is space the final frontier?

EPA Science Inventory

To support community decision-making, we need to evaluate sources of stress and impact at a variety of spatial scales, whether local or watershed-based. Increasingly, we are using stable isotope-based approaches to determine those scales of impact, and using these approaches in v...

Profile-IQ: Web-based data query system for local health department infrastructure and activities.

PubMed

Shah, Gulzar H; Leep, Carolyn J; Alexander, Dayna

2014-01-01

To demonstrate the use of National Association of County & City Health Officials' Profile-IQ, a Web-based data query system, and how policy makers, researchers, the general public, and public health professionals can use the system to generate descriptive statistics on local health departments. This article is a descriptive account of an important health informatics tool based on information from the project charter for Profile-IQ and the authors' experience and knowledge in design and use of this query system. Profile-IQ is a Web-based data query system that is based on open-source software: MySQL 5.5, Google Web Toolkit 2.2.0, Apache Commons Math library, Google Chart API, and Tomcat 6.0 Web server deployed on an Amazon EC2 server. It supports dynamic queries of National Profile of Local Health Departments data on local health department finances, workforce, and activities. Profile-IQ's customizable queries provide a variety of statistics not available in published reports and support the growing information needs of users who do not wish to work directly with data files for lack of staff skills or time, or to avoid a data use agreement. Profile-IQ also meets the growing demand of public health practitioners and policy makers for data to support quality improvement, community health assessment, and other processes associated with voluntary public health accreditation. It represents a step forward in the recent health informatics movement of data liberation and use of open source information technology solutions to promote public health.

An Open Source Web Map Server Implementation For California and the Digital Earth: Lessons Learned

NASA Technical Reports Server (NTRS)

Sullivan, D. V.; Sheffner, E. J.; Skiles, J. W.; Brass, J. A.; Condon, Estelle (Technical Monitor)

2000-01-01

This paper describes an Open Source implementation of the Open GIS Consortium's Web Map interface. It is based on the very popular Apache WWW Server, the Sun Microsystems Java ServIet Development Kit, and a C language shared library interface to a spatial datastore. This server was initially written as a proof of concept, to support a National Aeronautics and Space Administration (NASA) Digital Earth test bed demonstration. It will also find use in the California Land Science Information Partnership (CaLSIP), a joint program between NASA and the state of California. At least one WebMap enabled server will be installed in every one of the state's 58 counties. This server will form a basis for a simple, easily maintained installation for those entities that do not yet require one of the larger, more expensive, commercial offerings.

BingEO: Enable Distributed Earth Observation Data for Environmental Research

NASA Astrophysics Data System (ADS)

Wu, H.; Yang, C.; Xu, Y.

2010-12-01

Our planet is facing great environmental challenges including global climate change, environmental vulnerability, extreme poverty, and a shortage of clean cheap energy. To address these problems, scientists are developing various models to analysis, forecast, simulate various geospatial phenomena to support critical decision making. These models not only challenge our computing technology, but also challenge us to feed huge demands of earth observation data. Through various policies and programs, open and free sharing of earth observation data are advocated in earth science. Currently, thousands of data sources are freely available online through open standards such as Web Map Service (WMS), Web Feature Service (WFS) and Web Coverage Service (WCS). Seamless sharing and access to these resources call for a spatial Cyberinfrastructure (CI) to enable the use of spatial data for the advancement of related applied sciences including environmental research. Based on Microsoft Bing Search Engine and Bing Map, a seamlessly integrated and visual tool is under development to bridge the gap between researchers/educators and earth observation data providers. With this tool, earth science researchers/educators can easily and visually find the best data sets for their research and education. The tool includes a registry and its related supporting module at server-side and an integrated portal as its client. The proposed portal, Bing Earth Observation (BingEO), is based on Bing Search and Bing Map to: 1) Use Bing Search to discover Web Map Services (WMS) resources available over the internet; 2) Develop and maintain a registry to manage all the available WMS resources and constantly monitor their service quality; 3) Allow users to manually register data services; 4) Provide a Bing Maps-based Web application to visualize the data on a high-quality and easy-to-manipulate map platform and enable users to select the best data layers online. Given the amount of observation data accumulated already and still growing, BingEO will allow these resources to be utilized more widely, intensively, efficiently and economically in earth science applications.

Virtualization of open-source secure web services to support data exchange in a pediatric critical care research network

PubMed Central

Sward, Katherine A; Newth, Christopher JL; Khemani, Robinder G; Cryer, Martin E; Thelen, Julie L; Enriquez, Rene; Shaoyu, Su; Pollack, Murray M; Harrison, Rick E; Meert, Kathleen L; Berg, Robert A; Wessel, David L; Shanley, Thomas P; Dalton, Heidi; Carcillo, Joseph; Jenkins, Tammara L; Dean, J Michael

2015-01-01

Objectives To examine the feasibility of deploying a virtual web service for sharing data within a research network, and to evaluate the impact on data consistency and quality. Material and Methods Virtual machines (VMs) encapsulated an open-source, semantically and syntactically interoperable secure web service infrastructure along with a shadow database. The VMs were deployed to 8 Collaborative Pediatric Critical Care Research Network Clinical Centers. Results Virtual web services could be deployed in hours. The interoperability of the web services reduced format misalignment from 56% to 1% and demonstrated that 99% of the data consistently transferred using the data dictionary and 1% needed human curation. Conclusions Use of virtualized open-source secure web service technology could enable direct electronic abstraction of data from hospital databases for research purposes. PMID:25796596

Ontology Based Quality Evaluation for Spatial Data

NASA Astrophysics Data System (ADS)

Yılmaz, C.; Cömert, Ç.

2015-08-01

Many institutions will be providing data to the National Spatial Data Infrastructure (NSDI). Current technical background of the NSDI is based on syntactic web services. It is expected that this will be replaced by semantic web services. The quality of the data provided is important in terms of the decision-making process and the accuracy of transactions. Therefore, the data quality needs to be tested. This topic has been neglected in Turkey. Data quality control for NSDI may be done by private or public "data accreditation" institutions. A methodology is required for data quality evaluation. There are studies for data quality including ISO standards, academic studies and software to evaluate spatial data quality. ISO 19157 standard defines the data quality elements. Proprietary software such as, 1Spatial's 1Validate and ESRI's Data Reviewer offers quality evaluation based on their own classification of rules. Commonly, rule based approaches are used for geospatial data quality check. In this study, we look for the technical components to devise and implement a rule based approach with ontologies using free and open source software in semantic web context. Semantic web uses ontologies to deliver well-defined web resources and make them accessible to end-users and processes. We have created an ontology conforming to the geospatial data and defined some sample rules to show how to test data with respect to data quality elements including; attribute, topo-semantic and geometrical consistency using free and open source software. To test data against rules, sample GeoSPARQL queries are created, associated with specifications.

Prototype development of a web-based participative decision support platform in risk management

NASA Astrophysics Data System (ADS)

Aye, Zar Chi; Olyazadeh, Roya; Jaboyedoff, Michel; Derron, Marc-Henri

2014-05-01

This paper discusses the proposed background architecture and prototype development of an internet-based decision support system (DSS) in the field of natural hazards and risk management using open-source geospatial software and web technologies. It is based on a three-tier, client-server architecture with the support of boundless (opengeo) framework and its client side SDK application environment using customized gxp components and data utility classes. The main purpose of the system is to integrate the workflow of risk management systematically with the diverse involvement of stakeholders from different organizations dealing with natural hazards and risk for evaluation of management measures through the active online participation approach. It aims to develop an adaptive user friendly, web-based environment that allows the users to set up risk management strategies based on actual context and data by integrating web-GIS and DSS functionality associated with process flow and other visualization tools. Web-GIS interface has been integrated within the DSS to deliver maps and provide certain geo-processing capabilities on the web, which can be easily accessible and shared by different organizations located in case study sites of the project. This platform could be envisaged not only as a common web-based platform for the centralized sharing of data such as hazard maps, elements at risk maps and additional information but also to ensure an integrated platform of risk management where the users could upload data, analyze risk and identify possible alternative scenarios for risk reduction especially for floods and landslides, either quantitatively or qualitatively depending on the risk information provided by the stakeholders in case study regions. The level of involvement, access to and interaction with the provided functionality of the system varies depending on the roles and responsibilities of the stakeholders, for example, only the experts (planners, geological services, etc.) can have access to the alternative definition component to formulate the risk reduction measures. The development of such a participative platform would finally lead to an integrated risk management approach highlighting the needs to deal with involved experts and civil society in the decision-making process for evaluation of risk management measures through the active participation approach. The system will be applied and evaluated in four case study areas of the CHANGES project in Europe: Romania, North Eastern Italy, French Alps and Poland. However, the framework of the system is designed in a generic way so as to be applicable in other regions to achieve the high adaptability and flexibility of the system. The research has been undertaken as a part of the CHANGES project funded by the European Commission's 7th framework program.

Deciding to Change OpenURL Link Resolvers

ERIC Educational Resources Information Center

Johnson, Megan; Leonard, Andrea; Wiswell, John

2015-01-01

This article will be of interest to librarians, particularly those in consortia that are evaluating OpenURL link resolvers. This case study contrasts WebBridge (an Innovative Interface product) and LinkSource (EBSCO's product). This study assisted us in the decision-making process of choosing an OpenURL link resolver that was sustainable to…

FloorspaceJS - A New, Open Source, Web-Based Geometry Editor for Building Energy Modeling (BEM): Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Macumber, Daniel L; Horowitz, Scott G; Schott, Marjorie

Across most industries, desktop applications are being rapidly migrated to web applications for a variety of reasons. Web applications are inherently cross platform, mobile, and easier to distribute than desktop applications. Fueling this trend are a wide range of free, open source libraries and frameworks that make it incredibly easy to develop powerful web applications. The building energy modeling community is just beginning to pick up on these larger trends, with a small but growing number of building energy modeling applications starting on or moving to the web. This paper presents a new, open source, web based geometry editor formore » Building Energy Modeling (BEM). The editor is written completely in JavaScript and runs in a modern web browser. The editor works on a custom JSON file format and is designed to be integrated into a variety of web and desktop applications. The web based editor is available to use as a standalone web application at: https://nrel.github.io/openstudio-geometry-editor/. An example integration is demonstrated with the OpenStudio desktop application. Finally, the editor can be easily integrated with a wide range of possible building energy modeling web applications.« less

Development of Web Mapping Service Capabilities to Support NASA Disasters Applications/App Development

NASA Technical Reports Server (NTRS)

Burks, Jason E.; Molthan, Andrew L.; McGrath, Kevin M.

2014-01-01

During the last year several significant disasters have occurred such as Superstorm Sandy on the East coast of the United States, and Typhoon Bopha in the Phillipines, along with several others. In support of these disasters NASA's Short-term Prediction Research and Transition (SPoRT) Center delivered various products derived from satellite imagery to help in the assessment of damage and recovery of the affected areas. To better support the decision makers responding to the disasters SPoRT quickly developed several solutions to provide the data using open Geographical Information Service (GIS) formats. Providing the data in open GIS standard formats allowed the end user to easily integrate the data into existing Decision Support Systems (DSS). Both Tile Mapping Service (TMS) and Web Mapping Service (WMS) were leveraged to quickly provide the data to the end-user. Development of the deliver methodology allowed quick response to rapidly developing disasters and enabled NASA SPoRT to bring science data to decision makers in a successful research to operations transition.

Development of Web Mapping Service Capabilities to Support NASA Disasters Applications / App Development

NASA Technical Reports Server (NTRS)

Burks, Jason E.; Molthan, Andrew L.; McGrath, Kevin M.

2014-01-01

During the last year several significant disasters have occurred such as Superstorm Sandy on the East coast of the United States, and Typhoon Bopha in the Phillipines, along with several others. In support of these disasters NASA's Short-term Prediction Research and Transition (SPoRT) Center delivered various products derived from satellite imagery to help in the assessment of damage and recovery of the affected areas. To better support the decision makers responding to the disasters SPoRT quickly developed several solutions to provide the data using open Geographical Information Service (GIS) formats. Providing the data in open GIS standard formats allowed the end user to easily integrate the data into existing Decision Support Systems (DSS). Both Tile Mapping Service (TMS) and Web Mapping Service (WMS) were leveraged to quickly provide the data to the end-user. Development of the deliver methodology allowed quick response to rapidly developing disasters and enabled NASA SPoRT to bring science data to decision makers in a successful research to operations transition.

Use of Open Standards and Technologies at the Lunar Mapping and Modeling Project

NASA Astrophysics Data System (ADS)

Law, E.; Malhotra, S.; Bui, B.; Chang, G.; Goodale, C. E.; Ramirez, P.; Kim, R. M.; Sadaqathulla, S.; Rodriguez, L.

2011-12-01

The Lunar Mapping and Modeling Project (LMMP), led by the Marshall Space Flight center (MSFC), is tasked by NASA. The project is responsible for the development of an information system to support lunar exploration activities. It provides lunar explorers a set of tools and lunar map and model products that are predominantly derived from present lunar missions (e.g., the Lunar Reconnaissance Orbiter (LRO)) and from historical missions (e.g., Apollo). At Jet Propulsion Laboratory (JPL), we have built the LMMP interoperable geospatial information system's underlying infrastructure and a single point of entry - the LMMP Portal by employing a number of open standards and technologies. The Portal exposes a set of services to users to allow search, visualization, subset, and download of lunar data managed by the system. Users also have access to a set of tools that visualize, analyze and annotate the data. The infrastructure and Portal are based on web service oriented architecture. We designed the system to support solar system bodies in general including asteroids, earth and planets. We employed a combination of custom software, commercial and open-source components, off-the-shelf hardware and pay-by-use cloud computing services. The use of open standards and web service interfaces facilitate platform and application independent access to the services and data, offering for instances, iPad and Android mobile applications and large screen multi-touch with 3-D terrain viewing functions, for a rich browsing and analysis experience from a variety of platforms. The web services made use of open standards including: Representational State Transfer (REST); and Open Geospatial Consortium (OGC)'s Web Map Service (WMS), Web Coverage Service (WCS), Web Feature Service (WFS). Its data management services have been built on top of a set of open technologies including: Object Oriented Data Technology (OODT) - open source data catalog, archive, file management, data grid framework; openSSO - open source access management and federation platform; solr - open source enterprise search platform; redmine - open source project collaboration and management framework; GDAL - open source geospatial data abstraction library; and others. Its data products are compliant with Federal Geographic Data Committee (FGDC) metadata standard. This standardization allows users to access the data products via custom written applications or off-the-shelf applications such as GoogleEarth. We will demonstrate this ready-to-use system for data discovery and visualization by walking through the data services provided through the portal such as browse, search, and other tools. We will further demonstrate image viewing and layering of lunar map images from the Internet, via mobile devices such as Apple's iPad.

DISPLA: decision information system for procurement and logistics analysis

NASA Astrophysics Data System (ADS)

Calvo, Alberto B.; Danish, Alexander J.; Lamonakis, Gregory G.

2002-08-01

This paper describes an information-exchange system for Display systems acquisition and logistics support. DISPLA (Decision Information System for Procurement and Logistics Analysis) is an Internet-based system concept for bringing sellers (display system and component suppliers) and buyers (Government Program Offices and System Integrators) together in an electronic exchange to improve the acquisition and logistics analysis support of Flat Panel Displays for the military. A proof-of-concept demonstration is presented in this paper using sample data from vendor Web sites and Government data sources.

Web-based health services and clinical decision support.

PubMed

Jegelevicius, Darius; Marozas, Vaidotas; Lukosevicius, Arunas; Patasius, Martynas

2004-01-01

The purpose of this study was the development of a Web-based e-health service for comprehensive assistance and clinical decision support. The service structure consists of a Web server, a PHP-based Web interface linked to a clinical SQL database, Java applets for interactive manipulation and visualization of signals and a Matlab server linked with signal and data processing algorithms implemented by Matlab programs. The service ensures diagnostic signal- and image analysis-sbased clinical decision support. By using the discussed methodology, a pilot service for pathology specialists for automatic calculation of the proliferation index has been developed. Physicians use a simple Web interface for uploading the pictures under investigation to the server; subsequently a Java applet interface is used for outlining the region of interest and, after processing on the server, the requested proliferation index value is calculated. There is also an "expert corner", where experts can submit their index estimates and comments on particular images, which is especially important for system developers. These expert evaluations are used for optimization and verification of automatic analysis algorithms. Decision support trials have been conducted for ECG and ophthalmology ultrasonic investigations of intraocular tumor differentiation. Data mining algorithms have been applied and decision support trees constructed. These services are under implementation by a Web-based system too. The study has shown that the Web-based structure ensures more effective, flexible and accessible services compared with standalone programs and is very convenient for biomedical engineers and physicians, especially in the development phase.

Web-GIS-based SARS epidemic situation visualization

NASA Astrophysics Data System (ADS)

Lu, Xiaolin

2004-03-01

In order to research, perform statistical analysis and broadcast the information of SARS epidemic situation according to the relevant spatial position, this paper proposed a unified global visualization information platform for SARS epidemic situation based on Web-GIS and scientific virtualization technology. To setup the unified global visual information platform, the architecture of Web-GIS based interoperable information system is adopted to enable public report SARS virus information to health cure center visually by using the web visualization technology. A GIS java applet is used to visualize the relationship between spatial graphical data and virus distribution, and other web based graphics figures such as curves, bars, maps and multi-dimensional figures are used to visualize the relationship between SARS virus tendency with time, patient number or locations. The platform is designed to display the SARS information in real time, simulate visually for real epidemic situation and offer an analyzing tools for health department and the policy-making government department to support the decision-making for preventing against the SARS epidemic virus. It could be used to analyze the virus condition through visualized graphics interface, isolate the areas of virus source, and control the virus condition within shortest time. It could be applied to the visualization field of SARS preventing systems for SARS information broadcasting, data management, statistical analysis, and decision supporting.

Evaluating a Web-Based MMR Decision Aid to Support Informed Decision-Making by UK Parents: A Before-and-After Feasibility Study

ERIC Educational Resources Information Center

Jackson, Cath; Cheater, Francine M.; Peacock, Rose; Leask, Julie; Trevena, Lyndal

2010-01-01

Objective: The objective of this feasibility study was to evaluate the acceptability and potential effectiveness of a web-based MMR decision aid in supporting informed decision-making for the MMR vaccine. Design: This was a prospective before-and-after evaluation. Setting: Thirty parents of children eligible for MMR vaccination were recruited from…

Open-Source Electronic Health Record Systems for Low-Resource Settings: Systematic Review

PubMed Central

Zolfo, Maria; Diro, Ermias

2017-01-01

Background Despite the great impact of information and communication technologies on clinical practice and on the quality of health services, this trend has been almost exclusive to developed countries, whereas countries with poor resources suffer from many economic and social issues that have hindered the real benefits of electronic health (eHealth) tools. As a component of eHealth systems, electronic health records (EHRs) play a fundamental role in patient management and effective medical care services. Thus, the adoption of EHRs in regions with a lack of infrastructure, untrained staff, and ill-equipped health care providers is an important task. However, the main barrier to adopting EHR software in low- and middle-income countries is the cost of its purchase and maintenance, which highlights the open-source approach as a good solution for these underserved areas. Objective The aim of this study was to conduct a systematic review of open-source EHR systems based on the requirements and limitations of low-resource settings. Methods First, we reviewed existing literature on the comparison of available open-source solutions. In close collaboration with the University of Gondar Hospital, Ethiopia, we identified common limitations in poor resource environments and also the main requirements that EHRs should support. Then, we extensively evaluated the current open-source EHR solutions, discussing their strengths and weaknesses, and their appropriateness to fulfill a predefined set of features relevant for low-resource settings. Results The evaluation methodology allowed assessment of several key aspects of available solutions that are as follows: (1) integrated applications, (2) configurable reports, (3) custom reports, (4) custom forms, (5) interoperability, (6) coding systems, (7) authentication methods, (8) patient portal, (9) access control model, (10) cryptographic features, (11) flexible data model, (12) offline support, (13) native client, (14) Web client,(15) other clients, (16) code-based language, (17) development activity, (18) modularity, (19) user interface, (20) community support, and (21) customization. The quality of each feature is discussed for each of the evaluated solutions and a final comparison is presented. Conclusions There is a clear demand for open-source, reliable, and flexible EHR systems in low-resource settings. In this study, we have evaluated and compared five open-source EHR systems following a multidimensional methodology that can provide informed recommendations to other implementers, developers, and health care professionals. We hope that the results of this comparison can guide decision making when needing to adopt, install, and maintain an open-source EHR solution in low-resource settings. PMID:29133283

Tank Information System (tis): a Case Study in Migrating Web Mapping Application from Flex to Dojo for Arcgis Server and then to Open Source

NASA Astrophysics Data System (ADS)

Pulsani, B. R.

2017-11-01

Tank Information System is a web application which provides comprehensive information about minor irrigation tanks of Telangana State. As part of the program, a web mapping application using Flex and ArcGIS server was developed to make the data available to the public. In course of time as Flex be-came outdated, a migration of the client interface to the latest JavaScript based technologies was carried out. Initially, the Flex based application was migrated to ArcGIS JavaScript API using Dojo Toolkit. Both the client applications used published services from ArcGIS server. To check the migration pattern from proprietary to open source, the JavaScript based ArcGIS application was later migrated to OpenLayers and Dojo Toolkit which used published service from GeoServer. The migration pattern noticed in the study especially emphasizes upon the use of Dojo Toolkit and PostgreSQL database for ArcGIS server so that migration to open source could be performed effortlessly. The current ap-plication provides a case in study which could assist organizations in migrating their proprietary based ArcGIS web applications to open source. Furthermore, the study reveals cost benefits of adopting open source against commercial software's.

Open source software integrated into data services of Japanese planetary explorations

NASA Astrophysics Data System (ADS)

Yamamoto, Y.; Ishihara, Y.; Otake, H.; Imai, K.; Masuda, K.

2015-12-01

Scientific data obtained by Japanese scientific satellites and lunar and planetary explorations are archived in DARTS (Data ARchives and Transmission System). DARTS provides the data with a simple method such as HTTP directory listing for long-term preservation while DARTS tries to provide rich web applications for ease of access with modern web technologies based on open source software. This presentation showcases availability of open source software through our services. KADIAS is a web-based application to search, analyze, and obtain scientific data measured by SELENE(Kaguya), a Japanese lunar orbiter. KADIAS uses OpenLayers to display maps distributed from Web Map Service (WMS). As a WMS server, open source software MapServer is adopted. KAGUYA 3D GIS (KAGUYA 3D Moon NAVI) provides a virtual globe for the SELENE's data. The main purpose of this application is public outreach. NASA World Wind Java SDK is used to develop. C3 (Cross-Cutting Comparisons) is a tool to compare data from various observations and simulations. It uses Highcharts to draw graphs on web browsers. Flow is a tool to simulate a Field-Of-View of an instrument onboard a spacecraft. This tool itself is open source software developed by JAXA/ISAS, and the license is BSD 3-Caluse License. SPICE Toolkit is essential to compile FLOW. SPICE Toolkit is also open source software developed by NASA/JPL, and the website distributes many spacecrafts' data. Nowadays, open source software is an indispensable tool to integrate DARTS services.

Leveraging Open Standard Interfaces in Providing Efficient Discovery, Retrieval, and Information of NASA-Sponsored Observations and Predictions

NASA Astrophysics Data System (ADS)

Cole, M.; Alameh, N.; Bambacus, M.

2006-05-01

The Applied Sciences Program at NASA focuses on extending the results of NASA's Earth-Sun system science research beyond the science and research communities to contribute to national priority applications with societal benefits. By employing a systems engineering approach, supporting interoperable data discovery and access, and developing partnerships with federal agencies and national organizations, the Applied Sciences Program facilitates the transition from research to operations in national applications. In particular, the Applied Sciences Program identifies twelve national applications, listed at http://science.hq.nasa.gov/earth-sun/applications/, which can be best served by the results of NASA aerospace research and development of science and technologies. The ability to use and integrate NASA data and science results into these national applications results in enhanced decision support and significant socio-economic benefits for each of the applications. This paper focuses on leveraging the power of interoperability and specifically open standard interfaces in providing efficient discovery, retrieval, and integration of NASA's science research results. Interoperability (the ability to access multiple, heterogeneous geoprocessing environments, either local or remote by means of open and standard software interfaces) can significantly increase the value of NASA-related data by increasing the opportunities to discover, access and integrate that data in the twelve identified national applications (particularly in non-traditional settings). Furthermore, access to data, observations, and analytical models from diverse sources can facilitate interdisciplinary and exploratory research and analysis. To streamline this process, the NASA GeoSciences Interoperability Office (GIO) is developing the NASA Earth-Sun System Gateway (ESG) to enable access to remote geospatial data, imagery, models, and visualizations through open, standard web protocols. The gateway (online at http://esg.gsfc.nasa.gov) acts as a flexible and searchable registry of NASA-related resources (files, services, models, etc) and allows scientists, decision makers and others to discover and retrieve a wide variety of observations and predictions of natural and human phenomena related to Earth Science from NASA and other sources. To support the goals of the Applied Sciences national applications, GIO staff is also working with the national applications communities to identify opportunities where open standards-based discovery and access to NASA data can enhance the decision support process of the national applications. This paper describes the work performed to-date on that front, and summarizes key findings in terms of identified data sources and benefiting national applications. The paper also highlights the challenges encountered in making NASA-related data accessible in a cross-cutting fashion and identifies areas where interoperable approaches can be leveraged.

A Clinician-Centered Evaluation of the Usability of AHLTA and Automated Clinical Practice Guidelines at TAMC

DTIC Science & Technology

2011-03-31

evidence based medicine into clinical practice. It will decrease costs and enable multiple stakeholders to work in an open content/source environment to exchange clinical content, develop and test technology and explore processes in applied CDS. Design: Comparative study between the KMR infrastructure and capabilities developed as an open source, vendor agnostic solution for aCPG execution within AHLTA and the current DoD/MHS standard evaluating: H1: An open source, open standard KMR and Clinical Decision Support Engine can enable organizations to share domain

Web-Based Versus Usual Care and Other Formats of Decision Aids to Support Prostate Cancer Screening Decisions: Systematic Review and Meta-Analysis.

PubMed

Baptista, Sofia; Teles Sampaio, Elvira; Heleno, Bruno; Azevedo, Luís Filipe; Martins, Carlos

2018-06-26

Prostate cancer is a leading cause of cancer among men. Because screening for prostate cancer is a controversial issue, many experts in the field have defended the use of shared decision making using validated decision aids, which can be presented in different formats (eg, written, multimedia, Web). Recent studies have concluded that decision aids improve knowledge and reduce decisional conflict. This meta-analysis aimed to investigate the impact of using Web-based decision aids to support men's prostate cancer screening decisions in comparison with usual care and other formats of decision aids. We searched PubMed, CINAHL, PsycINFO, and Cochrane CENTRAL databases up to November 2016. This search identified randomized controlled trials, which assessed Web-based decision aids for men making a prostate cancer screening decision and reported quality of decision-making outcomes. Two reviewers independently screened citations for inclusion criteria, extracted data, and assessed risk of bias. Using a random-effects model, meta-analyses were conducted pooling results using mean differences (MD), standardized mean differences (SMD), and relative risks (RR). Of 2406 unique citations, 7 randomized controlled trials met the inclusion criteria. For risk of bias, selective outcome reporting and participant/personnel blinding were mostly rated as unclear due to inadequate reporting. Based on seven items, two studies had high risk of bias for one item. Compared to usual care, Web-based decision aids increased knowledge (SMD 0.46; 95% CI 0.18-0.75), reduced decisional conflict (MD -7.07%; 95% CI -9.44 to -4.71), and reduced the practitioner control role in the decision-making process (RR 0.50; 95% CI 0.31-0.81). Web-based decision aids compared to printed decision aids yielded no differences in knowledge, decisional conflict, and participation in decision or screening behaviors. Compared to video decision aids, Web-based decision aids showed lower average knowledge scores (SMD -0.50; 95% CI -0.88 to -0.12) and a slight decrease in prostate-specific antigen screening (RR 1.12; 95% CI 1.01-1.25). According to this analysis, Web-based decision aids performed similarly to alternative formats (ie, printed, video) for the assessed decision-quality outcomes. The low cost, readiness, availability, and anonymity of the Web can be an advantage for increasing access to decision aids that support prostate cancer screening decisions among men. ©Sofia Baptista, Elvira Teles Sampaio, Bruno Heleno, Luís Filipe Azevedo, Carlos Martins. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 26.06.2018.

Tele-healthcare for diabetes management: A low cost automatic approach.

PubMed

Benaissa, M; Malik, B; Kanakis, A; Wright, N P

2012-01-01

In this paper, a telemedicine system for managing diabetic patients with better care is presented. The system is an end to end solution which relies on the integration of front end (patient unit) and backend web server. A key feature of the system developed is the very low cost automated approach. The front-end of the system is capable of reading glucose measurements from any glucose meter and sending them automatically via existing networks to the back-end server. The back-end is designed and developed using n-tier web client architecture based on model-view-controller design pattern using open source technology, a cost effective solution. The back-end helps the health-care provider with data analysis; data visualization and decision support, and allows them to send feedback and therapeutic advice to patients from anywhere using a browser enabled device. This system will be evaluated during the trials which will be conducted in collaboration with a local hospital in phased manner.

Baobab Laboratory Information Management System: Development of an Open-Source Laboratory Information Management System for Biobanking

PubMed Central

Bendou, Hocine; Sizani, Lunga; Reid, Tim; Swanepoel, Carmen; Ademuyiwa, Toluwaleke; Merino-Martinez, Roxana; Meuller, Heimo; Abayomi, Akin

2017-01-01

A laboratory information management system (LIMS) is central to the informatics infrastructure that underlies biobanking activities. To date, a wide range of commercial and open-source LIMSs are available and the decision to opt for one LIMS over another is often influenced by the needs of the biobank clients and researchers, as well as available financial resources. The Baobab LIMS was developed by customizing the Bika LIMS software (www.bikalims.org) to meet the requirements of biobanking best practices. The need to implement biobank standard operation procedures as well as stimulate the use of standards for biobank data representation motivated the implementation of Baobab LIMS, an open-source LIMS for Biobanking. Baobab LIMS comprises modules for biospecimen kit assembly, shipping of biospecimen kits, storage management, analysis requests, reporting, and invoicing. The Baobab LIMS is based on the Plone web-content management framework. All the system requirements for Plone are applicable to Baobab LIMS, including the need for a server with at least 8 GB RAM and 120 GB hard disk space. Baobab LIMS is a server–client-based system, whereby the end user is able to access the system securely through the internet on a standard web browser, thereby eliminating the need for standalone installations on all machines. PMID:28375759

Baobab Laboratory Information Management System: Development of an Open-Source Laboratory Information Management System for Biobanking.

PubMed

Bendou, Hocine; Sizani, Lunga; Reid, Tim; Swanepoel, Carmen; Ademuyiwa, Toluwaleke; Merino-Martinez, Roxana; Meuller, Heimo; Abayomi, Akin; Christoffels, Alan

2017-04-01

A laboratory information management system (LIMS) is central to the informatics infrastructure that underlies biobanking activities. To date, a wide range of commercial and open-source LIMSs are available and the decision to opt for one LIMS over another is often influenced by the needs of the biobank clients and researchers, as well as available financial resources. The Baobab LIMS was developed by customizing the Bika LIMS software ( www.bikalims.org ) to meet the requirements of biobanking best practices. The need to implement biobank standard operation procedures as well as stimulate the use of standards for biobank data representation motivated the implementation of Baobab LIMS, an open-source LIMS for Biobanking. Baobab LIMS comprises modules for biospecimen kit assembly, shipping of biospecimen kits, storage management, analysis requests, reporting, and invoicing. The Baobab LIMS is based on the Plone web-content management framework. All the system requirements for Plone are applicable to Baobab LIMS, including the need for a server with at least 8 GB RAM and 120 GB hard disk space. Baobab LIMS is a server-client-based system, whereby the end user is able to access the system securely through the internet on a standard web browser, thereby eliminating the need for standalone installations on all machines.

Design and implementation of the standards-based personal intelligent self-management system (PICS).

PubMed

von Bargen, Tobias; Gietzelt, Matthias; Britten, Matthias; Song, Bianying; Wolf, Klaus-Hendrik; Kohlmann, Martin; Marschollek, Michael; Haux, Reinhold

2013-01-01

Against the background of demographic change and a diminishing care workforce there is a growing need for personalized decision support. The aim of this paper is to describe the design and implementation of the standards-based personal intelligent care systems (PICS). PICS makes consistent use of internationally accepted standards such as the Health Level 7 (HL7) Arden syntax for the representation of the decision logic, HL7 Clinical Document Architecture for information representation and is based on a open-source service-oriented architecture framework and a business process management system. Its functionality is exemplified for the application scenario of a patient suffering from congestive heart failure. Several vital signs sensors provide data for the decision support system, and a number of flexible communication channels are available for interaction with patient or caregiver. PICS is a standards-based, open and flexible system enabling personalized decision support. Further development will include the implementation of components on small computers and sensor nodes.

A Multimodal Search Engine for Medical Imaging Studies.

PubMed

Pinho, Eduardo; Godinho, Tiago; Valente, Frederico; Costa, Carlos

2017-02-01

The use of digital medical imaging systems in healthcare institutions has increased significantly, and the large amounts of data in these systems have led to the conception of powerful support tools: recent studies on content-based image retrieval (CBIR) and multimodal information retrieval in the field hold great potential in decision support, as well as for addressing multiple challenges in healthcare systems, such as computer-aided diagnosis (CAD). However, the subject is still under heavy research, and very few solutions have become part of Picture Archiving and Communication Systems (PACS) in hospitals and clinics. This paper proposes an extensible platform for multimodal medical image retrieval, integrated in an open-source PACS software with profile-based CBIR capabilities. In this article, we detail a technical approach to the problem by describing its main architecture and each sub-component, as well as the available web interfaces and the multimodal query techniques applied. Finally, we assess our implementation of the engine with computational performance benchmarks.

Virtualization of open-source secure web services to support data exchange in a pediatric critical care research network.

PubMed

Frey, Lewis J; Sward, Katherine A; Newth, Christopher J L; Khemani, Robinder G; Cryer, Martin E; Thelen, Julie L; Enriquez, Rene; Shaoyu, Su; Pollack, Murray M; Harrison, Rick E; Meert, Kathleen L; Berg, Robert A; Wessel, David L; Shanley, Thomas P; Dalton, Heidi; Carcillo, Joseph; Jenkins, Tammara L; Dean, J Michael

2015-11-01

To examine the feasibility of deploying a virtual web service for sharing data within a research network, and to evaluate the impact on data consistency and quality. Virtual machines (VMs) encapsulated an open-source, semantically and syntactically interoperable secure web service infrastructure along with a shadow database. The VMs were deployed to 8 Collaborative Pediatric Critical Care Research Network Clinical Centers. Virtual web services could be deployed in hours. The interoperability of the web services reduced format misalignment from 56% to 1% and demonstrated that 99% of the data consistently transferred using the data dictionary and 1% needed human curation. Use of virtualized open-source secure web service technology could enable direct electronic abstraction of data from hospital databases for research purposes. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A web-based screening tool for near-port air quality assessments

PubMed Central

Isakov, Vlad; Barzyk, Timothy M.; Smith, Elizabeth R.; Arunachalam, Saravanan; Naess, Brian; Venkatram, Akula

2018-01-01

The Community model for near-PORT applications (C-PORT) is a screening tool with an intended purpose of calculating differences in annual averaged concentration patterns and relative contributions of various source categories over the spatial domain within about 10 km of the port. C-PORT can inform decision-makers and concerned citizens about local air quality due to mobile source emissions related to commercial port activities. It allows users to visualize and evaluate different planning scenarios, helping them identify the best alternatives for making long-term decisions that protect community health and sustainability. The web-based, easy-to-use interface currently includes data from 21 seaports primarily in the Southeastern U.S., and has a map-based interface based on Google Maps. The tool was developed to visualize and assess changes in air quality due to changes in emissions and/or meteorology in order to analyze development scenarios, and is not intended to support or replace any regulatory models or programs. PMID:29681760

Web accessibility and open source software.

PubMed

Obrenović, Zeljko

2009-07-01

A Web browser provides a uniform user interface to different types of information. Making this interface universally accessible and more interactive is a long-term goal still far from being achieved. Universally accessible browsers require novel interaction modalities and additional functionalities, for which existing browsers tend to provide only partial solutions. Although functionality for Web accessibility can be found as open source and free software components, their reuse and integration is complex because they were developed in diverse implementation environments, following standards and conventions incompatible with the Web. To address these problems, we have started several activities that aim at exploiting the potential of open-source software for Web accessibility. The first of these activities is the development of Adaptable Multi-Interface COmmunicator (AMICO):WEB, an infrastructure that facilitates efficient reuse and integration of open source software components into the Web environment. The main contribution of AMICO:WEB is in enabling the syntactic and semantic interoperability between Web extension mechanisms and a variety of integration mechanisms used by open source and free software components. Its design is based on our experiences in solving practical problems where we have used open source components to improve accessibility of rich media Web applications. The second of our activities involves improving education, where we have used our platform to teach students how to build advanced accessibility solutions from diverse open-source software. We are also partially involved in the recently started Eclipse projects called Accessibility Tools Framework (ACTF), the aim of which is development of extensible infrastructure, upon which developers can build a variety of utilities that help to evaluate and enhance the accessibility of applications and content for people with disabilities. In this article we briefly report on these activities.

Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects

PubMed Central

Hyam, Roger; Hagedorn, Gregor; Chagnoux, Simon; Röpert, Dominik; Casino, Ana; Droege, Gabi; Glöckler, Falko; Gödderz, Karsten; Groom, Quentin; Hoffmann, Jana; Holleman, Ayco; Kempa, Matúš; Koivula, Hanna; Marhold, Karol; Nicolson, Nicky; Smith, Vincent S.; Triebel, Dagmar

2017-01-01

With biodiversity research activities being increasingly shifted to the web, the need for a system of persistent and stable identifiers for physical collection objects becomes increasingly pressing. The Consortium of European Taxonomic Facilities agreed on a common system of HTTP-URI-based stable identifiers which is now rolled out to its member organizations. The system follows Linked Open Data principles and implements redirection mechanisms to human-readable and machine-readable representations of specimens facilitating seamless integration into the growing semantic web. The implementation of stable identifiers across collection organizations is supported with open source provider software scripts, best practices documentations and recommendations for RDF metadata elements facilitating harmonized access to collection information in web portals. Database URL: http://cetaf.org/cetaf-stable-identifiers PMID:28365724

Data Mining Meets HCI: Making Sense of Large Graphs

DTIC Science & Technology

2012-07-01

graph algo- rithms, won the Open Source Software World Challenge, Silver Award. We have released Pegasus as free , open-source software, downloaded by...METIS [77], spectral clustering [108], and the parameter- free “Cross-associations” (CA) [26]. Belief Propagation can also be used for clus- tering, as...number of tools have been developed to support “ landscape ” views of information. These include WebBook and Web- Forager [23], which use a book metaphor

High performance geospatial and climate data visualization using GeoJS

NASA Astrophysics Data System (ADS)

Chaudhary, A.; Beezley, J. D.

2015-12-01

GeoJS (https://github.com/OpenGeoscience/geojs) is an open-source library developed to support interactive scientific and geospatial visualization of climate and earth science datasets in a web environment. GeoJS has a convenient application programming interface (API) that enables users to harness the fast performance of WebGL and Canvas 2D APIs with sophisticated Scalable Vector Graphics (SVG) features in a consistent and convenient manner. We started the project in response to the need for an open-source JavaScript library that can combine traditional geographic information systems (GIS) and scientific visualization on the web. Many libraries, some of which are open source, support mapping or other GIS capabilities, but lack the features required to visualize scientific and other geospatial datasets. For instance, such libraries are not be capable of rendering climate plots from NetCDF files, and some libraries are limited in regards to geoinformatics (infovis in a geospatial environment). While libraries such as d3.js are extremely powerful for these kinds of plots, in order to integrate them into other GIS libraries, the construction of geoinformatics visualizations must be completed manually and separately, or the code must somehow be mixed in an unintuitive way.We developed GeoJS with the following motivations:• To create an open-source geovisualization and GIS library that combines scientific visualization with GIS and informatics• To develop an extensible library that can combine data from multiple sources and render them using multiple backends• To build a library that works well with existing scientific visualizations tools such as VTKWe have successfully deployed GeoJS-based applications for multiple domains across various projects. The ClimatePipes project funded by the Department of Energy, for example, used GeoJS to visualize NetCDF datasets from climate data archives. Other projects built visualizations using GeoJS for interactively exploring data and analysis regarding 1) the human trafficking domain, 2) New York City taxi drop-offs and pick-ups, and 3) the Ebola outbreak. GeoJS supports advanced visualization features such as picking and selecting, as well as clustering. It also supports 2D contour plots, vector plots, heat maps, and geospatial graphs.

FEMA's Earthquake Incident Journal: A Web-Based Data Integration and Decision Support Tool for Emergency Management

NASA Astrophysics Data System (ADS)

Jones, M.; Pitts, R.

2017-12-01

For emergency managers, government officials, and others who must respond to rapidly changing natural disasters, timely access to detailed information related to affected terrain, population and infrastructure is critical for planning, response and recovery operations. Accessing, analyzing and disseminating such disparate information in near real-time are critical decision support components. However, finding a way to handle a variety of informative yet complex datasets poses a challenge when preparing for and responding to disasters. Here, we discuss the implementation of a web-based data integration and decision support tool for earthquakes developed by the Federal Emergency Management Agency (FEMA) as a solution to some of these challenges. While earthquakes are among the most well- monitored and measured of natural hazards, the spatially broad impacts of shaking, ground deformation, landslides, liquefaction, and even tsunamis, are extremely difficult to quantify without accelerated access to data, modeling, and analytics. This web-based application, deemed the "Earthquake Incident Journal", provides real-time access to authoritative and event-specific data from external (e.g. US Geological Survey, NASA, state and local governments, etc.) and internal (FEMA) data sources. The journal includes a GIS-based model for exposure analytics, allowing FEMA to assess the severity of an event, estimate impacts to structures and population in near real-time, and then apply planning factors to exposure estimates to answer questions such as: What geographic areas are impacted? Will federal support be needed? What resources are needed to support survivors? And which infrastructure elements or essential facilities are threatened? This presentation reviews the development of the Earthquake Incident Journal, detailing the data integration solutions, the methodology behind the GIS-based automated exposure model, and the planning factors as well as other analytical advances that provide near real-time decision support to the federal government.

Using Mobile App Development Tools to Build a GIS Application

NASA Astrophysics Data System (ADS)

Mital, A.; Catchen, M.; Mital, K.

2014-12-01

Our group designed and built working web, android, and IOS applications using different mapping libraries as bases on which to overlay fire data from NASA. The group originally planned to make app versions for Google Maps, Leaflet, and OpenLayers. However, because the Leaflet library did not properly load on Android, the group focused efforts on the other two mapping libraries. For Google Maps, the group first designed a UI for the web app and made a working version of the app. After updating the source of fire data to one which also provided historical fire data, the design had to be modified to include the extra data. After completing a working version of the web app, the group used webview in android, a built in resource which allowed porting the web app to android without rewriting the code for android. Upon completing this, the group found Apple IOS devices had a similar capability, and so decided to add an IOS app to the project using a function similar to webview. Alongside this effort, the group began implementing an OpenLayers fire map using a simpler UI. This web app was completed fairly quickly relative to Google Maps; however, it did not include functionality such as satellite imagery or searchable locations. The group finished the project with a working android version of the Google Maps based app supporting API levels 14-19 and an OpenLayers based app supporting API levels 8-19, as well as a Google Maps based IOS app supporting both old and new screen formats. This project was implemented by high school and college students under an SGT Inc. STEM internship program

Computational toxicology using the OpenTox application programming interface and Bioclipse

PubMed Central

2011-01-01

Background Toxicity is a complex phenomenon involving the potential adverse effect on a range of biological functions. Predicting toxicity involves using a combination of experimental data (endpoints) and computational methods to generate a set of predictive models. Such models rely strongly on being able to integrate information from many sources. The required integration of biological and chemical information sources requires, however, a common language to express our knowledge ontologically, and interoperating services to build reliable predictive toxicology applications. Findings This article describes progress in extending the integrative bio- and cheminformatics platform Bioclipse to interoperate with OpenTox, a semantic web framework which supports open data exchange and toxicology model building. The Bioclipse workbench environment enables functionality from OpenTox web services and easy access to OpenTox resources for evaluating toxicity properties of query molecules. Relevant cases and interfaces based on ten neurotoxins are described to demonstrate the capabilities provided to the user. The integration takes advantage of semantic web technologies, thereby providing an open and simplifying communication standard. Additionally, the use of ontologies ensures proper interoperation and reliable integration of toxicity information from both experimental and computational sources. Conclusions A novel computational toxicity assessment platform was generated from integration of two open science platforms related to toxicology: Bioclipse, that combines a rich scriptable and graphical workbench environment for integration of diverse sets of information sources, and OpenTox, a platform for interoperable toxicology data and computational services. The combination provides improved reliability and operability for handling large data sets by the use of the Open Standards from the OpenTox Application Programming Interface. This enables simultaneous access to a variety of distributed predictive toxicology databases, and algorithm and model resources, taking advantage of the Bioclipse workbench handling the technical layers. PMID:22075173

Visual DMDX: A web-based authoring tool for DMDX, a Windows display program with millisecond accuracy.

PubMed

Garaizar, Pablo; Reips, Ulf-Dietrich

2015-09-01

DMDX is a software package for the experimental control and timing of stimulus display for Microsoft Windows systems. DMDX is reliable, flexible, millisecond accurate, and can be downloaded free of charge; therefore it has become very popular among experimental researchers. However, setting up a DMDX-based experiment is burdensome because of its command-based interface. Further, DMDX relies on RTF files in which parts of the stimuli, design, and procedure of an experiment are defined in a complicated (DMASTR-compatible) syntax. Other experiment software, such as E-Prime, Psychopy, and WEXTOR, became successful as a result of integrated visual authoring tools. Such an intuitive interface was lacking for DMDX. We therefore created and present here Visual DMDX (http://visualdmdx.com/), a HTML5-based web interface to set up experiments and export them to DMDX item files format in RTF. Visual DMDX offers most of the features available from the rich DMDX/DMASTR syntax, and it is a useful tool to support researchers who are new to DMDX. Both old and modern versions of DMDX syntax are supported. Further, with Visual DMDX, we go beyond DMDX by having added export to JSON (a versatile web format), easy backup, and a preview option for experiments. In two examples, one experiment each on lexical decision making and affective priming, we explain in a step-by-step fashion how to create experiments using Visual DMDX. We release Visual DMDX under an open-source license to foster collaboration in its continuous improvement.

AN OPEN-SOURCE COMMUNITY WEB SITE TO SUPPORT GROUND-WATER MODEL TESTING

EPA Science Inventory

A community wiki wiki web site has been created as a resource to support ground-water model development and testing. The Groundwater Gourmet wiki is a repository for user supplied analytical and numerical recipes, how-to's, and examples. Members are encouraged to submit analyti...

Phynx: an open source software solution supporting data management and web-based patient-level data review for drug safety studies in the general practice research database and other health care databases.

PubMed

Egbring, Marco; Kullak-Ublick, Gerd A; Russmann, Stefan

2010-01-01

To develop a software solution that supports management and clinical review of patient data from electronic medical records databases or claims databases for pharmacoepidemiological drug safety studies. We used open source software to build a data management system and an internet application with a Flex client on a Java application server with a MySQL database backend. The application is hosted on Amazon Elastic Compute Cloud. This solution named Phynx supports data management, Web-based display of electronic patient information, and interactive review of patient-level information in the individual clinical context. This system was applied to a dataset from the UK General Practice Research Database (GPRD). Our solution can be setup and customized with limited programming resources, and there is almost no extra cost for software. Access times are short, the displayed information is structured in chronological order and visually attractive, and selected information such as drug exposure can be blinded. External experts can review patient profiles and save evaluations and comments via a common Web browser. Phynx provides a flexible and economical solution for patient-level review of electronic medical information from databases considering the individual clinical context. It can therefore make an important contribution to an efficient validation of outcome assessment in drug safety database studies.

Cloud computing geospatial application for water resources based on free and open source software and open standards - a prototype

NASA Astrophysics Data System (ADS)

Delipetrev, Blagoj

2016-04-01

Presently, most of the existing software is desktop-based, designed to work on a single computer, which represents a major limitation in many ways, starting from limited computer processing, storage power, accessibility, availability, etc. The only feasible solution lies in the web and cloud. This abstract presents research and development of a cloud computing geospatial application for water resources based on free and open source software and open standards using hybrid deployment model of public - private cloud, running on two separate virtual machines (VMs). The first one (VM1) is running on Amazon web services (AWS) and the second one (VM2) is running on a Xen cloud platform. The presented cloud application is developed using free and open source software, open standards and prototype code. The cloud application presents a framework how to develop specialized cloud geospatial application that needs only a web browser to be used. This cloud application is the ultimate collaboration geospatial platform because multiple users across the globe with internet connection and browser can jointly model geospatial objects, enter attribute data and information, execute algorithms, and visualize results. The presented cloud application is: available all the time, accessible from everywhere, it is scalable, works in a distributed computer environment, it creates a real-time multiuser collaboration platform, the programing languages code and components are interoperable, and it is flexible in including additional components. The cloud geospatial application is implemented as a specialized water resources application with three web services for 1) data infrastructure (DI), 2) support for water resources modelling (WRM), 3) user management. The web services are running on two VMs that are communicating over the internet providing services to users. The application was tested on the Zletovica river basin case study with concurrent multiple users. The application is a state-of-the-art cloud geospatial collaboration platform. The presented solution is a prototype and can be used as a foundation for developing of any specialized cloud geospatial applications. Further research will be focused on distributing the cloud application on additional VMs, testing the scalability and availability of services.

Adaptation of a web-based, open source electronic medical record system platform to support a large study of tuberculosis epidemiology

PubMed Central

2012-01-01

Background In 2006, we were funded by the US National Institutes of Health to implement a study of tuberculosis epidemiology in Peru. The study required a secure information system to manage data from a target goal of 16,000 subjects who needed to be followed for at least one year. With previous experience in the development and deployment of web-based medical record systems for TB treatment in Peru, we chose to use the OpenMRS open source electronic medical record system platform to develop the study information system. Supported by a core technical and management team and a large and growing worldwide community, OpenMRS is now being used in more than 40 developing countries. We adapted the OpenMRS platform to better support foreign languages. We added a new module to support double data entry, linkage to an existing laboratory information system, automatic upload of GPS data from handheld devices, and better security and auditing of data changes. We added new reports for study managers, and developed data extraction tools for research staff and statisticians. Further adaptation to handle direct entry of laboratory data occurred after the study was launched. Results Data collection in the OpenMRS system began in September 2009. By August 2011 a total of 9,256 participants had been enrolled, 102,274 forms and 13,829 laboratory results had been entered, and there were 208 users. The system is now entirely supported by the Peruvian study staff and programmers. Conclusions The information system served the study objectives well despite requiring some significant adaptations mid-stream. OpenMRS has more tools and capabilities than it did in 2008, and requires less adaptations for future projects. OpenMRS can be an effective research data system in resource poor environments, especially for organizations using or considering it for clinical care as well as research. PMID:23131180

Web-based Traffic Noise Control Support System for Sustainable Transportation

NASA Astrophysics Data System (ADS)

Fan, Lisa; Dai, Liming; Li, Anson

Traffic noise is considered as one of the major pollutions that will affect our communities in the future. This paper presents a framework of web-based traffic noise control support system (WTNCSS) for a sustainable transportation. WTNCSS is to provide the decision makers, engineers and publics a platform to efficiently access the information, and effectively making decisions related to traffic control. The system is based on a Service Oriented Architecture (SOA) which takes the advantages of the convenience of World Wide Web system with the data format of XML. The whole system is divided into different modules such as the prediction module, ontology-based expert module and dynamic online survey module. Each module of the system provides a distinct information service to the decision support center through the HTTP protocol.

Recent advancements on the development of web-based applications for the implementation of seismic analysis and surveillance systems

NASA Astrophysics Data System (ADS)

Friberg, P. A.; Luis, R. S.; Quintiliani, M.; Lisowski, S.; Hunter, S.

2014-12-01

Recently, a novel set of modules has been included in the Open Source Earthworm seismic data processing system, supporting the use of web applications. These include the Mole sub-system, for storing relevant event data in a MySQL database (see M. Quintiliani and S. Pintore, SRL, 2013), and an embedded webserver, Moleserv, for serving such data to web clients in QuakeML format. These modules have enabled, for the first time using Earthworm, the use of web applications for seismic data processing. These can greatly simplify the operation and maintenance of seismic data processing centers by having one or more servers providing the relevant data as well as the data processing applications themselves to client machines running arbitrary operating systems.Web applications with secure online web access allow operators to work anywhere, without the often cumbersome and bandwidth hungry use of secure shell or virtual private networks. Furthermore, web applications can seamlessly access third party data repositories to acquire additional information, such as maps. Finally, the usage of HTML email brought the possibility of specialized web applications, to be used in email clients. This is the case of EWHTMLEmail, which produces event notification emails that are in fact simple web applications for plotting relevant seismic data.Providing web services as part of Earthworm has enabled a number of other tools as well. One is ISTI's EZ Earthworm, a web based command and control system for an otherwise command line driven system; another is a waveform web service. The waveform web service serves Earthworm data to additional web clients for plotting, picking, and other web-based processing tools. The current Earthworm waveform web service hosts an advanced plotting capability for providing views of event-based waveforms from a Mole database served by Moleserve.The current trend towards the usage of cloud services supported by web applications is driving improvements in JavaScript, css and HTML, as well as faster and more efficient web browsers, including mobile. It is foreseeable that in the near future, web applications are as powerful and efficient as native applications. Hence the work described here has been the first step towards bringing the Open Source Earthworm seismic data processing system to this new paradigm.

Open-Source Electronic Health Record Systems for Low-Resource Settings: Systematic Review.

PubMed

Syzdykova, Assel; Malta, André; Zolfo, Maria; Diro, Ermias; Oliveira, José Luis

2017-11-13

Despite the great impact of information and communication technologies on clinical practice and on the quality of health services, this trend has been almost exclusive to developed countries, whereas countries with poor resources suffer from many economic and social issues that have hindered the real benefits of electronic health (eHealth) tools. As a component of eHealth systems, electronic health records (EHRs) play a fundamental role in patient management and effective medical care services. Thus, the adoption of EHRs in regions with a lack of infrastructure, untrained staff, and ill-equipped health care providers is an important task. However, the main barrier to adopting EHR software in low- and middle-income countries is the cost of its purchase and maintenance, which highlights the open-source approach as a good solution for these underserved areas. The aim of this study was to conduct a systematic review of open-source EHR systems based on the requirements and limitations of low-resource settings. First, we reviewed existing literature on the comparison of available open-source solutions. In close collaboration with the University of Gondar Hospital, Ethiopia, we identified common limitations in poor resource environments and also the main requirements that EHRs should support. Then, we extensively evaluated the current open-source EHR solutions, discussing their strengths and weaknesses, and their appropriateness to fulfill a predefined set of features relevant for low-resource settings. The evaluation methodology allowed assessment of several key aspects of available solutions that are as follows: (1) integrated applications, (2) configurable reports, (3) custom reports, (4) custom forms, (5) interoperability, (6) coding systems, (7) authentication methods, (8) patient portal, (9) access control model, (10) cryptographic features, (11) flexible data model, (12) offline support, (13) native client, (14) Web client,(15) other clients, (16) code-based language, (17) development activity, (18) modularity, (19) user interface, (20) community support, and (21) customization. The quality of each feature is discussed for each of the evaluated solutions and a final comparison is presented. There is a clear demand for open-source, reliable, and flexible EHR systems in low-resource settings. In this study, we have evaluated and compared five open-source EHR systems following a multidimensional methodology that can provide informed recommendations to other implementers, developers, and health care professionals. We hope that the results of this comparison can guide decision making when needing to adopt, install, and maintain an open-source EHR solution in low-resource settings. ©Assel Syzdykova, André Malta, Maria Zolfo, Ermias Diro, José Luis Oliveira. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 13.11.2017.

OntoMaton: a bioportal powered ontology widget for Google Spreadsheets.

PubMed

Maguire, Eamonn; González-Beltrán, Alejandra; Whetzel, Patricia L; Sansone, Susanna-Assunta; Rocca-Serra, Philippe

2013-02-15

Data collection in spreadsheets is ubiquitous, but current solutions lack support for collaborative semantic annotation that would promote shared and interdisciplinary annotation practices, supporting geographically distributed players. OntoMaton is an open source solution that brings ontology lookup and tagging capabilities into a cloud-based collaborative editing environment, harnessing Google Spreadsheets and the NCBO Web services. It is a general purpose, format-agnostic tool that may serve as a component of the ISA software suite. OntoMaton can also be used to assist the ontology development process. OntoMaton is freely available from Google widgets under the CPAL open source license; documentation and examples at: https://github.com/ISA-tools/OntoMaton.

Online Hydrologic Impact Assessment Decision Support System using Internet and Web-GIS Capability

NASA Astrophysics Data System (ADS)

Choi, J.; Engel, B. A.; Harbor, J.

2002-05-01

Urban sprawl and the corresponding land use change from lower intensity uses, such as agriculture and forests, to higher intensity uses including high density residential and commercial has various long- and short-term environment impacts on ground water recharge, water pollution, and storm water drainage. A web-based Spatial Decision Support System, SDSS, for Web-based operation of long-term hydrologic impact modeling and analysis was developed. The system combines a hydrologic model, databases, web-GIS capability and HTML user interfaces to create a comprehensive hydrologic analysis system. The hydrologic model estimates daily direct runoff using the NRCS Curve Number technique and annual nonpoint source pollution loading by an event mean concentration approach. This is supported by a rainfall database with over 30 years of daily rainfall for the continental US. A web-GIS interface and a robust Web-based watershed delineation capability were developed to simplify the spatial data preparation task that is often a barrier to hydrologic model operation. The web-GIS supports browsing of map layers including hydrologic soil groups, roads, counties, streams, lakes and railroads, as well as on-line watershed delineation for any geographic point the user selects with a simple mouse click. The watershed delineation results can also be used to generate data for the hydrologic and water quality models available in the DSS. This system is already being used by city and local government planners for hydrologic impact evaluation of land use change from urbanization, and can be found at http://pasture.ecn.purdue.edu/~watergen/hymaps. This system can assist local community, city and watershed planners, and even professionals when they are examining impacts of land use change on water resources. They can estimate the hydrologic impact of possible land use changes using this system with readily available data supported through the Internet. This system provides a cost effective approach to serve potential users who require easy-to-use tools.

Decision support methodology to establish priorities on the inspection of structures

NASA Astrophysics Data System (ADS)

Cortes, V. Juliette; Sterlacchini, Simone; Bogaard, Thom; Frigerio, Simone; Schenato, Luca; Pasuto, Alessandro

2014-05-01

For hydro-meteorological hazards in mountain areas, the regular inspection of check dams and bridges is important due to the effect of their functional status on water-sediment processes. Moreover, the inspection of these structures is time consuming for organizations due to their extensive number in many regions. However, trained citizen-volunteers can support civil protection and technical services in the frequency, timeliness and coverage of monitoring the functional status of hydraulic structures. Technicians should evaluate and validate these reports to get an index for the status of the structure. Thus, preventive actions could initiate such as the cleaning of obstructions or to pre-screen potential problems for a second level inspection. This study proposes a decision support methodology that technicians can use to assess an index for three parameters representing the functional status of the structure: a) condition of the structure at the opening of the stream flow, b) level of obstruction at the structure and c) the level of erosion in the stream bank. The calculation of the index for each parameter is based upon fuzzy logic theory to handle ranges in precision of the reports and to convert the linguistic rating scales into numbers representing the structure's status. A weighting method and multi-criteria method (Analytic Hierarchy Process- AHP and TOPSIS), can be used by technicians to combine the different ratings according to the component elements of the structure and the completeness of the reports. Finally, technicians can set decision rules based on the worst rating and a threshold for the functional indexes. The methodology was implemented as a prototype web-based tool to be tested with technicians of the Civil Protection in the Fella basin, Northern Italy. Results at this stage comprise the design and implementation of the web-based tool with GIS interaction to evaluate available reports and to set priorities on the inspection of structures. Keywords Decision-making, Multi-criteria methods, Torrent control structures, Web-based tools.

Community-based Early Warning and Adaptive Response System (EWARS) for mosquito borne diseases: An open source/open community approach

NASA Astrophysics Data System (ADS)

Babu, A. N.; Soman, B.; Niehaus, E.; Shah, J.; Sarda, N. L.; Ramkumar, P. S.; Unnithan, C.

2014-11-01

A variety of studies around the world have evaluated the use of remote sensing with and without GIS in communicable diseases. The ongoing Ebola epidemic has highlighted the risks that can arise for the global community from rapidly spreading diseases which may outpace attempts at control and eradication. This paper presents an approach to the development, deployment, validation and wide-spread adoption of a GIS-based temporo-spatial decision support system which is being collaboratively developed in open source/open community mode by an international group that came together under UN auspices. The group believes in an open source/open community approach to make the fruits of knowledge as widely accessible as possible. A core initiative of the groups is the EWARS project. It proposes to strengthen existing public health systems by the development and validation a model for a community based surveillance and response system which will initially address mosquito borne diseases in the developing world. At present mathematical modeling to support EWARS is at an advanced state, and it planned to embark on a pilot project

ClimatePipes: User-Friendly Data Access, Manipulation, Analysis & Visualization of Community Climate Models

NASA Astrophysics Data System (ADS)

Chaudhary, A.; DeMarle, D.; Burnett, B.; Harris, C.; Silva, W.; Osmari, D.; Geveci, B.; Silva, C.; Doutriaux, C.; Williams, D. N.

2013-12-01

The impact of climate change will resonate through a broad range of fields including public health, infrastructure, water resources, and many others. Long-term coordinated planning, funding, and action are required for climate change adaptation and mitigation. Unfortunately, widespread use of climate data (simulated and observed) in non-climate science communities is impeded by factors such as large data size, lack of adequate metadata, poor documentation, and lack of sufficient computational and visualization resources. We present ClimatePipes to address many of these challenges by creating an open source platform that provides state-of-the-art, user-friendly data access, analysis, and visualization for climate and other relevant geospatial datasets, making the climate data available to non-researchers, decision-makers, and other stakeholders. The overarching goals of ClimatePipes are: - Enable users to explore real-world questions related to climate change. - Provide tools for data access, analysis, and visualization. - Facilitate collaboration by enabling users to share datasets, workflows, and visualization. ClimatePipes uses a web-based application platform for its widespread support on mainstream operating systems, ease-of-use, and inherent collaboration support. The front-end of ClimatePipes uses HTML5 (WebGL, Canvas2D, CSS3) to deliver state-of-the-art visualization and to provide a best-in-class user experience. The back-end of the ClimatePipes is built around Python using the Visualization Toolkit (VTK, http://vtk.org), Climate Data Analysis Tools (CDAT, http://uv-cdat.llnl.gov), and other climate and geospatial data processing tools such as GDAL and PROJ4. ClimatePipes web-interface to query and access data from remote sources (such as ESGF). Shown in the figure is climate data layer from ESGF on top of map data layer from OpenStreetMap. The ClimatePipes workflow editor provides flexibility and fine grained control, and uses the VisTrails (http://www.vistrails.org) workflow engine in the backend.

A web-based decision support tool for prognosis simulation in multiple sclerosis.

PubMed

Veloso, Mário

2014-09-01

A multiplicity of natural history studies of multiple sclerosis provides valuable knowledge of the disease progression but individualized prognosis remains elusive. A few decision support tools that assist the clinician in such task have emerged but have not received proper attention from clinicians and patients. The objective of the current work is to implement a web-based tool, conveying decision relevant prognostic scientific evidence, which will help clinicians discuss prognosis with individual patients. Data were extracted from a set of reference studies, especially those dealing with the natural history of multiple sclerosis. The web-based decision support tool for individualized prognosis simulation was implemented with NetLogo, a program environment suited for the development of complex adaptive systems. Its prototype has been launched online; it enables clinicians to predict both the likelihood of CIS to CDMS conversion, and the long-term prognosis of disability level and SPMS conversion, as well as assess and monitor the effects of treatment. More robust decision support tools, which convey scientific evidence and satisfy the needs of clinical practice by helping clinicians discuss prognosis expectations with individual patients, are required. The web-based simulation model herein introduced proposes to be a step forward toward this purpose. Copyright © 2014 Elsevier B.V. All rights reserved.

Use of a remote clinical decision support service for a multicenter trial to implement prediction rules for children with minor blunt head trauma.

PubMed

Goldberg, Howard S; Paterno, Marilyn D; Grundmeier, Robert W; Rocha, Beatriz H; Hoffman, Jeffrey M; Tham, Eric; Swietlik, Marguerite; Schaeffer, Molly H; Pabbathi, Deepika; Deakyne, Sara J; Kuppermann, Nathan; Dayan, Peter S

2016-03-01

To evaluate the architecture, integration requirements, and execution characteristics of a remote clinical decision support (CDS) service used in a multicenter clinical trial. The trial tested the efficacy of implementing brain injury prediction rules for children with minor blunt head trauma. We integrated the Epic(®) electronic health record (EHR) with the Enterprise Clinical Rules Service (ECRS), a web-based CDS service, at two emergency departments. Patterns of CDS review included either a delayed, near-real-time review, where the physician viewed CDS recommendations generated by the nursing assessment, or a real-time review, where the physician viewed recommendations generated by their own documentation. A backstopping, vendor-based CDS triggered with zero delay when no recommendation was available in the EHR from the web-service. We assessed the execution characteristics of the integrated system and the source of the generated recommendations viewed by physicians. The ECRS mean execution time was 0.74 ±0.72 s. Overall execution time was substantially different at the two sites, with mean total transaction times of 19.67 and 3.99 s. Of 1930 analyzed transactions from the two sites, 60% (310/521) of all physician documentation-initiated recommendations and 99% (1390/1409) of all nurse documentation-initiated recommendations originated from the remote web service. The remote CDS system was the source of recommendations in more than half of the real-time cases and virtually all the near-real-time cases. Comparisons are limited by allowable variation in user workflow and resolution of the EHR clock. With maturation and adoption of standards for CDS services, remote CDS shows promise to decrease time-to-trial for multicenter evaluations of candidate decision support interventions. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Sirepo for Synchrotron Radiation Workshop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nagler, Robert; Moeller, Paul; Rakitin, Maksim

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jinja, which is a secure andmore » widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is the Synchrotron Radiation Workshop (SRW). SRW computes synchrotron radiation from relativistic electrons in arbitrary magnetic fields and propagates the radiation wavefronts through optical beamlines. SRW is open source and is primarily supported by Dr. Oleg Chubar of NSLS-II at Brookhaven National Laboratory.« less

An open-source, mobile-friendly search engine for public medical knowledge.

PubMed

Samwald, Matthias; Hanbury, Allan

2014-01-01

The World Wide Web has become an important source of information for medical practitioners. To complement the capabilities of currently available web search engines we developed FindMeEvidence, an open-source, mobile-friendly medical search engine. In a preliminary evaluation, the quality of results from FindMeEvidence proved to be competitive with those from TRIP Database, an established, closed-source search engine for evidence-based medicine.

Development of transportation asset management decision support tools : final report.

DOT National Transportation Integrated Search

2017-08-09

This study developed a web-based prototype decision support platform to demonstrate the benefits of transportation asset management in monitoring asset performance, supporting asset funding decisions, planning budget tradeoffs, and optimizing resourc...

Fusion Analytics: A Data Integration System for Public Health and Medical Disaster Response Decision Support

PubMed Central

Passman, Dina B.

2013-01-01

Objective The objective of this demonstration is to show conference attendees how they can integrate, analyze, and visualize diverse data type data from across a variety of systems by leveraging an off-the-shelf enterprise business intelligence (EBI) solution to support decision-making in disasters. Introduction Fusion Analytics is the data integration system developed by the Fusion Cell at the U.S. Department of Health and Human Services (HHS), Office of the Assistant Secretary for Preparedness and Response (ASPR). Fusion Analytics meaningfully augments traditional public and population health surveillance reporting by providing web-based data analysis and visualization tools. Methods Fusion Analytics serves as a one-stop-shop for the web-based data visualizations of multiple real-time data sources within ASPR. The 24-7 web availability makes it an ideal analytic tool for situational awareness and response allowing stakeholders to access the portal from any internet-enabled device without installing any software. The Fusion Analytics data integration system was built using off-the-shelf EBI software. Fusion Analytics leverages the full power of statistical analysis software and delivers reports to users in a secure web-based environment. Fusion Analytics provides an example of how public health staff can develop and deploy a robust public health informatics solution using an off-the shelf product and with limited development funding. It also provides the unique example of a public health information system that combines patient data for traditional disease surveillance with manpower and resource data to provide overall decision support for federal public health and medical disaster response operations. Conclusions We are currently in a unique position within public health. One the one hand, we have been gaining greater and greater access to electronic data of all kinds over the last few years. On the other, we are working in a time of reduced government spending to support leveraging this data for decision support with robust analytics and visualizations. Fusion Analytics provides an opportunity for attendees to see how various types of data are integrated into a single application for population health decision support. It also can provide them with ideas of how they can use their own staff to create analyses and reports that support their public health activities.

Open-source web-enabled data management, analyses, and visualization of very large data in geosciences using Jupyter, Apache Spark, and community tools

NASA Astrophysics Data System (ADS)

Chaudhary, A.

2017-12-01

Current simulation models and sensors are producing high-resolution, high-velocity data in geosciences domain. Knowledge discovery from these complex and large size datasets require tools that are capable of handling very large data and providing interactive data analytics features to researchers. To this end, Kitware and its collaborators are producing open-source tools GeoNotebook, GeoJS, Gaia, and Minerva for geosciences that are using hardware accelerated graphics and advancements in parallel and distributed processing (Celery and Apache Spark) and can be loosely coupled to solve real-world use-cases. GeoNotebook (https://github.com/OpenGeoscience/geonotebook) is co-developed by Kitware and NASA-Ames and is an extension to the Jupyter Notebook. It provides interactive visualization and python-based analysis of geospatial data and depending the backend (KTile or GeoPySpark) can handle data sizes of Hundreds of Gigabytes to Terabytes. GeoNotebook uses GeoJS (https://github.com/OpenGeoscience/geojs) to render very large geospatial data on the map using WebGL and Canvas2D API. GeoJS is more than just a GIS library as users can create scientific plots such as vector and contour and can embed InfoVis plots using D3.js. GeoJS aims for high-performance visualization and interactive data exploration of scientific and geospatial location aware datasets and supports features such as Point, Line, Polygon, and advanced features such as Pixelmap, Contour, Heatmap, and Choropleth. Our another open-source tool Minerva ((https://github.com/kitware/minerva) is a geospatial application that is built on top of open-source web-based data management system Girder (https://github.com/girder/girder) which provides an ability to access data from HDFS or Amazon S3 buckets and provides capabilities to perform visualization and analyses on geosciences data in a web environment using GDAL and GeoPandas wrapped in a unified API provided by Gaia (https://github.com/OpenDataAnalytics/gaia). In this presentation, we will discuss core features of each of these tools and will present lessons learned on handling large data in the context of data management, analyses and visualization.

An open source web interface for linking models to infrastructure system databases

NASA Astrophysics Data System (ADS)

Knox, S.; Mohamed, K.; Harou, J. J.; Rheinheimer, D. E.; Medellin-Azuara, J.; Meier, P.; Tilmant, A.; Rosenberg, D. E.

2016-12-01

Models of networked engineered resource systems such as water or energy systems are often built collaboratively with developers from different domains working at different locations. These models can be linked to large scale real world databases, and they are constantly being improved and extended. As the development and application of these models becomes more sophisticated, and the computing power required for simulations and/or optimisations increases, so has the need for online services and tools which enable the efficient development and deployment of these models. Hydra Platform is an open source, web-based data management system, which allows modellers of network-based models to remotely store network topology and associated data in a generalised manner, allowing it to serve multiple disciplines. Hydra Platform uses a web API using JSON to allow external programs (referred to as `Apps') to interact with its stored networks and perform actions such as importing data, running models, or exporting the networks to different formats. Hydra Platform supports multiple users accessing the same network and has a suite of functions for managing users and data. We present ongoing development in Hydra Platform, the Hydra Web User Interface, through which users can collaboratively manage network data and models in a web browser. The web interface allows multiple users to graphically access, edit and share their networks, run apps and view results. Through apps, which are located on the server, the web interface can give users access to external data sources and models without the need to install or configure any software. This also ensures model results can be reproduced by removing platform or version dependence. Managing data and deploying models via the web interface provides a way for multiple modellers to collaboratively manage data, deploy and monitor model runs and analyse results.

A WebGIS service for managing, sharing and communicating information on mountain risks: a pilot study at the Barcelonnette Basin (South French Alps)

NASA Astrophysics Data System (ADS)

Frigerio, Simone; Skupinski, Grzegorz; Kappes, Melanie; Malet, Jean-Philippe; Puissant, Anne

2010-05-01

Integrative analysis, assessment and management of mountain hazards and risks require (1) the intense cooperation among scientists, local practitioners and stakeholders, (2) the compilation of multi-source GIS database on both the sources of the dangers and their impacts, and (3) the communication of scientific results which is still a challenge. Within the European project Mountain Risks and the French-research initiative OMIV (Multi-disciplinary Observatory on Slope Instabilities; http://eost.u-strasbg.fr/omiv), several approaches are under development aiming at a coherent communication of scientific results to the population in order to inform about hazards and risks and support practical risk management measures. A simple and user-friendly approach with a visual-web-based interface is proposed, able (1) to incorporate geographical information on past events and on controlling factors, (2) to include administrative boundaries and official risk regulation maps, and(3) to integrate all modeling results obtained in the study area (already performed or in progress). The possibility to share information by means of web services offers a double utility: firstly it is a way to decrease the gap between scientific community's results and stakeholders' practical needs (simple interface, easy-to-use buttons in a generally user-friendly approach). Secondly the wide collection of diverse information (records of historical events, conditioning and triggering factors, information on elements at risk and their vulnerability, modeling results) in combination with the possibility of comparison among the data offers a great support in the decision-making process. As first case study, the Barcelonnette Basin (South French Alps) has been chosen for the pilot development of the interface. The objective is to organize, manage and share a wide range of information and calibrate a correct web-service solution. Several steps are planned to achieve this goal: the creation of a hierarchical GeoDB that includes all information available for the area (high resolution airborne and satellite imagery, various DEMs, geo-environmental factor maps, susceptibility and hazard maps, historical events and old photographs, maps of elements at risk, potential consequence maps, existing risk scenarios and risk maps) using different organizational folders (splitted in web-switches), the definition of an OpenSource Cartoweb web-platform (based on GeoDB structure) and finally the adjustment of a POSTGIS and POSTGRESQL environment to accomplish query actions, a metadata support system, and a WMS for external data connection and layer control.

Effects of Using a Web-Based Individualized Education Program Decision Making Tutorial

ERIC Educational Resources Information Center

Shriner, James G.; Carty, Susan J.; Rose, Chad A.; Shogren, Karrie A.; Kim, Myungjin; Trach, John S.

2013-01-01

This study explored the effects of a web-based decision support system ("Tutorial") for writing standards-based Individualized Education Programs (IEPs). A total of 35 teachers and 154 students participated across two academic years. Participants were assigned to one of three intervention groups based on level of "Tutorial"…

Effects of Using a Web-Based Individualized Education Program Decision-Making Tutorial

ERIC Educational Resources Information Center

Shriner, James G.; Carty, Susan J.; Rose, Chad A.; Shogren, Karrie A.; Kim, Myungjin; Trach, John S.

2013-01-01

This study explored the effects of a web-based decision support system ("Tutorial") for writing standards-based Individualized Education Programs (IEPs). A total of 35 teachers and 154 students participated across two academic years. Participants were assigned to one of three intervention groups based on level of "Tutorial"…

Smart Cities Intelligence System (SMACiSYS) Integrating Sensor Web with Spatial Data Infrastructures (sensdi)

NASA Astrophysics Data System (ADS)

Bhattacharya, D.; Painho, M.

2017-09-01

The paper endeavours to enhance the Sensor Web with crucial geospatial analysis capabilities through integration with Spatial Data Infrastructure. The objective is development of automated smart cities intelligence system (SMACiSYS) with sensor-web access (SENSDI) utilizing geomatics for sustainable societies. There has been a need to develop automated integrated system to categorize events and issue information that reaches users directly. At present, no web-enabled information system exists which can disseminate messages after events evaluation in real time. Research work formalizes a notion of an integrated, independent, generalized, and automated geo-event analysing system making use of geo-spatial data under popular usage platform. Integrating Sensor Web With Spatial Data Infrastructures (SENSDI) aims to extend SDIs with sensor web enablement, converging geospatial and built infrastructure, and implement test cases with sensor data and SDI. The other benefit, conversely, is the expansion of spatial data infrastructure to utilize sensor web, dynamically and in real time for smart applications that smarter cities demand nowadays. Hence, SENSDI augments existing smart cities platforms utilizing sensor web and spatial information achieved by coupling pairs of otherwise disjoint interfaces and APIs formulated by Open Geospatial Consortium (OGC) keeping entire platform open access and open source. SENSDI is based on Geonode, QGIS and Java, that bind most of the functionalities of Internet, sensor web and nowadays Internet of Things superseding Internet of Sensors as well. In a nutshell, the project delivers a generalized real-time accessible and analysable platform for sensing the environment and mapping the captured information for optimal decision-making and societal benefit.

OpenClimateGIS - A Web Service Providing Climate Model Data in Commonly Used Geospatial Formats

NASA Astrophysics Data System (ADS)

Erickson, T. A.; Koziol, B. W.; Rood, R. B.

2011-12-01

The goal of the OpenClimateGIS project is to make climate model datasets readily available in commonly used, modern geospatial formats used by GIS software, browser-based mapping tools, and virtual globes.The climate modeling community typically stores climate data in multidimensional gridded formats capable of efficiently storing large volumes of data (such as netCDF, grib) while the geospatial community typically uses flexible vector and raster formats that are capable of storing small volumes of data (relative to the multidimensional gridded formats). OpenClimateGIS seeks to address this difference in data formats by clipping climate data to user-specified vector geometries (i.e. areas of interest) and translating the gridded data on-the-fly into multiple vector formats. The OpenClimateGIS system does not store climate data archives locally, but rather works in conjunction with external climate archives that expose climate data via the OPeNDAP protocol. OpenClimateGIS provides a RESTful API web service for accessing climate data resources via HTTP, allowing a wide range of applications to access the climate data.The OpenClimateGIS system has been developed using open source development practices and the source code is publicly available. The project integrates libraries from several other open source projects (including Django, PostGIS, numpy, Shapely, and netcdf4-python).OpenClimateGIS development is supported by a grant from NOAA's Climate Program Office.

Comparison of Physics Frameworks for WebGL-Based Game Engine

NASA Astrophysics Data System (ADS)

Yogya, Resa; Kosala, Raymond

2014-03-01

Recently, a new technology called WebGL shows a lot of potentials for developing games. However since this technology is still new, there are still many potentials in the game development area that are not explored yet. This paper tries to uncover the potential of integrating physics frameworks with WebGL technology in a game engine for developing 2D or 3D games. Specifically we integrated three open source physics frameworks: Bullet, Cannon, and JigLib into a WebGL-based game engine. Using experiment, we assessed these frameworks in terms of their correctness or accuracy, performance, completeness and compatibility. The results show that it is possible to integrate open source physics frameworks into a WebGLbased game engine, and Bullet is the best physics framework to be integrated into the WebGL-based game engine.

Web-based recruitment: effects of information, organizational brand, and attitudes toward a Web site on applicant attraction.

PubMed

Allen, David G; Mahto, Raj V; Otondo, Robert F

2007-11-01

Recruitment theory and research show that objective characteristics, subjective considerations, and critical contact send signals to prospective applicants about the organization and available opportunities. In the generating applicants phase of recruitment, critical contact may consist largely of interactions with recruitment sources (e.g., newspaper ads, job fairs, organization Web sites); however, research has yet to fully address how all 3 types of signaling mechanisms influence early job pursuit decisions in the context of organizational recruitment Web sites. Results based on data from 814 student participants searching actual organization Web sites support and extend signaling and brand equity theories by showing that job information (directly) and organization information (indirectly) are related to intentions to pursue employment when a priori perceptions of image are controlled. A priori organization image is related to pursuit intentions when subsequent information search is controlled, but organization familiarity is not, and attitudes about a recruitment source also influence attraction and partially mediate the effects of organization information. Theoretical and practical implications for recruitment are discussed. (c) 2007 APA

Mercury- Distributed Metadata Management, Data Discovery and Access System

NASA Astrophysics Data System (ADS)

Palanisamy, Giri; Wilson, Bruce E.; Devarakonda, Ranjeet; Green, James M.

2007-12-01

Mercury is a federated metadata harvesting, search and retrieval tool based on both open source and ORNL- developed software. It was originally developed for NASA, and the Mercury development consortium now includes funding from NASA, USGS, and DOE. Mercury supports various metadata standards including XML, Z39.50, FGDC, Dublin-Core, Darwin-Core, EML, and ISO-19115 (under development). Mercury provides a single portal to information contained in disparate data management systems. It collects metadata and key data from contributing project servers distributed around the world and builds a centralized index. The Mercury search interfaces then allow the users to perform simple, fielded, spatial and temporal searches across these metadata sources. This centralized repository of metadata with distributed data sources provides extremely fast search results to the user, while allowing data providers to advertise the availability of their data and maintain complete control and ownership of that data. Mercury supports various projects including: ORNL DAAC, NBII, DADDI, LBA, NARSTO, CDIAC, OCEAN, I3N, IAI, ESIP and ARM. The new Mercury system is based on a Service Oriented Architecture and supports various services such as Thesaurus Service, Gazetteer Web Service and UDDI Directory Services. This system also provides various search services including: RSS, Geo-RSS, OpenSearch, Web Services and Portlets. Other features include: Filtering and dynamic sorting of search results, book-markable search results, save, retrieve, and modify search criteria.

Advancing translational research with the Semantic Web.

PubMed

Ruttenberg, Alan; Clark, Tim; Bug, William; Samwald, Matthias; Bodenreider, Olivier; Chen, Helen; Doherty, Donald; Forsberg, Kerstin; Gao, Yong; Kashyap, Vipul; Kinoshita, June; Luciano, Joanne; Marshall, M Scott; Ogbuji, Chimezie; Rees, Jonathan; Stephens, Susie; Wong, Gwendolyn T; Wu, Elizabeth; Zaccagnini, Davide; Hongsermeier, Tonya; Neumann, Eric; Herman, Ivan; Cheung, Kei-Hoi

2007-05-09

A fundamental goal of the U.S. National Institute of Health (NIH) "Roadmap" is to strengthen Translational Research, defined as the movement of discoveries in basic research to application at the clinical level. A significant barrier to translational research is the lack of uniformly structured data across related biomedical domains. The Semantic Web is an extension of the current Web that enables navigation and meaningful use of digital resources by automatic processes. It is based on common formats that support aggregation and integration of data drawn from diverse sources. A variety of technologies have been built on this foundation that, together, support identifying, representing, and reasoning across a wide range of biomedical data. The Semantic Web Health Care and Life Sciences Interest Group (HCLSIG), set up within the framework of the World Wide Web Consortium, was launched to explore the application of these technologies in a variety of areas. Subgroups focus on making biomedical data available in RDF, working with biomedical ontologies, prototyping clinical decision support systems, working on drug safety and efficacy communication, and supporting disease researchers navigating and annotating the large amount of potentially relevant literature. We present a scenario that shows the value of the information environment the Semantic Web can support for aiding neuroscience researchers. We then report on several projects by members of the HCLSIG, in the process illustrating the range of Semantic Web technologies that have applications in areas of biomedicine. Semantic Web technologies present both promise and challenges. Current tools and standards are already adequate to implement components of the bench-to-bedside vision. On the other hand, these technologies are young. Gaps in standards and implementations still exist and adoption is limited by typical problems with early technology, such as the need for a critical mass of practitioners and installed base, and growing pains as the technology is scaled up. Still, the potential of interoperable knowledge sources for biomedicine, at the scale of the World Wide Web, merits continued work.

Advancing translational research with the Semantic Web

PubMed Central

Ruttenberg, Alan; Clark, Tim; Bug, William; Samwald, Matthias; Bodenreider, Olivier; Chen, Helen; Doherty, Donald; Forsberg, Kerstin; Gao, Yong; Kashyap, Vipul; Kinoshita, June; Luciano, Joanne; Marshall, M Scott; Ogbuji, Chimezie; Rees, Jonathan; Stephens, Susie; Wong, Gwendolyn T; Wu, Elizabeth; Zaccagnini, Davide; Hongsermeier, Tonya; Neumann, Eric; Herman, Ivan; Cheung, Kei-Hoi

2007-01-01

Background A fundamental goal of the U.S. National Institute of Health (NIH) "Roadmap" is to strengthen Translational Research, defined as the movement of discoveries in basic research to application at the clinical level. A significant barrier to translational research is the lack of uniformly structured data across related biomedical domains. The Semantic Web is an extension of the current Web that enables navigation and meaningful use of digital resources by automatic processes. It is based on common formats that support aggregation and integration of data drawn from diverse sources. A variety of technologies have been built on this foundation that, together, support identifying, representing, and reasoning across a wide range of biomedical data. The Semantic Web Health Care and Life Sciences Interest Group (HCLSIG), set up within the framework of the World Wide Web Consortium, was launched to explore the application of these technologies in a variety of areas. Subgroups focus on making biomedical data available in RDF, working with biomedical ontologies, prototyping clinical decision support systems, working on drug safety and efficacy communication, and supporting disease researchers navigating and annotating the large amount of potentially relevant literature. Results We present a scenario that shows the value of the information environment the Semantic Web can support for aiding neuroscience researchers. We then report on several projects by members of the HCLSIG, in the process illustrating the range of Semantic Web technologies that have applications in areas of biomedicine. Conclusion Semantic Web technologies present both promise and challenges. Current tools and standards are already adequate to implement components of the bench-to-bedside vision. On the other hand, these technologies are young. Gaps in standards and implementations still exist and adoption is limited by typical problems with early technology, such as the need for a critical mass of practitioners and installed base, and growing pains as the technology is scaled up. Still, the potential of interoperable knowledge sources for biomedicine, at the scale of the World Wide Web, merits continued work. PMID:17493285

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics.

PubMed

Bonnal, Raoul J P; Aerts, Jan; Githinji, George; Goto, Naohisa; MacLean, Dan; Miller, Chase A; Mishima, Hiroyuki; Pagani, Massimiliano; Ramirez-Gonzalez, Ricardo; Smant, Geert; Strozzi, Francesco; Syme, Rob; Vos, Rutger; Wennblom, Trevor J; Woodcroft, Ben J; Katayama, Toshiaki; Prins, Pjotr

2012-04-01

Biogem provides a software development environment for the Ruby programming language, which encourages community-based software development for bioinformatics while lowering the barrier to entry and encouraging best practices. Biogem, with its targeted modular and decentralized approach, software generator, tools and tight web integration, is an improved general model for scaling up collaborative open source software development in bioinformatics. Biogem and modules are free and are OSS. Biogem runs on all systems that support recent versions of Ruby, including Linux, Mac OS X and Windows. Further information at http://www.biogems.info. A tutorial is available at http://www.biogems.info/howto.html bonnal@ingm.org.

Web-Based Tools for Data Visualization and Decision Support for South Asia

NASA Astrophysics Data System (ADS)

Jones, N.; Nelson, J.; Pulla, S. T.; Ames, D. P.; Souffront, M.; David, C. H.; Zaitchik, B. F.; Gatlin, P. N.; Matin, M. A.

2017-12-01

The objective of the NASA SERVIR project is to assist developing countries in using information provided by Earth observing satellites to assess and manage climate risks, land use, and water resources. We present a collection of web apps that integrate earth observations and in situ data to facilitate deployment of data and water resources models as decision-making tools in support of this effort. The interactive nature of web apps makes this an excellent medium for creating decision support tools that harness cutting edge modeling techniques. Thin client apps hosted in a cloud portal eliminates the need for the decision makers to procure and maintain the high performance hardware required by the models, deal with issues related to software installation and platform incompatibilities, or monitor and install software updates, a problem that is exacerbated for many of the regional SERVIR hubs where both financial and technical capacity may be limited. All that is needed to use the system is an Internet connection and a web browser. We take advantage of these technologies to develop tools which can be centrally maintained but openly accessible. Advanced mapping and visualization make results intuitive and information derived actionable. We also take advantage of the emerging standards for sharing water information across the web using the OGC and WMO approved WaterML standards. This makes our tools interoperable and extensible via application programming interfaces (APIs) so that tools and data from other projects can both consume and share the tools developed in our project. Our approach enables the integration of multiple types of data and models, thus facilitating collaboration between science teams in SERVIR. The apps developed thus far by our team process time-varying netCDF files from Earth observations and large-scale computer simulations and allow visualization and exploration via raster animation and extraction of time series at selected points and/or regions.

Collaborative development of predictive toxicology applications

PubMed Central

2010-01-01

OpenTox provides an interoperable, standards-based Framework for the support of predictive toxicology data management, algorithms, modelling, validation and reporting. It is relevant to satisfying the chemical safety assessment requirements of the REACH legislation as it supports access to experimental data, (Quantitative) Structure-Activity Relationship models, and toxicological information through an integrating platform that adheres to regulatory requirements and OECD validation principles. Initial research defined the essential components of the Framework including the approach to data access, schema and management, use of controlled vocabularies and ontologies, architecture, web service and communications protocols, and selection and integration of algorithms for predictive modelling. OpenTox provides end-user oriented tools to non-computational specialists, risk assessors, and toxicological experts in addition to Application Programming Interfaces (APIs) for developers of new applications. OpenTox actively supports public standards for data representation, interfaces, vocabularies and ontologies, Open Source approaches to core platform components, and community-based collaboration approaches, so as to progress system interoperability goals. The OpenTox Framework includes APIs and services for compounds, datasets, features, algorithms, models, ontologies, tasks, validation, and reporting which may be combined into multiple applications satisfying a variety of different user needs. OpenTox applications are based on a set of distributed, interoperable OpenTox API-compliant REST web services. The OpenTox approach to ontology allows for efficient mapping of complementary data coming from different datasets into a unifying structure having a shared terminology and representation. Two initial OpenTox applications are presented as an illustration of the potential impact of OpenTox for high-quality and consistent structure-activity relationship modelling of REACH-relevant endpoints: ToxPredict which predicts and reports on toxicities for endpoints for an input chemical structure, and ToxCreate which builds and validates a predictive toxicity model based on an input toxicology dataset. Because of the extensible nature of the standardised Framework design, barriers of interoperability between applications and content are removed, as the user may combine data, models and validation from multiple sources in a dependable and time-effective way. PMID:20807436

Collaborative development of predictive toxicology applications.

PubMed

Hardy, Barry; Douglas, Nicki; Helma, Christoph; Rautenberg, Micha; Jeliazkova, Nina; Jeliazkov, Vedrin; Nikolova, Ivelina; Benigni, Romualdo; Tcheremenskaia, Olga; Kramer, Stefan; Girschick, Tobias; Buchwald, Fabian; Wicker, Joerg; Karwath, Andreas; Gütlein, Martin; Maunz, Andreas; Sarimveis, Haralambos; Melagraki, Georgia; Afantitis, Antreas; Sopasakis, Pantelis; Gallagher, David; Poroikov, Vladimir; Filimonov, Dmitry; Zakharov, Alexey; Lagunin, Alexey; Gloriozova, Tatyana; Novikov, Sergey; Skvortsova, Natalia; Druzhilovsky, Dmitry; Chawla, Sunil; Ghosh, Indira; Ray, Surajit; Patel, Hitesh; Escher, Sylvia

2010-08-31

OpenTox provides an interoperable, standards-based Framework for the support of predictive toxicology data management, algorithms, modelling, validation and reporting. It is relevant to satisfying the chemical safety assessment requirements of the REACH legislation as it supports access to experimental data, (Quantitative) Structure-Activity Relationship models, and toxicological information through an integrating platform that adheres to regulatory requirements and OECD validation principles. Initial research defined the essential components of the Framework including the approach to data access, schema and management, use of controlled vocabularies and ontologies, architecture, web service and communications protocols, and selection and integration of algorithms for predictive modelling. OpenTox provides end-user oriented tools to non-computational specialists, risk assessors, and toxicological experts in addition to Application Programming Interfaces (APIs) for developers of new applications. OpenTox actively supports public standards for data representation, interfaces, vocabularies and ontologies, Open Source approaches to core platform components, and community-based collaboration approaches, so as to progress system interoperability goals.The OpenTox Framework includes APIs and services for compounds, datasets, features, algorithms, models, ontologies, tasks, validation, and reporting which may be combined into multiple applications satisfying a variety of different user needs. OpenTox applications are based on a set of distributed, interoperable OpenTox API-compliant REST web services. The OpenTox approach to ontology allows for efficient mapping of complementary data coming from different datasets into a unifying structure having a shared terminology and representation.Two initial OpenTox applications are presented as an illustration of the potential impact of OpenTox for high-quality and consistent structure-activity relationship modelling of REACH-relevant endpoints: ToxPredict which predicts and reports on toxicities for endpoints for an input chemical structure, and ToxCreate which builds and validates a predictive toxicity model based on an input toxicology dataset. Because of the extensible nature of the standardised Framework design, barriers of interoperability between applications and content are removed, as the user may combine data, models and validation from multiple sources in a dependable and time-effective way.

Adaptable Information Models in the Global Change Information System

NASA Astrophysics Data System (ADS)

Duggan, B.; Buddenberg, A.; Aulenbach, S.; Wolfe, R.; Goldstein, J.

2014-12-01

The US Global Change Research Program has sponsored the creation of the Global Change Information System () to provide a web based source of accessible, usable, and timely information about climate and global change for use by scientists, decision makers, and the public. The GCIS played multiple roles during the assembly and release of the Third National Climate Assessment. It provided human and programmable interfaces, relational and semantic representations of information, and discrete identifiers for various types of resources, which could then be manipulated by a distributed team with a wide range of specialties. The GCIS also served as a scalable backend for the web based version of the report. In this talk, we discuss the infrastructure decisions made during the design and deployment of the GCIS, as well as ongoing work to adapt to new types of information. Both a constrained relational database and an open ended triple store are used to ensure data integrity while maintaining fluidity. Using natural primary keys allows identifiers to propagate through both models. Changing identifiers are accomodated through fine grained auditing and explicit mappings to external lexicons. A practical RESTful API is used whose endpoints are also URIs in an ontology. Both the relational schema and the ontology are maleable, and stability is ensured through test driven development and continuous integration testing using modern open source techniques. Content is also validated through continuous testing techniques. A high degres of scalability is achieved through caching.

Mantis BT Cluster Support

DOE Office of Scientific and Technical Information (OSTI.GOV)

Riot, V.

2009-06-05

The software is a modidication to the Mantis BT V1.5 open source application provided by the mantis BT group to support cluster web servers. It also provides various cosmetic modifications used a LLNL.

gemcWeb: A Cloud Based Nuclear Physics Simulation Software

NASA Astrophysics Data System (ADS)

Markelon, Sam

2017-09-01

gemcWeb allows users to run nuclear physics simulations from the web. Being completely device agnostic, scientists can run simulations from anywhere with an Internet connection. Having a full user system, gemcWeb allows users to revisit and revise their projects, and share configurations and results with collaborators. gemcWeb is based on simulation software gemc, which is based on standard GEant4. gemcWeb requires no C++, gemc, or GEant4 knowledge. Using a simple but powerful GUI allows users to configure their project from geometries and configurations stored on the deployment server. Simulations are then run on the server, with results being posted to the user, and then securely stored. Python based and open-source, the main version of gemcWeb is hosted internally at Jefferson National Labratory and used by the CLAS12 and Electron-Ion Collider Project groups. However, as the software is open-source, and hosted as a GitHub repository, an instance can be deployed on the open web, or any institution's intra-net. An instance can be configured to host experiments specific to an institution, and the code base can be modified by any individual or group. Special thanks to: Maurizio Ungaro, PhD., creator of gemc; Markus Diefenthaler, PhD., advisor; and Kyungseon Joo, PhD., advisor.

GIS Tool for Real-time Decision Making and Analysis of Multidisciplinary Cryosphere Datasets.

NASA Astrophysics Data System (ADS)

Roberts, S. D.; Moore, J. A.

2004-12-01

In support of the Western Arctic Shelf-Basin Interaction Project(SBI) a web-based interactive mapping server was installed on the USCGC Healy's on-board science computer network during its 2004 spring(HLY-04-02) and summer cruises (HLY-04-03) in the Chukchi and Beaufort Seas. SBI is a National Science Foundation sponsored multi-year and multidisciplinary project studying the biological productivity in the region. The mapping server was developed by the UCAR Joint Office of Science Support(JOSS) using OpenSource GIS tools(University of Minnesota Mapserver and USGS MapSurfer). Additional OpenSource tools such as GMT and MB-Systems were also utilized. The key layers in this system are the current ship track, station locations, multibeam bottom bathymetry, IBCAO bathymetry, DMSP satellite imagery , NOAA AVHRR Sea Surface temperature and all past SBI Project ship tracks and station locations. The ship track and multibeam layers are updated in real-time and the satellite layers are updated daily only during clear weather. In addition to using current high resolution multibeam bathymetry data, a composite high resolution bathymetry layer was created using multibeam data from past cruises in the SBI region. The server provides click-and-drag zooms, pan, feature query, distance measure and lat/lon/depth querys on a polar projection map of the arctic ocean. The main use of the system on the ship was for cruise track and station position planning by the scientists utilizing all available historical data and high resolution bathymetry. It was also the main source of information to all the scientist on board as to the cruise progress and plans. The system permitted on-board scientists to integrate historical cruise information for comparative purposes. A mirror web site was set up on land and the current ship track/station information was copied once a day to this site via a satellite link so people interested SBI research could follow the cruise progress.

The charged particle accelerators subsystems modeling

NASA Astrophysics Data System (ADS)

Averyanov, G. P.; Kobylyatskiy, A. V.

2017-01-01

Presented web-based resource for information support the engineering, science and education in Electrophysics, containing web-based tools for simulation subsystems charged particle accelerators. Formulated the development motivation of Web-Environment for Virtual Electrophysical Laboratories. Analyzes the trends of designs the dynamic web-environments for supporting of scientific research and E-learning, within the framework of Open Education concept.

Application of Open Source Software by the Lunar Mapping and Modeling Project

NASA Astrophysics Data System (ADS)

Ramirez, P.; Goodale, C. E.; Bui, B.; Chang, G.; Kim, R. M.; Law, E.; Malhotra, S.; Rodriguez, L.; Sadaqathullah, S.; Mattmann, C. A.; Crichton, D. J.

2011-12-01

The Lunar Mapping and Modeling Project (LMMP), led by the Marshall Space Flight center (MSFC), is responsible for the development of an information system to support lunar exploration, decision analysis, and release of lunar data to the public. The data available through the lunar portal is predominantly derived from present lunar missions (e.g., the Lunar Reconnaissance Orbiter (LRO)) and from historical missions (e.g., Apollo). This project has created a gold source of data, models, and tools for lunar explorers to exercise and incorporate into their activities. At Jet Propulsion Laboratory (JPL), we focused on engineering and building the infrastructure to support cataloging, archiving, accessing, and delivery of lunar data. We decided to use a RESTful service-oriented architecture to enable us to abstract from the underlying technology choices and focus on interfaces to be used internally and externally. This decision allowed us to leverage several open source software components and integrate them by either writing a thin REST service layer or relying on the API they provided; the approach chosen was dependent on the targeted consumer of a given interface. We will discuss our varying experience using open source products; namely Apache OODT, Oracle Berkley DB XML, Apache Solr, and Oracle OpenSSO (now named OpenAM). Apache OODT, developed at NASA's Jet Propulsion Laboratory and recently migrated over to Apache, provided the means for ingestion and cataloguing of products within the infrastructure. Its usage was based upon team experience with the project and past benefit received on other projects internal and external to JPL. Berkeley DB XML, distributed by Oracle for both commercial and open source use, was the storage technology chosen for our metadata. This decision was in part based on our use Federal Geographic Data Committee (FGDC) Metadata, which is expressed in XML, and the desire to keep it in its native form and exploit other technologies built on top of XML. Apache Solr, an open source search engine, was used to drive our search interface and as way to store references to metadata and data exposed via REST endpoints. As was the case with Apache OODT there was team experience with this component that helped drive this choice. Lastly, OpenSSO, an open source single sign on service, was used to secure and provide access constraints to our REST based services. For this product there was little past experience but given our service based approach seemed to be a natural fit. Given our exposure to open source we will discuss the tradeoffs and benefits received by the choices made. Moreover, we will dive into the context of how the software packages were used and the impact of their design and extensibility had on the construction of the infrastructure. Finally, we will compare our encounter across open source solutions and attributes that can vary the impression one will get. This comprehensive account of our endeavor should aid others in their assessment and use of open source.

Web-based Tsunami Early Warning System with instant Tsunami Propagation Calculations in the GPU Cloud

NASA Astrophysics Data System (ADS)

Hammitzsch, M.; Spazier, J.; Reißland, S.

2014-12-01

Usually, tsunami early warning and mitigation systems (TWS or TEWS) are based on several software components deployed in a client-server based infrastructure. The vast majority of systems importantly include desktop-based clients with a graphical user interface (GUI) for the operators in early warning centers. However, in times of cloud computing and ubiquitous computing the use of concepts and paradigms, introduced by continuously evolving approaches in information and communications technology (ICT), have to be considered even for early warning systems (EWS). Based on the experiences and the knowledge gained in three research projects - 'German Indonesian Tsunami Early Warning System' (GITEWS), 'Distant Early Warning System' (DEWS), and 'Collaborative, Complex, and Critical Decision-Support in Evolving Crises' (TRIDEC) - new technologies are exploited to implement a cloud-based and web-based prototype to open up new prospects for EWS. This prototype, named 'TRIDEC Cloud', merges several complementary external and in-house cloud-based services into one platform for automated background computation with graphics processing units (GPU), for web-mapping of hazard specific geospatial data, and for serving relevant functionality to handle, share, and communicate threat specific information in a collaborative and distributed environment. The prototype in its current version addresses tsunami early warning and mitigation. The integration of GPU accelerated tsunami simulation computations have been an integral part of this prototype to foster early warning with on-demand tsunami predictions based on actual source parameters. However, the platform is meant for researchers around the world to make use of the cloud-based GPU computation to analyze other types of geohazards and natural hazards and react upon the computed situation picture with a web-based GUI in a web browser at remote sites. The current website is an early alpha version for demonstration purposes to give the concept a whirl and to shape science's future. Further functionality, improvements and possible profound changes have to implemented successively based on the users' evolving needs.

TethysCluster: A comprehensive approach for harnessing cloud resources for hydrologic modeling

NASA Astrophysics Data System (ADS)

Nelson, J.; Jones, N.; Ames, D. P.

2015-12-01

Advances in water resources modeling are improving the information that can be supplied to support decisions affecting the safety and sustainability of society. However, as water resources models become more sophisticated and data-intensive they require more computational power to run. Purchasing and maintaining the computing facilities needed to support certain modeling tasks has been cost-prohibitive for many organizations. With the advent of the cloud, the computing resources needed to address this challenge are now available and cost-effective, yet there still remains a significant technical barrier to leverage these resources. This barrier inhibits many decision makers and even trained engineers from taking advantage of the best science and tools available. Here we present the Python tools TethysCluster and CondorPy, that have been developed to lower the barrier to model computation in the cloud by providing (1) programmatic access to dynamically scalable computing resources, (2) a batch scheduling system to queue and dispatch the jobs to the computing resources, (3) data management for job inputs and outputs, and (4) the ability to dynamically create, submit, and monitor computing jobs. These Python tools leverage the open source, computing-resource management, and job management software, HTCondor, to offer a flexible and scalable distributed-computing environment. While TethysCluster and CondorPy can be used independently to provision computing resources and perform large modeling tasks, they have also been integrated into Tethys Platform, a development platform for water resources web apps, to enable computing support for modeling workflows and decision-support systems deployed as web apps.

The Reactome pathway knowledgebase

PubMed Central

Croft, David; Mundo, Antonio Fabregat; Haw, Robin; Milacic, Marija; Weiser, Joel; Wu, Guanming; Caudy, Michael; Garapati, Phani; Gillespie, Marc; Kamdar, Maulik R.; Jassal, Bijay; Jupe, Steven; Matthews, Lisa; May, Bruce; Palatnik, Stanislav; Rothfels, Karen; Shamovsky, Veronica; Song, Heeyeon; Williams, Mark; Birney, Ewan; Hermjakob, Henning; Stein, Lincoln; D'Eustachio, Peter

2014-01-01

Reactome (http://www.reactome.org) is a manually curated open-source open-data resource of human pathways and reactions. The current version 46 describes 7088 human proteins (34% of the predicted human proteome), participating in 6744 reactions based on data extracted from 15 107 research publications with PubMed links. The Reactome Web site and analysis tool set have been completely redesigned to increase speed, flexibility and user friendliness. The data model has been extended to support annotation of disease processes due to infectious agents and to mutation. PMID:24243840

The Reactome pathway knowledgebase.

PubMed

Croft, David; Mundo, Antonio Fabregat; Haw, Robin; Milacic, Marija; Weiser, Joel; Wu, Guanming; Caudy, Michael; Garapati, Phani; Gillespie, Marc; Kamdar, Maulik R; Jassal, Bijay; Jupe, Steven; Matthews, Lisa; May, Bruce; Palatnik, Stanislav; Rothfels, Karen; Shamovsky, Veronica; Song, Heeyeon; Williams, Mark; Birney, Ewan; Hermjakob, Henning; Stein, Lincoln; D'Eustachio, Peter

2014-01-01

Reactome (http://www.reactome.org) is a manually curated open-source open-data resource of human pathways and reactions. The current version 46 describes 7088 human proteins (34% of the predicted human proteome), participating in 6744 reactions based on data extracted from 15 107 research publications with PubMed links. The Reactome Web site and analysis tool set have been completely redesigned to increase speed, flexibility and user friendliness. The data model has been extended to support annotation of disease processes due to infectious agents and to mutation.

Informatics in radiology: web-based preliminary reporting system for radiology residents with PACS integration.

PubMed

O'Connell, Timothy; Chang, Debra

2012-01-01

While on call, radiology residents review imaging studies and issue preliminary reports to referring clinicians. In the absence of an integrated reporting system at the training sites of the authors' institution, residents were typing and faxing preliminary reports. To partially automate the on-call resident workflow, a Web-based system for resident reporting was developed by using the free open-source xAMP Web application framework and an open-source DICOM (Digital Imaging and Communications in Medicine) software toolkit, with the goals of reducing errors and lowering barriers to education. This reporting system integrates with the picture archiving and communication system to display a worklist of studies. Patient data are automatically entered in the preliminary report to prevent identification errors and simplify the report creation process. When the final report for a resident's on-call study is available, the reporting system queries the report broker for the final report, and then displays the preliminary report side by side with the final report, thus simplifying the review process and encouraging review of all of the resident's reports. The xAMP Web application framework should be considered for development of radiology department informatics projects owing to its zero cost, minimal hardware requirements, ease of programming, and large support community.

A prototype web-GIS application for risk analysis of natural hazards in Switzerland

NASA Astrophysics Data System (ADS)

Aye, Zar Chi; Nicolet, Pierrick; Jaboyedoff, Michel; Derron, Marc-Henri; Gerber, Christian; Lévy, Sebastien

2016-04-01

Following changes in the system of Swiss subsidy in January 2008, the Swiss cantons and the Federal Office for the Environment (FOEN) were forced to prioritize different natural hazard protection projects based on their cost-effectiveness, as a response to limited financial resources (Bründl et al., 2009). For this purpose, applications such as EconoMe (OFEV, 2016) and Valdorisk (DGE, 2016) were developed for risk evaluation and prioritization of mitigation projects. These tools serve as a useful decision-making instrument to the community of practitioners and responsible authorities for natural hazard risk management in Switzerland. However, there are several aspects which could be improved, in particular, the integration and visualization of spatial information interactively through a web-GIS interface for better risk planning and evaluation. Therefore, in this study, we aim to develop an interactive web-GIS application based on the risk concepts applied in Switzerland. The purpose of this tool is to provide a rapid evaluation of risk before and after protection measures, and to test the efficiency of measures by using a simplified cost-benefit analysis within the context of different protection projects. This application allows to integrate different layers which are necessary to calculate risk, in particular, hazard intensity (vector) maps for different scenarios (such as 30, 100 and 300 years of return periods based on Swiss guidelines), exposed objects (such as buildings) and vulnerability information of these objects. Based on provided information and additional parameters, risk is calculated automatically and results are visualized within the web-GIS interface of the application. The users can modify these input information and parameters to create different risk scenarios. Based on the resultant risk scenarios, the users can propose and visualize (preliminary) risk reduction measures before realizing the actual design and dimensions of such protective measures in the area. After designing measures, the users can re-calculate risk by updating hazard intensity and object layers. This is achieved by manual editing of shape (vector) layers in the web-GIS interface interactively. Within the application, a cost-benefit analysis tool is also integrated to support the decision-making process for the selection of different protection measures. Finally, the resultant risk information (vector layers and data) can be exported in the form of shapefiles and excel sheets. A prototype application is realized using open-source geospatial software and technologies. Boundless framework with its client-side SDK environment is applied for the rapid prototyping. Free and open source components such as PostGIS spatial database, GeoServer and GeoWebCache, GeoExt and OpenLayers are used for the development of the platform. This developed prototype is demonstrated with a case study area located in Les Diablerets, Switzerland. This research work is carried out within a project funded by the Canton of Vaud, Switzerland. References: Bründl, M., Romang, H. E., Bischof, N., and Rheinberger, C. M.: The risk concept and its application in natural hazard risk management in Switzerland, Nat. Hazards Earth Syst. Sci., 9, 801-813, 2009. DGE: Valdorisk - Direction Générale de l'Environnement, www.vd.ch, accessed 9 January 2016, 2016. OFEV: EconoMe - Office fédéral de l'environnement, www.econome.admin.ch, accessed 9 January 2016, 2016.

Merging Air Quality and Public Health Decision Support Systems

NASA Astrophysics Data System (ADS)

Hudspeth, W. B.; Bales, C. L.

2003-12-01

The New Mexico Air Quality Mapper (NMAQM) is a Web-based, open source GIS prototype application that Earth Data Analysis Center is developing under a NASA Cooperative Agreement. NMAQM enhances and extends existing data and imagery delivery systems with an existing Public Health system called the Rapid Syndrome Validation Project (RSVP). RSVP is a decision support system operating in several medical and public health arenas. It is evolving to ingest remote sensing data as input to provide early warning of human health threats, especially those related to anthropogenic atmospheric pollutants and airborne pathogens. The NMAQM project applies measurements of these atmospheric pollutants, derived from both remotely sensed data as well as from in-situ air quality networks, to both forecasting and retrospective analyses that influence human respiratory health. NMAQM provides a user-friendly interface for visualizing and interpreting environmentally-linked epidemiological phenomena. The results, and the systems made to provide the information, will be applicable not only to decision-makers in the public health realm, but also to air quality organizations, demographers, community planners, and other professionals in information technology, and social and engineering sciences. As an accessible and interactive mapping and analysis application, it allows environment and health personnel to study historic data for hypothesis generation and trend analysis, and then, potentially, to predict air quality conditions from daily data acquisitions. Additional spin off benefits to such users include the identification of gaps in the distribution of in-situ monitoring stations, the dissemination of air quality data to the public, and the discrimination of local vs. more regional sources of air pollutants that may bear on decisions relating to public health and public policy.

ASK-LDT 2.0: A Web-Based Graphical Tool for Authoring Learning Designs

ERIC Educational Resources Information Center

Zervas, Panagiotis; Fragkos, Konstantinos; Sampson, Demetrios G.

2013-01-01

During the last decade, Open Educational Resources (OERs) have gained increased attention for their potential to support open access, sharing and reuse of digital educational resources. Therefore, a large amount of digital educational resources have become available worldwide through web-based open access repositories which are referred to as…

Sirepo - Warp

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nagler, Robert; Moeller, Paul

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jin-ja, which is a secure andmore » widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is Warp. Warp is a particle-in-cell (PIC) code de-signed to simulate high-intensity charged particle beams and plasmas in both the electrostatic and electromagnetic regimes, with a wide variety of integrated physics models and diagnostics. At pre-sent, Sirepo supports a small subset of Warp’s capabilities. Warp is open source and is part of the Berkeley Lab Accelerator Simulation Toolkit.« less

Sensor Web Interoperability Testbed Results Incorporating Earth Observation Satellites

NASA Technical Reports Server (NTRS)

Frye, Stuart; Mandl, Daniel J.; Alameh, Nadine; Bambacus, Myra; Cappelaere, Pat; Falke, Stefan; Derezinski, Linda; Zhao, Piesheng

2007-01-01

This paper describes an Earth Observation Sensor Web scenario based on the Open Geospatial Consortium s Sensor Web Enablement and Web Services interoperability standards. The scenario demonstrates the application of standards in describing, discovering, accessing and tasking satellites and groundbased sensor installations in a sequence of analysis activities that deliver information required by decision makers in response to national, regional or local emergencies.

CorRECTreatment: A Web-based Decision Support Tool for Rectal Cancer Treatment that Uses the Analytic Hierarchy Process and Decision Tree

PubMed Central

Karakülah, G.; Dicle, O.; Sökmen, S.; Çelikoğlu, C.C.

2015-01-01

Summary Background The selection of appropriate rectal cancer treatment is a complex multi-criteria decision making process, in which clinical decision support systems might be used to assist and enrich physicians’ decision making. Objective The objective of the study was to develop a web-based clinical decision support tool for physicians in the selection of potentially beneficial treatment options for patients with rectal cancer. Methods The updated decision model contained 8 and 10 criteria in the first and second steps respectively. The decision support model, developed in our previous study by combining the Analytic Hierarchy Process (AHP) method which determines the priority of criteria and decision tree that formed using these priorities, was updated and applied to 388 patients data collected retrospectively. Later, a web-based decision support tool named corRECTreatment was developed. The compatibility of the treatment recommendations by the expert opinion and the decision support tool was examined for its consistency. Two surgeons were requested to recommend a treatment and an overall survival value for the treatment among 20 different cases that we selected and turned into a scenario among the most common and rare treatment options in the patient data set. Results In the AHP analyses of the criteria, it was found that the matrices, generated for both decision steps, were consistent (consistency ratio<0.1). Depending on the decisions of experts, the consistency value for the most frequent cases was found to be 80% for the first decision step and 100% for the second decision step. Similarly, for rare cases consistency was 50% for the first decision step and 80% for the second decision step. Conclusions The decision model and corRECTreatment, developed by applying these on real patient data, are expected to provide potential users with decision support in rectal cancer treatment processes and facilitate them in making projections about treatment options. PMID:25848413

CorRECTreatment: a web-based decision support tool for rectal cancer treatment that uses the analytic hierarchy process and decision tree.

PubMed

Suner, A; Karakülah, G; Dicle, O; Sökmen, S; Çelikoğlu, C C

2015-01-01

The selection of appropriate rectal cancer treatment is a complex multi-criteria decision making process, in which clinical decision support systems might be used to assist and enrich physicians' decision making. The objective of the study was to develop a web-based clinical decision support tool for physicians in the selection of potentially beneficial treatment options for patients with rectal cancer. The updated decision model contained 8 and 10 criteria in the first and second steps respectively. The decision support model, developed in our previous study by combining the Analytic Hierarchy Process (AHP) method which determines the priority of criteria and decision tree that formed using these priorities, was updated and applied to 388 patients data collected retrospectively. Later, a web-based decision support tool named corRECTreatment was developed. The compatibility of the treatment recommendations by the expert opinion and the decision support tool was examined for its consistency. Two surgeons were requested to recommend a treatment and an overall survival value for the treatment among 20 different cases that we selected and turned into a scenario among the most common and rare treatment options in the patient data set. In the AHP analyses of the criteria, it was found that the matrices, generated for both decision steps, were consistent (consistency ratio<0.1). Depending on the decisions of experts, the consistency value for the most frequent cases was found to be 80% for the first decision step and 100% for the second decision step. Similarly, for rare cases consistency was 50% for the first decision step and 80% for the second decision step. The decision model and corRECTreatment, developed by applying these on real patient data, are expected to provide potential users with decision support in rectal cancer treatment processes and facilitate them in making projections about treatment options.

A web-based personalized risk communication and decision-making tool for women with dense breasts: Design and methods of a randomized controlled trial within an integrated health care system.

PubMed

Knerr, Sarah; Wernli, Karen J; Leppig, Kathleen; Ehrlich, Kelly; Graham, Amanda L; Farrell, David; Evans, Chalanda; Luta, George; Schwartz, Marc D; O'Neill, Suzanne C

2017-05-01

Mammographic breast density is one of the strongest risk factors for breast cancer after age and family history. Mandatory breast density disclosure policies are increasing nationally without clear guidance on how to communicate density status to women. Coupling density disclosure with personalized risk counseling and decision support through a web-based tool may be an effective way to allow women to make informed, values-consistent risk management decisions without increasing distress. This paper describes the design and methods of Engaged, a prospective, randomized controlled trial examining the effect of online personalized risk counseling and decision support on risk management decisions in women with dense breasts and increased breast cancer risk. The trial is embedded in a large integrated health care system in the Pacific Northwest. A total of 1250 female health plan members aged 40-69 with a recent negative screening mammogram who are at increased risk for interval cancer based on their 5-year breast cancer risk and BI-RADS® breast density will be randomly assigned to access either a personalized web-based counseling and decision support tool or standard educational content. Primary outcomes will be assessed using electronic health record data (i.e., chemoprevention and breast MRI utilization) and telephone surveys (i.e., distress) at baseline, six weeks, and twelve months. Engaged will provide evidence about whether a web-based personalized risk counseling and decision support tool is an effective method for communicating with women about breast density and risk management. An effective intervention could be disseminated with minimal clinical burden to align with density disclosure mandates. Clinical Trials Registration Number:NCT03029286. Copyright © 2017 Elsevier Inc. All rights reserved.

Facilitating knowledge transfer: decision support tools in environment and health.

PubMed

Liu, Hai-Ying; Bartonova, Alena; Neofytou, Panagiotis; Yang, Aileen; Kobernus, Michael J; Negrenti, Emanuele; Housiadas, Christos

2012-06-28

The HENVINET Health and Environment Network aimed to enhance the use of scientific knowledge in environmental health for policy making. One of the goals was to identify and evaluate Decision Support Tools (DST) in current use. Special attention was paid to four "priority" health issues: asthma and allergies, cancer, neurodevelopment disorders, and endocrine disruptors.We identified a variety of tools that are used for decision making at various levels and by various stakeholders. We developed a common framework for information acquisition about DSTs, translated this to a database structure and collected the information in an online Metadata Base (MDB).The primary product is an open access web-based MDB currently filled with 67 DSTs, accessible through the HENVINET networking portal http://www.henvinet.eu and http://henvinet.nilu.no. Quality assurance and control of the entries and evaluation of requirements to use the DSTs were also a focus of the work. The HENVINET DST MDB is an open product that enables the public to get basic information about the DSTs, and to search the DSTs using pre-designed attributes or free text. Registered users are able to 1) review and comment on existing DSTs; 2) evaluate each DST's functionalities, and 3) add new DSTs, or change the entry for their own DSTs. Assessment of the available 67 DSTs showed: 1) more than 25% of the DSTs address only one pollution source; 2) 25% of the DSTs address only one environmental stressor; 3) almost 50% of the DSTs are only applied to one disease; 4) 41% of the DSTs can only be applied to one decision making area; 5) 60% of the DSTs' results are used only by national authority and/or municipality/urban level administration; 6) almost half of the DSTs are used only by environmental professionals and researchers. This indicates that there is a need to develop DSTs covering an increasing number of pollution sources, environmental stressors and health end points, and considering links to other 'Driving forces-Pressures-State-Exposure-Effects-Actions' (DPSEEA) elements. Of interest to both researchers and decision makers should be the standardization of the way DSTs are described for easier access to the knowledge, and the identification of coverage gaps.

Mapping Application for Penguin Populations and Projected Dynamics (MAPPPD): Data and Tools for Dynamic Management and Decision Support

NASA Technical Reports Server (NTRS)

Humphries, G. R. W.; Naveen, R.; Schwaller, M.; Che-Castaldo, C.; McDowall, P.; Schrimpf, M.; Schrimpf, Michael; Lynch, H. J.

2017-01-01

The Mapping Application for Penguin Populations and Projected Dynamics (MAPPPD) is a web-based, open access, decision-support tool designed to assist scientists, non-governmental organizations and policy-makers working to meet the management objectives as set forth by the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) and other components of the Antarctic Treaty System (ATS) (that is, Consultative Meetings and the ATS Committee on Environmental Protection). MAPPPD was designed specifically to complement existing efforts such as the CCAMLR Ecosystem Monitoring Program (CEMP) and the ATS site guidelines for visitors. The database underlying MAPPPD includes all publicly available (published and unpublished) count data on emperor, gentoo, Adelie) and chinstrap penguins in Antarctica. Penguin population models are used to assimilate available data into estimates of abundance for each site and year.Results are easily aggregated across multiple sites to obtain abundance estimates over any user-defined area of interest. A front end web interface located at www.penguinmap.com provides free and ready access to the most recent count and modelled data, and can act as a facilitator for data transfer between scientists and Antarctic stakeholders to help inform management decisions for the continent.

Developing a GIS for CO2 analysis using lightweight, open source components

NASA Astrophysics Data System (ADS)

Verma, R.; Goodale, C. E.; Hart, A. F.; Kulawik, S. S.; Law, E.; Osterman, G. B.; Braverman, A.; Nguyen, H. M.; Mattmann, C. A.; Crichton, D. J.; Eldering, A.; Castano, R.; Gunson, M. R.

2012-12-01

There are advantages to approaching the realm of geographic information systems (GIS) using lightweight, open source components in place of a more traditional web map service (WMS) solution. Rapid prototyping, schema-less data storage, the flexible interchange of components, and open source community support are just some of the benefits. In our effort to develop an application supporting the geospatial and temporal rendering of remote sensing carbon-dioxide (CO2) data for the CO2 Virtual Science Data Environment project, we have connected heterogeneous open source components together to form a GIS. Utilizing widely popular open source components including the schema-less database MongoDB, Leaflet interactive maps, the HighCharts JavaScript graphing library, and Python Bottle web-services, we have constructed a system for rapidly visualizing CO2 data with reduced up-front development costs. These components can be aggregated together, resulting in a configurable stack capable of replicating features provided by more standard GIS technologies. The approach we have taken is not meant to replace the more established GIS solutions, but to instead offer a rapid way to provide GIS features early in the development of an application and to offer a path towards utilizing more capable GIS technology in the future.

Combining data from multiple sources using the CUAHSI Hydrologic Information System

NASA Astrophysics Data System (ADS)

Tarboton, D. G.; Ames, D. P.; Horsburgh, J. S.; Goodall, J. L.

2012-12-01

The Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) has developed a Hydrologic Information System (HIS) to provide better access to data by enabling the publication, cataloging, discovery, retrieval, and analysis of hydrologic data using web services. The CUAHSI HIS is an Internet based system comprised of hydrologic databases and servers connected through web services as well as software for data publication, discovery and access. The HIS metadata catalog lists close to 100 web services registered to provide data through this system, ranging from large federal agency data sets to experimental watersheds managed by University investigators. The system's flexibility in storing and enabling public access to similarly formatted data and metadata has created a community data resource from governmental and academic data that might otherwise remain private or analyzed only in isolation. Comprehensive understanding of hydrology requires integration of this information from multiple sources. HydroDesktop is the client application developed as part of HIS to support data discovery and access through this system. HydroDesktop is founded on an open source GIS client and has a plug-in architecture that has enabled the integration of modeling and analysis capability with the functionality for data discovery and access. Model integration is possible through a plug-in built on the OpenMI standard and data visualization and analysis is supported by an R plug-in. This presentation will demonstrate HydroDesktop, showing how it provides an analysis environment within which data from multiple sources can be discovered, accessed and integrated.

Resources monitoring and automatic management system for multi-VO distributed computing system

NASA Astrophysics Data System (ADS)

Chen, J.; Pelevanyuk, I.; Sun, Y.; Zhemchugov, A.; Yan, T.; Zhao, X. H.; Zhang, X. M.

2017-10-01

Multi-VO supports based on DIRAC have been set up to provide workload and data management for several high energy experiments in IHEP. To monitor and manage the heterogeneous resources which belong to different Virtual Organizations in a uniform way, a resources monitoring and automatic management system based on Resource Status System(RSS) of DIRAC has been presented in this paper. The system is composed of three parts: information collection, status decision and automatic control, and information display. The information collection includes active and passive way of gathering status from different sources and stores them in databases. The status decision and automatic control is used to evaluate the resources status and take control actions on resources automatically through some pre-defined policies and actions. The monitoring information is displayed on a web portal. Both the real-time information and historical information can be obtained from the web portal. All the implementations are based on DIRAC framework. The information and control including sites, policies, web portal for different VOs can be well defined and distinguished within DIRAC user and group management infrastructure.

Implementation of a web-based national child health-care programme in a local context: A complex facilitator role.

PubMed

Tell, Johanna; Olander, Ewy; Anderberg, Peter; Berglund, Johan Sanmartin

2018-02-01

The aim of this study was to investigate child health-care coordinators' experiences of being a facilitator for the implementation of a new national child health-care programme in the form of a web-based national guide. The study was based on eight remote, online focus groups, using Skype for Business. A qualitative content analysis was performed. The analysis generated three categories: adapt to a local context, transition challenges and led by strong incentives. There were eight subcategories. In the latent analysis, the theme 'Being a facilitator: a complex role' was formed to express the child health-care coordinators' experiences. Facilitating a national guideline or decision support in a local context is a complex task that requires an advocating and mediating role. For successful implementation, guidelines and decision support, such as a web-based guide and the new child health-care programme, must match professional consensus and needs and be seen as relevant by all. Participation in the development and a strong bottom-up approach was important, making the web-based guide and the programme relevant to whom it is intended to serve, and for successful implementation. The study contributes valuable knowledge when planning to implement a national web-based decision support and policy programme in a local health-care context.

Strategic and integrated planning for healthy, connected cities: Chattanooga case study.

PubMed

Elwell Bostrom, Holly; Shulaker, Bianca; Rippon, Jasmin; Wood, Rick

2017-02-01

The United States is facing unprecedented health challenges - such as obesity and cardiovascular disease - many of which are related to a lack of or insufficient physical activity. Maintaining or creating parks and other public recreation facilities that promote physical activity is particularly important for combating these. This brief describes a strategic planning initiative, known as "Healthy, Connected Chattanooga." The City of Chattanooga, Tennessee, partnered with The Trust for Public Land, a national nonprofit organization, to analyze the city for physical activity opportunities and identify areas where interventions were of highest need. Interventions include the creation of new parks and the activation of existing ones through the installation of fitness facilities known as Fitness Zones®. Maps and an on-line decision-support tool (web portal) were developed between 2013 and 2015, and are being used by the city to make strategic investment decisions. The decision-support analysis described in this brief has engaged a wide variety of stakeholders, opened the door to a broader base of funding sources for health-related interventions, and provided evidence for discussions about equity, access to resources, and prioritization of future projects. This brief presents a framework for integrating scientific models with community and social metrics, enabling more complete and accurate understanding of cities and the identification of more equitable, strategic, and investable solutions to current and pressing challenges. Copyright © 2016 Elsevier Inc. All rights reserved.

Pharmacogenomic knowledge representation, reasoning and genome-based clinical decision support based on OWL 2 DL ontologies.

PubMed

Samwald, Matthias; Miñarro Giménez, Jose Antonio; Boyce, Richard D; Freimuth, Robert R; Adlassnig, Klaus-Peter; Dumontier, Michel

2015-02-22

Every year, hundreds of thousands of patients experience treatment failure or adverse drug reactions (ADRs), many of which could be prevented by pharmacogenomic testing. However, the primary knowledge needed for clinical pharmacogenomics is currently dispersed over disparate data structures and captured in unstructured or semi-structured formalizations. This is a source of potential ambiguity and complexity, making it difficult to create reliable information technology systems for enabling clinical pharmacogenomics. We developed Web Ontology Language (OWL) ontologies and automated reasoning methodologies to meet the following goals: 1) provide a simple and concise formalism for representing pharmacogenomic knowledge, 2) finde errors and insufficient definitions in pharmacogenomic knowledge bases, 3) automatically assign alleles and phenotypes to patients, 4) match patients to clinically appropriate pharmacogenomic guidelines and clinical decision support messages and 5) facilitate the detection of inconsistencies and overlaps between pharmacogenomic treatment guidelines from different sources. We evaluated different reasoning systems and test our approach with a large collection of publicly available genetic profiles. Our methodology proved to be a novel and useful choice for representing, analyzing and using pharmacogenomic data. The Genomic Clinical Decision Support (Genomic CDS) ontology represents 336 SNPs with 707 variants; 665 haplotypes related to 43 genes; 22 rules related to drug-response phenotypes; and 308 clinical decision support rules. OWL reasoning identified CDS rules with overlapping target populations but differing treatment recommendations. Only a modest number of clinical decision support rules were triggered for a collection of 943 public genetic profiles. We found significant performance differences across available OWL reasoners. The ontology-based framework we developed can be used to represent, organize and reason over the growing wealth of pharmacogenomic knowledge, as well as to identify errors, inconsistencies and insufficient definitions in source data sets or individual patient data. Our study highlights both advantages and potential practical issues with such an ontology-based approach.

Data-Driven Geospatial Visual Analytics for Real-Time Urban Flooding Decision Support

NASA Astrophysics Data System (ADS)

Liu, Y.; Hill, D.; Rodriguez, A.; Marini, L.; Kooper, R.; Myers, J.; Wu, X.; Minsker, B. S.

2009-12-01

Urban flooding is responsible for the loss of life and property as well as the release of pathogens and other pollutants into the environment. Previous studies have shown that spatial distribution of intense rainfall significantly impacts the triggering and behavior of urban flooding. However, no general purpose tools yet exist for deriving rainfall data and rendering them in real-time at the resolution of hydrologic units used for analyzing urban flooding. This paper presents a new visual analytics system that derives and renders rainfall data from the NEXRAD weather radar system at the sewershed (i.e. urban hydrologic unit) scale in real-time for a Chicago stormwater management project. We introduce a lightweight Web 2.0 approach which takes advantages of scientific workflow management and publishing capabilities developed at NCSA (National Center for Supercomputing Applications), streaming data-aware semantic content management repository, web-based Google Earth/Map and time-aware KML (Keyhole Markup Language). A collection of polygon-based virtual sensors is created from the NEXRAD Level II data using spatial, temporal and thematic transformations at the sewershed level in order to produce persistent virtual rainfall data sources for the animation. Animated color-coded rainfall map in the sewershed can be played in real-time as a movie using time-aware KML inside the web browser-based Google Earth for visually analyzing the spatiotemporal patterns of the rainfall intensity in the sewershed. Such system provides valuable information for situational awareness and improved decision support during extreme storm events in an urban area. Our further work includes incorporating additional data (such as basement flooding events data) or physics-based predictive models that can be used for more integrated data-driven decision support.

Building Successful GitHub Communities

NASA Astrophysics Data System (ADS)

Smith, A.

2014-12-01

Building successful online communities is hard, whether it's in open source software or web-based citizen science. In this presentation I'll share some lessons learned and outline some techniques employed by successful open source projects.

Data Mining for Web-Based Support Systems: A Case Study in e-Custom Systems

NASA Astrophysics Data System (ADS)

Razmerita, Liana; Kirchner, Kathrin

This chapter provides an example of a Web-based support system (WSS) used to streamline trade procedures, prevent potential security threats, and reduce tax-related fraud in cross-border trade. The architecture is based on a service-oriented architecture that includes smart seals and Web services. We discuss the implications and suggest further enhancements to demonstrate how such systems can move toward a Web-based decision support system with the support of data mining methods. We provide a concrete example of how data mining can help to analyze the vast amount of data collected while monitoring the container movements along its supply chain.

From open source communications to knowledge

NASA Astrophysics Data System (ADS)

Preece, Alun; Roberts, Colin; Rogers, David; Webberley, Will; Innes, Martin; Braines, Dave

2016-05-01

Rapid processing and exploitation of open source information, including social media sources, in order to shorten decision-making cycles, has emerged as an important issue in intelligence analysis in recent years. Through a series of case studies and natural experiments, focussed primarily upon policing and counter-terrorism scenarios, we have developed an approach to information foraging and framing to inform decision making, drawing upon open source intelligence, in particular Twitter, due to its real-time focus and frequent use as a carrier for links to other media. Our work uses a combination of natural language (NL) and controlled natural language (CNL) processing to support information collection from human sensors, linking and schematising of collected information, and the framing of situational pictures. We illustrate the approach through a series of vignettes, highlighting (1) how relatively lightweight and reusable knowledge models (schemas) can rapidly be developed to add context to collected social media data, (2) how information from open sources can be combined with reports from trusted observers, for corroboration or to identify con icting information; and (3) how the approach supports users operating at or near the tactical edge, to rapidly task information collection and inform decision-making. The approach is supported by bespoke software tools for social media analytics and knowledge management.

Enabling Cross-Platform Clinical Decision Support through Web-Based Decision Support in Commercial Electronic Health Record Systems: Proposal and Evaluation of Initial Prototype Implementations

PubMed Central

Zhang, Mingyuan; Velasco, Ferdinand T.; Musser, R. Clayton; Kawamoto, Kensaku

2013-01-01

Enabling clinical decision support (CDS) across multiple electronic health record (EHR) systems has been a desired but largely unattained aim of clinical informatics, especially in commercial EHR systems. A potential opportunity for enabling such scalable CDS is to leverage vendor-supported, Web-based CDS development platforms along with vendor-supported application programming interfaces (APIs). Here, we propose a potential staged approach for enabling such scalable CDS, starting with the use of custom EHR APIs and moving towards standardized EHR APIs to facilitate interoperability. We analyzed three commercial EHR systems for their capabilities to support the proposed approach, and we implemented prototypes in all three systems. Based on these analyses and prototype implementations, we conclude that the approach proposed is feasible, already supported by several major commercial EHR vendors, and potentially capable of enabling cross-platform CDS at scale. PMID:24551426

Intelligent Information Fusion in the Aviation Domain: A Semantic-Web based Approach

NASA Technical Reports Server (NTRS)

Ashish, Naveen; Goforth, Andre

2005-01-01

Information fusion from multiple sources is a critical requirement for System Wide Information Management in the National Airspace (NAS). NASA and the FAA envision creating an "integrated pool" of information originally coming from different sources, which users, intelligent agents and NAS decision support tools can tap into. In this paper we present the results of our initial investigations into the requirements and prototype development of such an integrated information pool for the NAS. We have attempted to ascertain key requirements for such an integrated pool based on a survey of DSS tools that will benefit from this integrated pool. We then advocate key technologies from computer science research areas such as the semantic web, information integration, and intelligent agents that we believe are well suited to achieving the envisioned system wide information management capabilities.

WE-E-BRB-11: Riview a Web-Based Viewer for Radiotherapy.

PubMed

Apte, A; Wang, Y; Deasy, J

2012-06-01

Collaborations involving radiotherapy data collection, such as the recently proposed international radiogenomics consortium, require robust, web-based tools to facilitate reviewing treatment planning information. We present the architecture and prototype characteristics for a web-based radiotherapy viewer. The web-based environment developed in this work consists of the following components: 1) Import of DICOM/RTOG data: CERR was leveraged to import DICOM/RTOG data and to convert to database friendly RT objects. 2) Extraction and Storage of RT objects: The scan and dose distributions were stored as .png files per slice and view plane. The file locations were written to the MySQL database. Structure contours and DVH curves were written to the database as numeric data. 3) Web interfaces to query, retrieve and visualize the RT objects: The Web application was developed using HTML 5 and Ruby on Rails (RoR) technology following the MVC philosophy. The open source ImageMagick library was utilized to overlay scan, dose and structures. The application allows users to (i) QA the treatment plans associated with a study, (ii) Query and Retrieve patients matching anonymized ID and study, (iii) Review up to 4 plans simultaneously in 4 window panes (iv) Plot DVH curves for the selected structures and dose distributions. A subset of data for lung cancer patients was used to prototype the system. Five user accounts were created to have access to this study. The scans, doses, structures and DVHs for 10 patients were made available via the web application. A web-based system to facilitate QA, and support Query, Retrieve and the Visualization of RT data was prototyped. The RIVIEW system was developed using open source and free technology like MySQL and RoR. We plan to extend the RIVIEW system further to be useful in clinical trial data collection, outcomes research, cohort plan review and evaluation. © 2012 American Association of Physicists in Medicine.

A smarter way to search, share and utilize open-spatial online data for energy R&D - Custom machine learning and GIS tools in U.S. DOE's virtual data library & laboratory, EDX

NASA Astrophysics Data System (ADS)

Rose, K.; Bauer, J.; Baker, D.; Barkhurst, A.; Bean, A.; DiGiulio, J.; Jones, K.; Jones, T.; Justman, D.; Miller, R., III; Romeo, L.; Sabbatino, M.; Tong, A.

2017-12-01

As spatial datasets are increasingly accessible through open, online systems, the opportunity to use these resources to address a range of Earth system questions grows. Simultaneously, there is a need for better infrastructure and tools to find and utilize these resources. We will present examples of advanced online computing capabilities, hosted in the U.S. DOE's Energy Data eXchange (EDX), that address these needs for earth-energy research and development. In one study the computing team developed a custom, machine learning, big data computing tool designed to parse the web and return priority datasets to appropriate servers to develop an open-source global oil and gas infrastructure database. The results of this spatial smart search approach were validated against expert-driven, manual search results which required a team of seven spatial scientists three months to produce. The custom machine learning tool parsed online, open systems, including zip files, ftp sites and other web-hosted resources, in a matter of days. The resulting resources were integrated into a geodatabase now hosted for open access via EDX. Beyond identifying and accessing authoritative, open spatial data resources, there is also a need for more efficient tools to ingest, perform, and visualize multi-variate, spatial data analyses. Within the EDX framework, there is a growing suite of processing, analytical and visualization capabilities that allow multi-user teams to work more efficiently in private, virtual workspaces. An example of these capabilities are a set of 5 custom spatio-temporal models and data tools that form NETL's Offshore Risk Modeling suite that can be used to quantify oil spill risks and impacts. Coupling the data and advanced functions from EDX with these advanced spatio-temporal models has culminated with an integrated web-based decision-support tool. This platform has capabilities to identify and combine data across scales and disciplines, evaluate potential environmental, social, and economic impacts, highlight knowledge or technology gaps, and reduce uncertainty for a range of `what if' scenarios relevant to oil spill prevention efforts. These examples illustrate EDX's growing capabilities for advanced spatial data search and analysis to support geo-data science needs.

An open, interoperable, transdisciplinary approach to a point cloud data service using OGC standards and open source software.

NASA Astrophysics Data System (ADS)

Steer, Adam; Trenham, Claire; Druken, Kelsey; Evans, Benjamin; Wyborn, Lesley

2017-04-01

High resolution point clouds and other topology-free point data sources are widely utilised for research, management and planning activities. A key goal for research and management users is making these data and common derivatives available in a way which is seamlessly interoperable with other observed and modelled data. The Australian National Computational Infrastructure (NCI) stores point data from a range of disciplines, including terrestrial and airborne LiDAR surveys, 3D photogrammetry, airborne and ground-based geophysical observations, bathymetric observations and 4D marine tracers. These data are stored alongside a significant store of Earth systems data including climate and weather, ecology, hydrology, geoscience and satellite observations, and available from NCI's National Environmental Research Data Interoperability Platform (NERDIP) [1]. Because of the NERDIP requirement for interoperability with gridded datasets, the data models required to store these data may not conform to the LAS/LAZ format - the widely accepted community standard for point data storage and transfer. The goal for NCI is making point data discoverable, accessible and useable in ways which allow seamless integration with earth observation datasets and model outputs - in turn assisting researchers and decision-makers in the often-convoluted process of handling and analyzing massive point datasets. With a use-case of providing a web data service and supporting a derived product workflow, NCI has implemented and tested a web-based point cloud service using the Open Geospatial Consortium (OGC) Web Processing Service [2] as a transaction handler between a web-based client and server-side computing tools based on a native Linux operating system. Using this model, the underlying toolset for driving a data service is flexible and can take advantage of NCI's highly scalable research cloud. Present work focusses on the Point Data Abstraction Library (PDAL) [3] as a logical choice for efficiently handling LAS/LAZ based point workflows, and native HDF5 libraries for handling point data kept in HDF5-based structures (eg NetCDF4, SPDlib [4]). Points stored in database tables (eg postgres-pointcloud [5]) will be considered as testing continues. Visualising and exploring massive point datasets in a web browser alongside multiple datasets has been demonstrated by the entwine-3D tiles project [6]. This is a powerful interface which enables users to investigate and select appropriate data, and is also being investigated as a potential front-end to a WPS-based point data service. In this work we show preliminary results for a WPS-based point data access system, in preparation for demonstration at FOSS4G 2017, Boston (http://2017.foss4g.org/) [1] http://nci.org.au/data-collections/nerdip/ [2] http://www.opengeospatial.org/standards/wps [3] http://www.pdal.io [4] http://www.spdlib.org/doku.php [5] https://github.com/pgpointcloud/pointcloud [6] http://cesium.entwine.io

Cognitive Readiness Assessment and Reporting: An Open Source Mobile Framework for Operational Decision Support and Performance Improvement

ERIC Educational Resources Information Center

Heric, Matthew; Carter, Jenn

2011-01-01

Cognitive readiness (CR) and performance for operational time-critical environments are continuing points of focus for military and academic communities. In response to this need, we designed an open source interactive CR assessment application as a highly adaptive and efficient open source testing administration and analysis tool. It is capable…

Genes2WordCloud: a quick way to identify biological themes from gene lists and free text.

PubMed

Baroukh, Caroline; Jenkins, Sherry L; Dannenfelser, Ruth; Ma'ayan, Avi

2011-10-13

Word-clouds recently emerged on the web as a solution for quickly summarizing text by maximizing the display of most relevant terms about a specific topic in the minimum amount of space. As biologists are faced with the daunting amount of new research data commonly presented in textual formats, word-clouds can be used to summarize and represent biological and/or biomedical content for various applications. Genes2WordCloud is a web application that enables users to quickly identify biological themes from gene lists and research relevant text by constructing and displaying word-clouds. It provides users with several different options and ideas for the sources that can be used to generate a word-cloud. Different options for rendering and coloring the word-clouds give users the flexibility to quickly generate customized word-clouds of their choice. Genes2WordCloud is a word-cloud generator and a word-cloud viewer that is based on WordCram implemented using Java, Processing, AJAX, mySQL, and PHP. Text is fetched from several sources and then processed to extract the most relevant terms with their computed weights based on word frequencies. Genes2WordCloud is freely available for use online; it is open source software and is available for installation on any web-site along with supporting documentation at http://www.maayanlab.net/G2W. Genes2WordCloud provides a useful way to summarize and visualize large amounts of textual biological data or to find biological themes from several different sources. The open source availability of the software enables users to implement customized word-clouds on their own web-sites and desktop applications.

Genes2WordCloud: a quick way to identify biological themes from gene lists and free text

PubMed Central

2011-01-01

Background Word-clouds recently emerged on the web as a solution for quickly summarizing text by maximizing the display of most relevant terms about a specific topic in the minimum amount of space. As biologists are faced with the daunting amount of new research data commonly presented in textual formats, word-clouds can be used to summarize and represent biological and/or biomedical content for various applications. Results Genes2WordCloud is a web application that enables users to quickly identify biological themes from gene lists and research relevant text by constructing and displaying word-clouds. It provides users with several different options and ideas for the sources that can be used to generate a word-cloud. Different options for rendering and coloring the word-clouds give users the flexibility to quickly generate customized word-clouds of their choice. Methods Genes2WordCloud is a word-cloud generator and a word-cloud viewer that is based on WordCram implemented using Java, Processing, AJAX, mySQL, and PHP. Text is fetched from several sources and then processed to extract the most relevant terms with their computed weights based on word frequencies. Genes2WordCloud is freely available for use online; it is open source software and is available for installation on any web-site along with supporting documentation at http://www.maayanlab.net/G2W. Conclusions Genes2WordCloud provides a useful way to summarize and visualize large amounts of textual biological data or to find biological themes from several different sources. The open source availability of the software enables users to implement customized word-clouds on their own web-sites and desktop applications. PMID:21995939

IASMHYN: A web tool for mapping Soil Water Budget and agro-hydrological assessment trough the integration of monitoring and remote sensing data

NASA Astrophysics Data System (ADS)

Bagli, Stefano; Pistocchi, Alberto; Mazzoli, Paolo; Borga, Marco; Bertoldi, Giacomo; Brenner, Johannes; Luzzi, Valerio

2016-04-01

Climate change, increasing pressure on farmland to satisfy the growing demand, and need to ensure environmental quality for agriculture in order to be competitive require an increasing capacity of water management. In this context, web-based for forecasting and monitoring the hydrological conditions of topsoil can be an effective means to save water, maximize crop protection and reduce soil loss and the leaching of pollutants. Such tools need to be targeted to the users and be accessible in a simple way in order to allow adequate take up in the practice. IASMHYN "Improved management of Agricultural Systems by Monitoring and Hydrological evaluation" is a web mapping service designed to provide and update on a daily basis the main water budget variables for farmland management. A beta version of the tool is available at www.gecosistema.com/iasmhyn . IASMHYN is an instrument for "second level monitoring" that takes into account accurate hydro-meteorological information's from ground stations and remote sensing sources, and turns them into practically usable decision variables for precision farming, making use of geostatistical analysis and hydrological models The main routines embedded in IASMYHN exclusively use open source libraries (R packages and Python), to perform following operations: (1) Automatic acquisition of observed data, both from ground stations and remote sensing, concerning precipitation (RADAR) and temperature (MODIS-LST) available from various sources; (2) Interpolation of acquisitions through regression kriging in order to spatially map the meteorological data; (3) Run of hydrological models to obtain spatial information of hydrological soil variables of immediate interest in agriculture. The real time results that are produced are available trough a web interface and provide the user with spatial maps and time series of the following variables, supporting decision on irrigation, soil protection from erosion, pollution risk of groundwater and streams: - Daily precipitation and its characteristics (rain, snow or hail, rain erosiveness); - Maximum, minimum and average daily temperature; - Soil Water Content (SWC); - Infiltration into the deep layers of the soil and surface runoff; - Potential loss of soil due to erosion - Residence time of a possible chemical (pesticides, fertilizers) applied to the soil. Thematic real time maps are produced give the user support decision on irrigation, soil management and pesticide/fertilizer application. The ongoing project will also lead to validation and improvement of estimates of hydrological variables from satellite imagery and radar data. The tool has been cross-validated with estimates of evapotranspiration and soil water content in agricultural sites in South Tyrol (Italy) in the framework of MONALISA project (http://www.monalisa-project.eu). A comparison with physical based models, satellite imagery and radar data will allow further generalization of the product. The ultimate goal of the tool is to make available on the market a service that is generally applicable in Europe , using commonly available data, to provide single farmers and organizations effective and up to date information for planning and programming their activities.

Brandenburg 3D - a comprehensive 3D Subsurface Model, Conception of an Infrastructure Node and a Web Application

NASA Astrophysics Data System (ADS)

Kerschke, Dorit; Schilling, Maik; Simon, Andreas; Wächter, Joachim

2014-05-01

The Energiewende and the increasing scarcity of raw materials will lead to an intensified utilization of the subsurface in Germany. Within this context, geological 3D modeling is a fundamental approach for integrated decision and planning processes. Initiated by the development of the European Geospatial Infrastructure INSPIRE, the German State Geological Offices started digitizing their predominantly analog archive inventory. Until now, a comprehensive 3D subsurface model of Brandenburg did not exist. Therefore the project B3D strived to develop a new 3D model as well as a subsequent infrastructure node to integrate all geological and spatial data within the Geodaten-Infrastruktur Brandenburg (Geospatial Infrastructure, GDI-BB) and provide it to the public through an interactive 2D/3D web application. The functionality of the web application is based on a client-server architecture. Server-sided, all available spatial data is published through GeoServer. GeoServer is designed for interoperability and acts as the reference implementation of the Open Geospatial Consortium (OGC) Web Feature Service (WFS) standard that provides the interface that allows requests for geographical features. In addition, GeoServer implements, among others, the high performance certified compliant Web Map Service (WMS) that serves geo-referenced map images. For publishing 3D data, the OGC Web 3D Service (W3DS), a portrayal service for three-dimensional geo-data, is used. The W3DS displays elements representing the geometry, appearance, and behavior of geographic objects. On the client side, the web application is solely based on Free and Open Source Software and leans on the JavaScript API WebGL that allows the interactive rendering of 2D and 3D graphics by means of GPU accelerated usage of physics and image processing as part of the web page canvas without the use of plug-ins. WebGL is supported by most web browsers (e.g., Google Chrome, Mozilla Firefox, Safari, and Opera). The web application enables an intuitive navigation through all available information and allows the visualization of geological maps (2D), seismic transects (2D/3D), wells (2D/3D), and the 3D-model. These achievements will alleviate spatial and geological data management within the German State Geological Offices and foster the interoperability of heterogeneous systems. It will provide guidance to a systematic subsurface management across system, domain and administrative boundaries on the basis of a federated spatial data infrastructure, and include the public in the decision processes (e-Governance). Yet, the interoperability of the systems has to be strongly propelled forward through agreements on standards that need to be decided upon in responsible committees. The project B3D is funded with resources from the European Fund for Regional Development (EFRE).

Integrating Data Distribution and Data Assimilation Between the OOI CI and the NOAA DIF

NASA Astrophysics Data System (ADS)

Meisinger, M.; Arrott, M.; Clemesha, A.; Farcas, C.; Farcas, E.; Im, T.; Schofield, O.; Krueger, I.; Klacansky, I.; Orcutt, J.; Peach, C.; Chave, A.; Raymer, D.; Vernon, F.

2008-12-01

The Ocean Observatories Initiative (OOI) is an NSF funded program to establish the ocean observing infrastructure of the 21st century benefiting research and education. It is currently approaching final design and promises to deliver cyber and physical observatory infrastructure components as well as substantial core instrumentation to study environmental processes of the ocean at various scales, from coastal shelf-slope exchange processes to the deep ocean. The OOI's data distribution network lies at the heart of its cyber- infrastructure, which enables a multitude of science and education applications, ranging from data analysis, to processing, visualization and ontology supported query and mediation. In addition, it fundamentally supports a class of applications exploiting the knowledge gained from analyzing observational data for objective-driven ocean observing applications, such as automatically triggered response to episodic environmental events and interactive instrument tasking and control. The U.S. Department of Commerce through NOAA operates the Integrated Ocean Observing System (IOOS) providing continuous data in various formats, rates and scales on open oceans and coastal waters to scientists, managers, businesses, governments, and the public to support research and inform decision-making. The NOAA IOOS program initiated development of the Data Integration Framework (DIF) to improve management and delivery of an initial subset of ocean observations with the expectation of achieving improvements in a select set of NOAA's decision-support tools. Both OOI and NOAA through DIF collaborate on an effort to integrate the data distribution, access and analysis needs of both programs. We present details and early findings from this collaboration; one part of it is the development of a demonstrator combining web-based user access to oceanographic data through ERDDAP, efficient science data distribution, and scalable, self-healing deployment in a cloud computing environment. ERDDAP is a web-based front-end application integrating oceanographic data sources of various formats, for instance CDF data files as aggregated through NcML or presented using a THREDDS server. The OOI-designed data distribution network provides global traffic management and computational load balancing for observatory resources; it makes use of the OpenDAP Data Access Protocol (DAP) for efficient canonical science data distribution over the network. A cloud computing strategy is the basis for scalable, self-healing organization of an observatory's computing and storage resources, independent of the physical location and technical implementation of these resources.

Capturing Trust in Social Web Applications

NASA Astrophysics Data System (ADS)

O'Donovan, John

The Social Web constitutes a shift in information flow from the traditional Web. Previously, content was provided by the owners of a website, for consumption by the end-user. Nowadays, these websites are being replaced by Social Web applications which are frameworks for the publication of user-provided content. Traditionally, Web content could be `trusted' to some extent based on the site it originated from. Algorithms such as Google's PageRank were (and still are) used to compute the importance of a website, based on analysis of underlying link topology. In the Social Web, analysis of link topology merely tells us about the importance of the information framework which hosts the content. Consumers of information still need to know about the importance/reliability of the content they are reading, and therefore about the reliability of the producers of that content. Research into trust and reputation of the producers of information in the Social Web is still very much in its infancy. Every day, people are forced to make trusting decisions about strangers on the Web based on a very limited amount of information. For example, purchasing a product from an eBay seller with a `reputation' of 99%, downloading a file from a peer-to-peer application such as Bit-Torrent, or allowing Amazon.com tell you what products you will like. Even something as simple as reading comments on a Web-blog requires the consumer to make a trusting decision about the quality of that information. In all of these example cases, and indeed throughout the Social Web, there is a pressing demand for increased information upon which we can make trusting decisions. This chapter examines the diversity of sources from which trust information can be harnessed within Social Web applications and discusses a high level classification of those sources. Three different techniques for harnessing and using trust from a range of sources are presented. These techniques are deployed in two sample Social Web applications—a recommender system and an online auction. In all cases, it is shown that harnessing an increased amount of information upon which to make trust decisions greatly enhances the user experience with the Social Web application.

ERDDAP - An Easier Way for Diverse Clients to Access Scientific Data From Diverse Sources

NASA Astrophysics Data System (ADS)

Mendelssohn, R.; Simons, R. A.

2008-12-01

ERDDAP is a new open-source, web-based service that aggregates data from other web services: OPeNDAP grid servers (THREDDS), OPeNDAP sequence servers (Dapper), NOS SOAP service, SOS (IOOS, OOStethys), microWFS, DiGIR (OBIS, BMDE). Regardless of the data source, ERDDAP makes all datasets available to clients via standard (and enhanced) DAP requests and makes some datasets accessible via WMS. A client's request also specifies the desired format for the results, e.g., .asc, .csv, .das, .dds, .dods, htmlTable, XHTML, .mat, netCDF, .kml, .png, or .pdf (formats more directly useful to clients). ERDDAP interprets a client request, requests the data from the data source (in the appropriate way), reformats the data source's response, and sends the result to the client. Thus ERDDAP makes data from diverse sources available to diverse clients via standardized interfaces. Clients don't have to install libraries to get data from ERDDAP because ERDDAP is RESTful and resource-oriented: a URL completely defines a data request and the URL can be used in any application that can send a URL and receive a file. This also makes it easy to use ERDDAP in mashups with other web services. ERDDAP could be extended to support other protocols. ERDDAP's hub and spoke architecture simplifies adding support for new types of data sources and new types of clients. ERDDAP includes metadata management support, catalog services, and services to make graphs and maps.

An Extensible, Modular Architecture Coupling HydroShare and Tethys Platform to Deploy Water Science Web Apps

NASA Astrophysics Data System (ADS)

Nelson, J.; Ames, D. P.; Jones, N.; Tarboton, D. G.; Li, Z.; Qiao, X.; Crawley, S.

2016-12-01

As water resources data continue to move to the web in the form of well-defined, open access, machine readable web services provided by government, academic, and private institutions, there is increased opportunity to move additional parts of the water science workflow to the web (e.g. analysis, modeling, decision support, and collaboration.) Creating such web-based functionality can be extremely time-consuming and resource-intensive and can lead the erstwhile water scientist down a veritable cyberinfrastructure rabbit hole, through an unintended tunnel of transformation to become a Cyber-Wonderland software engineer. We posit that such transformations were never the intention of the research programs that fund earth science cyberinfrastructure, nor is it in the best interest of water researchers to spend exorbitant effort developing and deploying such technologies. This presentation will introduce a relatively simple and ready-to-use water science web app environment funded by the National Science Foundation that couples the new HydroShare data publishing system with the Tethys Platform web app development toolkit. The coupled system has already been shown to greatly lower the barrier to deploying of web based visualization and analysis tools for the CUAHSI Water Data Center and for the National Weather Service's National Water Model. The design and implementation of the developed web app architecture will be presented together key examples of existing apps created using this system. In each of the cases presented, water resources students with basic programming skills were able to develop and deploy highly functional web apps in a relatively short period of time (days to weeks) - allowing the focus to remain on water science rather on cyberinfrastructure. This presentation is accompanied by an open invitation for new collaborations that use the HydroShare-Tethys web app environment.

plas.io: Open Source, Browser-based WebGL Point Cloud Visualization

NASA Astrophysics Data System (ADS)

Butler, H.; Finnegan, D. C.; Gadomski, P. J.; Verma, U. K.

2014-12-01

Point cloud data, in the form of Light Detection and Ranging (LiDAR), RADAR, or semi-global matching (SGM) image processing, are rapidly becoming a foundational data type to quantify and characterize geospatial processes. Visualization of these data, due to overall volume and irregular arrangement, is often difficult. Technological advancement in web browsers, in the form of WebGL and HTML5, have made interactivity and visualization capabilities ubiquitously available which once only existed in desktop software. plas.io is an open source JavaScript application that provides point cloud visualization, exploitation, and compression features in a web-browser platform, reducing the reliance for client-based desktop applications. The wide reach of WebGL and browser-based technologies mean plas.io's capabilities can be delivered to a diverse list of devices -- from phones and tablets to high-end workstations -- with very little custom software development. These properties make plas.io an ideal open platform for researchers and software developers to communicate visualizations of complex and rich point cloud data to devices to which everyone has easy access.

Description and testing of the Geo Data Portal: Data integration framework and Web processing services for environmental science collaboration

USGS Publications Warehouse

Blodgett, David L.; Booth, Nathaniel L.; Kunicki, Thomas C.; Walker, Jordan I.; Viger, Roland J.

2011-01-01

Interest in sharing interdisciplinary environmental modeling results and related data is increasing among scientists. The U.S. Geological Survey Geo Data Portal project enables data sharing by assembling open-standard Web services into an integrated data retrieval and analysis Web application design methodology that streamlines time-consuming and resource-intensive data management tasks. Data-serving Web services allow Web-based processing services to access Internet-available data sources. The Web processing services developed for the project create commonly needed derivatives of data in numerous formats. Coordinate reference system manipulation and spatial statistics calculation components implemented for the Web processing services were confirmed using ArcGIS 9.3.1, a geographic information science software package. Outcomes of the Geo Data Portal project support the rapid development of user interfaces for accessing and manipulating environmental data.

Generalized Intelligent Framework for Tutoring (GIFT) Cloud/Virtual Open Campus Quick Start Guide (Revision 1)

DTIC Science & Technology

2017-06-01

for GIFT Cloud, the web -based application version of the Generalized Intelligent Framework for Tutoring (GIFT). GIFT is a modular, open-source...external applications. GIFT is available to users with a GIFT Account at no cost. GIFT Cloud is an implementation of GIFT. This web -based application...section. Approved for public release; distribution is unlimited. 3 3. Requirements for GIFT Cloud GIFT Cloud is accessed via a web browser

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application.

PubMed

Hanwell, Marcus D; de Jong, Wibe A; Harris, Christopher J

2017-10-30

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction-connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platform with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web-going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

DOE PAGES

Hanwell, Marcus D.; de Jong, Wibe A.; Harris, Christopher J.

2017-10-30

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction - connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platformmore » with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web - going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.« less

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hanwell, Marcus D.; de Jong, Wibe A.; Harris, Christopher J.

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction - connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platformmore » with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web - going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.« less

Collaborative GIS for flood susceptibility mapping: An example from Mekong river basin of Viet Nam

NASA Astrophysics Data System (ADS)

Thanh, B.

2016-12-01

Flooding is one of the most dangerous natural disasters in Vietnam. Floods have caused serious damages to people and made adverse impact on social economic development across the country, especially in lower river basin where there is high risk of flooding as consequences of the climate change and social activities. This paper presents a collaborative platform of a combination of an interactive web-GIS framework and a multi-criteria evaluation (MCE) tool. MCE is carried out in server side through web interface, in which parameters used for evaluation are groups into three major categories, including (1) climatic factor: precipitation, typhoon frequency, temperature, humidity (2) physiographic data: DEM, topographic wetness index, NDVI, stream power index, soil texture, distance to river (3) social factor: NDBI, land use pattern. Web-based GIS is based on open-source technology that includes an information page, a page for MCE tool that users can interactively alter parameters in flood susceptible mapping, and a discussion page. The system is designed for local participation in prediction of the flood risk magnitude under impacts of natural processes and human intervention. The proposed flood susceptibility assessment prototype was implemented in the Mekong river basin, Viet Nam. Index images were calculated using Landsat data, and other were collected from authorized agencies. This study shows the potential to combine web-GIS and spatial analysis tool to flood hazard risk assessment. The combination can be a supportive solution that potentially assists the interaction between stakeholders in information exchange and in disaster management, thus provides for better analysis, control and decision-making.

Open Source Cloud-Based Technologies for Bim

NASA Astrophysics Data System (ADS)

Logothetis, S.; Karachaliou, E.; Valari, E.; Stylianidis, E.

2018-05-01

This paper presents a Cloud-based open source system for storing and processing data from a 3D survey approach. More specifically, we provide an online service for viewing, storing and analysing BIM. Cloud technologies were used to develop a web interface as a BIM data centre, which can handle large BIM data using a server. The server can be accessed by many users through various electronic devices anytime and anywhere so they can view online 3D models using browsers. Nowadays, the Cloud computing is engaged progressively in facilitating BIM-based collaboration between the multiple stakeholders and disciplinary groups for complicated Architectural, Engineering and Construction (AEC) projects. Besides, the development of Open Source Software (OSS) has been rapidly growing and their use tends to be united. Although BIM and Cloud technologies are extensively known and used, there is a lack of integrated open source Cloud-based platforms able to support all stages of BIM processes. The present research aims to create an open source Cloud-based BIM system that is able to handle geospatial data. In this effort, only open source tools will be used; from the starting point of creating the 3D model with FreeCAD to its online presentation through BIMserver. Python plug-ins will be developed to link the two software which will be distributed and freely available to a large community of professional for their use. The research work will be completed by benchmarking four Cloud-based BIM systems: Autodesk BIM 360, BIMserver, Graphisoft BIMcloud and Onuma System, which present remarkable results.

Development of WMS Capabilities to Support NASA Disasters Applications and App Development

NASA Astrophysics Data System (ADS)

Bell, J. R.; Burks, J. E.; Molthan, A.; McGrath, K. M.

2013-12-01

During the last year several significant disasters have occurred such as Superstorm Sandy on the East coast of the United States, and Typhoon Bopha in the Phillipines, along with several others. In support of these disasters NASA's Short-term Prediction Research and Transition (SPoRT) Center delivered various products derived from satellite imagery to help in the assessment of damage and recovery of the affected areas. To better support the decision makers responding to the disasters SPoRT quickly developed several solutions to provide the data using open Geographical Information Service (GIS) formats. Providing the data in open GIS standard formats allowed the end user to easily integrate the data into existing Decision Support Systems (DSS). Both Tile Mapping Service (TMS) and Web Mapping Service (WMS) were leveraged to quickly provide the data to the end-user. Development of the deliver methodology allowed quick response to rapidly developing disasters and enabled NASA SPoRT to bring science data to decision makers in a successful research to operations transition.

Development of WMS Capabilities to Support NASA Disasters Applications and App Development

NASA Technical Reports Server (NTRS)

Bell, Jordan R.; Burks, Jason E.; Molthan, Andrew L.; McGrath, Kevin M.

2013-01-01

During the last year several significant disasters have occurred such as Superstorm Sandy on the East coast of the United States, and Typhoon Bopha in the Phillipines, along with several others. In support of these disasters NASA's Short-term Prediction Research and Transition (SPoRT) Center delivered various products derived from satellite imagery to help in the assessment of damage and recovery of the affected areas. To better support the decision makers responding to the disasters SPoRT quickly developed several solutions to provide the data using open Geographical Information Service (GIS) formats. Providing the data in open GIS standard formats allowed the end user to easily integrate the data into existing Decision Support Systems (DSS). Both Tile Mapping Service (TMS) and Web Mapping Service (WMS) were leveraged to quickly provide the data to the end-user. Development of the deliver methodology allowed quick response to rapidly developing disasters and enabled NASA SPoRT to bring science data to decision makers in a successful research to operations transition.

Internet use in pregnancy informs women's decision making: a web-based survey.

PubMed

Lagan, Briege M; Sinclair, Marlene; Kernohan, W George

2010-06-01

Internet access and usage is almost ubiquitous, providing new opportunities and increasing challenges for health care practitioners and users. With pregnant women reportedly turning to the Internet for information during pregnancy, a better understanding of this behavior is needed. The objective of this study was to ascertain why and how pregnant women use the Internet as a health information source, and the overall effect it had on their decision making. Kuhlthau's (1993) information-seeking model was adapted to provide the underpinning theoretical framework for the study. The design was exploratory and descriptive. Data were collected using a valid and reliable web-based questionnaire. Over a 12-week period, 613 women from 24 countries who had confirmed that they had used the Internet for pregnancy-related information during their pregnancy completed and submitted a questionnaire. Most women (97%) used search engines such as Google to identify online web pages to access a large variety of pregnancy-related information and to use the Internet for pregnancy-related social networking, support, and electronic commerce (i.e., e-commerce). Almost 94 percent of women used the Internet to supplement information already provided by health professionals and 83 percent used it to influence their pregnancy decision making. Nearly half of the respondents reported dissatisfaction with information given by health professionals (48.6%) and lack of time to ask health professionals questions (46.5%) as key factors influencing them to access the Internet. Statistically, women's confidence levels significantly increased with respect to making decisions about their pregnancy after Internet usage (p < 0.05). In this study, the Internet played a significant part in the respondents' health information seeking and decision making in pregnancy. Health professionals need to be ready to support pregnant women in online data retrieval, interpretation, and application.

Using Cesium for 3D Thematic Visualisations on the Web

NASA Astrophysics Data System (ADS)

Gede, Mátyás

2018-05-01

Cesium (http://cesiumjs.org) is an open source, WebGL-based JavaScript library for virtual globes and 3D maps. It is an excellent tool for 3D thematic visualisations, but to use its full functionality it has to be feed with its own file format, CZML. Unfortunately, this format is not yet supported by any major GIS software. This paper intro- duces a plugin for QGIS, developed by the author, which facilitates the creation of CZML file for various types of visualisations. The usability of Cesium is also examined in various hardware/software environments.

Choosing Open Source ERP Systems: What Reasons Are There For Doing So?

NASA Astrophysics Data System (ADS)

Johansson, Björn; Sudzina, Frantisek

Enterprise resource planning (ERP) systems attract a high attention and open source software does it as well. The question is then if, and if so, when do open source ERP systems take off. The paper describes the status of open source ERP systems. Based on literature review of ERP system selection criteria based on Web of Science articles, it discusses reported reasons for choosing open source or proprietary ERP systems. Last but not least, the article presents some conclusions that could act as input for future research. The paper aims at building up a foundation for the basic question: What are the reasons for an organization to adopt open source ERP systems.

Regulating outdoor advertisement boards; employing spatial decision support system to control urban visual pollution

NASA Astrophysics Data System (ADS)

Wakil, K.; Hussnain, MQ; Tahir, A.; Naeem, M. A.

2016-06-01

Unmanaged placement, size, location, structure and contents of outdoor advertisement boards have resulted in severe urban visual pollution and deterioration of the socio-physical living environment in urban centres of Pakistan. As per the regulatory instruments, the approval decision for a new advertisement installation is supposed to be based on the locational density of existing boards and their proximity or remoteness to certain land- uses. In cities, where regulatory tools for the control of advertisement boards exist, responsible authorities are handicapped in effective implementation due to the absence of geospatial analysis capacity. This study presents the development of a spatial decision support system (SDSS) for regularization of advertisement boards in terms of their location and placement. The knowledge module of the proposed SDSS is based on provisions and restrictions prescribed in regulatory documents. While the user interface allows visualization and scenario evaluation to understand if the new board will affect existing linear density on a particular road and if it violates any buffer restrictions around a particular land use. Technically the structure of the proposed SDSS is a web-based solution which includes open geospatial tools such as OpenGeo Suite, GeoExt, PostgreSQL, and PHP. It uses three key data sets including road network, locations of existing billboards and building parcels with land use information to perform the analysis. Locational suitability has been calculated using pairwise comparison through analytical hierarchy process (AHP) and weighted linear combination (WLC). Our results indicate that open geospatial tools can be helpful in developing an SDSS which can assist solving space related iterative decision challenges on outdoor advertisements. Employing such a system will result in effective implementation of regulations resulting in visual harmony and aesthetic improvement in urban communities.

Design, implementation, use, and preliminary evaluation of SEBASTIAN, a standards-based Web service for clinical decision support.

PubMed

Kawamoto, Kensaku; Lobach, David F

2005-01-01

Despite their demonstrated ability to improve care quality, clinical decision support systems are not widely used. In part, this limited use is due to the difficulty of sharing medical knowledge in a machine-executable format. To address this problem, we developed a decision support Web service known as SEBASTIAN. In SEBASTIAN, individual knowledge modules define the data requirements for assessing a patient, the conclusions that can be drawn using that data, and instructions on how to generate those conclusions. Using standards-based XML messages transmitted over HTTP, client decision support applications provide patient data to SEBASTIAN and receive patient-specific assessments and recommendations. SEBASTIAN has been used to implement four distinct decision support systems; an architectural overview is provided for one of these systems. Preliminary assessments indicate that SEBASTIAN fulfills all original design objectives, including the re-use of executable medical knowledge across diverse applications and care settings, the straightforward authoring of knowledge modules, and use of the framework to implement decision support applications with significant clinical utility.

Development of spatial density maps based on geoprocessing web services: application to tuberculosis incidence in Barcelona, Spain.

PubMed

Dominkovics, Pau; Granell, Carlos; Pérez-Navarro, Antoni; Casals, Martí; Orcau, Angels; Caylà, Joan A

2011-11-29

Health professionals and authorities strive to cope with heterogeneous data, services, and statistical models to support decision making on public health. Sophisticated analysis and distributed processing capabilities over geocoded epidemiological data are seen as driving factors to speed up control and decision making in these health risk situations. In this context, recent Web technologies and standards-based web services deployed on geospatial information infrastructures have rapidly become an efficient way to access, share, process, and visualize geocoded health-related information. Data used on this study is based on Tuberculosis (TB) cases registered in Barcelona city during 2009. Residential addresses are geocoded and loaded into a spatial database that acts as a backend database. The web-based application architecture and geoprocessing web services are designed according to the Representational State Transfer (REST) principles. These web processing services produce spatial density maps against the backend database. The results are focused on the use of the proposed web-based application to the analysis of TB cases in Barcelona. The application produces spatial density maps to ease the monitoring and decision making process by health professionals. We also include a discussion of how spatial density maps may be useful for health practitioners in such contexts. In this paper, we developed web-based client application and a set of geoprocessing web services to support specific health-spatial requirements. Spatial density maps of TB incidence were generated to help health professionals in analysis and decision-making tasks. The combined use of geographic information tools, map viewers, and geoprocessing services leads to interesting possibilities in handling health data in a spatial manner. In particular, the use of spatial density maps has been effective to identify the most affected areas and its spatial impact. This study is an attempt to demonstrate how web processing services together with web-based mapping capabilities suit the needs of health practitioners in epidemiological analysis scenarios.

Development of spatial density maps based on geoprocessing web services: application to tuberculosis incidence in Barcelona, Spain

PubMed Central

2011-01-01

Background Health professionals and authorities strive to cope with heterogeneous data, services, and statistical models to support decision making on public health. Sophisticated analysis and distributed processing capabilities over geocoded epidemiological data are seen as driving factors to speed up control and decision making in these health risk situations. In this context, recent Web technologies and standards-based web services deployed on geospatial information infrastructures have rapidly become an efficient way to access, share, process, and visualize geocoded health-related information. Methods Data used on this study is based on Tuberculosis (TB) cases registered in Barcelona city during 2009. Residential addresses are geocoded and loaded into a spatial database that acts as a backend database. The web-based application architecture and geoprocessing web services are designed according to the Representational State Transfer (REST) principles. These web processing services produce spatial density maps against the backend database. Results The results are focused on the use of the proposed web-based application to the analysis of TB cases in Barcelona. The application produces spatial density maps to ease the monitoring and decision making process by health professionals. We also include a discussion of how spatial density maps may be useful for health practitioners in such contexts. Conclusions In this paper, we developed web-based client application and a set of geoprocessing web services to support specific health-spatial requirements. Spatial density maps of TB incidence were generated to help health professionals in analysis and decision-making tasks. The combined use of geographic information tools, map viewers, and geoprocessing services leads to interesting possibilities in handling health data in a spatial manner. In particular, the use of spatial density maps has been effective to identify the most affected areas and its spatial impact. This study is an attempt to demonstrate how web processing services together with web-based mapping capabilities suit the needs of health practitioners in epidemiological analysis scenarios. PMID:22126392

The NIAID Division of AIDS enterprise information system: integrated decision support for global clinical research programs

PubMed Central

Gupta, Nitin; Varghese, Suresh; Virkar, Hemant

2011-01-01

The National Institute of Allergy and Infectious Diseases (NIAID) Division of AIDS (DAIDS) Enterprise Information System (DAIDS-ES) is a web-based system that supports NIAID in the scientific, strategic, and tactical management of its global clinical research programs for HIV/AIDS vaccines, prevention, and therapeutics. Different from most commercial clinical trials information systems, which are typically protocol-driven, the DAIDS-ES was built to exchange information with those types of systems and integrate it in ways that help scientific program directors lead the research effort and keep pace with the complex and ever-changing global HIV/AIDS pandemic. Whereas commercially available clinical trials support systems are not usually disease-focused, DAIDS-ES was specifically designed to capture and incorporate unique scientific, demographic, and logistical aspects of HIV/AIDS treatment, prevention, and vaccine research in order to provide a rich source of information to guide informed decision-making. Sharing data across its internal components and with external systems, using defined vocabularies, open standards and flexible interfaces, the DAIDS-ES enables NIAID, its global collaborators and stakeholders, access to timely, quality information about NIAID-supported clinical trials which is utilized to: (1) analyze the research portfolio, assess capacity, identify opportunities, and avoid redundancies; (2) help support study safety, quality, ethics, and regulatory compliance; (3) conduct evidence-based policy analysis and business process re-engineering for improved efficiency. This report summarizes how the DAIDS-ES was conceptualized, how it differs from typical clinical trial support systems, the rationale for key design choices, and examples of how it is being used to advance the efficiency and effectiveness of NIAID's HIV/AIDS clinical research programs. PMID:21816958

The NIAID Division of AIDS enterprise information system: integrated decision support for global clinical research programs.

PubMed

Kagan, Jonathan M; Gupta, Nitin; Varghese, Suresh; Virkar, Hemant

2011-12-01

The National Institute of Allergy and Infectious Diseases (NIAID) Division of AIDS (DAIDS) Enterprise Information System (DAIDS-ES) is a web-based system that supports NIAID in the scientific, strategic, and tactical management of its global clinical research programs for HIV/AIDS vaccines, prevention, and therapeutics. Different from most commercial clinical trials information systems, which are typically protocol-driven, the DAIDS-ES was built to exchange information with those types of systems and integrate it in ways that help scientific program directors lead the research effort and keep pace with the complex and ever-changing global HIV/AIDS pandemic. Whereas commercially available clinical trials support systems are not usually disease-focused, DAIDS-ES was specifically designed to capture and incorporate unique scientific, demographic, and logistical aspects of HIV/AIDS treatment, prevention, and vaccine research in order to provide a rich source of information to guide informed decision-making. Sharing data across its internal components and with external systems, using defined vocabularies, open standards and flexible interfaces, the DAIDS-ES enables NIAID, its global collaborators and stakeholders, access to timely, quality information about NIAID-supported clinical trials which is utilized to: (1) analyze the research portfolio, assess capacity, identify opportunities, and avoid redundancies; (2) help support study safety, quality, ethics, and regulatory compliance; (3) conduct evidence-based policy analysis and business process re-engineering for improved efficiency. This report summarizes how the DAIDS-ES was conceptualized, how it differs from typical clinical trial support systems, the rationale for key design choices, and examples of how it is being used to advance the efficiency and effectiveness of NIAID's HIV/AIDS clinical research programs.

An Open Source Model for Open Access Journal Publication

PubMed Central

Blesius, Carl R.; Williams, Michael A.; Holzbach, Ana; Huntley, Arthur C.; Chueh, Henry

2005-01-01

We describe an electronic journal publication infrastructure that allows a flexible publication workflow, academic exchange around different forms of user submissions, and the exchange of articles between publishers and archives using a common XML based standard. This web-based application is implemented on a freely available open source software stack. This publication demonstrates the Dermatology Online Journal's use of the platform for non-biased independent open access publication. PMID:16779183

Using open source software for the supervision and management of the water resources system of Athens

NASA Astrophysics Data System (ADS)

Kozanis, S.; Christofides, A.; Efstratiadis, A.; Koukouvinos, A.; Karavokiros, G.; Mamassis, N.; Koutsoyiannis, D.; Nikolopoulos, D.

2012-04-01

The water supply of Athens, Greece, is implemented through a complex water resource system, extending over an area of around 4 000 km2 and including surface water and groundwater resources. It incorporates four reservoirs, 350 km of main aqueducts, 15 pumping stations, more than 100 boreholes and 5 small hydropower plants. The system is run by the Athens Water Supply and Sewerage Company (EYDAP) Over more than 10 years we have developed, information technology tools such as GIS, database and decision support systems, to assist the management of the system. Among the software components, "Enhydris", a web application for the visualization and management of geographical and hydrometeorological data, and "Hydrognomon", a data analysis and processing tool, are now free software. Enhydris is entirely based on free software technologies such as Python, Django, PostgreSQL, and JQuery. We also created http://openmeteo.org/, a web site hosting our free software products as well as a free database system devoted to the dissemination of free data. In particular, "Enhydris" is used for the management of the hydrometeorological stations and the major hydraulic structures (aqueducts, reservoirs, boreholes, etc.), as well as for the retrieval of time series, online graphs etc. For the specific needs of EYDAP, additional GIS functionality was introduced for the display and monitoring of the water supply network. This functionality is also implemented as free software and can be reused in similar projects. Except for "Hydrognomon" and "Enhydris", we have developed a number of advanced modeling applications, which are also generic-purpose tools that have been used for a long time to provide decision support for the water resource system of Athens. These are "Hydronomeas", which optimizes the operation of complex water resource systems, based on a stochastic simulation framework, "Castalia", which implements the generation of synthetic time series, and "Hydrogeios", which employs conjunctive hydrological and hydrogeological simulation, with emphasis to human-modified river basins. These tools are currently available as executable files that are free for download though the ITIA web site (http://itia.ntua.gr/). Currently, we are working towards releasing their source code as well, through making them free software, after some licensing issues are resolved.

Next generation of weather generators on web service framework

NASA Astrophysics Data System (ADS)

Chinnachodteeranun, R.; Hung, N. D.; Honda, K.; Ines, A. V. M.

2016-12-01

Weather generator is a statistical model that synthesizes possible realization of long-term historical weather in future. It generates several tens to hundreds of realizations stochastically based on statistical analysis. Realization is essential information as a crop modeling's input for simulating crop growth and yield. Moreover, they can be contributed to analyzing uncertainty of weather to crop development stage and to decision support system on e.g. water management and fertilizer management. Performing crop modeling requires multidisciplinary skills which limit the usage of weather generator only in a research group who developed it as well as a barrier for newcomers. To improve the procedures of performing weather generators as well as the methodology to acquire the realization in a standard way, we implemented a framework for providing weather generators as web services, which support service interoperability. Legacy weather generator programs were wrapped in the web service framework. The service interfaces were implemented based on an international standard that was Sensor Observation Service (SOS) defined by Open Geospatial Consortium (OGC). Clients can request realizations generated by the model through SOS Web service. Hierarchical data preparation processes required for weather generator are also implemented as web services and seamlessly wired. Analysts and applications can invoke services over a network easily. The services facilitate the development of agricultural applications and also reduce the workload of analysts on iterative data preparation and handle legacy weather generator program. This architectural design and implementation can be a prototype for constructing further services on top of interoperable sensor network system. This framework opens an opportunity for other sectors such as application developers and scientists in other fields to utilize weather generators.

Mobile service for open data visualization on geo-based images

NASA Astrophysics Data System (ADS)

Lee, Kiwon; Kim, Kwangseob; Kang, Sanggoo

2015-12-01

Since the early 2010s, governments in most countries have adopted and promoted open data policy and open data platform. Korea are in the same situation, and government and public organizations have operated the public-accessible open data portal systems since 2011. The number of open data and data type have been increasing every year. These trends are more expandable or extensible on mobile environments. The purpose of this study is to design and implement a mobile application service to visualize various typed or formatted public open data with geo-based images on the mobile web. Open data cover downloadable data sets or open-accessible data application programming interface API. Geo-based images mean multi-sensor satellite imageries which are referred in geo-coordinates and matched with digital map sets. System components for mobile service are fully based on open sources and open development environments without any commercialized tools: PostgreSQL for database management system, OTB for remote sensing image processing, GDAL for data conversion, GeoServer for application server, OpenLayers for mobile web mapping, R for data analysis and D3.js for web-based data graphic processing. Mobile application in client side was implemented by using HTML5 for cross browser and cross platform. The result shows many advantageous points such as linking open data and geo-based data, integrating open data and open source, and demonstrating mobile applications with open data. It is expected that this approach is cost effective and process efficient implementation strategy for intelligent earth observing data.

Sustainability of Open-Source Software Organizations as Underpinning for Sustainable Interoperability on Large Scales

NASA Astrophysics Data System (ADS)

Fulker, D. W.; Gallagher, J. H. R.

2015-12-01

OPeNDAP's Hyrax data server is an open-source framework fostering interoperability via easily-deployed Web services. Compatible with solutions listed in the (PA001) session description—federation, rigid standards and brokering/mediation—the framework can support tight or loose coupling, even with dependence on community-contributed software. Hyrax is a Web-services framework with a middleware-like design and a handler-style architecture that together reduce the interoperability challenge (for N datatypes and M user contexts) to an O(N+M) problem, similar to brokering. Combined with an open-source ethos, this reduction makes Hyrax a community tool for gaining interoperability. E.g., in its response to the Big Earth Data Initiative (BEDI), NASA references OPeNDAP-based interoperability. Assuming its suitability, the question becomes: how sustainable is OPeNDAP, a small not-for-profit that produces open-source software, i.e., has no software-sales? In other words, if geoscience interoperability depends on OPeNDAP and similar organizations, are those entities in turn sustainable? Jim Collins (in Good to Great) highlights three questions that successful companies can answer (paraphrased here): What is your passion? Where is your world-class excellence? What drives your economic engine? We attempt to shed light on OPeNDAP sustainability by examining these. Passion: OPeNDAP has a focused passion for improving the effectiveness of scientific data sharing and use, as deeply-cooperative community endeavors. Excellence: OPeNDAP has few peers in remote, scientific data access. Skills include computer science with experience in data science, (operational, secure) Web services, and software design (for servers and clients, where the latter vary from Web pages to standalone apps and end-user programs). Economic Engine: OPeNDAP is an engineering services organization more than a product company, despite software being key to OPeNDAP's reputation. In essence, provision of engineering expertise, via contracts and grants, is the economic engine. Hence sustainability, as needed to address global grand challenges in geoscience, depends on agencies' and others' abilities and willingness to offer grants and let contracts for continually upgrading open-source software from OPeNDAP and others.

National Geothermal Data System: Open Access to Geoscience Data, Maps, and Documents

NASA Astrophysics Data System (ADS)

Caudill, C. M.; Richard, S. M.; Musil, L.; Sonnenschein, A.; Good, J.

2014-12-01

The U.S. National Geothermal Data System (NGDS) provides free open access to millions of geoscience data records, publications, maps, and reports via distributed web services to propel geothermal research, development, and production. NGDS is built on the US Geoscience Information Network (USGIN) data integration framework, which is a joint undertaking of the USGS and the Association of American State Geologists (AASG), and is compliant with international standards and protocols. NGDS currently serves geoscience information from 60+ data providers in all 50 states. Free and open source software is used in this federated system where data owners maintain control of their data. This interactive online system makes geoscience data easily discoverable, accessible, and interoperable at no cost to users. The dynamic project site http://geothermaldata.org serves as the information source and gateway to the system, allowing data and applications discovery and availability of the system's data feed. It also provides access to NGDS specifications and the free and open source code base (on GitHub), a map-centric and library style search interface, other software applications utilizing NGDS services, NGDS tutorials (via YouTube and USGIN site), and user-created tools and scripts. The user-friendly map-centric web-based application has been created to support finding, visualizing, mapping, and acquisition of data based on topic, location, time, provider, or key words. Geographic datasets visualized through the map interface also allow users to inspect the details of individual GIS data points (e.g. wells, geologic units, etc.). In addition, the interface provides the information necessary for users to access the GIS data from third party software applications such as GoogleEarth, UDig, and ArcGIS. A redistributable, free and open source software package called GINstack (USGIN software stack) was also created to give data providers a simple way to release data using interoperable and shareable standards, upload data and documents, and expose those data as a node in the NGDS or any larger data system through a CSW endpoint. The easy-to-use interface is supported by back-end software including Postgres, GeoServer, and custom CKAN extensions among others.

A WebGIS platform for the monitoring of Farm Animal Genetic Resources (GENMON)

PubMed Central

Flury, Christine; Matasci, Giona; Joerin, Florent; Widmer, Ivo; Joost, Stéphane

2017-01-01

Background In 2007, the Food and Agriculture Organization of the United Nations (FAO) initiated the Global plan of action for Farm Animal Genetic Resources (FAnGR). The main goal of this plan is to reduce further loss of genetic diversity in farm animals, so as to protect and promote the diversity of farm animal resources. An important step to reach this goal is to monitor and prioritize endangered breeds in the context of conservation programs. Methodology/Web portal implementation The GENMON WebGIS platform is able to monitor FAnGR and to evaluate the degree of endangerment of livestock breeds. The system takes into account pedigree and introgression information, the geographical concentration of animals, the cryo-conservation plan and the sustainability of breeding activities based on socio-economic data as well as present and future land use conditions. A multi-criteria decision tool supports the aggregation of the multi-thematic indices mentioned above using the MACBETH method, which is based on a weighted average using satisfaction thresholds. GENMON is a monitoring tool to reach subjective decisions made by a government agency. It relies on open source software and is available at http://lasigsrv2.epfl.ch/genmon-ch. Results/Significance GENMON allows users to upload pedigree-information (animal ID, parents, birthdate, sex, location and introgression) from a specific livestock breed and to define species and/or region-specific weighting parameters and thresholds. The program then completes a pedigree analysis and derives several indices that are used to calculate an integrated score of conservation prioritization for the breeds under investigation. The score can be visualized on a geographic map and allows a fast, intuitive and regional identification of breeds in danger. Appropriate conservation actions and breeding programs can thus be undertaken in order to promote the recovery of the genetic diversity in livestock breeds in need. The use of the platform is illustrated by means of an example based on three local livestock breeds from different species in Switzerland. PMID:28453561

Expert System Shells for Rapid Clinical Decision Support Module Development: An ESTA Demonstration of a Simple Rule-Based System for the Diagnosis of Vaginal Discharge

PubMed Central

2012-01-01

Objectives This study demonstrates the feasibility of using expert system shells for rapid clinical decision support module development. Methods A readily available expert system shell was used to build a simple rule-based system for the crude diagnosis of vaginal discharge. Pictures and 'canned text explanations' are extensively used throughout the program to enhance its intuitiveness and educational dimension. All the steps involved in developing the system are documented. Results The system runs under Microsoft Windows and is available as a free download at http://healthcybermap.org/vagdisch.zip (the distribution archive includes both the program's executable and the commented knowledge base source as a text document). The limitations of the demonstration system, such as the lack of provisions for assessing uncertainty or various degrees of severity of a sign or symptom, are discussed in detail. Ways of improving the system, such as porting it to the Web and packaging it as an app for smartphones and tablets, are also presented. Conclusions An easy-to-use expert system shell enables clinicians to rapidly become their own 'knowledge engineers' and develop concise evidence-based decision support modules of simple to moderate complexity, targeting clinical practitioners, medical and nursing students, as well as patients, their lay carers and the general public (where appropriate). In the spirit of the social Web, it is hoped that an online repository can be created to peer review, share and re-use knowledge base modules covering various clinical problems and algorithms, as a service to the clinical community. PMID:23346475

ADEpedia: a scalable and standardized knowledge base of Adverse Drug Events using semantic web technology.

PubMed

Jiang, Guoqian; Solbrig, Harold R; Chute, Christopher G

2011-01-01

A source of semantically coded Adverse Drug Event (ADE) data can be useful for identifying common phenotypes related to ADEs. We proposed a comprehensive framework for building a standardized ADE knowledge base (called ADEpedia) through combining ontology-based approach with semantic web technology. The framework comprises four primary modules: 1) an XML2RDF transformation module; 2) a data normalization module based on NCBO Open Biomedical Annotator; 3) a RDF store based persistence module; and 4) a front-end module based on a Semantic Wiki for the review and curation. A prototype is successfully implemented to demonstrate the capability of the system to integrate multiple drug data and ontology resources and open web services for the ADE data standardization. A preliminary evaluation is performed to demonstrate the usefulness of the system, including the performance of the NCBO annotator. In conclusion, the semantic web technology provides a highly scalable framework for ADE data source integration and standard query service.

Building CHAOS: An Operating System for Livermore Linux Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garlick, J E; Dunlap, C M

2003-02-21

The Livermore Computing (LC) Linux Integration and Development Project (the Linux Project) produces and supports the Clustered High Availability Operating System (CHAOS), a cluster operating environment based on Red Hat Linux. Each CHAOS release begins with a set of requirements and ends with a formally tested, packaged, and documented release suitable for use on LC's production Linux clusters. One characteristic of CHAOS is that component software packages come from different sources under varying degrees of project control. Some are developed by the Linux Project, some are developed by other LC projects, some are external open source projects, and some aremore » commercial software packages. A challenge to the Linux Project is to adhere to release schedules and testing disciplines in a diverse, highly decentralized development environment. Communication channels are maintained for externally developed packages in order to obtain support, influence development decisions, and coordinate/understand release schedules. The Linux Project embraces open source by releasing locally developed packages under open source license, by collaborating with open source projects where mutually beneficial, and by preferring open source over proprietary software. Project members generally use open source development tools. The Linux Project requires system administrators and developers to work together to resolve problems that arise in production. This tight coupling of production and development is a key strategy for making a product that directly addresses LC's production requirements. It is another challenge to balance support and development activities in such a way that one does not overwhelm the other.« less

A web-based system for supporting global land cover data production

NASA Astrophysics Data System (ADS)

Han, Gang; Chen, Jun; He, Chaoying; Li, Songnian; Wu, Hao; Liao, Anping; Peng, Shu

2015-05-01

Global land cover (GLC) data production and verification process is very complicated, time consuming and labor intensive, requiring huge amount of imagery data and ancillary data and involving many people, often from different geographic locations. The efficient integration of various kinds of ancillary data and effective collaborative classification in large area land cover mapping requires advanced supporting tools. This paper presents the design and development of a web-based system for supporting 30-m resolution GLC data production by combining geo-spatial web-service and Computer Support Collaborative Work (CSCW) technology. Based on the analysis of the functional and non-functional requirements from GLC mapping, a three tiers system model is proposed with four major parts, i.e., multisource data resources, data and function services, interactive mapping and production management. The prototyping and implementation of the system have been realised by a combination of Open Source Software (OSS) and commercially available off-the-shelf system. This web-based system not only facilitates the integration of heterogeneous data and services required by GLC data production, but also provides online access, visualization and analysis of the images, ancillary data and interim 30 m global land-cover maps. The system further supports online collaborative quality check and verification workflows. It has been successfully applied to China's 30-m resolution GLC mapping project, and has improved significantly the efficiency of GLC data production and verification. The concepts developed through this study should also benefit other GLC or regional land-cover data production efforts.

Scalable Decision Support at the Point of Care: A Substitutable Electronic Health Record App for Monitoring Medication Adherence

PubMed Central

Mandel, Joshua; Jonikas, Magdalena; Ramoni, Rachel Badovinac; Kohane, Isaac S; Mandl, Kenneth D

2013-01-01

Background Non-adherence to prescribed medications is a serious health problem in the United States, costing an estimated $100 billion per year. While poor adherence should be addressable with point of care health information technology, integrating new solutions with existing electronic health records (EHR) systems require customization within each organization, which is difficult because of the monolithic software design of most EHR products. Objective The objective of this study was to create a published algorithm for predicting medication adherence problems easily accessible at the point of care through a Web application that runs on the Substitutable Medical Apps, Reusuable Technologies (SMART) platform. The SMART platform is an emerging framework that enables EHR systems to behave as “iPhone like platforms” by exhibiting an application programming interface for easy addition and deletion of third party apps. The app is presented as a point of care solution to monitoring medication adherence as well as a sufficiently general, modular application that may serve as an example and template for other SMART apps. Methods The widely used, open source Django framework was used together with the SMART platform to create the interoperable components of this app. Django uses Python as its core programming language. This allows statistical and mathematical modules to be created from a large array of Python numerical libraries and assembled together with the core app to create flexible and sophisticated EHR functionality. Algorithms that predict individual adherence are derived from a retrospective study of dispensed medication claims from a large private insurance plan. Patients’ prescription fill information is accessed through the SMART framework and the embedded algorithms compute adherence information, including predicted adherence one year after the first prescription fill. Open source graphing software is used to display patient medication information and the results of statistical prediction of future adherence on a clinician-facing Web interface. Results The user interface allows the physician to quickly review all medications in a patient record for potential non-adherence problems. A gap-check and current medication possession ratio (MPR) threshold test are applied to all medications in the record to test for current non-adherence. Predictions of 1-year non-adherence are made for certain drug classes for which external data was available. Information is presented graphically to indicate present non-adherence, or predicted non-adherence at one year, based on early prescription fulfillment patterns. The MPR Monitor app is installed in the SMART reference container as the “MPR Monitor”, where it is publically available for use and testing. MPR is an acronym for Medication Possession Ratio, a commonly used measure of adherence to a prescribed medication regime. This app may be used as an example for creating additional functionality by replacing statistical and display algorithms with new code in a cycle of rapid prototyping and implementation or as a framework for a new SMART app. Conclusions The MPR Monitor app is a useful pilot project for monitoring medication adherence. It also provides an example that integrates several open source software components, including the Python-based Django Web framework and python-based graphics, to build a SMART app that allows complex decision support methods to be encapsulated to enhance EHR functionality. PMID:23876796

Scalable decision support at the point of care: a substitutable electronic health record app for monitoring medication adherence.

PubMed

Bosl, William; Mandel, Joshua; Jonikas, Magdalena; Ramoni, Rachel Badovinac; Kohane, Isaac S; Mandl, Kenneth D

2013-07-22

Non-adherence to prescribed medications is a serious health problem in the United States, costing an estimated $100 billion per year. While poor adherence should be addressable with point of care health information technology, integrating new solutions with existing electronic health records (EHR) systems require customization within each organization, which is difficult because of the monolithic software design of most EHR products. The objective of this study was to create a published algorithm for predicting medication adherence problems easily accessible at the point of care through a Web application that runs on the Substitutable Medical Apps, Reusuable Technologies (SMART) platform. The SMART platform is an emerging framework that enables EHR systems to behave as "iPhone like platforms" by exhibiting an application programming interface for easy addition and deletion of third party apps. The app is presented as a point of care solution to monitoring medication adherence as well as a sufficiently general, modular application that may serve as an example and template for other SMART apps. The widely used, open source Django framework was used together with the SMART platform to create the interoperable components of this app. Django uses Python as its core programming language. This allows statistical and mathematical modules to be created from a large array of Python numerical libraries and assembled together with the core app to create flexible and sophisticated EHR functionality. Algorithms that predict individual adherence are derived from a retrospective study of dispensed medication claims from a large private insurance plan. Patients' prescription fill information is accessed through the SMART framework and the embedded algorithms compute adherence information, including predicted adherence one year after the first prescription fill. Open source graphing software is used to display patient medication information and the results of statistical prediction of future adherence on a clinician-facing Web interface. The user interface allows the physician to quickly review all medications in a patient record for potential non-adherence problems. A gap-check and current medication possession ratio (MPR) threshold test are applied to all medications in the record to test for current non-adherence. Predictions of 1-year non-adherence are made for certain drug classes for which external data was available. Information is presented graphically to indicate present non-adherence, or predicted non-adherence at one year, based on early prescription fulfillment patterns. The MPR Monitor app is installed in the SMART reference container as the "MPR Monitor", where it is publically available for use and testing. MPR is an acronym for Medication Possession Ratio, a commonly used measure of adherence to a prescribed medication regime. This app may be used as an example for creating additional functionality by replacing statistical and display algorithms with new code in a cycle of rapid prototyping and implementation or as a framework for a new SMART app. The MPR Monitor app is a useful pilot project for monitoring medication adherence. It also provides an example that integrates several open source software components, including the Python-based Django Web framework and python-based graphics, to build a SMART app that allows complex decision support methods to be encapsulated to enhance EHR functionality.

A GIS Based 3D Online Decision Assistance System for Underground Energy Storage in Northern Germany

NASA Astrophysics Data System (ADS)

Nolde, M.; Schwanebeck, M.; Biniyaz, E.; Duttmann, R.

2014-12-01

We would like to present a GIS-based 3D online decision assistance system for underground energy storage. Its aim is to support the local land use planning authorities through pre-selection of possible sites for thermal, electrical and substantial underground energy storages. Since the extension of renewable energies has become legal requirement in Germany, the underground storing of superfluously produced green energy (such as during a heavy wind event) in the form of compressed air, gas or heated water has become increasingly important. However, the selection of suitable sites is a complex task. The assistance system uses data of geological features such as rock layers, salt caverns and faults enriched with attribute data such as rock porosity and permeability. This information is combined with surface data of the existing energy infrastructure, such as locations of wind and biogas stations, power line arrangement and cable capacity, and energy distribution stations. Furthermore, legal obligations such as protected areas on the surface and current underground mining permissions are used for the decision finding process. Not only the current situation but also prospective scenarios, such as expected growth in produced amount of energy are incorporated in the system. The decision process is carried out via the 'Analytic Hierarchy Process' (AHP) methodology of the 'Multi Object Decision Making' (MODM) approach. While the process itself is completely automated, the user has full control of the weighting of the different factors via the web interface. The system is implemented as an online 3D server GIS environment, with no software needed to be installed on the user side. The results are visualized as interactive 3d graphics. The implementation of the assistance system is based exclusively on free and open source software, and utilizes the 'Python' programming language in combination with current web technologies, such as 'HTML5', 'CSS3' and 'JavaScript'. It is developed at Kiel University for the federal state of Schleswig-Holstein in northern Germany. This work is part of project 'ANGUS+', lead by Prof. Dr. Sebastian Bauer and funded by the German Ministry for Education and Research (BMBF).

Open Biomedical Engineering education in Africa.

PubMed

Ahluwalia, Arti; Atwine, Daniel; De Maria, Carmelo; Ibingira, Charles; Kipkorir, Emmauel; Kiros, Fasil; Madete, June; Mazzei, Daniele; Molyneux, Elisabeth; Moonga, Kando; Moshi, Mainen; Nzomo, Martin; Oduol, Vitalice; Okuonzi, John

2015-08-01

Despite the virtual revolution, the mainstream academic community in most countries remains largely ignorant of the potential of web-based teaching resources and of the expansion of open source software, hardware and rapid prototyping. In the context of Biomedical Engineering (BME), where human safety and wellbeing is paramount, a high level of supervision and quality control is required before open source concepts can be embraced by universities and integrated into the curriculum. In the meantime, students, more than their teachers, have become attuned to continuous streams of digital information, and teaching methods need to adapt rapidly by giving them the skills to filter meaningful information and by supporting collaboration and co-construction of knowledge using open, cloud and crowd based technology. In this paper we present our experience in bringing these concepts to university education in Africa, as a way of enabling rapid development and self-sufficiency in health care. We describe the three summer schools held in sub-Saharan Africa where both students and teachers embraced the philosophy of open BME education with enthusiasm, and discuss the advantages and disadvantages of opening education in this way in the developing and developed world.

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments.

PubMed

MacLean, Brendan; Tomazela, Daniela M; Shulman, Nicholas; Chambers, Matthew; Finney, Gregory L; Frewen, Barbara; Kern, Randall; Tabb, David L; Liebler, Daniel C; MacCoss, Michael J

2010-04-01

Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. It is open source and freely available for academic and commercial use. The Skyline user interface simplifies the development of mass spectrometer methods and the analysis of data from targeted proteomics experiments performed using selected reaction monitoring (SRM). Skyline supports using and creating MS/MS spectral libraries from a wide variety of sources to choose SRM filters and verify results based on previously observed ion trap data. Skyline exports transition lists to and imports the native output files from Agilent, Applied Biosystems, Thermo Fisher Scientific and Waters triple quadrupole instruments, seamlessly connecting mass spectrometer output back to the experimental design document. The fast and compact Skyline file format is easily shared, even for experiments requiring many sample injections. A rich array of graphs displays results and provides powerful tools for inspecting data integrity as data are acquired, helping instrument operators to identify problems early. The Skyline dynamic report designer exports tabular data from the Skyline document model for in-depth analysis with common statistical tools. Single-click, self-updating web installation is available at http://proteome.gs.washington.edu/software/skyline. This web site also provides access to instructional videos, a support board, an issues list and a link to the source code project.

moocRP: Enabling Open Learning Analytics with an Open Source Platform for Data Distribution, Analysis, and Visualization

ERIC Educational Resources Information Center

Pardos, Zachary A.; Whyte, Anthony; Kao, Kevin

2016-01-01

In this paper, we address issues of transparency, modularity, and privacy with the introduction of an open source, web-based data repository and analysis tool tailored to the Massive Open Online Course community. The tool integrates data request/authorization and distribution workflow features as well as provides a simple analytics module upload…

GobyWeb: Simplified Management and Analysis of Gene Expression and DNA Methylation Sequencing Data

PubMed Central

Dorff, Kevin C.; Chambwe, Nyasha; Zeno, Zachary; Simi, Manuele; Shaknovich, Rita; Campagne, Fabien

2013-01-01

We present GobyWeb, a web-based system that facilitates the management and analysis of high-throughput sequencing (HTS) projects. The software provides integrated support for a broad set of HTS analyses and offers a simple plugin extension mechanism. Analyses currently supported include quantification of gene expression for messenger and small RNA sequencing, estimation of DNA methylation (i.e., reduced bisulfite sequencing and whole genome methyl-seq), or the detection of pathogens in sequenced data. In contrast to previous analysis pipelines developed for analysis of HTS data, GobyWeb requires significantly less storage space, runs analyses efficiently on a parallel grid, scales gracefully to process tens or hundreds of multi-gigabyte samples, yet can be used effectively by researchers who are comfortable using a web browser. We conducted performance evaluations of the software and found it to either outperform or have similar performance to analysis programs developed for specialized analyses of HTS data. We found that most biologists who took a one-hour GobyWeb training session were readily able to analyze RNA-Seq data with state of the art analysis tools. GobyWeb can be obtained at http://gobyweb.campagnelab.org and is freely available for non-commercial use. GobyWeb plugins are distributed in source code and licensed under the open source LGPL3 license to facilitate code inspection, reuse and independent extensions http://github.com/CampagneLaboratory/gobyweb2-plugins. PMID:23936070

PopHR: a knowledge-based platform to support integration, analysis, and visualization of population health data.

PubMed

Shaban-Nejad, Arash; Lavigne, Maxime; Okhmatovskaia, Anya; Buckeridge, David L

2017-01-01

Population health decision makers must consider complex relationships between multiple concepts measured with differential accuracy from heterogeneous data sources. Population health information systems are currently limited in their ability to integrate data and present a coherent portrait of population health. Consequentially, these systems can provide only basic support for decision makers. The Population Health Record (PopHR) is a semantic web application that automates the integration and extraction of massive amounts of heterogeneous data from multiple distributed sources (e.g., administrative data, clinical records, and survey responses) to support the measurement and monitoring of population health and health system performance for a defined population. The design of the PopHR draws on the theories of the determinants of health and evidence-based public health to harmonize and explicitly link information about a population with evidence about the epidemiology and control of chronic diseases. Organizing information in this manner and linking it explicitly to evidence is expected to improve decision making related to the planning, implementation, and evaluation of population health and health system interventions. In this paper, we describe the PopHR platform and discuss the architecture, design, key modules, and its implementation and use. © 2016 New York Academy of Sciences.

GOC-TX: A Reliable Ticket Synchronization Application for the Open Science Grid

NASA Astrophysics Data System (ADS)

Hayashi, Soichi; Gopu, Arvind; Quick, Robert

2011-12-01

One of the major operational issues faced by large multi-institutional collaborations is permitting its users and support staff to use their native ticket tracking environment while also exchanging these tickets with collaborators. After several failed attempts at email-parser based ticket exchanges, the OSG Operations Group has designed a comprehensive ticket synchronizing application. The GOC-TX application uses web-service interfaces offered by various commercial, open source and other homegrown ticketing systems, to synchronize tickets between two or more of these systems. GOC-TX operates independently from any ticketing system. It can be triggered by one ticketing system via email, active messaging, or a web-services call to check for current sync-status, pull applicable recent updates since prior synchronizations to the source ticket, and apply the updates to a destination ticket. The currently deployed production version of GOC-TX is able to synchronize tickets between the Numara Footprints ticketing system used by the OSG and the following systems: European Grid Initiative's system Global Grid User Support (GGUS) and the Request Tracker (RT) system used by Brookhaven. Additional interfaces to the BMC Remedy system used by Fermilab, and to other instances of RT used by other OSG partners, are expected to be completed in summer 2010. A fully configurable open source version is expected to be made available by early autumn 2010. This paper will cover the structure of the GOC-TX application, its evolution, and the problems encountered by OSG Operations group with ticket exchange within the OSG Collaboration.

OpenTox predictive toxicology framework: toxicological ontology and semantic media wiki-based OpenToxipedia

PubMed Central

2012-01-01

Background The OpenTox Framework, developed by the partners in the OpenTox project (http://www.opentox.org), aims at providing a unified access to toxicity data, predictive models and validation procedures. Interoperability of resources is achieved using a common information model, based on the OpenTox ontologies, describing predictive algorithms, models and toxicity data. As toxicological data may come from different, heterogeneous sources, a deployed ontology, unifying the terminology and the resources, is critical for the rational and reliable organization of the data, and its automatic processing. Results The following related ontologies have been developed for OpenTox: a) Toxicological ontology – listing the toxicological endpoints; b) Organs system and Effects ontology – addressing organs, targets/examinations and effects observed in in vivo studies; c) ToxML ontology – representing semi-automatic conversion of the ToxML schema; d) OpenTox ontology– representation of OpenTox framework components: chemical compounds, datasets, types of algorithms, models and validation web services; e) ToxLink–ToxCast assays ontology and f) OpenToxipedia community knowledge resource on toxicology terminology. OpenTox components are made available through standardized REST web services, where every compound, data set, and predictive method has a unique resolvable address (URI), used to retrieve its Resource Description Framework (RDF) representation, or to initiate the associated calculations and generate new RDF-based resources. The services support the integration of toxicity and chemical data from various sources, the generation and validation of computer models for toxic effects, seamless integration of new algorithms and scientifically sound validation routines and provide a flexible framework, which allows building arbitrary number of applications, tailored to solving different problems by end users (e.g. toxicologists). Availability The OpenTox toxicological ontology projects may be accessed via the OpenTox ontology development page http://www.opentox.org/dev/ontology; the OpenTox ontology is available as OWL at http://opentox.org/api/1 1/opentox.owl, the ToxML - OWL conversion utility is an open source resource available at http://ambit.svn.sourceforge.net/viewvc/ambit/branches/toxml-utils/ PMID:22541598

OpenTox predictive toxicology framework: toxicological ontology and semantic media wiki-based OpenToxipedia.

PubMed

Tcheremenskaia, Olga; Benigni, Romualdo; Nikolova, Ivelina; Jeliazkova, Nina; Escher, Sylvia E; Batke, Monika; Baier, Thomas; Poroikov, Vladimir; Lagunin, Alexey; Rautenberg, Micha; Hardy, Barry

2012-04-24

The OpenTox Framework, developed by the partners in the OpenTox project (http://www.opentox.org), aims at providing a unified access to toxicity data, predictive models and validation procedures. Interoperability of resources is achieved using a common information model, based on the OpenTox ontologies, describing predictive algorithms, models and toxicity data. As toxicological data may come from different, heterogeneous sources, a deployed ontology, unifying the terminology and the resources, is critical for the rational and reliable organization of the data, and its automatic processing. The following related ontologies have been developed for OpenTox: a) Toxicological ontology - listing the toxicological endpoints; b) Organs system and Effects ontology - addressing organs, targets/examinations and effects observed in in vivo studies; c) ToxML ontology - representing semi-automatic conversion of the ToxML schema; d) OpenTox ontology- representation of OpenTox framework components: chemical compounds, datasets, types of algorithms, models and validation web services; e) ToxLink-ToxCast assays ontology and f) OpenToxipedia community knowledge resource on toxicology terminology.OpenTox components are made available through standardized REST web services, where every compound, data set, and predictive method has a unique resolvable address (URI), used to retrieve its Resource Description Framework (RDF) representation, or to initiate the associated calculations and generate new RDF-based resources.The services support the integration of toxicity and chemical data from various sources, the generation and validation of computer models for toxic effects, seamless integration of new algorithms and scientifically sound validation routines and provide a flexible framework, which allows building arbitrary number of applications, tailored to solving different problems by end users (e.g. toxicologists). The OpenTox toxicological ontology projects may be accessed via the OpenTox ontology development page http://www.opentox.org/dev/ontology; the OpenTox ontology is available as OWL at http://opentox.org/api/1 1/opentox.owl, the ToxML - OWL conversion utility is an open source resource available at http://ambit.svn.sourceforge.net/viewvc/ambit/branches/toxml-utils/

A Web-based Visualization System for Three Dimensional Geological Model using Open GIS

NASA Astrophysics Data System (ADS)

Nemoto, T.; Masumoto, S.; Nonogaki, S.

2017-12-01

A three dimensional geological model is an important information in various fields such as environmental assessment, urban planning, resource development, waste management and disaster mitigation. In this study, we have developed a web-based visualization system for 3D geological model using free and open source software. The system has been successfully implemented by integrating web mapping engine MapServer and geographic information system GRASS. MapServer plays a role of mapping horizontal cross sections of 3D geological model and a topographic map. GRASS provides the core components for management, analysis and image processing of the geological model. Online access to GRASS functions has been enabled using PyWPS that is an implementation of WPS (Web Processing Service) Open Geospatial Consortium (OGC) standard. The system has two main functions. Two dimensional visualization function allows users to generate horizontal and vertical cross sections of 3D geological model. These images are delivered via WMS (Web Map Service) and WPS OGC standards. Horizontal cross sections are overlaid on the topographic map. A vertical cross section is generated by clicking a start point and an end point on the map. Three dimensional visualization function allows users to visualize geological boundary surfaces and a panel diagram. The user can visualize them from various angles by mouse operation. WebGL is utilized for 3D visualization. WebGL is a web technology that brings hardware-accelerated 3D graphics to the browser without installing additional software. The geological boundary surfaces can be downloaded to incorporate the geologic structure in a design on CAD and model for various simulations. This study was supported by JSPS KAKENHI Grant Number JP16K00158.

Building a Snow Data Management System using Open Source Software (and IDL)

NASA Astrophysics Data System (ADS)

Goodale, C. E.; Mattmann, C. A.; Ramirez, P.; Hart, A. F.; Painter, T.; Zimdars, P. A.; Bryant, A.; Brodzik, M.; Skiles, M.; Seidel, F. C.; Rittger, K. E.

2012-12-01

At NASA's Jet Propulsion Laboratory free and open source software is used everyday to support a wide range of projects, from planetary to climate to research and development. In this abstract I will discuss the key role that open source software has played in building a robust science data processing pipeline for snow hydrology research, and how the system is also able to leverage programs written in IDL, making JPL's Snow Data System a hybrid of open source and proprietary software. Main Points: - The Design of the Snow Data System (illustrate how the collection of sub-systems are combined to create a complete data processing pipeline) - Discuss the Challenges of moving from a single algorithm on a laptop, to running 100's of parallel algorithms on a cluster of servers (lesson's learned) - Code changes - Software license related challenges - Storage Requirements - System Evolution (from data archiving, to data processing, to data on a map, to near-real-time products and maps) - Road map for the next 6 months (including how easily we re-used the snowDS code base to support the Airborne Snow Observatory Mission) Software in Use and their Software Licenses: IDL - Used for pre and post processing of data. Licensed under a proprietary software license held by Excelis. Apache OODT - Used for data management and workflow processing. Licensed under the Apache License Version 2. GDAL - Geospatial Data processing library used for data re-projection currently. Licensed under the X/MIT license. GeoServer - WMS Server. Licensed under the General Public License Version 2.0 Leaflet.js - Javascript web mapping library. Licensed under the Berkeley Software Distribution License. Python - Glue code and miscellaneous data processing support. Licensed under the Python Software Foundation License. Perl - Script wrapper for running the SCAG algorithm. Licensed under the General Public License Version 3. PHP - Front-end web application programming. Licensed under the PHP License Version 3.01

Openness, Web 2.0 Technology, and Open Science

ERIC Educational Resources Information Center

Peters, Michael A.

2010-01-01

Open science is a term that is being used in the literature to designate a form of science based on open source models or that utilizes principles of open access, open archiving and open publishing to promote scientific communication. Open science increasingly also refers to open governance and more democratized engagement and control of science…

MyMolDB: a micromolecular database solution with open source and free components.

PubMed

Xia, Bing; Tai, Zheng-Fu; Gu, Yu-Cheng; Li, Bang-Jing; Ding, Li-Sheng; Zhou, Yan

2011-10-01

To manage chemical structures in small laboratories is one of the important daily tasks. Few solutions are available on the internet, and most of them are closed source applications. The open-source applications typically have limited capability and basic cheminformatics functionalities. In this article, we describe an open-source solution to manage chemicals in research groups based on open source and free components. It has a user-friendly interface with the functions of chemical handling and intensive searching. MyMolDB is a micromolecular database solution that supports exact, substructure, similarity, and combined searching. This solution is mainly implemented using scripting language Python with a web-based interface for compound management and searching. Almost all the searches are in essence done with pure SQL on the database by using the high performance of the database engine. Thus, impressive searching speed has been archived in large data sets for no external Central Processing Unit (CPU) consuming languages were involved in the key procedure of the searching. MyMolDB is an open-source software and can be modified and/or redistributed under GNU General Public License version 3 published by the Free Software Foundation (Free Software Foundation Inc. The GNU General Public License, Version 3, 2007. Available at: http://www.gnu.org/licenses/gpl.html). The software itself can be found at http://code.google.com/p/mymoldb/. Copyright © 2011 Wiley Periodicals, Inc.

R package CityWaterBalance | Science Inventory | US EPA

EPA Pesticide Factsheets

CityWaterBalance provides a reproducible workflow for studying an urban water system. The network of urban water flows and storages can be modeled and visualized. Any city may be modeled with preassembled data, but data for US cities can be gathered via web services using this package and dependencies, geoknife and dataRetrieval. Urban water flows are difficult to comprehensively quantify. Although many important data sources are openly available, they are published by a variety of agencies in different formats, units, spatial and temporal resolutions. Increasingly, open data are made available via web services, which allow for automated, current retrievals. Integrating data streams and estimating the values of unmeasured urban water flows, however, remains needlessly time-consuming. In order to streamline a reproducible analysis, we have developed the CityWaterBalance package for the open source R language. The CityWaterBalance package for R is based on a simple model of the network of urban water flows and storages. The model may be run with data that has been pre-assembled by the user, or data can be retrieved by functions in CityWaterBalance and dependencies. CityWaterBalance can be used to quickly assemble a quantitative portrait of any urban water system. The systemic effects of water management decisions can be readily explored. Much of the data acquisition process for US cities can already be automated, while the package serves as a place-hold

The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science

PubMed Central

Bruskiewich, Richard; Senger, Martin; Davenport, Guy; Ruiz, Manuel; Rouard, Mathieu; Hazekamp, Tom; Takeya, Masaru; Doi, Koji; Satoh, Kouji; Costa, Marcos; Simon, Reinhard; Balaji, Jayashree; Akintunde, Akinnola; Mauleon, Ramil; Wanchana, Samart; Shah, Trushar; Anacleto, Mylah; Portugal, Arllet; Ulat, Victor Jun; Thongjuea, Supat; Braak, Kyle; Ritter, Sebastian; Dereeper, Alexis; Skofic, Milko; Rojas, Edwin; Martins, Natalia; Pappas, Georgios; Alamban, Ryan; Almodiel, Roque; Barboza, Lord Hendrix; Detras, Jeffrey; Manansala, Kevin; Mendoza, Michael Jonathan; Morales, Jeffrey; Peralta, Barry; Valerio, Rowena; Zhang, Yi; Gregorio, Sergio; Hermocilla, Joseph; Echavez, Michael; Yap, Jan Michael; Farmer, Andrew; Schiltz, Gary; Lee, Jennifer; Casstevens, Terry; Jaiswal, Pankaj; Meintjes, Ayton; Wilkinson, Mark; Good, Benjamin; Wagner, James; Morris, Jane; Marshall, David; Collins, Anthony; Kikuchi, Shoshi; Metz, Thomas; McLaren, Graham; van Hintum, Theo

2008-01-01

The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the following: (i) shared, public platform-independent domain models, ontology, and data formats to enable interoperability of data and analysis flows within the platform; (ii) web service and registry technologies to identify, share, and integrate information across diverse, globally dispersed data sources, as well as to access high-performance computational (HPC) facilities for computationally intensive, high-throughput analyses of project data; (iii) platform-specific middleware reference implementations of the domain model integrating a suite of public (largely open-access/-source) databases and software tools into a workbench to facilitate biodiversity analysis, comparative analysis of crop genomic data, and plant breeding decision making. PMID:18483570

Extensions to regret-based decision curve analysis: an application to hospice referral for terminal patients.

PubMed

Tsalatsanis, Athanasios; Barnes, Laura E; Hozo, Iztok; Djulbegovic, Benjamin

2011-12-23

Despite the well documented advantages of hospice care, most terminally ill patients do not reap the maximum benefit from hospice services, with the majority of them receiving hospice care either prematurely or delayed. Decision systems to improve the hospice referral process are sorely needed. We present a novel theoretical framework that is based on well-established methodologies of prognostication and decision analysis to assist with the hospice referral process for terminally ill patients. We linked the SUPPORT statistical model, widely regarded as one of the most accurate models for prognostication of terminally ill patients, with the recently developed regret based decision curve analysis (regret DCA). We extend the regret DCA methodology to consider harms associated with the prognostication test as well as harms and effects of the management strategies. In order to enable patients and physicians in making these complex decisions in real-time, we developed an easily accessible web-based decision support system available at the point of care. The web-based decision support system facilitates the hospice referral process in three steps. First, the patient or surrogate is interviewed to elicit his/her personal preferences regarding the continuation of life-sustaining treatment vs. palliative care. Then, regret DCA is employed to identify the best strategy for the particular patient in terms of threshold probability at which he/she is indifferent between continuation of treatment and of hospice referral. Finally, if necessary, the probabilities of survival and death for the particular patient are computed based on the SUPPORT prognostication model and contrasted with the patient's threshold probability. The web-based design of the CDSS enables patients, physicians, and family members to participate in the decision process from anywhere internet access is available. We present a theoretical framework to facilitate the hospice referral process. Further rigorous clinical evaluation including testing in a prospective randomized controlled trial is required and planned.

Extensions to Regret-based Decision Curve Analysis: An application to hospice referral for terminal patients

PubMed Central

2011-01-01

Background Despite the well documented advantages of hospice care, most terminally ill patients do not reap the maximum benefit from hospice services, with the majority of them receiving hospice care either prematurely or delayed. Decision systems to improve the hospice referral process are sorely needed. Methods We present a novel theoretical framework that is based on well-established methodologies of prognostication and decision analysis to assist with the hospice referral process for terminally ill patients. We linked the SUPPORT statistical model, widely regarded as one of the most accurate models for prognostication of terminally ill patients, with the recently developed regret based decision curve analysis (regret DCA). We extend the regret DCA methodology to consider harms associated with the prognostication test as well as harms and effects of the management strategies. In order to enable patients and physicians in making these complex decisions in real-time, we developed an easily accessible web-based decision support system available at the point of care. Results The web-based decision support system facilitates the hospice referral process in three steps. First, the patient or surrogate is interviewed to elicit his/her personal preferences regarding the continuation of life-sustaining treatment vs. palliative care. Then, regret DCA is employed to identify the best strategy for the particular patient in terms of threshold probability at which he/she is indifferent between continuation of treatment and of hospice referral. Finally, if necessary, the probabilities of survival and death for the particular patient are computed based on the SUPPORT prognostication model and contrasted with the patient's threshold probability. The web-based design of the CDSS enables patients, physicians, and family members to participate in the decision process from anywhere internet access is available. Conclusions We present a theoretical framework to facilitate the hospice referral process. Further rigorous clinical evaluation including testing in a prospective randomized controlled trial is required and planned. PMID:22196308

Evaluating Student Response to WeBWorK, a Web-Based Homework Delivery and Grading System

ERIC Educational Resources Information Center

Roth, Vicki; Ivanchenko, Volodymyr; Record, Nicholas

2008-01-01

As the use of web-based homework delivery and checking systems expands, we have greater need to evaluate how students engage with these systems and how changes in the systems influence student behavior. Reported here is the assessment of WeBWorK, an open-source web-based homework program used largely in postsecondary math and science courses, with…

SNPversity: A web-based tool for visualizing diversity

USDA-ARS?s Scientific Manuscript database

Background: Many stand-alone desktop software suites exist to visualize single nucleotide polymorphisms (SNP) diversity, but web-based software that can be easily implemented and used for biological databases is absent. SNPversity was created to answer this need by building an open-source visualizat...

Exploring U.S Cropland - A Web Service based Cropland Data Layer Visualization, Dissemination and Querying System (Invited)

NASA Astrophysics Data System (ADS)

Yang, Z.; Han, W.; di, L.

2010-12-01

The National Agricultural Statistics Service (NASS) of the USDA produces the Cropland Data Layer (CDL) product, which is a raster-formatted, geo-referenced, U.S. crop specific land cover classification. These digital data layers are widely used for a variety of applications by universities, research institutions, government agencies, and private industry in climate change studies, environmental ecosystem studies, bioenergy production & transportation planning, environmental health research and agricultural production decision making. The CDL is also used internally by NASS for crop acreage and yield estimation. Like most geospatial data products, the CDL product is only available by CD/DVD delivery or online bulk file downloading via the National Research Conservation Research (NRCS) Geospatial Data Gateway (external users) or in a printed paper map format. There is no online geospatial information access and dissemination, no crop visualization & browsing, no geospatial query capability, nor online analytics. To facilitate the application of this data layer and to help disseminating the data, a web-service based CDL interactive map visualization, dissemination, querying system is proposed. It uses Web service based service oriented architecture, adopts open standard geospatial information science technology and OGC specifications and standards, and re-uses functions/algorithms from GeoBrain Technology (George Mason University developed). This system provides capabilities of on-line geospatial crop information access, query and on-line analytics via interactive maps. It disseminates all data to the decision makers and users via real time retrieval, processing and publishing over the web through standards-based geospatial web services. A CDL region of interest can also be exported directly to Google Earth for mashup or downloaded for use with other desktop application. This web service based system greatly improves equal-accessibility, interoperability, usability, and data visualization, facilitates crop geospatial information usage, and enables US cropland online exploring capability without any client-side software installation. It also greatly reduces the need for paper map and analysis report printing and media usages, and thus enhances low-carbon Agro-geoinformation dissemination for decision support.

Developing a Web-based system by integrating VGI and SDI for real estate management and marketing

NASA Astrophysics Data System (ADS)

Salajegheh, J.; Hakimpour, F.; Esmaeily, A.

2014-10-01

Property importance of various aspects, especially the impact on various sectors of the economy and the country's macroeconomic is clear. Because of the real, multi-dimensional and heterogeneous nature of housing as a commodity, the lack of an integrated system includes comprehensive information of property, the lack of awareness of some actors in this field about comprehensive information about property and the lack of clear and comprehensive rules and regulations for the trading and pricing, several problems arise for the people involved in this field. In this research implementation of a crowd-sourced Web-based real estate support system is desired. Creating a Spatial Data Infrastructure (SDI) in this system for collecting, updating and integrating all official data about property is also desired in this study. In this system a Web2.0 broker and technologies such as Web services and service composition has been used. This work aims to provide comprehensive and diverse information about property from different sources. For this purpose five-level real estate support system architecture is used. PostgreSql DBMS is used to implement the desired system. Geoserver software is also used as map server and reference implementation of OGC (Open Geospatial Consortium) standards. And Apache server is used to run web pages and user interfaces. Integration introduced methods and technologies provide a proper environment for various users to use the system and share their information. This goal is only achieved by cooperation between all involved organizations in real estate with implementation their required infrastructures in interoperability Web services format.

Parameter selection for and implementation of a web-based decision-support tool to predict extubation outcome in premature infants.

PubMed

Mueller, Martina; Wagner, Carol L; Annibale, David J; Knapp, Rebecca G; Hulsey, Thomas C; Almeida, Jonas S

2006-03-01

Approximately 30% of intubated preterm infants with respiratory distress syndrome (RDS) will fail attempted extubation, requiring reintubation and mechanical ventilation. Although ventilator technology and monitoring of premature infants have improved over time, optimal extubation remains challenging. Furthermore, extubation decisions for premature infants require complex informational processing, techniques implicitly learned through clinical practice. Computer-aided decision-support tools would benefit inexperienced clinicians, especially during peak neonatal intensive care unit (NICU) census. A five-step procedure was developed to identify predictive variables. Clinical expert (CE) thought processes comprised one model. Variables from that model were used to develop two mathematical models for the decision-support tool: an artificial neural network (ANN) and a multivariate logistic regression model (MLR). The ranking of the variables in the three models was compared using the Wilcoxon Signed Rank Test. The best performing model was used in a web-based decision-support tool with a user interface implemented in Hypertext Markup Language (HTML) and the mathematical model employing the ANN. CEs identified 51 potentially predictive variables for extubation decisions for an infant on mechanical ventilation. Comparisons of the three models showed a significant difference between the ANN and the CE (p = 0.0006). Of the original 51 potentially predictive variables, the 13 most predictive variables were used to develop an ANN as a web-based decision-tool. The ANN processes user-provided data and returns the prediction 0-1 score and a novelty index. The user then selects the most appropriate threshold for categorizing the prediction as a success or failure. Furthermore, the novelty index, indicating the similarity of the test case to the training case, allows the user to assess the confidence level of the prediction with regard to how much the new data differ from the data originally used for the development of the prediction tool. State-of-the-art, machine-learning methods can be employed for the development of sophisticated tools to aid clinicians' decisions. We identified numerous variables considered relevant for extubation decisions for mechanically ventilated premature infants with RDS. We then developed a web-based decision-support tool for clinicians which can be made widely available and potentially improve patient care world wide.

BioenergyKDF: Enabling Spatiotemporal Data Synthesis and Research Collaboration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Myers, Aaron T; Movva, Sunil; Karthik, Rajasekar

2014-01-01

The Bioenergy Knowledge Discovery Framework (BioenergyKDF) is a scalable, web-based collaborative environment for scientists working on bioenergy related research in which the connections between data, literature, and models can be explored and more clearly understood. The fully-operational and deployed system, built on multiple open source libraries and architectures, stores contributions from the community of practice and makes them easy to find, but that is just its base functionality. The BioenergyKDF provides a national spatiotemporal decision support capability that enables data sharing, analysis, modeling, and visualization as well as fosters the development and management of the U.S. bioenergy infrastructure, which ismore » an essential component of the national energy infrastructure. The BioenergyKDF is built on a flexible, customizable platform that can be extended to support the requirements of any user community especially those that work with spatiotemporal data. While there are several community data-sharing software platforms available, some developed and distributed by national governments, none of them have the full suite of capabilities available in BioenergyKDF. For example, this component-based platform and database independent architecture allows it to be quickly deployed to existing infrastructure and to connect to existing data repositories (spatial or otherwise). As new data, analysis, and features are added; the BioenergyKDF will help lead research and support decisions concerning bioenergy into the future, but will also enable the development and growth of additional communities of practice both inside and outside of the Department of Energy. These communities will be able to leverage the substantial investment the agency has made in the KDF platform to quickly stand up systems that are customized to their data and research needs.« less

Crawling The Web for Libre: Selecting, Integrating, Extending and Releasing Open Source Software

NASA Astrophysics Data System (ADS)

Truslove, I.; Duerr, R. E.; Wilcox, H.; Savoie, M.; Lopez, L.; Brandt, M.

2012-12-01

Libre is a project developed by the National Snow and Ice Data Center (NSIDC). Libre is devoted to liberating science data from its traditional constraints of publication, location, and findability. Libre embraces and builds on the notion of making knowledge freely available, and both Creative Commons licensed content and Open Source Software are crucial building blocks for, as well as required deliverable outcomes of the project. One important aspect of the Libre project is to discover cryospheric data published on the internet without prior knowledge of the location or even existence of that data. Inspired by well-known search engines and their underlying web crawling technologies, Libre has explored tools and technologies required to build a search engine tailored to allow users to easily discover geospatial data related to the polar regions. After careful consideration, the Libre team decided to base its web crawling work on the Apache Nutch project (http://nutch.apache.org). Nutch is "an open source web-search software project" written in Java, with good documentation, a significant user base, and an active development community. Nutch was installed and configured to search for the types of data of interest, and the team created plugins to customize the default Nutch behavior to better find and categorize these data feeds. This presentation recounts the Libre team's experiences selecting, using, and extending Nutch, and working with the Nutch user and developer community. We will outline the technical and organizational challenges faced in order to release the project's software as Open Source, and detail the steps actually taken. We distill these experiences into a set of heuristics and recommendations for using, contributing to, and releasing Open Source Software.

Omics Metadata Management Software v. 1 (OMMS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Our application, the Omics Metadata Management Software (OMMS), answers both needs, empowering experimentalists to generate intuitive, consistent metadata, and to perform bioinformatics analyses and information management tasks via a simple and intuitive web-based interface. Several use cases with short-read sequence datasets are provided to showcase the full functionality of the OMMS, from metadata curation tasks, to bioinformatics analyses and results management and downloading. The OMMS can be implemented as a stand alone-package for individual laboratories, or can be configured for web-based deployment supporting geographically dispersed research teams. Our software was developed with open-source bundles, is flexible, extensible and easily installedmore » and run by operators with general system administration and scripting language literacy.« less

Web-based decision support system to predict risk level of long term rice production

NASA Astrophysics Data System (ADS)

Mukhlash, Imam; Maulidiyah, Ratna; Sutikno; Setiyono, Budi

2017-09-01

Appropriate decision making in risk management of rice production is very important in agricultural planning, especially for Indonesia which is an agricultural country. Good decision would be obtained if the supporting data required are satisfied and using appropriate methods. This study aims to develop a Decision Support System that can be used to predict the risk level of rice production in some districts which are central of rice production in East Java. Web-based decision support system is constructed so that the information can be easily accessed and understood. Components of the system are data management, model management, and user interface. This research uses regression models of OLS and Copula. OLS model used to predict rainfall while Copula model used to predict harvested area. Experimental results show that the models used are successfully predict the harvested area of rice production in some districts which are central of rice production in East Java at any given time based on the conditions and climate of a region. Furthermore, it can predict the amount of rice production with the level of risk. System generates prediction of production risk level in the long term for some districts that can be used as a decision support for the authorities.

Decision Support Framework Implementation Of The Web-Based Environmental Decision Analysis DASEES: Decision Analysis For A Sustainable Environment, Economy, And Society

EPA Science Inventory

Solutions to pervasive environmental problems often are not amenable to a straightforward application of science-based actions. These problems encompass large-scale environmental policy questions where environmental concerns, economic constraints, and societal values conflict ca...

A Web-based open-source database for the distribution of hyperspectral signatures

NASA Astrophysics Data System (ADS)

Ferwerda, J. G.; Jones, S. D.; Du, Pei-Jun

2006-10-01

With the coming of age of field spectroscopy as a non-destructive means to collect information on the physiology of vegetation, there is a need for storage of signatures, and, more importantly, their metadata. Without the proper organisation of metadata, the signatures itself become limited. In order to facilitate re-distribution of data, a database for the storage & distribution of hyperspectral signatures and their metadata was designed. The database was built using open-source software, and can be used by the hyperspectral community to share their data. Data is uploaded through a simple web-based interface. The database recognizes major file-formats by ASD, GER and International Spectronics. The database source code is available for download through the hyperspectral.info web domain, and we happily invite suggestion for additions & modification for the database to be submitted through the online forums on the same website.

Data access and decision tools for coastal water resources ...

EPA Pesticide Factsheets

US EPA has supported the development of numerous models and tools to support implementation of environmental regulations. However, transfer of knowledge and methods from detailed technical models to support practical problem solving by local communities and watershed or coastal management organizations remains a challenge. We have developed the Estuary Data Mapper (EDM) to facilitate data discovery, visualization and access to support environmental problem solving for coastal watersheds and estuaries. EDM is a stand-alone application based on open-source software which requires only internet access for operation. Initially, development of EDM focused on delivery of raw data streams from distributed web services, ranging from atmospheric deposition to hydrologic, tidal, and water quality time series, estuarine habitat characteristics, and remote sensing products. We have transitioned to include access to value-added products which provide end-users with results of future scenario analysis, facilitate extension of models across geographic regions, and/or promote model interoperability. Here we present three examples: 1) the delivery of input data for the development of seagrass models across estuaries, 2) scenarios illustrating the implications of riparian buffer management (loss or restoration) for stream thermal regimes and fish communities, and 3) access to hydrology model outputs to foster connections across models at different scales, ultimately feeding

Open Source Web-Based Solutions for Disseminating and Analyzing Flood Hazard Information at the Community Level

NASA Astrophysics Data System (ADS)

Santillan, M. M.-M.; Santillan, J. R.; Morales, E. M. O.

2017-09-01

We discuss in this paper the development, including the features and functionalities, of an open source web-based flood hazard information dissemination and analytical system called "Flood EViDEns". Flood EViDEns is short for "Flood Event Visualization and Damage Estimations", an application that was developed by the Caraga State University to address the needs of local disaster managers in the Caraga Region in Mindanao, Philippines in accessing timely and relevant flood hazard information before, during and after the occurrence of flood disasters at the community (i.e., barangay and household) level. The web application made use of various free/open source web mapping and visualization technologies (GeoServer, GeoDjango, OpenLayers, Bootstrap), various geospatial datasets including LiDAR-derived elevation and information products, hydro-meteorological data, and flood simulation models to visualize various scenarios of flooding and its associated damages to infrastructures. The Flood EViDEns application facilitates the release and utilization of this flood-related information through a user-friendly front end interface consisting of web map and tables. A public version of the application can be accessed at http://121.97.192.11:8082/. The application is currently expanded to cover additional sites in Mindanao, Philippines through the "Geo-informatics for the Systematic Assessment of Flood Effects and Risks for a Resilient Mindanao" or the "Geo-SAFER Mindanao" Program.

Harvest: a web-based biomedical data discovery and reporting application development platform.

PubMed

Italia, Michael J; Pennington, Jeffrey W; Ruth, Byron; Wrazien, Stacey; Loutrel, Jennifer G; Crenshaw, E Bryan; Miller, Jeffrey; White, Peter S

2013-01-01

Biomedical researchers share a common challenge of making complex data understandable and accessible. This need is increasingly acute as investigators seek opportunities for discovery amidst an exponential growth in the volume and complexity of laboratory and clinical data. To address this need, we developed Harvest, an open source framework that provides a set of modular components to aid the rapid development and deployment of custom data discovery software applications. Harvest incorporates visual representations of multidimensional data types in an intuitive, web-based interface that promotes a real-time, iterative approach to exploring complex clinical and experimental data. The Harvest architecture capitalizes on standards-based, open source technologies to address multiple functional needs critical to a research and development environment, including domain-specific data modeling, abstraction of complex data models, and a customizable web client.

A Semantic Sensor Web for Environmental Decision Support Applications

PubMed Central

Gray, Alasdair J. G.; Sadler, Jason; Kit, Oles; Kyzirakos, Kostis; Karpathiotakis, Manos; Calbimonte, Jean-Paul; Page, Kevin; García-Castro, Raúl; Frazer, Alex; Galpin, Ixent; Fernandes, Alvaro A. A.; Paton, Norman W.; Corcho, Oscar; Koubarakis, Manolis; De Roure, David; Martinez, Kirk; Gómez-Pérez, Asunción

2011-01-01

Sensing devices are increasingly being deployed to monitor the physical world around us. One class of application for which sensor data is pertinent is environmental decision support systems, e.g., flood emergency response. For these applications, the sensor readings need to be put in context by integrating them with other sources of data about the surrounding environment. Traditional systems for predicting and detecting floods rely on methods that need significant human resources. In this paper we describe a semantic sensor web architecture for integrating multiple heterogeneous datasets, including live and historic sensor data, databases, and map layers. The architecture provides mechanisms for discovering datasets, defining integrated views over them, continuously receiving data in real-time, and visualising on screen and interacting with the data. Our approach makes extensive use of web service standards for querying and accessing data, and semantic technologies to discover and integrate datasets. We demonstrate the use of our semantic sensor web architecture in the context of a flood response planning web application that uses data from sensor networks monitoring the sea-state around the coast of England. PMID:22164110

The EarthServer Federation: State, Role, and Contribution to GEOSS

NASA Astrophysics Data System (ADS)

Merticariu, Vlad; Baumann, Peter

2016-04-01

The intercontinental EarthServer initiative has established a European datacube platform with proven scalability: known databases exceed 100 TB, and single queries have been split across more than 1,000 cloud nodes. Its service interface being rigorously based on the OGC "Big Geo Data" standards, Web Coverage Service (WCS) and Web Coverage Processing Service (WCPS), a series of clients can dock into the services, ranging from open-source OpenLayers and QGIS over open-source NASA WorldWind to proprietary ESRI ArcGIS. Datacube fusion in a "mix and match" style is supported by the platform technolgy, the rasdaman Array Database System, which transparently federates queries so that users simply approach any node of the federation to access any data item, internally optimized for minimal data transfer. Notably, rasdaman is part of GEOSS GCI. NASA is contributing its Web WorldWind virtual globe for user-friendly data extraction, navigation, and analysis. Integrated datacube / metadata queries are contributed by CITE. Current federation members include ESA (managed by MEEO sr.l.), Plymouth Marine Laboratory (PML), the European Centre for Medium-Range Weather Forecast (ECMWF), Australia's National Computational Infrastructure, and Jacobs University (adding in Planetary Science). Further data centers have expressed interest in joining. We present the EarthServer approach, discuss its underlying technology, and illustrate the contribution this datacube platform can make to GEOSS.

Implementation of a near-real time cross-border web-mapping platform on airborne particulate matter (PM) concentration with open-source software

NASA Astrophysics Data System (ADS)

Knörchen, Achim; Ketzler, Gunnar; Schneider, Christoph

2015-01-01

Although Europe has been growing together for the past decades, cross-border information platforms on environmental issues are still scarce. With regard to the establishment of a web-mapping tool on airborne particulate matter (PM) concentration for the Euregio Meuse-Rhine located in the border region of Belgium, Germany and the Netherlands, this article describes the research on methodical and technical backgrounds implementing such a platform. An open-source solution was selected for presenting the data in a Web GIS (OpenLayers/GeoExt; both JavaScript-based), applying other free tools for data handling (Python), data management (PostgreSQL), geo-statistical modelling (Octave), geoprocessing (GRASS GIS/GDAL) and web mapping (MapServer). The multilingual, made-to-order online platform provides access to near-real time data on PM concentration as well as additional background information. In an open data section, commented configuration files for the Web GIS client are being made available for download. Furthermore, all geodata generated by the project is being published under public domain and can be retrieved in various formats or integrated into Desktop GIS as Web Map Services (WMS).

Modernizing the MagIC Paleomagnetic and Rock Magnetic Database Technology Stack to Encourage Code Reuse and Reproducible Science

NASA Astrophysics Data System (ADS)

Minnett, R.; Koppers, A. A. P.; Jarboe, N.; Jonestrask, L.; Tauxe, L.; Constable, C.

2016-12-01

The Magnetics Information Consortium (https://earthref.org/MagIC/) develops and maintains a database and web application for supporting the paleo-, geo-, and rock magnetic scientific community. Historically, this objective has been met with an Oracle database and a Perl web application at the San Diego Supercomputer Center (SDSC). The Oracle Enterprise Cluster at SDSC, however, was decommissioned in July of 2016 and the cost for MagIC to continue using Oracle became prohibitive. This provided MagIC with a unique opportunity to reexamine the entire technology stack and data model. MagIC has developed an open-source web application using the Meteor (http://meteor.com) framework and a MongoDB database. The simplicity of the open-source full-stack framework that Meteor provides has improved MagIC's development pace and the increased flexibility of the data schema in MongoDB encouraged the reorganization of the MagIC Data Model. As a result of incorporating actively developed open-source projects into the technology stack, MagIC has benefited from their vibrant software development communities. This has translated into a more modern web application that has significantly improved the user experience for the paleo-, geo-, and rock magnetic scientific community.

Integrating hydrologic modeling web services with online data sharing to prepare, store, and execute models in hydrology

NASA Astrophysics Data System (ADS)

Gan, T.; Tarboton, D. G.; Dash, P. K.; Gichamo, T.; Horsburgh, J. S.

2017-12-01

Web based apps, web services and online data and model sharing technology are becoming increasingly available to support research. This promises benefits in terms of collaboration, platform independence, transparency and reproducibility of modeling workflows and results. However, challenges still exist in real application of these capabilities and the programming skills researchers need to use them. In this research we combined hydrologic modeling web services with an online data and model sharing system to develop functionality to support reproducible hydrologic modeling work. We used HydroDS, a system that provides web services for input data preparation and execution of a snowmelt model, and HydroShare, a hydrologic information system that supports the sharing of hydrologic data, model and analysis tools. To make the web services easy to use, we developed a HydroShare app (based on the Tethys platform) to serve as a browser based user interface for HydroDS. In this integration, HydroDS receives web requests from the HydroShare app to process the data and execute the model. HydroShare supports storage and sharing of the results generated by HydroDS web services. The snowmelt modeling example served as a use case to test and evaluate this approach. We show that, after the integration, users can prepare model inputs or execute the model through the web user interface of the HydroShare app without writing program code. The model input/output files and metadata describing the model instance are stored and shared in HydroShare. These files include a Python script that is automatically generated by the HydroShare app to document and reproduce the model input preparation workflow. Once stored in HydroShare, inputs and results can be shared with other users, or published so that other users can directly discover, repeat or modify the modeling work. This approach provides a collaborative environment that integrates hydrologic web services with a data and model sharing system to enable model development and execution. The entire system comprised of the HydroShare app, HydroShare and HydroDS web services is open source and contributes to capability for web based modeling research.

A Web-Based Treatment Decision Support Tool for Patients With Advanced Knee Arthritis: Evaluation of User Interface and Content Design

PubMed Central

Zheng, Hua; Rosal, Milagros C; Li, Wenjun; Borg, Amy; Yang, Wenyun; Ayers, David C

2018-01-01

Background Data-driven surgical decisions will ensure proper use and timing of surgical care. We developed a Web-based patient-centered treatment decision and assessment tool to guide treatment decisions among patients with advanced knee osteoarthritis who are considering total knee replacement surgery. Objective The aim of this study was to examine user experience and acceptance of the Web-based treatment decision support tool among older adults. Methods User-centered formative and summative evaluations were conducted for the tool. A sample of 28 patients who were considering total knee replacement participated in the study. Participants’ responses to the user interface design, the clarity of information, as well as usefulness, satisfaction, and acceptance of the tool were collected through qualitative (ie, individual patient interviews) and quantitative (ie, standardized Computer System Usability Questionnaire) methods. Results Participants were older adults with a mean age of 63 (SD 11) years. Three-quarters of them had no technical questions using the tool. User interface design recommendations included larger fonts, bigger buttons, less colors, simpler navigation without extra “next page” click, less mouse movement, and clearer illustrations with simple graphs. Color-coded bar charts and outcome-specific graphs with positive action were easiest for them to understand the outcomes data. Questionnaire data revealed high satisfaction with the tool usefulness and interface quality, and also showed ease of use of the tool, regardless of age or educational status. Conclusions We evaluated the usability of a patient-centered decision support tool designed for advanced knee arthritis patients to facilitate their knee osteoarthritis treatment decision making. The lessons learned can inform other decision support tools to improve interface and content design for older patients’ use. PMID:29712620

Web Mapping Architectures Based on Open Specifications and Free and Open Source Software in the Water Domain

NASA Astrophysics Data System (ADS)

Arias Muñoz, C.; Brovelli, M. A.; Kilsedar, C. E.; Moreno-Sanchez, R.; Oxoli, D.

2017-09-01

The availability of water-related data and information across different geographical and jurisdictional scales is of critical importance for the conservation and management of water resources in the 21st century. Today information assets are often found fragmented across multiple agencies that use incompatible data formats and procedures for data collection, storage, maintenance, analysis, and distribution. The growing adoption of Web mapping systems in the water domain is reducing the gap between data availability and its practical use and accessibility. Nevertheless, more attention must be given to the design and development of these systems to achieve high levels of interoperability and usability while fulfilling different end user informational needs. This paper first presents a brief overview of technologies used in the water domain, and then presents three examples of Web mapping architectures based on free and open source software (FOSS) and the use of open specifications (OS) that address different users' needs for data sharing, visualization, manipulation, scenario simulations, and map production. The purpose of the paper is to illustrate how the latest developments in OS for geospatial and water-related data collection, storage, and sharing, combined with the use of mature FOSS projects facilitate the creation of sophisticated interoperable Web-based information systems in the water domain.

Information Management Systems for Monitoring and Documenting World Heritage - the Silk Roads Chris

NASA Astrophysics Data System (ADS)

Vileikis, O.; Serruys, E.; Dumont, B.; van Balen, K.; Santana Quinterod, M.; de Maeyer, P.; Tigny, V.

2012-07-01

This paper discusses the application of Information Management Systems (IMS) for documenting and monitoring World Heritage (WH) properties. The application of IMS in WH can support all stakeholders involved in conservation, and management of cultural heritage by more easily inventorying, mining and exchanging information from multiple sources based on international standards. Moreover, IMS could assist in detecting damages and preparing management strategies to mitigate risks, and slowing down the deterioration of the integrity of WH properties. The case study of the Silk Roads Cultural Heritage Resource Information System (CHRIS), a Belgian Federal Science Policy Office funded project, illustrates the capabilities of IMS in the context of the nomination of the Central Asian Silk Roads on the WH List. This multi-lingual, web-based IMS will act as a collaborative platform allowing for the completion of improved transnational nomination dossiers and subsequent monitoring activities with all necessary baseline information to easily verify consistency and quality of the proposal. The Silk Roads CHRIS Geospatial Content Management System uses open source technologies and allows to georeference data from different scales and sources including data from field recording methods and combine it with historical and heritage features documented through various means such as textual descriptions, documents, photographs, 3D models or videos. Moreover, tailored maps can also be generated by overlaying a selection of available layers and then be exported to support the nomination dossier. Finally, by using this innovative information and decision support system, the State Parties and other interested stakeholders will have access to a complete nomination dossier and could therefore respond more effectively to hazards and disaster phenomena.

Evidence-informed decision-making by professionals working in addiction agencies serving women: a descriptive qualitative study.

PubMed

Jack, Susan M; Dobbins, Maureen; Sword, Wendy; Novotna, Gabriela; Brooks, Sandy; Lipman, Ellen L; Niccols, Alison

2011-11-07

Effective approaches to the prevention and treatment of substance abuse among mothers have been developed but not widely implemented. Implementation studies suggest that the adoption of evidence-based practices in the field of addictions remains low. There is a need, therefore, to better understand decision making processes in addiction agencies in order to develop more effective approaches to promote the translation of knowledge gained from addictions research into clinical practice. A descriptive qualitative study was conducted to explore: 1) the types and sources of evidence used to inform practice-related decisions within Canadian addiction agencies serving women; 2) how decision makers at different levels report using research evidence; and 3) factors that influence evidence-informed decision making. A purposeful sample of 26 decision-makers providing addiction treatment services to women completed in-depth qualitative interviews. Interview data were coded and analyzed using directed and summative content analysis strategies as well as constant comparison techniques. Across all groups, individuals reported locating and using multiple types of evidence to inform decisions. Some decision-makers rely on their experiential knowledge of addiction and recovery in decision-making. Research evidence is often used directly in decision-making at program management and senior administrative levels. Information for decision-making is accessed from a range of sources, including web-based resources and experts in the field. Individual and organizational facilitators and barriers to using research evidence in decision making were identified. There is support at administrative levels for integrating EIDM in addiction agencies. Knowledge transfer and exchange strategies should be focussed towards program managers and administrators and include capacity building for locating, appraising and using research evidence, knowledge brokering, and for partnering with universities. Resources are required to maintain web-based databases of searchable evidence to facilitate access to research evidence. A need exists to address the perception that there is a paucity of research evidence available to inform program decisions. Finally, there is a need to consider how experiential knowledge influences decision-making and what guidance research evidence has to offer regarding the implementation of different treatment approaches within the field of addictions.

Evidence-informed decision-making by professionals working in addiction agencies serving women: a descriptive qualitative study

PubMed Central

2011-01-01

Background Effective approaches to the prevention and treatment of substance abuse among mothers have been developed but not widely implemented. Implementation studies suggest that the adoption of evidence-based practices in the field of addictions remains low. There is a need, therefore, to better understand decision making processes in addiction agencies in order to develop more effective approaches to promote the translation of knowledge gained from addictions research into clinical practice. Methods A descriptive qualitative study was conducted to explore: 1) the types and sources of evidence used to inform practice-related decisions within Canadian addiction agencies serving women; 2) how decision makers at different levels report using research evidence; and 3) factors that influence evidence-informed decision making. A purposeful sample of 26 decision-makers providing addiction treatment services to women completed in-depth qualitative interviews. Interview data were coded and analyzed using directed and summative content analysis strategies as well as constant comparison techniques. Results Across all groups, individuals reported locating and using multiple types of evidence to inform decisions. Some decision-makers rely on their experiential knowledge of addiction and recovery in decision-making. Research evidence is often used directly in decision-making at program management and senior administrative levels. Information for decision-making is accessed from a range of sources, including web-based resources and experts in the field. Individual and organizational facilitators and barriers to using research evidence in decision making were identified. Conclusions There is support at administrative levels for integrating EIDM in addiction agencies. Knowledge transfer and exchange strategies should be focussed towards program managers and administrators and include capacity building for locating, appraising and using research evidence, knowledge brokering, and for partnering with universities. Resources are required to maintain web-based databases of searchable evidence to facilitate access to research evidence. A need exists to address the perception that there is a paucity of research evidence available to inform program decisions. Finally, there is a need to consider how experiential knowledge influences decision-making and what guidance research evidence has to offer regarding the implementation of different treatment approaches within the field of addictions. PMID:22059528

RiskChanges Spatial Decision Support system for the analysis of changing multi-hazard risk

NASA Astrophysics Data System (ADS)

van Westen, Cees; Zhang, Kaixi; Bakker, Wim; Andrejchenko, Vera; Berlin, Julian; Olyazadeh, Roya; Cristal, Irina

2015-04-01

Within the framework of the EU FP7 Marie Curie Project CHANGES and the EU FP7 Copernicus project INCREO a spatial decision support system was developed with the aim to analyse the effect of risk reduction planning alternatives on reducing the risk now and in the future, and support decision makers in selecting the best alternatives. Central to the SDSS are the stakeholders. The envisaged users of the system are organizations involved in planning of risk reduction measures, and that have staff capable of visualizing and analyzing spatial data at a municipal scale. The SDSS should be able to function in different countries with different legal frameworks and with organizations with different mandates. These could be subdivided into Civil protection organization with the mandate to design disaster response plans, Expert organizations with the mandate to design structural risk reduction measures (e.g. dams, dikes, check-dams etc), and planning organizations with the mandate to make land development plans. The SDSS can be used in different ways: analyzing the current level of risk, analyzing the best alternatives for risk reduction, the evaluation of the consequences of possible future scenarios to the risk levels, and the evaluation how different risk reduction alternatives will lead to risk reduction under different future scenarios. The SDSS is developed based on open source software and following open standards, for code as well as for data formats and service interfaces. Code development was based upon open source software as well. The architecture of the system is modular. The various parts of the system are loosely coupled, extensible, using standards for interoperability, flexible and web-based. The Spatial Decision Support System is composed of a number of integrated components. The Risk Assessment component allows to carry out spatial risk analysis, with different degrees of complexity, ranging from simple exposure (overlay of hazard and assets maps) to quantitative analysis (using different hazard types, temporal scenarios and vulnerability curves) resulting into risk curves. The platform does not include a component to calculate hazard maps, and existing hazard maps are used as input data for the risk component. The second component of the SDSS is a risk reduction planning component, which forms the core of the platform. This component includes the definition of risk reduction alternatives (related to disaster response planning, risk reduction measures and spatial planning) and links back to the risk assessment module to calculate the new level of risk if the measure is implemented, and a cost-benefit (or cost-effectiveness/ Spatial Multi Criteria Evaluation) component to compare the alternatives and make decision on the optimal one. The third component of the SDSS is a temporal scenario component, which allows to define future scenarios in terms of climate change, land use change and population change, and the time periods for which these scenarios will be made. The component doesn't generate these scenarios but uses input maps for the effect of the scenarios on the hazard and assets maps. The last component is a communication and visualization component, which can compare scenarios and alternatives, not only in the form of maps, but also in other forms (risk curves, tables, graphs)

HDDTOOLS: an R package serving Hydrological Data Discovery Tools

NASA Astrophysics Data System (ADS)

Vitolo, C.; Buytaert, W.

2014-12-01

Many governmental bodies and institutions are currently committed to publish open data as the result of a trend of increasing transparency, based on which a wide variety of information produced at public expense is now becoming open and freely available to improve public involvement in the process of decision and policy making. Discovery, access and retrieval of information is, however, not always a simple task. Especially when programmatic access to data resources is not allowed, downloading metadata catalogue, select the information needed, request datasets, de-compression, conversion, manual filtering and parsing can become rather tedious. The R package "hddtools" is an open source project, designed to make all the above operations more efficient by means of re-usable functions. The package facilitate non programmatic access to various online data sources such as the Global Runoff Data Centre, NASA's TRMM mission, the Data60UK database amongst others. This package complements R's growing functionality in environmental web technologies to bridge the gap between data providers and data consumers and it is designed to be the starting building block of scientific workflows for linking data and models in a seamless fashion.

The Matsu Wheel: A Cloud-Based Framework for Efficient Analysis and Reanalysis of Earth Satellite Imagery

NASA Technical Reports Server (NTRS)

Patterson, Maria T.; Anderson, Nicholas; Bennett, Collin; Bruggemann, Jacob; Grossman, Robert L.; Handy, Matthew; Ly, Vuong; Mandl, Daniel J.; Pederson, Shane; Pivarski, James;

[Patients' decision for aesthetic surgery].

PubMed

Fansa, H; Haller, S

2011-12-01

Aesthetic surgery is a service which entails a high degree of trust. Service evaluation prior to provision is difficult for the patient. This leads to the question of how to manage the service successfully while still focusing on the medical needs. The decision to undergo an operation is not influenced by the operation itself, but by preoperative events which induce the patient to have the operation done. According to "buying decisions" for products or in service management, the decision for an aesthetic operation is extensive; the patient is highly involved and actively searching for information using different directed sources of information. The real "buying decision" consists of 5 phases: problem recognition, gathering of information, alternative education, purchase decision, and post purchase behaviour. A retrospective survey of 40 female patients who have already undergone an aesthetic operation assessed for problem recognition, which types of information were collected prior to the appointment with the surgeon, and why the patients have had the operation at our hospital. They were also asked how many alternative surgeons they had been seen before. Most of the patients had been thinking about undergoing an operation for several years. They mainly used the web for their research and were informed by other (non-aesthetic) physicians/general practitioners. Requested information was about the aesthetic results and possible problems and complications. Patients came based on web information and because of recommendations from other physicians. 60% of all interviewees did not see another surgeon and decided to have the operation because of positive patient-doctor communication and the surgeon's good reputation. Competence was considered to be the most important quality of the surgeon. However, the attribute was judged on subjective parameters. Environment, office rooms and staff were assessed as important but not very important. Costs of surgery were ranked second. Influence on patients' decision is only possible by high quality operation results, which in turn lead to good reputation with (non-aesthetic) physicians and patients. In contrast to print advertisements, the provision of information via the internet is of tremendous importance and must be both information and comprehensible. Not only the aesthetic result should be depicted, but also questions such as "when will I be fit after surgery", and possible problems and complications should be described honestly. Besides the described word-of-mouth recommendations web fora resemble a virtual extension of recommendation. Whether such web based fora will prevail as a significant source of information remains unclear. Board certification in plastic and aesthetic surgery ("Facharzt" qualification) was assessed as very important. Thus, this is relevant information which should be emphasized. Most important for the patients' decision, however, was patient-doctor communication. To develop a basis of trust, communication should be open and reliable. An adequate time span has to be planned for the first appointment with the patient. In addition to aesthetic results, risks and possible complications have to be discussed. An open and comprehensible conversation which does not sugar-coat the operation is assessed as very positive. Finally, based on this consultation the surgeon is suggestive of his surgical competence. This underlines that core competence in aesthetic surgery is a medical one. © Georg Thieme Verlag KG Stuttgart · New York.

The GeoDataPortal: A Standards-based Environmental Modeling Data Access and Manipulation Toolkit

NASA Astrophysics Data System (ADS)

Blodgett, D. L.; Kunicki, T.; Booth, N.; Suftin, I.; Zoerb, R.; Walker, J.

2010-12-01

Environmental modelers from fields of study such as climatology, hydrology, geology, and ecology rely on many data sources and processing methods that are common across these disciplines. Interest in inter-disciplinary, loosely coupled modeling and data sharing is increasing among scientists from the USGS, other agencies, and academia. For example, hydrologic modelers need downscaled climate change scenarios and land cover data summarized for the watersheds they are modeling. Subsequently, ecological modelers are interested in soil moisture information for a particular habitat type as predicted by the hydrologic modeler. The USGS Center for Integrated Data Analytics Geo Data Portal (GDP) project seeks to facilitate this loose model coupling data sharing through broadly applicable open-source web processing services. These services simplify and streamline the time consuming and resource intensive tasks that are barriers to inter-disciplinary collaboration. The GDP framework includes a catalog describing projects, models, data, processes, and how they relate. Using newly introduced data, or sources already known to the catalog, the GDP facilitates access to sub-sets and common derivatives of data in numerous formats on disparate web servers. The GDP performs many of the critical functions needed to summarize data sources into modeling units regardless of scale or volume. A user can specify their analysis zones or modeling units as an Open Geospatial Consortium (OGC) standard Web Feature Service (WFS). Utilities to cache Shapefiles and other common GIS input formats have been developed to aid in making the geometry available for processing via WFS. Dataset access in the GDP relies primarily on the Unidata NetCDF-Java library’s common data model. Data transfer relies on methods provided by Unidata’s Thematic Real-time Environmental Data Distribution System Data Server (TDS). TDS services of interest include the Open-source Project for a Network Data Access Protocol (OPeNDAP) standard for gridded time series, the OGC’s Web Coverage Service for high-density static gridded data, and Unidata’s CDM-remote for point time series. OGC WFS and Sensor Observation Service (SOS) are being explored as mechanisms to serve and access static or time series data attributed to vector geometry. A set of standardized XML-based output formats allows easy transformation into a wide variety of “model-ready” formats. Interested users will have the option of submitting custom transformations to the GDP or transforming the XML output as a post-process. The GDP project aims to support simple, rapid development of thin user interfaces (like web portals) to commonly needed environmental modeling-related data access and manipulation tools. Standalone, service-oriented components of the GDP framework provide the metadata cataloging, data subset access, and spatial-statistics calculations needed to support interdisciplinary environmental modeling.

Dynamic online surveys and experiments with the free open-source software dynQuest.

PubMed

Rademacher, Jens D M; Lippke, Sonia

2007-08-01

With computers and the World Wide Web widely available, collecting data through Web browsers is an attractive method utilized by the social sciences. In this article, conducting PC- and Web-based trials with the software package dynQuest is described. The software manages dynamic questionnaire-based trials over the Internet or on single computers, possibly as randomized control trials (RCT), if two or more groups are involved. The choice of follow-up questions can depend on previous responses, as needed for matched interventions. Data are collected in a simple text-based database that can be imported easily into other programs for postprocessing and statistical analysis. The software consists of platform-independent scripts written in the programming language PERL that use the common gateway interface between Web browser and server for submission of data through HTML forms. Advantages of dynQuest are parsimony, simplicity in use and installation, transparency, and reliability. The program is available as open-source freeware from the authors.

Clinician accessible tools for GUI computational models of transcranial electrical stimulation: BONSAI and SPHERES.

PubMed

Truong, Dennis Q; Hüber, Mathias; Xie, Xihe; Datta, Abhishek; Rahman, Asif; Parra, Lucas C; Dmochowski, Jacek P; Bikson, Marom

2014-01-01

Computational models of brain current flow during transcranial electrical stimulation (tES), including transcranial direct current stimulation (tDCS) and transcranial alternating current stimulation (tACS), are increasingly used to understand and optimize clinical trials. We propose that broad dissemination requires a simple graphical user interface (GUI) software that allows users to explore and design montages in real-time, based on their own clinical/experimental experience and objectives. We introduce two complimentary open-source platforms for this purpose: BONSAI and SPHERES. BONSAI is a web (cloud) based application (available at neuralengr.com/bonsai) that can be accessed through any flash-supported browser interface. SPHERES (available at neuralengr.com/spheres) is a stand-alone GUI application that allow consideration of arbitrary montages on a concentric sphere model by leveraging an analytical solution. These open-source tES modeling platforms are designed go be upgraded and enhanced. Trade-offs between open-access approaches that balance ease of access, speed, and flexibility are discussed. Copyright © 2014 Elsevier Inc. All rights reserved.

EnviroAtlas Webinar

EPA Pesticide Factsheets

EnviroAtlas is a web-based decision support tool that combines maps, analysis tools, downloadable data and informational resources that states, tribes and communities can use to help inform policy and planning decisions impacting their surroundings.

HydroDesktop: An Open Source GIS-Based Platform for Hydrologic Data Discovery, Visualization, and Analysis

NASA Astrophysics Data System (ADS)

Ames, D. P.; Kadlec, J.; Cao, Y.; Grover, D.; Horsburgh, J. S.; Whiteaker, T.; Goodall, J. L.; Valentine, D. W.

2010-12-01

A growing number of hydrologic information servers are being deployed by government agencies, university networks, and individual researchers using the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) Hydrologic Information System (HIS). The CUAHSI HIS Project has developed a standard software stack, called HydroServer, for publishing hydrologic observations data. It includes the Observations Data Model (ODM) database and Water Data Service web services, which together enable publication of data on the Internet in a standard format called Water Markup Language (WaterML). Metadata describing available datasets hosted on these servers is compiled within a central metadata catalog called HIS Central at the San Diego Supercomputer Center and is searchable through a set of predefined web services based queries. Together, these servers and central catalog service comprise a federated HIS of a scale and comprehensiveness never previously available. This presentation will briefly review/introduce the CUAHSI HIS system with special focus on a new HIS software tool called "HydroDesktop" and the open source software development web portal, www.HydroDesktop.org, which supports community development and maintenance of the software. HydroDesktop is a client-side, desktop software application that acts as a search and discovery tool for exploring the distributed network of HydroServers, downloading specific data series, visualizing and summarizing data series and exporting these to formats needed for analysis by external software. HydroDesktop is based on the open source DotSpatial GIS developer toolkit which provides it with map-based data interaction and visualization, and a plug-in interface that can be used by third party developers and researchers to easily extend the software using Microsoft .NET programming languages. HydroDesktop plug-ins that are presently available or currently under development within the project and by third party collaborators include functions for data search and discovery, extensive graphing, data editing and export, HydroServer exploration, integration with the OpenMI workflow and modeling system, and an interface for data analysis through the R statistical package.

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

PubMed Central

MacLean, Brendan; Tomazela, Daniela M.; Shulman, Nicholas; Chambers, Matthew; Finney, Gregory L.; Frewen, Barbara; Kern, Randall; Tabb, David L.; Liebler, Daniel C.; MacCoss, Michael J.

2010-01-01

Summary: Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. It is open source and freely available for academic and commercial use. The Skyline user interface simplifies the development of mass spectrometer methods and the analysis of data from targeted proteomics experiments performed using selected reaction monitoring (SRM). Skyline supports using and creating MS/MS spectral libraries from a wide variety of sources to choose SRM filters and verify results based on previously observed ion trap data. Skyline exports transition lists to and imports the native output files from Agilent, Applied Biosystems, Thermo Fisher Scientific and Waters triple quadrupole instruments, seamlessly connecting mass spectrometer output back to the experimental design document. The fast and compact Skyline file format is easily shared, even for experiments requiring many sample injections. A rich array of graphs displays results and provides powerful tools for inspecting data integrity as data are acquired, helping instrument operators to identify problems early. The Skyline dynamic report designer exports tabular data from the Skyline document model for in-depth analysis with common statistical tools. Availability: Single-click, self-updating web installation is available at http://proteome.gs.washington.edu/software/skyline. This web site also provides access to instructional videos, a support board, an issues list and a link to the source code project. Contact: brendanx@u.washington.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20147306

Implementing a Dynamic Database-Driven Course Using LAMP

ERIC Educational Resources Information Center

Laverty, Joseph Packy; Wood, David; Turchek, John

2011-01-01

This paper documents the formulation of a database driven open source architecture web development course. The design of a web-based curriculum faces many challenges: a) relative emphasis of client and server-side technologies, b) choice of a server-side language, and c) the cost and efficient delivery of a dynamic web development, database-driven…

Development and usability testing of a web-based decision support for users and health professionals in psychiatric services.

PubMed

Grim, Katarina; Rosenberg, David; Svedberg, Petra; Schön, Ulla-Karin

2017-09-01

Shared decision making (SMD) related to treatment and rehabilitation is considered a central component in recovery-oriented practice. Although decision aids are regarded as an essential component for successfully implementing SDM, these aids are often lacking within psychiatric services. The aim of this study was to use a participatory design to facilitate the development of a user-generated, web-based decision aid for individuals receiving psychiatric services. The results of this effort as well as the lessons learned during the development and usability processes are reported. The participatory design included 4 iterative cycles of development. Various qualitative methods for data collection were used with potential end users participating as informants in focus group and individual interviews and as usability and pilot testers. Interviewing and testing identified usability problems that then led to refinements and making the subsequent prototypes increasingly user-friendly and relevant. In each phase of the process, feedback from potential end-users provided guidance in developing the formation of the web-based decision aid that strengthens the position of users by integrating access to information regarding alternative supports, interactivity between staff and users, and user preferences as a continual focus in the tool. This web-based decision aid has the potential to strengthen service users' experience of self-efficacy and control as well as provide staff access to user knowledge and preferences. Studies employing participatory models focusing on usability have potential to significantly contribute to the development and implementation of tools that reflect user perspectives. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Data-driven decision support for radiologists: re-using the National Lung Screening Trial dataset for pulmonary nodule management.

PubMed

Morrison, James J; Hostetter, Jason; Wang, Kenneth; Siegel, Eliot L

2015-02-01

Real-time mining of large research trial datasets enables development of case-based clinical decision support tools. Several applicable research datasets exist including the National Lung Screening Trial (NLST), a dataset unparalleled in size and scope for studying population-based lung cancer screening. Using these data, a clinical decision support tool was developed which matches patient demographics and lung nodule characteristics to a cohort of similar patients. The NLST dataset was converted into Structured Query Language (SQL) tables hosted on a web server, and a web-based JavaScript application was developed which performs real-time queries. JavaScript is used for both the server-side and client-side language, allowing for rapid development of a robust client interface and server-side data layer. Real-time data mining of user-specified patient cohorts achieved a rapid return of cohort cancer statistics and lung nodule distribution information. This system demonstrates the potential of individualized real-time data mining using large high-quality clinical trial datasets to drive evidence-based clinical decision-making.

The Shared Decision Making Frontier: a Feasibility and Usability Study for Managing Non-Critical Chronic Illness by Combining Behavioural & Decision Theory with Online Technology.

PubMed

Russell, Amina; Van Woensel, William; Abidi, Samina Raza

2015-01-01

The objective of this study is to determine if shared decisions for managing non-critical chronic illness, made through an online biomedical technology intervention, us feasible and usable. The technology intervention incorporates behavioural and decision theories to increase patient engagement, and ultimately long term adherence to health behaviour change. We devised the iheart web intervention as a "proof of concept" in five phases. The implementation incorporates the Vaadin web application framework, Drools, EclipseLink and a MySQL database. Two-thirds of the study participants favoured the technology intervention, based on Likert-scale questions from a post-study questionnaire. Qualitative analysis of think aloud feedback, video screen captures and open-ended questions from the post-study questionnaire uncovered six main areas or themes for improvement. We conclude that online shared decisions for managing a non-critical chronic illness are feasible and usable through the iheart web intervention.

SensorWeb Hub infrastructure for open access to scientific research data

NASA Astrophysics Data System (ADS)

de Filippis, Tiziana; Rocchi, Leandro; Rapisardi, Elena

2015-04-01

The sharing of research data is a new challenge for the scientific community that may benefit from a large amount of information to solve environmental issues and sustainability in agriculture and urban contexts. Prerequisites for this challenge is the development of an infrastructure that ensure access, management and preservation of data, technical support for a coordinated and harmonious management of data that, in the framework of Open Data Policies, should encourages the reuse and the collaboration. The neogeography and the citizen as sensors approach, highlight that new data sources need a new set of tools and practices so to collect, validate, categorize, and use / access these "crowdsourced" data, that integrate the data sets produced in the scientific field, thus "feeding" the overall available data for analysis and research. When the scientific community embraces the dimension of collaboration and sharing, access and re-use, in order to accept the open innovation approach, it should redesign and reshape the processes of data management: the challenges of technological and cultural innovation, enabled by web 2.0 technologies, bring to the scenario where the sharing of structured and interoperable data will constitute the unavoidable building block to set up a new paradigm of scientific research. In this perspective the Institute of Biometeorology, CNR, whose aim is contributing to sharing and development of research data, has developed the "SensorWebHub" (SWH) infrastructure to support the scientific activities carried out in several research projects at national and international level. It is designed to manage both mobile and fixed open source meteorological and environmental sensors, in order to integrate the existing agro-meteorological and urban monitoring networks. The proposed architecture uses open source tools to ensure sustainability in the development and deployment of web applications with geographic features and custom analysis, as requested by the different research projects. The SWH components are organized in typical client-server architecture and interact from the sensing process to the representation of the results to the end-users. The Web Application enables to view and analyse the data stored in the GeoDB. The interface is designed following Internet browsers specifications allowing the visualization of collected data in different formats (tabular, chart and geographic map). The services for the dissemination of geo-referenced information, adopt the OGC specifications. SWH is a bottom-up collaborative initiative to share real time research data and pave the way for a open innovation approach in the scientific research. Until now this framework has been used for several WebGIS applications and WebApp for environmental monitoring at different temporal and spatial scales.

Developing an electronic health record (EHR) for methadone treatment recording and decision support

PubMed Central

2011-01-01

Background In this paper, we give an overview of methadone treatment in Ireland and outline the rationale for designing an electronic health record (EHR) with extensibility, interoperability and decision support functionality. Incorporating several international standards, a conceptual model applying a problem orientated approach in a hierarchical structure has been proposed for building the EHR. Methods A set of archetypes has been designed in line with the current best practice and clinical guidelines which guide the information-gathering process. A web-based data entry system has been implemented, incorporating elements of the paper-based prescription form, while at the same time facilitating the decision support function. Results The use of archetypes was found to capture the ever changing requirements in the healthcare domain and externalises them in constrained data structures. The solution is extensible enabling the EHR to cover medicine management in general as per the programme of the HRB Centre for Primary Care Research. Conclusions The data collected via this Irish system can be aggregated into a larger dataset, if necessary, for analysis and evidence-gathering, since we adopted the openEHR standard. It will be later extended to include the functionalities of prescribing drugs other than methadone along with the research agenda at the HRB Centre for Primary Care Research in Ireland. PMID:21284849

DEIVA: a web application for interactive visual analysis of differential gene expression profiles.

PubMed

Harshbarger, Jayson; Kratz, Anton; Carninci, Piero

2017-01-07

Differential gene expression (DGE) analysis is a technique to identify statistically significant differences in RNA abundance for genes or arbitrary features between different biological states. The result of a DGE test is typically further analyzed using statistical software, spreadsheets or custom ad hoc algorithms. We identified a need for a web-based system to share DGE statistical test results, and locate and identify genes in DGE statistical test results with a very low barrier of entry. We have developed DEIVA, a free and open source, browser-based single page application (SPA) with a strong emphasis on being user friendly that enables locating and identifying single or multiple genes in an immediate, interactive, and intuitive manner. By design, DEIVA scales with very large numbers of users and datasets. Compared to existing software, DEIVA offers a unique combination of design decisions that enable inspection and analysis of DGE statistical test results with an emphasis on ease of use.

3D-Lab: a collaborative web-based platform for molecular modeling.

PubMed

Grebner, Christoph; Norrby, Magnus; Enström, Jonatan; Nilsson, Ingemar; Hogner, Anders; Henriksson, Jonas; Westin, Johan; Faramarzi, Farzad; Werner, Philip; Boström, Jonas

2016-09-01

The use of 3D information has shown impact in numerous applications in drug design. However, it is often under-utilized and traditionally limited to specialists. We want to change that, and present an approach making 3D information and molecular modeling accessible and easy-to-use 'for the people'. A user-friendly and collaborative web-based platform (3D-Lab) for 3D modeling, including a blazingly fast virtual screening capability, was developed. 3D-Lab provides an interface to automatic molecular modeling, like conformer generation, ligand alignments, molecular dockings and simple quantum chemistry protocols. 3D-Lab is designed to be modular, and to facilitate sharing of 3D-information to promote interactions between drug designers. Recent enhancements to our open-source virtual reality tool Molecular Rift are described. The integrated drug-design platform allows drug designers to instantaneously access 3D information and readily apply advanced and automated 3D molecular modeling tasks, with the aim to improve decision-making in drug design projects.

Embodying Our Values in Our Teaching Practices: Building Open and Critical Discourse through Computer Mediated Communication

ERIC Educational Resources Information Center

Geelan, David R.; Taylor, Peter C.

2004-01-01

Computer mediated communication--including web pages, email and web-based bulletin boards--was used to support the development of a cooperative learning community among students in a web-based distance education unit for practicing science and mathematics educators. The students lived in several Australian states and a number of Pacific Rim…

Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities

PubMed Central

2010-01-01

Background Shared-usage high throughput screening (HTS) facilities are becoming more common in academe as large-scale small molecule and genome-scale RNAi screening strategies are adopted for basic research purposes. These shared facilities require a unique informatics infrastructure that must not only provide access to and analysis of screening data, but must also manage the administrative and technical challenges associated with conducting numerous, interleaved screening efforts run by multiple independent research groups. Results We have developed Screensaver, a free, open source, web-based lab information management system (LIMS), to address the informatics needs of our small molecule and RNAi screening facility. Screensaver supports the storage and comparison of screening data sets, as well as the management of information about screens, screeners, libraries, and laboratory work requests. To our knowledge, Screensaver is one of the first applications to support the storage and analysis of data from both genome-scale RNAi screening projects and small molecule screening projects. Conclusions The informatics and administrative needs of an HTS facility may be best managed by a single, integrated, web-accessible application such as Screensaver. Screensaver has proven useful in meeting the requirements of the ICCB-Longwood/NSRB Screening Facility at Harvard Medical School, and has provided similar benefits to other HTS facilities. PMID:20482787

Migrating a lecture in nursing informatics to a blended learning format--A bottom-up approach to implement an open-source web-based learning management system.

PubMed

Schrader, Ulrich

2006-01-01

At the university of applied sciences in Germany a learning management system has been implemented. The migration of classic courses to a web-enhances curriculum can be categorized into three phases independent of the technology used. The first two phases "dedicated website" and "database supported content management system" are mainly concerned with bringing the learning material and current information online and making it available to the students. The goal is here to make the maintenance of the learning material easier. The third phase characterized by the use of a learning management system offers the support of more modern didactic principles like social constructionism or problem-oriented learning. In this papers the phases as they occurred with the migration of a course of nursing informatics are described and experiences discussed.. The absence of institutional goals associated with the use of a learning management system led to a bottom-up approach triggered by faculty activities that can be described by a promoter model rather than by a process management model. The use of an open source learning management systems made this process easier to realize since no financial commitment is required up front.

Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities.

PubMed

Tolopko, Andrew N; Sullivan, John P; Erickson, Sean D; Wrobel, David; Chiang, Su L; Rudnicki, Katrina; Rudnicki, Stewart; Nale, Jennifer; Selfors, Laura M; Greenhouse, Dara; Muhlich, Jeremy L; Shamu, Caroline E

2010-05-18

Shared-usage high throughput screening (HTS) facilities are becoming more common in academe as large-scale small molecule and genome-scale RNAi screening strategies are adopted for basic research purposes. These shared facilities require a unique informatics infrastructure that must not only provide access to and analysis of screening data, but must also manage the administrative and technical challenges associated with conducting numerous, interleaved screening efforts run by multiple independent research groups. We have developed Screensaver, a free, open source, web-based lab information management system (LIMS), to address the informatics needs of our small molecule and RNAi screening facility. Screensaver supports the storage and comparison of screening data sets, as well as the management of information about screens, screeners, libraries, and laboratory work requests. To our knowledge, Screensaver is one of the first applications to support the storage and analysis of data from both genome-scale RNAi screening projects and small molecule screening projects. The informatics and administrative needs of an HTS facility may be best managed by a single, integrated, web-accessible application such as Screensaver. Screensaver has proven useful in meeting the requirements of the ICCB-Longwood/NSRB Screening Facility at Harvard Medical School, and has provided similar benefits to other HTS facilities.

Cardiac catheterization laboratory inpatient forecast tool: a prospective evaluation

PubMed Central

Flanagan, Eleni; Siddiqui, Sauleh; Appelbaum, Jeff; Kasper, Edward K; Levin, Scott

2016-01-01

Objective To develop and prospectively evaluate a web-based tool that forecasts the daily bed need for admissions from the cardiac catheterization laboratory using routinely available clinical data within electronic medical records (EMRs). Methods The forecast model was derived using a 13-month retrospective cohort of 6384 catheterization patients. Predictor variables such as demographics, scheduled procedures, and clinical indicators mined from free-text notes were input to a multivariable logistic regression model that predicted the probability of inpatient admission. The model was embedded into a web-based application connected to the local EMR system and used to support bed management decisions. After implementation, the tool was prospectively evaluated for accuracy on a 13-month test cohort of 7029 catheterization patients. Results The forecast model predicted admission with an area under the receiver operating characteristic curve of 0.722. Daily aggregate forecasts were accurate to within one bed for 70.3% of days and within three beds for 97.5% of days during the prospective evaluation period. The web-based application housing the forecast model was used by cardiology providers in practice to estimate daily admissions from the catheterization laboratory. Discussion The forecast model identified older age, male gender, invasive procedures, coronary artery bypass grafts, and a history of congestive heart failure as qualities indicating a patient was at increased risk for admission. Diagnostic procedures and less acute clinical indicators decreased patients’ risk of admission. Despite the site-specific limitations of the model, these findings were supported by the literature. Conclusion Data-driven predictive analytics may be used to accurately forecast daily demand for inpatient beds for cardiac catheterization patients. Connecting these analytics to EMR data sources has the potential to provide advanced operational decision support. PMID:26342217

A Comparison of Web-Based and Paper-and-Pencil Homework on Student Performance in College Algebra

ERIC Educational Resources Information Center

Hauk, Shandy; Powers, Robert A.; Segalla, Angelo

2015-01-01

College algebra fulfills general education requirements at many colleges in the United States. The study reported here investigated differences in mathematics achievement between undergraduates in college algebra classes using one of two homework methods: "WeBWorK," an open-source system for web-based homework, or traditional…

Supporting Open Access to European Academic Courses: The ASK-CDM-ECTS Tool

ERIC Educational Resources Information Center

Sampson, Demetrios G.; Zervas, Panagiotis

2013-01-01

Purpose: This paper aims to present and evaluate a web-based tool, namely ASK-CDM-ECTS, which facilitates authoring and publishing on the web descriptions of (open) academic courses in machine-readable format using an application profile of the Course Description Metadata (CDM) specification, namely CDM-ECTS. Design/methodology/approach: The paper…

Development of a Web-Based Registry to Support Diabetes Care in Free Medical Clinics.

PubMed

McFadden, Norman; Daniel, Bryan; Hoyt, Robert; Snider, Dallas

2017-01-01

The United States has more than 1,000 free medical clinics. Because these clinics do not bill Medicare or Medicaid, they are not eligible for federal reimbursement for electronic health record (EHR) adoption. As a result, most do not have EHRs or electronic disease registries. A web-based diabetes registry was created with all open-source components for use in an urban free clinic to manage patients with type 2 diabetes and comorbidities. The registry was modeled after the Chronic Disease Electronic Management System and recommendations of the American Diabetes Association. The software was enhanced to include multiple other features, such as progress notes, so that it can function as a simple EHR. The configuration permits other free clinics to join securely, and the software can be shared.

Foundations for context-aware information retrieval for proactive decision support

NASA Astrophysics Data System (ADS)

Mittu, Ranjeev; Lin, Jessica; Li, Qingzhe; Gao, Yifeng; Rangwala, Huzefa; Shargo, Peter; Robinson, Joshua; Rose, Carolyn; Tunison, Paul; Turek, Matt; Thomas, Stephen; Hanselman, Phil

2016-05-01

Intelligence analysts and military decision makers are faced with an onslaught of information. From the now ubiquitous presence of intelligence, surveillance, and reconnaissance (ISR) platforms providing large volumes of sensor data, to vast amounts of open source data in the form of news reports, blog postings, or social media postings, the amount of information available to a modern decision maker is staggering. Whether tasked with leading a military campaign or providing support for a humanitarian mission, being able to make sense of all the information available is a challenge. Due to the volume and velocity of this data, automated tools are required to help support reasoned, human decisions. In this paper we describe several automated techniques that are targeted at supporting decision making. Our approaches include modeling the kinematics of moving targets as motifs; developing normalcy models and detecting anomalies in kinematic data; automatically classifying the roles of users in social media; and modeling geo-spatial regions based on the behavior that takes place in them. These techniques cover a wide-range of potential decision maker needs.

Application of WebGIS for traffic risk assessment

NASA Astrophysics Data System (ADS)

Voumard, Jérémie; Aye, Zar Chi; Derron, Marc-Henri; Jaboyedoff, Michel

2015-04-01

Roads and railways are threatened throughout the year by several natural hazards around the world, leading to the closing of transportation corridors, loss of access, deviation travels and potentially infrastructures damages and loss of human lives and also financial, social and economic consequences. Protection measures used to reduce the exposure to natural hazards are usually expensive and cannot be deployed on an entire transportation network. It is thus necessary to choose priority areas where protection measures need to be built. The aim of this study is to propose a friendly tool to evaluate and to understand issues and consequences of section closing and affected parts of a transportation network at small region scale. The proposed tool, currently in its design and building phase, will provide ways to simulate different closure scenarios and to analyze their consequences on transportation network; like deviating traffic on others roads and railways sections, additional time and distance travel or accessibility for emergency services like police, firefighters and ambulances. The tool is based on OpenGeo architecture, which is composed of open-source components. It integrates PostGIS for database, GeoServer and GeoWebCache for application servers and finally GeoExt and OpenLayers for user interface. Users will be able to attribute quantitative (like roads and railway type and closure consequences) and qualitative (like section unavailability duration, season, etc.) data to the different roads and railways sections based on their user rights. They will also be able to evaluate different track closures consequences in terms of different scenarios. Once finalized, the goal of this project including natural hazards, traffic and geomatic thematic is to propose a decision support tool for public authorities firstly and for specialists secondly so that they can evaluate easily and accurately as much as possible to highlight the weakpoints of the transportation network in the case track closures due to natural hazards.

A web access script language to support clinical application development.

PubMed

O'Kane, K C; McColligan, E E

1998-02-01

This paper describes the development of a script language to support the implementation of decentralized, clinical information applications on the World Wide Web (Web). The goal of this work is to facilitate construction of low overhead, fully functional clinical information systems that can be accessed anywhere by low cost Web browsers to search, retrieve and analyze stored patient data. The Web provides a model of network access to data bases on a global scale. Although it was originally conceived as a means to exchange scientific documents, Web browsers and servers currently support access to a wide variety of audio, video, graphical and text based data to a rapidly growing community. Access to these services is via inexpensive client software browsers that connect to servers by means of the open architecture of the Internet. In this paper, the design and implementation of a script language that supports the development of low cost, Web-based, distributed clinical information systems for both Inter- and Intra-Net use is presented. The language is based on the Mumps language and, consequently, supports many legacy applications with few modifications. Several enhancements, however, have been made to support modern programming practices and the Web interface. The interpreter for the language also supports standalone program execution on Unix, MS-Windows, OS/2 and other operating systems.

Web Monitoring of EOS Front-End Ground Operations, Science Downlinks and Level 0 Processing

NASA Technical Reports Server (NTRS)

Cordier, Guy R.; Wilkinson, Chris; McLemore, Bruce

2008-01-01

This paper addresses the efforts undertaken and the technology deployed to aggregate and distribute the metadata characterizing the real-time operations associated with NASA Earth Observing Systems (EOS) high-rate front-end systems and the science data collected at multiple ground stations and forwarded to the Goddard Space Flight Center for level 0 processing. Station operators, mission project management personnel, spacecraft flight operations personnel and data end-users for various EOS missions can retrieve the information at any time from any location having access to the internet. The users are distributed and the EOS systems are distributed but the centralized metadata accessed via an external web server provide an effective global and detailed view of the enterprise-wide events as they are happening. The data-driven architecture and the implementation of applied middleware technology, open source database, open source monitoring tools, and external web server converge nicely to fulfill the various needs of the enterprise. The timeliness and content of the information provided are key to making timely and correct decisions which reduce project risk and enhance overall customer satisfaction. The authors discuss security measures employed to limit access of data to authorized users only.

Tatool: a Java-based open-source programming framework for psychological studies.

PubMed

von Bastian, Claudia C; Locher, André; Ruflin, Michael

2013-03-01

Tatool (Training and Testing Tool) was developed to assist researchers with programming training software, experiments, and questionnaires. Tatool is Java-based, and thus is a platform-independent and object-oriented framework. The architecture was designed to meet the requirements of experimental designs and provides a large number of predefined functions that are useful in psychological studies. Tatool comprises features crucial for training studies (e.g., configurable training schedules, adaptive training algorithms, and individual training statistics) and allows for running studies online via Java Web Start. The accompanying "Tatool Online" platform provides the possibility to manage studies and participants' data easily with a Web-based interface. Tatool is published open source under the GNU Lesser General Public License, and is available at www.tatool.ch.

Web-based GIS for collaborative planning and public participation: an application to the strategic planning of wind farm sites.

PubMed

Simão, Ana; Densham, Paul J; Haklay, Mordechai Muki

2009-05-01

Spatial planning typically involves multiple stakeholders. To any specific planning problem, stakeholders often bring different levels of knowledge about the components of the problem and make assumptions, reflecting their individual experiences, that yield conflicting views about desirable planning outcomes. Consequently, stakeholders need to learn about the likely outcomes that result from their stated preferences; this learning can be supported through enhanced access to information, increased public participation in spatial decision-making and support for distributed collaboration amongst planners, stakeholders and the public. This paper presents a conceptual system framework for web-based GIS that supports public participation in collaborative planning. The framework combines an information area, a Multi-Criteria Spatial Decision Support System (MC-SDSS) and an argumentation map to support distributed and asynchronous collaboration in spatial planning. After analysing the novel aspects of this framework, the paper describes its implementation, as a proof of concept, in a system for Web-based Participatory Wind Energy Planning (WePWEP). Details are provided on the specific implementation of each of WePWEP's four tiers, including technical and structural aspects. Throughout the paper, particular emphasis is placed on the need to support user learning throughout the planning process.

An Open Source Tool to Test Interoperability

NASA Astrophysics Data System (ADS)

Bermudez, L. E.

2012-12-01

Scientists interact with information at various levels from gathering of the raw observed data to accessing portrayed processed quality control data. Geoinformatics tools help scientist on the acquisition, storage, processing, dissemination and presentation of geospatial information. Most of the interactions occur in a distributed environment between software components that take the role of either client or server. The communication between components includes protocols, encodings of messages and managing of errors. Testing of these communication components is important to guarantee proper implementation of standards. The communication between clients and servers can be adhoc or follow standards. By following standards interoperability between components increase while reducing the time of developing new software. The Open Geospatial Consortium (OGC), not only coordinates the development of standards but also, within the Compliance Testing Program (CITE), provides a testing infrastructure to test clients and servers. The OGC Web-based Test Engine Facility, based on TEAM Engine, allows developers to test Web services and clients for correct implementation of OGC standards. TEAM Engine is a JAVA open source facility, available at Sourceforge that can be run via command line, deployed in a web servlet container or integrated in developer's environment via MAVEN. The TEAM Engine uses the Compliance Test Language (CTL) and TestNG to test HTTP requests, SOAP services and XML instances against Schemas and Schematron based assertions of any type of web service, not only OGC services. For example, the OGC Web Feature Service (WFS) 1.0.0 test has more than 400 test assertions. Some of these assertions includes conformance of HTTP responses, conformance of GML-encoded data; proper values for elements and attributes in the XML; and, correct error responses. This presentation will provide an overview of TEAM Engine, introduction of how to test via the OGC Testing web site and description of performing local tests. It will also provide information about how to participate in the open source code development of TEAM Engine.

STRAD Wheel: Web-Based Library for Visualizing Temporal Data.

PubMed

Fernondez-Prieto, Diana; Naranjo-Valero, Carol; Hernandez, Jose Tiberio; Hagen, Hans

2017-01-01

Recent advances in web development, including the introduction of HTML5, have opened a door for visualization researchers and developers to quickly access larger audiences worldwide. Open source libraries for the creation of interactive visualizations are becoming more specialized but also modular, which makes them easy to incorporate in domain-specific applications. In this context, the authors developed STRAD (Spatio-Temporal-Radar) Wheel, a web-based library that focuses on the visualization and interactive query of temporal data in a compact view with multiple temporal granularities. This article includes two application examples in urban planning to help illustrate the proposed visualization's use in practice.

Spatial Information Processing: Standards-Based Open Source Visualization Technology

NASA Astrophysics Data System (ADS)

Hogan, P.

2009-12-01

. Spatial information intelligence is a global issue that will increasingly affect our ability to survive as a species. Collectively we must better appreciate the complex relationships that make life on Earth possible. Providing spatial information in its native context can accelerate our ability to process that information. To maximize this ability to process information, three basic elements are required: data delivery (server technology), data access (client technology), and data processing (information intelligence). NASA World Wind provides open source client and server technologies based on open standards. The possibilities for data processing and data sharing are enhanced by this inclusive infrastructure for geographic information. It is interesting that this open source and open standards approach, unfettered by proprietary constraints, simultaneously provides for entirely proprietary use of this same technology. 1. WHY WORLD WIND? NASA World Wind began as a single program with specific functionality, to deliver NASA content. But as the possibilities for virtual globe technology became more apparent, we found that while enabling a new class of information technology, we were also getting in the way. Researchers, developers and even users expressed their desire for World Wind functionality in ways that would service their specific needs. They want it in their web pages. They want to add their own features. They want to manage their own data. They told us that only with this kind of flexibility, could their objectives and the potential for this technology be truly realized. World Wind client technology is a set of development tools, a software development kit (SDK) that allows a software engineer to create applications requiring geographic visualization technology. 2. MODULAR COMPONENTRY Accelerated evolution of a technology requires that the essential elements of that technology be modular components such that each can advance independent of the other elements. World Wind therefore changed its mission from providing a single information browser to enabling a whole class of 3D geographic applications. Instead of creating a single program, World Wind is a suite of components that can be selectively used in any number of programs. World Wind technology can be a part of any application, or it can be a window in a web page. Or it can be extended with additional functionalities by application and web developers. World Wind makes it possible to include virtual globe visualization and server technology in support of any objective. The world community can continually benefit from advances made in the technology by NASA in concert with the world community. 3. OPEN SOURCE AND OPEN STANDARDS NASA World Wind is NASA Open Source software. This means that the source code is fully accessible for anyone to freely use, even in association with proprietary technology. Imagery and other data provided by the World Wind servers reside in the public domain, including the data server technology itself. This allows others to deliver their own geospatial data and to provide custom solutions based on users specific needs.

A discussion for integrating INSPIRE with volunteered geographic information (VGI) and the vision for a global spatial-based platform

NASA Astrophysics Data System (ADS)

Demetriou, Demetris; Campagna, Michele; Racetin, Ivana; Konecny, Milan

2017-09-01

INSPIRE is the EU's authoritative Spatial Data Infrastructure (SDI) in which each Member State provides access to their spatial data across a wide spectrum of data themes to support policy making. In contrast, Volunteered Geographic Information (VGI) is one type of user-generated geographic information where volunteers use the web and mobile devices to create, assemble and disseminate spatial information. There are similarities and differences between SDIs and VGI initiatives, as well as advantages and disadvantages. Thus, the integration of these two data sources will enhance what is offered to end users to facilitate decision makers and the wider community regarding solving complex spatial problems, managing emergency situations and getting useful information for peoples' daily activities. Although some efforts towards this direction have been arisen, several key issues need to be considered and resolved. Further to this integration, the vision is the development of a global integrated GIS platform, which extends the capabilities of a typical data-hub by embedding on-line spatial and non-spatial applications, to deliver both static and dynamic outputs to support planning and decision making. In this context, this paper discusses the challenges of integrating INSPIRE with VGI and outlines a generic framework towards creating a global integrated web-based GIS platform. The tremendous high speed evolution of the Web and Geospatial technologies suggest that this "super" global Geo-system is not far away.

Using Semantic Web technologies for the generation of domain-specific templates to support clinical study metadata standards.

PubMed

Jiang, Guoqian; Evans, Julie; Endle, Cory M; Solbrig, Harold R; Chute, Christopher G

2016-01-01

The Biomedical Research Integrated Domain Group (BRIDG) model is a formal domain analysis model for protocol-driven biomedical research, and serves as a semantic foundation for application and message development in the standards developing organizations (SDOs). The increasing sophistication and complexity of the BRIDG model requires new approaches to the management and utilization of the underlying semantics to harmonize domain-specific standards. The objective of this study is to develop and evaluate a Semantic Web-based approach that integrates the BRIDG model with ISO 21090 data types to generate domain-specific templates to support clinical study metadata standards development. We developed a template generation and visualization system based on an open source Resource Description Framework (RDF) store backend, a SmartGWT-based web user interface, and a "mind map" based tool for the visualization of generated domain-specific templates. We also developed a RESTful Web Service informed by the Clinical Information Modeling Initiative (CIMI) reference model for access to the generated domain-specific templates. A preliminary usability study is performed and all reviewers (n = 3) had very positive responses for the evaluation questions in terms of the usability and the capability of meeting the system requirements (with the average score of 4.6). Semantic Web technologies provide a scalable infrastructure and have great potential to enable computable semantic interoperability of models in the intersection of health care and clinical research.

A New Data Management System for Biological and Chemical Oceanography

NASA Astrophysics Data System (ADS)

Groman, R. C.; Chandler, C.; Allison, D.; Glover, D. M.; Wiebe, P. H.

2007-12-01

The Biological and Chemical Oceanography Data Management Office (BCO-DMO) was created to serve PIs principally funded by NSF to conduct marine chemical and ecological research. The new office is dedicated to providing open access to data and information developed in the course of scientific research on short and intermediate time-frames. The data management system developed in support of U.S. JGOFS and U.S. GLOBEC programs is being modified to support the larger scope of the BCO-DMO effort, which includes ultimately providing a way to exchange data with other data systems. The open access system is based on a philosophy of data stewardship, support for existing and evolving data standards, and use of public domain software. The DMO staff work closely with originating PIs to manage data gathered as part of their individual programs. In the new BCO-DMO data system, project and data set metadata records designed to support re-use of the data are stored in a relational database (MySQL) and the data are stored in or made accessible by the JGOFS/GLOBEC object- oriented, relational, data management system. Data access will be provided via any standard Web browser client user interface through a GIS application (Open Source, OGC-compliant MapServer), a directory listing from the data holdings catalog, or a custom search engine that facilitates data discovery. In an effort to maximize data system interoperability, data will also be available via Web Services; and data set descriptions will be generated to comply with a variety of metadata content standards. The office is located at the Woods Hole Oceanographic Institution and web access is via http://www.bco-dmo.org.

The Simple Concurrent Online Processing System (SCOPS) - An open-source interface for remotely sensed data processing

NASA Astrophysics Data System (ADS)

Warren, M. A.; Goult, S.; Clewley, D.

2018-06-01

Advances in technology allow remotely sensed data to be acquired with increasingly higher spatial and spectral resolutions. These data may then be used to influence government decision making and solve a number of research and application driven questions. However, such large volumes of data can be difficult to handle on a single personal computer or on older machines with slower components. Often the software required to process data is varied and can be highly technical and too advanced for the novice user to fully understand. This paper describes an open-source tool, the Simple Concurrent Online Processing System (SCOPS), which forms part of an airborne hyperspectral data processing chain that allows users accessing the tool over a web interface to submit jobs and process data remotely. It is demonstrated using Natural Environment Research Council Airborne Research Facility (NERC-ARF) instruments together with other free- and open-source tools to take radiometrically corrected data from sensor geometry into geocorrected form and to generate simple or complex band ratio products. The final processed data products are acquired via an HTTP download. SCOPS can cut data processing times and introduce complex processing software to novice users by distributing jobs across a network using a simple to use web interface.

VisBOL: Web-Based Tools for Synthetic Biology Design Visualization.

PubMed

McLaughlin, James Alastair; Pocock, Matthew; Mısırlı, Göksel; Madsen, Curtis; Wipat, Anil

2016-08-19

VisBOL is a Web-based application that allows the rendering of genetic circuit designs, enabling synthetic biologists to visually convey designs in SBOL visual format. VisBOL designs can be exported to formats including PNG and SVG images to be embedded in Web pages, presentations and publications. The VisBOL tool enables the automated generation of visualizations from designs specified using the Synthetic Biology Open Language (SBOL) version 2.0, as well as a range of well-known bioinformatics formats including GenBank and Pigeoncad notation. VisBOL is provided both as a user accessible Web site and as an open-source (BSD) JavaScript library that can be used to embed diagrams within other content and software.

Employing Virtual Humans for Education and Training in X3D/VRML Worlds

ERIC Educational Resources Information Center

Ieronutti, Lucio; Chittaro, Luca

2007-01-01

Web-based education and training provides a new paradigm for imparting knowledge; students can access the learning material anytime by operating remotely from any location. Web3D open standards, such as X3D and VRML, support Web-based delivery of Educational Virtual Environments (EVEs). EVEs have a great potential for learning and training…

Crowdsourcing, citizen sensing and Sensor Web technologies for public and environmental health surveillance and crisis management: trends, OGC standards and application examples

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kamel Boulos, Maged; Resch, Bernd; Crowley, David N.

The PIE Activity Awareness Environment is designed to be an adaptive data triage and decision support tool that allows role and activity based situation awareness through a dynamic, trainable filtering system. This paper discusses the process and methodology involved in the application as well as some of its capabilities. 'Wikification of GIS by the masses' is a phrase-term first coined by Kamel Boulos in 2005, two years earlier than Goodchild's term 'Volunteered Geographic Information'. Six years later (2005-2011), OpenStreetMap and Google Earth (GE) are now full-fledged, crowdsourced 'Wikipedias of the Earth' par excellence, with millions of users contributing their ownmore » layers to GE, attaching photos, videos, notes and even 3-D (three dimensional) models to locations in GE. From using Twitter in participatory sensing and bicycle-mounted sensors in pervasive environmental sensing, to creating a 100,000-sensor geo-mashup using Semantic Web technology, to the 3-D visualisation of indoor and outdoor surveillance data in real-time and the development of next-generation, collaborative natural user interfaces that will power the spatially-enabled public health and emergency situation rooms of the future, where sensor data and citizen reports can be triaged and acted upon in real-time by distributed teams of professionals, this paper offers a comprehensive state-of-the-art review of the overlapping domains of the Sensor Web, citizen sensing and 'human-in-the-loop sensing' in the era of the Mobile and Social Web, and the roles these domains can play in environmental and public health surveillance and crisis/disaster informatics. We provide an in-depth review of the key issues and trends in these areas, the challenges faced when reasoning and making decisions with real-time crowdsourced data (such as issues of information overload, 'noise', misinformation, bias and trust), the core technologies and Open Geospatial Consortium (OGC) standards involved (Sensor Web Enablement and Open GeoSMS), as well as a few outstanding project implementation examples from around the world.« less

Development of a real-time clinical decision support system upon the web mvc-based architecture for prostate cancer treatment

PubMed Central

2011-01-01

Background A real-time clinical decision support system (RTCDSS) with interactive diagrams enables clinicians to instantly and efficiently track patients' clinical records (PCRs) and improve their quality of clinical care. We propose a RTCDSS to process online clinical informatics from multiple databases for clinical decision making in the treatment of prostate cancer based on Web Model-View-Controller (MVC) architecture, by which the system can easily be adapted to different diseases and applications. Methods We designed a framework upon the Web MVC-based architecture in which the reusable and extractable models can be conveniently adapted to other hospital information systems and which allows for efficient database integration. Then, we determined the clinical variables of the prostate cancer treatment based on participating clinicians' opinions and developed a computational model to determine the pretreatment parameters. Furthermore, the components of the RTCDSS integrated PCRs and decision factors for real-time analysis to provide evidence-based diagrams upon the clinician-oriented interface for visualization of treatment guidance and health risk assessment. Results The resulting system can improve quality of clinical treatment by allowing clinicians to concurrently analyze and evaluate the clinical markers of prostate cancer patients with instantaneous clinical data and evidence-based diagrams which can automatically identify pretreatment parameters. Moreover, the proposed RTCDSS can aid interactions between patients and clinicians. Conclusions Our proposed framework supports online clinical informatics, evaluates treatment risks, offers interactive guidance, and provides real-time reference for decision making in the treatment of prostate cancer. The developed clinician-oriented interface can assist clinicians in conveniently presenting evidence-based information to patients and can be readily adapted to an existing hospital information system and be easily applied in other chronic diseases. PMID:21385459

Development of a real-time clinical decision support system upon the Web MVC-based architecture for prostate cancer treatment.

PubMed

Lin, Hsueh-Chun; Wu, Hsi-Chin; Chang, Chih-Hung; Li, Tsai-Chung; Liang, Wen-Miin; Wang, Jong-Yi Wang

2011-03-08

A real-time clinical decision support system (RTCDSS) with interactive diagrams enables clinicians to instantly and efficiently track patients' clinical records (PCRs) and improve their quality of clinical care. We propose a RTCDSS to process online clinical informatics from multiple databases for clinical decision making in the treatment of prostate cancer based on Web Model-View-Controller (MVC) architecture, by which the system can easily be adapted to different diseases and applications. We designed a framework upon the Web MVC-based architecture in which the reusable and extractable models can be conveniently adapted to other hospital information systems and which allows for efficient database integration. Then, we determined the clinical variables of the prostate cancer treatment based on participating clinicians' opinions and developed a computational model to determine the pretreatment parameters. Furthermore, the components of the RTCDSS integrated PCRs and decision factors for real-time analysis to provide evidence-based diagrams upon the clinician-oriented interface for visualization of treatment guidance and health risk assessment. The resulting system can improve quality of clinical treatment by allowing clinicians to concurrently analyze and evaluate the clinical markers of prostate cancer patients with instantaneous clinical data and evidence-based diagrams which can automatically identify pretreatment parameters. Moreover, the proposed RTCDSS can aid interactions between patients and clinicians. Our proposed framework supports online clinical informatics, evaluates treatment risks, offers interactive guidance, and provides real-time reference for decision making in the treatment of prostate cancer. The developed clinician-oriented interface can assist clinicians in conveniently presenting evidence-based information to patients and can be readily adapted to an existing hospital information system and be easily applied in other chronic diseases.

Open Clients for Distributed Databases

NASA Astrophysics Data System (ADS)

Chayes, D. N.; Arko, R. A.

2001-12-01

We are actively developing a collection of open source example clients that demonstrate use of our "back end" data management infrastructure. The data management system is reported elsewhere at this meeting (Arko and Chayes: A Scaleable Database Infrastructure). In addition to their primary goal of being examples for others to build upon, some of these clients may have limited utility in them selves. More information about the clients and the data infrastructure is available on line at http://data.ldeo.columbia.edu. The available examples to be demonstrated include several web-based clients including those developed for the Community Review System of the Digital Library for Earth System Education, a real-time watch standers log book, an offline interface to use log book entries, a simple client to search on multibeam metadata and others are Internet enabled and generally web-based front ends that support searches against one or more relational databases using industry standard SQL queries. In addition to the web based clients, simple SQL searches from within Excel and similar applications will be demonstrated. By defining, documenting and publishing a clear interface to the fully searchable databases, it becomes relatively easy to construct client interfaces that are optimized for specific applications in comparison to building a monolithic data and user interface system.

Methods, Knowledge Support, and Experimental Tools for Modeling

DTIC Science & Technology

2006-10-01

open source software entities: the PostgreSQL relational database management system (http://www.postgres.org), the Apache web server (http...past. The revision control system allows the program to capture disagreements, and allows users to explore the history of such disagreements by

Integrated Web-Based Access to and use of Satellite Remote Sensing Data for Improved Decision Making in Hydrologic Applications

NASA Astrophysics Data System (ADS)

Teng, W.; Chiu, L.; Kempler, S.; Liu, Z.; Nadeau, D.; Rui, H.

2006-12-01

Using NASA satellite remote sensing data from multiple sources for hydrologic applications can be a daunting task and requires a detailed understanding of the data's internal structure and physical implementation. Gaining this understanding and applying it to data reduction is a time-consuming task that must be undertaken before the core investigation can begin. In order to facilitate such investigations, the NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) has developed the GES-DISC Interactive Online Visualization ANd aNalysis Infrastructure or "Giovanni," which supports a family of Web interfaces (instances) that allow users to perform interactive visualization and analysis online without downloading any data. Two such Giovanni instances are particularly relevant to hydrologic applications: the Tropical Rainfall Measuring Mission (TRMM) Online Visualization and Analysis System (TOVAS) and the Agricultural Online Visualization and Analysis System (AOVAS), both highly popular and widely used for a variety of applications, including those related to several NASA Applications of National Priority, such as Agricultural Efficiency, Disaster Management, Ecological Forecasting, Homeland Security, and Public Health. Dynamic, context- sensitive Web services provided by TOVAS and AOVAS enable users to seamlessly access NASA data from within, and deeply integrate the data into, their local client environments. One example is between TOVAS and Florida International University's TerraFly, a Web-enabled system that serves a broad segment of the research and applications community, by facilitating access to various textual, remotely sensed, and vector data. Another example is between AOVAS and the U.S. Department of Agriculture Foreign Agricultural Service (USDA FAS)'s Crop Explorer, the primary decision support tool used by FAS to monitor the production, supply, and demand of agricultural commodities worldwide. AOVAS is also part of GES DISC's Agricultural Information System (AIS), which can operationally provide satellite remote sensing data products (e.g., near- real-time rainfall) and analysis services to agricultural users. AIS enables the remote, interoperable access to distributed data, by using the GrADS-Data Server (GDS) and the Open Geospatial Consortium (OGC)- compliant MapServer. The latter allows the access of AIS data from any OGC-compliant client, such as the Earth-Sun System Gateway (ESG) or Google Earth. The Giovanni system is evolving towards a Service- Oriented Architecture and is highly customizable (e.g., adding new products or services), thus availing the hydrologic applications user community of Giovanni's simple-to-use and powerful capabilities to improve decision-making.

Proteus - A Free and Open Source Sensor Observation Service (SOS) Client

NASA Astrophysics Data System (ADS)

Henriksson, J.; Satapathy, G.; Bermudez, L. E.

2013-12-01

The Earth's 'electronic skin' is becoming ever more sophisticated with a growing number of sensors measuring everything from seawater salinity levels to atmospheric pressure. To further the scientific application of this data collection effort, it is important to make the data easily available to anyone who wants to use it. Making Earth Science data readily available will allow the data to be used in new and potentially groundbreaking ways. The US National Science and Technology Council made this clear in its most recent National Strategy for Civil Earth Observations report, when it remarked that Earth observations 'are often found to be useful for additional purposes not foreseen during the development of the observation system'. On the road to this goal the Open Geospatial Consortium (OGC) is defining uniform data formats and service interfaces to facilitate the discovery and access of sensor data. This is being done through the Sensor Web Enablement (SWE) stack of standards, which include the Sensor Observation Service (SOS), Sensor Model Language (SensorML), Observations & Measurements (O&M) and Catalog Service for the Web (CSW). End-users do not have to use these standards directly, but can use smart tools that leverage and implement them. We have developed such a tool named Proteus. Proteus is an open-source sensor data discovery client. The goal of Proteus is to be a general-purpose client that can be used by anyone for discovering and accessing sensor data via OGC-based services. Proteus is a desktop client and supports a straightforward workflow for finding sensor data. The workflow takes the user through the process of selecting appropriate services, bounding boxes, observed properties, time periods and other search facets. NASA World Wind is used to display the matching sensor offerings on a map. Data from any sensor offering can be previewed in a time series. The user can download data from a single sensor offering, or download data in bulk from all matching sensor offerings. Proteus leverages NASA World Wind's WMS capabilities and allow overlaying sensor offerings on top of any map. Specific search criteria (i.e. user discoveries) can be saved and later restored. Proteus is supports two user types: 1) the researcher/scientist interested in discovering and downloading specific sensor data as input to research processes, and 2) the data manager responsible for maintaining sensor data services (e.g. SOSs) and wants to ensure proper data and metadata delivery, verify sensor data, and receive sensor data alerts. Proteus has a Web-based companion product named the Community Hub that is used to generate sensor data alerts. Alerts can be received via an RSS feed, viewed in a Web browser or displayed directly in Proteus via a Web-based API. To advance the vision of making Earth Science data easily discoverable and accessible to end-users, professional or laymen, Proteus is available as open-source on GitHub (https://github.com/intelligentautomation/proteus).

Kekule.js: An Open Source JavaScript Chemoinformatics Toolkit.

PubMed

Jiang, Chen; Jin, Xi; Dong, Ying; Chen, Ming

2016-06-27

Kekule.js is an open-source, object-oriented JavaScript toolkit for chemoinformatics. It provides methods for many common tasks in molecular informatics, including chemical data input/output (I/O), two- and three-dimensional (2D/3D) rendering of chemical structure, stereo identification, ring perception, structure comparison, and substructure search. Encapsulated widgets to display and edit chemical structures directly in web context are also supplied. Developed with web standards, the toolkit is ideal for building chemoinformatics applications over the Internet. Moreover, it is highly platform-independent and can also be used in desktop or mobile environments. Some initial applications, such as plugins for inputting chemical structures on the web and uses in chemistry education, have been developed based on the toolkit.

PaaS for web applications with OpenShift Origin

NASA Astrophysics Data System (ADS)

Lossent, A.; Rodriguez Peon, A.; Wagner, A.

2017-10-01

The CERN Web Frameworks team has deployed OpenShift Origin to facilitate deployment of web applications and to improving efficiency in terms of computing resource usage. OpenShift leverages Docker containers and Kubernetes orchestration to provide a Platform-as-a-service solution oriented for web applications. We will review use cases and how OpenShift was integrated with other services such as source control, web site management and authentication services.

OpenTrials: towards a collaborative open database of all available information on all clinical trials.

PubMed

Goldacre, Ben; Gray, Jonathan

2016-04-08

OpenTrials is a collaborative and open database for all available structured data and documents on all clinical trials, threaded together by individual trial. With a versatile and expandable data schema, it is initially designed to host and match the following documents and data for each trial: registry entries; links, abstracts, or texts of academic journal papers; portions of regulatory documents describing individual trials; structured data on methods and results extracted by systematic reviewers or other researchers; clinical study reports; and additional documents such as blank consent forms, blank case report forms, and protocols. The intention is to create an open, freely re-usable index of all such information and to increase discoverability, facilitate research, identify inconsistent data, enable audits on the availability and completeness of this information, support advocacy for better data and drive up standards around open data in evidence-based medicine. The project has phase I funding. This will allow us to create a practical data schema and populate the database initially through web-scraping, basic record linkage techniques, crowd-sourced curation around selected drug areas, and import of existing sources of structured and documents. It will also allow us to create user-friendly web interfaces onto the data and conduct user engagement workshops to optimise the database and interface designs. Where other projects have set out to manually and perfectly curate a narrow range of information on a smaller number of trials, we aim to use a broader range of techniques and attempt to match a very large quantity of information on all trials. We are currently seeking feedback and additional sources of structured data.

Implementation of workflow engine technology to deliver basic clinical decision support functionality.

PubMed

Huser, Vojtech; Rasmussen, Luke V; Oberg, Ryan; Starren, Justin B

2011-04-10

Workflow engine technology represents a new class of software with the ability to graphically model step-based knowledge. We present application of this novel technology to the domain of clinical decision support. Successful implementation of decision support within an electronic health record (EHR) remains an unsolved research challenge. Previous research efforts were mostly based on healthcare-specific representation standards and execution engines and did not reach wide adoption. We focus on two challenges in decision support systems: the ability to test decision logic on retrospective data prior prospective deployment and the challenge of user-friendly representation of clinical logic. We present our implementation of a workflow engine technology that addresses the two above-described challenges in delivering clinical decision support. Our system is based on a cross-industry standard of XML (extensible markup language) process definition language (XPDL). The core components of the system are a workflow editor for modeling clinical scenarios and a workflow engine for execution of those scenarios. We demonstrate, with an open-source and publicly available workflow suite, that clinical decision support logic can be executed on retrospective data. The same flowchart-based representation can also function in a prospective mode where the system can be integrated with an EHR system and respond to real-time clinical events. We limit the scope of our implementation to decision support content generation (which can be EHR system vendor independent). We do not focus on supporting complex decision support content delivery mechanisms due to lack of standardization of EHR systems in this area. We present results of our evaluation of the flowchart-based graphical notation as well as architectural evaluation of our implementation using an established evaluation framework for clinical decision support architecture. We describe an implementation of a free workflow technology software suite (available at http://code.google.com/p/healthflow) and its application in the domain of clinical decision support. Our implementation seamlessly supports clinical logic testing on retrospective data and offers a user-friendly knowledge representation paradigm. With the presented software implementation, we demonstrate that workflow engine technology can provide a decision support platform which evaluates well against an established clinical decision support architecture evaluation framework. Due to cross-industry usage of workflow engine technology, we can expect significant future functionality enhancements that will further improve the technology's capacity to serve as a clinical decision support platform.

Web-based objective structured clinical examination with remote standardized patients and Skype: resident experience.

PubMed

Langenau, Erik; Kachur, Elizabeth; Horber, Dot

2014-07-01

Using Skype and remote standardized patients (RSPs), investigators sought to evaluate user acceptance of a web-based objective structured clinical examination (OSCE) among resident physicians. After participating in four web-based clinical encounters addressing pain with RSPs, 59 residents from different training programs, disciplines and geographic locations completed a 52-item questionnaire regarding their experience with Skype and RSPs. Open-ended responses were solicited as well. The majority of participants (97%) agreed or strongly agreed the web-based format was convenient and a practical learning exercise, and 90% agreed or strongly agreed the format was effective in teaching communication skills. Although 93% agreed or strongly agreed they could communicate easily with RSPs using Skype, 80% preferred traditional face-to-face clinical encounters, and 58% reported technical difficulties during the encounters. Open-ended written responses supported survey results. Findings from this study expose challenges with technology and human factors, but positive experiences support the continued investigation of web-based OSCEs as a synchronous e-learning initiative for teaching and assessing doctor-patient communication. Such educational programs are valuable but unlikely to replace face-to-face encounters with patients. This web-based OSCE program provides physician learners with additional opportunity to improve doctor-patient communication. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Web-Based Learning Support System

NASA Astrophysics Data System (ADS)

Fan, Lisa

Web-based learning support system offers many benefits over traditional learning environments and has become very popular. The Web is a powerful environment for distributing information and delivering knowledge to an increasingly wide and diverse audience. Typical Web-based learning environments, such as Web-CT, Blackboard, include course content delivery tools, quiz modules, grade reporting systems, assignment submission components, etc. They are powerful integrated learning management systems (LMS) that support a number of activities performed by teachers and students during the learning process [1]. However, students who study a course on the Internet tend to be more heterogeneously distributed than those found in a traditional classroom situation. In order to achieve optimal efficiency in a learning process, an individual learner needs his or her own personalized assistance. For a web-based open and dynamic learning environment, personalized support for learners becomes more important. This chapter demonstrates how to realize personalized learning support in dynamic and heterogeneous learning environments by utilizing Adaptive Web technologies. It focuses on course personalization in terms of contents and teaching materials that is according to each student's needs and capabilities. An example of using Rough Set to analyze student personal information to assist students with effective learning and predict student performance is presented.

Open Standards in Practice: An OGC China Forum Initiative

NASA Astrophysics Data System (ADS)

Yue, Peng; Zhang, Mingda; Taylor, Trevor; Xie, Jibo; Zhang, Hongping; Tong, Xiaochong; Yu, Jinsongdi; Huang, Juntao

2016-11-01

Open standards like OGC standards can be used to improve interoperability and support machine-to-machine interaction over the Web. In the Big Data era, standard-based data and processing services from various vendors could be combined to automate the extraction of information and knowledge from heterogeneous and large volumes of geospatial data. This paper introduces an ongoing OGC China forum initiative, which will demonstrate how OGC standards can benefit the interaction among multiple organizations in China. The ability to share data and processing functions across organizations using standard services could change traditional manual interactions in their business processes, and provide on-demand decision support results by on-line service integration. In the initiative, six organizations are involved in two “MashUp” scenarios on disaster management. One “MashUp” is to derive flood maps in the Poyang Lake, Jiangxi. And the other one is to generate turbidity maps on demand in the East Lake, Wuhan, China. The two scenarios engage different organizations from the Chinese community by integrating sensor observations, data, and processing services from them, and improve the automation of data analysis process using open standards.

Evaluating the Utility of Web-Based Consumer Support Tools Using Rough Sets

NASA Astrophysics Data System (ADS)

Maciag, Timothy; Hepting, Daryl H.; Slezak, Dominik; Hilderman, Robert J.

On the Web, many popular e-commerce sites provide consumers with decision support tools to assist them in their commerce-related decision-making. Many consumers will rank the utility of these tools quite highly. Data obtained from web usage mining analyses, which may provide knowledge about a user's online experiences, could help indicate the utility of these tools. This type of analysis could provide insight into whether provided tools are adequately assisting consumers in conducting their online shopping activities or if new or additional enhancements need consideration. Although some research in this regard has been described in previous literature, there is still much that can be done. The authors of this paper hypothesize that a measurement of consumer decision accuracy, i.e. a measurement preferences, could help indicate the utility of these tools. This paper describes a procedure developed towards this goal using elements of rough set theory. The authors evaluated the procedure using two support tools, one based on a tool developed by the US-EPA and the other developed by one of the authors called cogito. Results from the evaluation did provide interesting insights on the utility of both support tools. Although it was shown that the cogito tool obtained slightly higher decision accuracy, both tools could be improved from additional enhancements. Details of the procedure developed and results obtained from the evaluation will be provided. Opportunities for future work are also discussed.

Data Mashups: Potential Contribution to Decision Support on Climate Change and Health

PubMed Central

Fleming, Lora E.; Haines, Andy; Golding, Brian; Kessel, Anthony; Cichowska, Anna; Sabel, Clive E.; Depledge, Michael H.; Sarran, Christophe; Osborne, Nicholas J.; Whitmore, Ceri; Cocksedge, Nicola; Bloomfield, Daniel

2014-01-01

Linking environmental, socioeconomic and health datasets provides new insights into the potential associations between climate change and human health and wellbeing, and underpins the development of decision support tools that will promote resilience to climate change, and thus enable more effective adaptation. This paper outlines the challenges and opportunities presented by advances in data collection, storage, analysis, and access, particularly focusing on “data mashups”. These data mashups are integrations of different types and sources of data, frequently using open application programming interfaces and data sources, to produce enriched results that were not necessarily the original reason for assembling the raw source data. As an illustration of this potential, this paper describes a recently funded initiative to create such a facility in the UK for use in decision support around climate change and health, and provides examples of suitable sources of data and the purposes to which they can be directed, particularly for policy makers and public health decision makers. PMID:24499879

Data mashups: potential contribution to decision support on climate change and health.

PubMed

Fleming, Lora E; Haines, Andy; Golding, Brian; Kessel, Anthony; Cichowska, Anna; Sabel, Clive E; Depledge, Michael H; Sarran, Christophe; Osborne, Nicholas J; Whitmore, Ceri; Cocksedge, Nicola; Bloomfield, Daniel

2014-02-04

Linking environmental, socioeconomic and health datasets provides new insights into the potential associations between climate change and human health and wellbeing, and underpins the development of decision support tools that will promote resilience to climate change, and thus enable more effective adaptation. This paper outlines the challenges and opportunities presented by advances in data collection, storage, analysis, and access, particularly focusing on "data mashups". These data mashups are integrations of different types and sources of data, frequently using open application programming interfaces and data sources, to produce enriched results that were not necessarily the original reason for assembling the raw source data. As an illustration of this potential, this paper describes a recently funded initiative to create such a facility in the UK for use in decision support around climate change and health, and provides examples of suitable sources of data and the purposes to which they can be directed, particularly for policy makers and public health decision makers.

Post hoc support vector machine learning for impedimetric biosensors based on weak protein-ligand interactions.

PubMed

Rong, Y; Padron, A V; Hagerty, K J; Nelson, N; Chi, S; Keyhani, N O; Katz, J; Datta, S P A; Gomes, C; McLamore, E S

2018-04-30

Impedimetric biosensors for measuring small molecules based on weak/transient interactions between bioreceptors and target analytes are a challenge for detection electronics, particularly in field studies or in the analysis of complex matrices. Protein-ligand binding sensors have enormous potential for biosensing, but achieving accuracy in complex solutions is a major challenge. There is a need for simple post hoc analytical tools that are not computationally expensive, yet provide near real time feedback on data derived from impedance spectra. Here, we show the use of a simple, open source support vector machine learning algorithm for analyzing impedimetric data in lieu of using equivalent circuit analysis. We demonstrate two different protein-based biosensors to show that the tool can be used for various applications. We conclude with a mobile phone-based demonstration focused on the measurement of acetone, an important biomarker related to the onset of diabetic ketoacidosis. In all conditions tested, the open source classifier was capable of performing as well as, or better, than the equivalent circuit analysis for characterizing weak/transient interactions between a model ligand (acetone) and a small chemosensory protein derived from the tsetse fly. In addition, the tool has a low computational requirement, facilitating use for mobile acquisition systems such as mobile phones. The protocol is deployed through Jupyter notebook (an open source computing environment available for mobile phone, tablet or computer use) and the code was written in Python. For each of the applications, we provide step-by-step instructions in English, Spanish, Mandarin and Portuguese to facilitate widespread use. All codes were based on scikit-learn, an open source software machine learning library in the Python language, and were processed in Jupyter notebook, an open-source web application for Python. The tool can easily be integrated with the mobile biosensor equipment for rapid detection, facilitating use by a broad range of impedimetric biosensor users. This post hoc analysis tool can serve as a launchpad for the convergence of nanobiosensors in planetary health monitoring applications based on mobile phone hardware.

SMARTE: IMPROVING REVITALIZATION DECISIONS - OCTOBER 3, 2006

EPA Science Inventory

SMARTe (Sustainable Management Approaches and Revitalization Tools -electronic) is a web-based decision support tool being developed by the Office of Research and Development (ORD) in partnership with the Office of Brownfields Cleanup and Revitalization (OBCR), the Interstate Tec...

Accessible Collaborative Learning Using Mobile Devices

ERIC Educational Resources Information Center

Wald, Mike; Li, Yunjia; Draffan, E. A.

2014-01-01

This paper describes accessible collaborative learning using mobile devices with mobile enhancements to Synote, the freely available, award winning, open source, web based application that makes web hosted recordings easier to access, search, manage, and exploit for all learners, teachers and other users. Notes taken live during lectures using…

Caching strategies for improving performance of web-based Geographic applications

NASA Astrophysics Data System (ADS)

Liu, M.; Brodzik, M.; Collins, J. A.; Lewis, S.; Oldenburg, J.

2012-12-01

The NASA Operation IceBridge mission collects airborne remote sensing measurements to bridge the gap between NASA's Ice, Cloud and Land Elevation Satellite (ICESat) mission and the upcoming ICESat-2 mission. The IceBridge Data Portal from the National Snow and Ice Data Center provides an intuitive web interface for accessing IceBridge mission observations and measurements. Scientists and users usually do not have knowledge about the individual campaigns but are interested in data collected in a specific place. We have developed a high-performance map interface to allow users to quickly zoom to an area of interest and see any Operation IceBridge overflights. The map interface consists of two layers: the user can pan and zoom on the base map layer; the flight line layer that overlays the base layer provides all the campaign missions that intersect with the current map view. The user can click on the flight campaigns and download the data as needed. The OpenGIS® Web Map Service Interface Standard (WMS) provides a simple HTTP interface for requesting geo-registered map images from one or more distributed geospatial databases. Web Feature Service (WFS) provides an interface allowing requests for geographical features across the web using platform-independent calls. OpenLayers provides vector support (points, polylines and polygons) to build a WMS/WFS client for displaying both layers on the screen. Map Server, an open source development environment for building spatially enabled internet applications, is serving the WMS and WFS spatial data to OpenLayers. Early releases of the portal displayed unacceptably poor load time performance for flight lines and the base map tiles. This issue was caused by long response times from the map server in generating all map tiles and flight line vectors. We resolved the issue by implementing various caching strategies on top of the WMS and WFS services, including the use of Squid (www.squid-cache.org) to cache frequently-used content. Our presentation includes the architectural design of the application, and how we use OpenLayers, WMS and WFS with Squid to build a responsive web application capable of efficiently displaying geospatial data to allow the user to quickly interact with the displayed information. We describe the design, implementation and performance improvement of our caching strategies, and the tools and techniques developed to assist our data caching strategies.

A Web-Based Treatment Decision Support Tool for Patients With Advanced Knee Arthritis: Evaluation of User Interface and Content Design.

PubMed

Zheng, Hua; Rosal, Milagros C; Li, Wenjun; Borg, Amy; Yang, Wenyun; Ayers, David C; Franklin, Patricia D

2018-04-30

Data-driven surgical decisions will ensure proper use and timing of surgical care. We developed a Web-based patient-centered treatment decision and assessment tool to guide treatment decisions among patients with advanced knee osteoarthritis who are considering total knee replacement surgery. The aim of this study was to examine user experience and acceptance of the Web-based treatment decision support tool among older adults. User-centered formative and summative evaluations were conducted for the tool. A sample of 28 patients who were considering total knee replacement participated in the study. Participants' responses to the user interface design, the clarity of information, as well as usefulness, satisfaction, and acceptance of the tool were collected through qualitative (ie, individual patient interviews) and quantitative (ie, standardized Computer System Usability Questionnaire) methods. Participants were older adults with a mean age of 63 (SD 11) years. Three-quarters of them had no technical questions using the tool. User interface design recommendations included larger fonts, bigger buttons, less colors, simpler navigation without extra "next page" click, less mouse movement, and clearer illustrations with simple graphs. Color-coded bar charts and outcome-specific graphs with positive action were easiest for them to understand the outcomes data. Questionnaire data revealed high satisfaction with the tool usefulness and interface quality, and also showed ease of use of the tool, regardless of age or educational status. We evaluated the usability of a patient-centered decision support tool designed for advanced knee arthritis patients to facilitate their knee osteoarthritis treatment decision making. The lessons learned can inform other decision support tools to improve interface and content design for older patients' use. ©Hua Zheng, Milagros C Rosal, Wenjun Li, Amy Borg, Wenyun Yang, David C Ayers, Patricia D Franklin. Originally published in JMIR Human Factors (http://humanfactors.jmir.org), 30.04.2018.

OpenFLUID: an open-source software environment for modelling fluxes in landscapes

NASA Astrophysics Data System (ADS)

Fabre, Jean-Christophe; Rabotin, Michaël; Crevoisier, David; Libres, Aline; Dagès, Cécile; Moussa, Roger; Lagacherie, Philippe; Raclot, Damien; Voltz, Marc

2013-04-01

Integrative landscape functioning has become a common concept in environmental management. Landscapes are complex systems where many processes interact in time and space. In agro-ecosystems, these processes are mainly physical processes, including hydrological-processes, biological processes and human activities. Modelling such systems requires an interdisciplinary approach, coupling models coming from different disciplines, developed by different teams. In order to support collaborative works, involving many models coupled in time and space for integrative simulations, an open software modelling platform is a relevant answer. OpenFLUID is an open source software platform for modelling landscape functioning, mainly focused on spatial fluxes. It provides an advanced object-oriented architecture allowing to i) couple models developed de novo or from existing source code, and which are dynamically plugged to the platform, ii) represent landscapes as hierarchical graphs, taking into account multi-scale, spatial heterogeneities and landscape objects connectivity, iii) run and explore simulations in many ways : using the OpenFLUID software interfaces for users (command line interface, graphical user interface), or using external applications such as GNU R through the provided ROpenFLUID package. OpenFLUID is developed in C++ and relies on open source libraries only (Boost, libXML2, GLib/GTK, OGR/GDAL, …). For modelers and developers, OpenFLUID provides a dedicated environment for model development, which is based on an open source toolchain, including the Eclipse editor, the GCC compiler and the CMake build system. OpenFLUID is distributed under the GPLv3 open source license, with a special exception allowing to plug existing models licensed under any license. It is clearly in the spirit of sharing knowledge and favouring collaboration in a community of modelers. OpenFLUID has been involved in many research applications, such as modelling of hydrological network transfer, diagnosis and prediction of water quality taking into account human activities, study of the effect of spatial organization on hydrological fluxes, modelling of surface-subsurface water exchanges, … At LISAH research unit, OpenFLUID is the supporting development platform of the MHYDAS model, which is a distributed model for agrosystems (Moussa et al., 2002, Hydrological Processes, 16, 393-412). OpenFLUID web site : http://www.openfluid-project.org

Visualization of Vgi Data Through the New NASA Web World Wind Virtual Globe

NASA Astrophysics Data System (ADS)

Brovelli, M. A.; Kilsedar, C. E.; Zamboni, G.

2016-06-01

GeoWeb 2.0, laying the foundations of Volunteered Geographic Information (VGI) systems, has led to platforms where users can contribute to the geographic knowledge that is open to access. Moreover, as a result of the advancements in 3D visualization, virtual globes able to visualize geographic data even on browsers emerged. However the integration of VGI systems and virtual globes has not been fully realized. The study presented aims to visualize volunteered data in 3D, considering also the ease of use aspects for general public, using Free and Open Source Software (FOSS). The new Application Programming Interface (API) of NASA, Web World Wind, written in JavaScript and based on Web Graphics Library (WebGL) is cross-platform and cross-browser, so that the virtual globe created using this API can be accessible through any WebGL supported browser on different operating systems and devices, as a result not requiring any installation or configuration on the client-side, making the collected data more usable to users, which is not the case with the World Wind for Java as installation and configuration of the Java Virtual Machine (JVM) is required. Furthermore, the data collected through various VGI platforms might be in different formats, stored in a traditional relational database or in a NoSQL database. The project developed aims to visualize and query data collected through Open Data Kit (ODK) platform and a cross-platform application, where data is stored in a relational PostgreSQL and NoSQL CouchDB databases respectively.

Applications of Satellite Data to Support Improvements in Irrigation and Groundwater Management in California

NASA Technical Reports Server (NTRS)

Melton, Forrest S.

2017-01-01

In agricultural regions around the world, threats to water supplies from drought and groundwater depletion are driving increased demand for tools to advance agricultural water use efficiency and support sustainable groundwater management. Satellite mapping of evapotranspiration (ET) from irrigated agricultural lands can provide agricultural producers and water resource managers with information that can be used to both optimize ag water use and improve estimates of groundwater withdrawals for irrigation. We describe the development of two remote sensing-based tools for ET mapping in California, including important lessons in terms of system design, partnership development, and transition to operations. For irrigation management, the integration of satellite data and surface sensor networks to provide timely delivery of information on crop water requirements can make irrigation scheduling more practical, convenient, and accurate.Developed through a partnership between NASA and the CA Department of Water Resources, the Satellite Irrigation Management Support (SIMS) framework integrates satellite data with information from agricultural weather networks to map crop canopy development and crop water requirements at the scale of individual fields. Information is distributed to agricultural producers and water managers via a web-based interface and web data services. SIMS also provides an API that facilitates integration with other irrigation decision support tools, such as CropManage and IrriQuest. Field trials using these integrated tools have shown that they can be used to sustain yields while improving water use efficiency and nutrient management. For sustainable groundwater management, the combination of satellite-derived estimates of ET and data on surface water deliveries for irrigation can increase the accuracy of estimates of groundwater pumping. We are developing an OpenET platform to facilitate access to ET data from multiple models and accelerate operational use of ET data in support of a range of water management applications, including implementation of the Sustainable Groundwater Management Act in CA. By providing a shared basis for decision making, we anticipate that the OpenET platform will accelerate implementation of solutions for sustainable groundwater management.

Applications of Satellite Data to Support Improvements in Irrigation and Groundwater Management in California

NASA Astrophysics Data System (ADS)

Melton, F. S.; Huntington, J. L.; Johnson, L.; Guzman, A.; Morton, C.; Zaragoza, I.; Dexter, J.; Rosevelt, C.; Michaelis, A.; Nemani, R. R.; Cahn, M.; Temesgen, B.; Trezza, R.; Frame, K.; Eching, S.; Grimm, R.; Hall, M.

2017-12-01

In agricultural regions around the world, threats to water supplies from drought and groundwater depletion are driving increased demand for tools to advance agricultural water use efficiency and support sustainable groundwater management. Satellite mapping of evapotranspiration (ET) from irrigated agricultural lands can provide agricultural producers and water resource managers with information that can be used to both optimize ag water use and improve estimates of groundwater withdrawals for irrigation. We describe the development of two remote sensing-based tools for ET mapping in California, including important lessons in terms of system design, partnership development, and transition to operations. For irrigation management, the integration of satellite data and surface sensor networks to provide timely delivery of information on crop water requirements can make irrigation scheduling more practical, convenient, and accurate. Developed through a partnership between NASA and the CA Department of Water Resources, the Satellite Irrigation Management Support (SIMS) framework integrates satellite data with information from agricultural weather networks to map crop canopy development and crop water requirements at the scale of individual fields. Information is distributed to agricultural producers and water managers via a web-based interface and web data services. SIMS also provides an API that facilitates integration with other irrigation decision support tools, such as CropManage and IrriQuest. Field trials using these integrated tools have shown that they can be used to sustain yields while improving water use efficiency and nutrient management. For sustainable groundwater management, the combination of satellite-derived estimates of ET and data on surface water deliveries for irrigation can increase the accuracy of estimates of groundwater pumping. We are developing an OpenET platform to facilitate access to ET data from multiple models and accelerate operational use of ET data in support of a range of water management applications, including implementation of the Sustainable Groundwater Management Act in CA. By providing a shared basis for decision making, we anticipate that the OpenET platform will accelerate implementation of solutions for sustainable groundwater management.

DE.SMARTe: US-German Bilateral Cooperation For The Development Of An Internet-Based Decision Support System For Sustainable Revitalisation of Contaminated Sites - June 2009

EPA Science Inventory

SMARTe (Sustainable Management Approaches and Revitalization Tools-electronic) is a web-based decision support tool developed by he Office of Research and Development (ORD) in partnership with the Office of Brownfields and Land Revitaliza...

The Space Environmental Impact System

NASA Astrophysics Data System (ADS)

Kihn, E. A.

2009-12-01

The Space Environmental Impact System (SEIS) is an operational tool for incorporating environmental data sets into DoD Modeling and Simulation (M&S) which allows for enhanced decision making regarding acquisitions, testing, operations and planning. The SEIS system creates, from the environmental archives and developed rule-base, a tool for describing the effects of the space environment on particular military systems, both historically and in real-time. The system uses data available over the web, and in particular data provided by NASA’s virtual observatory network, as well as modeled data generated specifically for this purpose. The rule base system developed to support SEIS is an open XML based model which can be extended to events from any environmental domain. This presentation will show how the SEIS tool allows users to easily and accurately evaluate the effect of space weather in terms that are meaningful to them as well as discuss the relevant standards used in its construction and go over lessons learned from fielding an operational environmental decision tool.

A dynamic simulation based water resources education tool.

PubMed

Williams, Alison; Lansey, Kevin; Washburne, James

2009-01-01

Educational tools to assist the public in recognizing impacts of water policy in a realistic context are not generally available. This project developed systems with modeling-based educational decision support simulation tools to satisfy this need. The goal of this model is to teach undergraduate students and the general public about the implications of common water management alternatives so that they can better understand or become involved in water policy and make more knowledgeable personal or community decisions. The model is based on Powersim, a dynamic simulation software package capable of producing web-accessible, intuitive, graphic, user-friendly interfaces. Modules are included to represent residential, agricultural, industrial, and turf uses, as well as non-market values, water quality, reservoir, flow, and climate conditions. Supplementary materials emphasize important concepts and lead learners through the model, culminating in an open-ended water management project. The model is used in a University of Arizona undergraduate class and within the Arizona Master Watershed Stewards Program. Evaluation results demonstrated improved understanding of concepts and system interactions, fulfilling the project's objectives.

Evaluating open-source cloud computing solutions for geosciences

NASA Astrophysics Data System (ADS)

Huang, Qunying; Yang, Chaowei; Liu, Kai; Xia, Jizhe; Xu, Chen; Li, Jing; Gui, Zhipeng; Sun, Min; Li, Zhenglong

2013-09-01

Many organizations start to adopt cloud computing for better utilizing computing resources by taking advantage of its scalability, cost reduction, and easy to access characteristics. Many private or community cloud computing platforms are being built using open-source cloud solutions. However, little has been done to systematically compare and evaluate the features and performance of open-source solutions in supporting Geosciences. This paper provides a comprehensive study of three open-source cloud solutions, including OpenNebula, Eucalyptus, and CloudStack. We compared a variety of features, capabilities, technologies and performances including: (1) general features and supported services for cloud resource creation and management, (2) advanced capabilities for networking and security, and (3) the performance of the cloud solutions in provisioning and operating the cloud resources as well as the performance of virtual machines initiated and managed by the cloud solutions in supporting selected geoscience applications. Our study found that: (1) no significant performance differences in central processing unit (CPU), memory and I/O of virtual machines created and managed by different solutions, (2) OpenNebula has the fastest internal network while both Eucalyptus and CloudStack have better virtual machine isolation and security strategies, (3) Cloudstack has the fastest operations in handling virtual machines, images, snapshots, volumes and networking, followed by OpenNebula, and (4) the selected cloud computing solutions are capable for supporting concurrent intensive web applications, computing intensive applications, and small-scale model simulations without intensive data communication.

An innovative approach to addressing childhood obesity: a knowledge-based infrastructure for supporting multi-stakeholder partnership decision-making in Quebec, Canada.

PubMed

Addy, Nii Antiaye; Shaban-Nejad, Arash; Buckeridge, David L; Dubé, Laurette

2015-01-23

Multi-stakeholder partnerships (MSPs) have become a widespread means for deploying policies in a whole of society strategy to address the complex problem of childhood obesity. However, decision-making in MSPs is fraught with challenges, as decision-makers are faced with complexity, and have to reconcile disparate conceptualizations of knowledge across multiple sectors with diverse sets of indicators and data. These challenges can be addressed by supporting MSPs with innovative tools for obtaining, organizing and using data to inform decision-making. The purpose of this paper is to describe and analyze the development of a knowledge-based infrastructure to support MSP decision-making processes. The paper emerged from a study to define specifications for a knowledge-based infrastructure to provide decision support for community-level MSPs in the Canadian province of Quebec. As part of the study, a process assessment was conducted to understand the needs of communities as they collect, organize, and analyze data to make decisions about their priorities. The result of this process is a "portrait", which is an epidemiological profile of health and nutrition in their community. Portraits inform strategic planning and development of interventions, and are used to assess the impact of interventions. Our key findings indicate ambiguities and disagreement among MSP decision-makers regarding causal relationships between actions and outcomes, and the relevant data needed for making decisions. MSP decision-makers expressed a desire for easy-to-use tools that facilitate the collection, organization, synthesis, and analysis of data, to enable decision-making in a timely manner. Findings inform conceptual modeling and ontological analysis to capture the domain knowledge and specify relationships between actions and outcomes. This modeling and analysis provide the foundation for an ontology, encoded using OWL 2 Web Ontology Language. The ontology is developed to provide semantic support for the MSP process, defining objectives, strategies, actions, indicators, and data sources. In the future, software interacting with the ontology can facilitate interactive browsing by decision-makers in the MSP in the form of concepts, instances, relationships, and axioms. Our ontology also facilitates the integration and interpretation of community data, and can help in managing semantic interoperability between different knowledge sources. Future work will focus on defining specifications for the development of a database of indicators and an information system to help decision-makers to view, analyze and organize indicators for their community. This work should improve MSP decision-making in the development of interventions to address childhood obesity.

An Innovative Approach to Addressing Childhood Obesity: A Knowledge-Based Infrastructure for Supporting Multi-Stakeholder Partnership Decision-Making in Quebec, Canada

PubMed Central

Addy, Nii Antiaye; Shaban-Nejad, Arash; Buckeridge, David L.; Dubé, Laurette

2015-01-01

Multi-stakeholder partnerships (MSPs) have become a widespread means for deploying policies in a whole of society strategy to address the complex problem of childhood obesity. However, decision-making in MSPs is fraught with challenges, as decision-makers are faced with complexity, and have to reconcile disparate conceptualizations of knowledge across multiple sectors with diverse sets of indicators and data. These challenges can be addressed by supporting MSPs with innovative tools for obtaining, organizing and using data to inform decision-making. The purpose of this paper is to describe and analyze the development of a knowledge-based infrastructure to support MSP decision-making processes. The paper emerged from a study to define specifications for a knowledge-based infrastructure to provide decision support for community-level MSPs in the Canadian province of Quebec. As part of the study, a process assessment was conducted to understand the needs of communities as they collect, organize, and analyze data to make decisions about their priorities. The result of this process is a “portrait”, which is an epidemiological profile of health and nutrition in their community. Portraits inform strategic planning and development of interventions, and are used to assess the impact of interventions. Our key findings indicate ambiguities and disagreement among MSP decision-makers regarding causal relationships between actions and outcomes, and the relevant data needed for making decisions. MSP decision-makers expressed a desire for easy-to-use tools that facilitate the collection, organization, synthesis, and analysis of data, to enable decision-making in a timely manner. Findings inform conceptual modeling and ontological analysis to capture the domain knowledge and specify relationships between actions and outcomes. This modeling and analysis provide the foundation for an ontology, encoded using OWL 2 Web Ontology Language. The ontology is developed to provide semantic support for the MSP process, defining objectives, strategies, actions, indicators, and data sources. In the future, software interacting with the ontology can facilitate interactive browsing by decision-makers in the MSP in the form of concepts, instances, relationships, and axioms. Our ontology also facilitates the integration and interpretation of community data, and can help in managing semantic interoperability between different knowledge sources. Future work will focus on defining specifications for the development of a database of indicators and an information system to help decision-makers to view, analyze and organize indicators for their community. This work should improve MSP decision-making in the development of interventions to address childhood obesity. PMID:25625409

The SURA Coastal Ocean Observing and Prediction (SCOOP) Program: Adapting Web 2.0 technologies to power next generation science

NASA Astrophysics Data System (ADS)

Bogden, P.; Partners, S.

2008-12-01

The Web 2.0 has helped globalize the economy and change social interactions, but the full impact on coastal sciences has yet to be realized. The SCOOP program (www.OpenIOOS.org/about/sura.html), an initiative of the Coastal Research Committee of the Southeastern Universities Research Association (SURA), has been using Web 2.0 technologies to create infrastructure for a multi-disciplinary Distributed Coastal Laboratory (DCL). In the spirit of the Web 2.0, SCOOP strives to provide an open-access virtual facility where "virtual visiting" scientists can log in, perform experiments (e.g., evaluate new wetting/drying algorithms in several different inundation models), potentially contribute to the assembly of resources (e.g., leave their algorithms for others), and then move on. The SCOOP prototype has focused on storm surge and waves (the initial science focus), and integrates a real-time data network to evaluate the predictions. The multi-purpose SCOOP components support a sensor-web initiative (www.OOSTethys.org) that is co-led by SURA. SCOOP also includes portals with real-time visualization, workflow configuration and decision-tool prototypes (www.OpenIOOS.org), powered by distributed computing resources from multiple universities across the nation (www.sura.org/SURAgrid). Based on our experience, we propose three key ingredients for initiatives to have the biggest impact on coastal science: (1) standards, (2) working prototypes and (3) communities of interest. We strongly endorse the Open Geospatial Consortium - a geospatial analog of the World Wide Web consortium - and other international consensus-standards bodies that engage government, private sector and academic involvement. But these standards are often highly complex, which can be an impediment to their use. We have overcome such hurdles with the second key ingredient: a focused working prototype. The prototype should include guides and resources that make it easy for others to apply, test, and revise the prototype, all without need to understand the standards in their overwhelming complexity. In addition, the prototype should support direct involvement of the third key ingredient: communities of interest that assess functional relevance. We expect that any two of these ingredients alone, without the third, will severely limit applicability and impact of any initiative.

A HTML5 open source tool to conduct studies based on Libet’s clock paradigm

PubMed Central

Garaizar, Pablo; Cubillas, Carmelo P.; Matute, Helena

2016-01-01

Libet’s clock is a well-known procedure in experiments in psychology and neuroscience. Examples of its use include experiments exploring the subjective sense of agency, action-effect binding, and subjective timing of conscious decisions and perceptions. However, the technical details of the apparatus used to conduct these types of experiments are complex, and are rarely explained in sufficient detail as to guarantee an exact replication of the procedure. With this in mind, we developed Labclock Web, a web tool designed to conduct online and offline experiments using Libet’s clock. After describing its technical features, we explain how to configure specific experiments using this tool. Its degree of accuracy and precision in the presentation of stimuli has been technically validated, including the use of two cognitive experiments conducted with voluntary participants who performed the experiment both in our laboratory and via the Internet. Labclock Web is distributed without charge under a free software license (GPLv3) since one of our main objectives is to facilitate the replication of experiments and hence the advancement of knowledge in this area. PMID:27623167

A HTML5 open source tool to conduct studies based on Libet's clock paradigm.

PubMed

Garaizar, Pablo; Cubillas, Carmelo P; Matute, Helena

2016-09-13

Libet's clock is a well-known procedure in experiments in psychology and neuroscience. Examples of its use include experiments exploring the subjective sense of agency, action-effect binding, and subjective timing of conscious decisions and perceptions. However, the technical details of the apparatus used to conduct these types of experiments are complex, and are rarely explained in sufficient detail as to guarantee an exact replication of the procedure. With this in mind, we developed Labclock Web, a web tool designed to conduct online and offline experiments using Libet's clock. After describing its technical features, we explain how to configure specific experiments using this tool. Its degree of accuracy and precision in the presentation of stimuli has been technically validated, including the use of two cognitive experiments conducted with voluntary participants who performed the experiment both in our laboratory and via the Internet. Labclock Web is distributed without charge under a free software license (GPLv3) since one of our main objectives is to facilitate the replication of experiments and hence the advancement of knowledge in this area.

The Lake Tahoe Basin Land Use Simulation Model

USGS Publications Warehouse

Forney, William M.; Oldham, I. Benson

2011-01-01

This U.S. Geological Survey Open-File Report describes the final modeling product for the Tahoe Decision Support System project for the Lake Tahoe Basin funded by the Southern Nevada Public Land Management Act and the U.S. Geological Survey's Geographic Analysis and Monitoring Program. This research was conducted by the U.S. Geological Survey Western Geographic Science Center. The purpose of this report is to describe the basic elements of the novel Lake Tahoe Basin Land Use Simulation Model, publish samples of the data inputs, basic outputs of the model, and the details of the Python code. The results of this report include a basic description of the Land Use Simulation Model, descriptions and summary statistics of model inputs, two figures showing the graphical user interface from the web-based tool, samples of the two input files, seven tables of basic output results from the web-based tool and descriptions of their parameters, and the fully functional Python code.

WebCN: A web-based computation tool for in situ-produced cosmogenic nuclides

NASA Astrophysics Data System (ADS)

Ma, Xiuzeng; Li, Yingkui; Bourgeois, Mike; Caffee, Marc; Elmore, David; Granger, Darryl; Muzikar, Paul; Smith, Preston

2007-06-01

Cosmogenic nuclide techniques are increasingly being utilized in geoscience research. For this it is critical to establish an effective, easily accessible and well defined tool for cosmogenic nuclide computations. We have been developing a web-based tool (WebCN) to calculate surface exposure ages and erosion rates based on the nuclide concentrations measured by the accelerator mass spectrometry. WebCN for 10Be and 26Al has been finished and published at http://www.physics.purdue.edu/primelab/for_users/rockage.html. WebCN for 36Cl is under construction. WebCN is designed as a three-tier client/server model and uses the open source PostgreSQL for the database management and PHP for the interface design and calculations. On the client side, an internet browser and Microsoft Access are used as application interfaces to access the system. Open Database Connectivity is used to link PostgreSQL and Microsoft Access. WebCN accounts for both spatial and temporal distributions of the cosmic ray flux to calculate the production rates of in situ-produced cosmogenic nuclides at the Earth's surface.

An IoT-Based Solution for Monitoring a Fleet of Educational Buildings Focusing on Energy Efficiency.

PubMed

Amaxilatis, Dimitrios; Akrivopoulos, Orestis; Mylonas, Georgios; Chatzigiannakis, Ioannis

2017-10-10

Raising awareness among young people and changing their behaviour and habits concerning energy usage is key to achieving sustained energy saving. Additionally, young people are very sensitive to environmental protection so raising awareness among children is much easier than with any other group of citizens. This work examines ways to create an innovative Information & Communication Technologies (ICT) ecosystem (including web-based, mobile, social and sensing elements) tailored specifically for school environments, taking into account both the users (faculty, staff, students, parents) and school buildings, thus motivating and supporting young citizens' behavioural change to achieve greater energy efficiency. A mixture of open-source IoT hardware and proprietary platforms on the infrastructure level, are currently being utilized for monitoring a fleet of 18 educational buildings across 3 countries, comprising over 700 IoT monitoring points. Hereon presented is the system's high-level architecture, as well as several aspects of its implementation, related to the application domain of educational building monitoring and energy efficiency. The system is developed based on open-source technologies and services in order to make it capable of providing open IT-infrastructure and support from different commercial hardware/sensor vendors as well as open-source solutions. The system presented can be used to develop and offer new app-based solutions that can be used either for educational purposes or for managing the energy efficiency of the building. The system is replicable and adaptable to settings that may be different than the scenarios envisioned here (e.g., targeting different climate zones), different IT infrastructures and can be easily extended to accommodate integration with other systems. The overall performance of the system is evaluated in real-world environment in terms of scalability, responsiveness and simplicity.

An IoT-Based Solution for Monitoring a Fleet of Educational Buildings Focusing on Energy Efficiency

PubMed Central

Akrivopoulos, Orestis

2017-01-01

Raising awareness among young people and changing their behaviour and habits concerning energy usage is key to achieving sustained energy saving. Additionally, young people are very sensitive to environmental protection so raising awareness among children is much easier than with any other group of citizens. This work examines ways to create an innovative Information & Communication Technologies (ICT) ecosystem (including web-based, mobile, social and sensing elements) tailored specifically for school environments, taking into account both the users (faculty, staff, students, parents) and school buildings, thus motivating and supporting young citizens’ behavioural change to achieve greater energy efficiency. A mixture of open-source IoT hardware and proprietary platforms on the infrastructure level, are currently being utilized for monitoring a fleet of 18 educational buildings across 3 countries, comprising over 700 IoT monitoring points. Hereon presented is the system’s high-level architecture, as well as several aspects of its implementation, related to the application domain of educational building monitoring and energy efficiency. The system is developed based on open-source technologies and services in order to make it capable of providing open IT-infrastructure and support from different commercial hardware/sensor vendors as well as open-source solutions. The system presented can be used to develop and offer new app-based solutions that can be used either for educational purposes or for managing the energy efficiency of the building. The system is replicable and adaptable to settings that may be different than the scenarios envisioned here (e.g., targeting different climate zones), different IT infrastructures and can be easily extended to accommodate integration with other systems. The overall performance of the system is evaluated in real-world environment in terms of scalability, responsiveness and simplicity. PMID:28994719

Web-based access to near real-time and archived high-density time-series data: cyber infrastructure challenges & developments in the open-source Waveform Server

NASA Astrophysics Data System (ADS)

Reyes, J. C.; Vernon, F. L.; Newman, R. L.; Steidl, J. H.

2010-12-01

The Waveform Server is an interactive web-based interface to multi-station, multi-sensor and multi-channel high-density time-series data stored in Center for Seismic Studies (CSS) 3.0 schema relational databases (Newman et al., 2009). In the last twelve months, based on expanded specifications and current user feedback, both the server-side infrastructure and client-side interface have been extensively rewritten. The Python Twisted server-side code-base has been fundamentally modified to now present waveform data stored in cluster-based databases using a multi-threaded architecture, in addition to supporting the pre-existing single database model. This allows interactive web-based access to high-density (broadband @ 40Hz to strong motion @ 200Hz) waveform data that can span multiple years; the common lifetime of broadband seismic networks. The client-side interface expands on it's use of simple JSON-based AJAX queries to now incorporate a variety of User Interface (UI) improvements including standardized calendars for defining time ranges, applying on-the-fly data calibration to display SI-unit data, and increased rendering speed. This presentation will outline the various cyber infrastructure challenges we have faced while developing this application, the use-cases currently in existence, and the limitations of web-based application development.

DXplain: a Web-based diagnostic decision support system for medical students.

PubMed

London, S

1998-01-01

DXplain is a diagnostic decision support program, with a new World Wide Web interface, designed to help medical students and physicians formulate differential diagnoses based on clinical findings. It covers over 2000 diseases and 5000 clinical manifestations. DXplain suggests possible diagnoses, and provides brief descriptions of every disease in the database. Not all diseases are included, nor does DXplain take into account preexisting conditions or the chronological sequence of clinical manifestations. Despite these limitations, it is a useful educational tool, particularly for problem-based learning (PBL) cases and for students in clinical rotations, as it fills a niche not adequately covered by MEDLINE or medical texts. The system is relatively self-explanatory, requiring little or no end-user training. Medical libraries offering, or planning to offer, their users access to Web-based materials and resources may find this system a valuable addition to their electronic collections. Should it prove popular with the local users, provision of access may also establish or enhance the library's image as a partner in medical education.

WebProtégé: A Collaborative Ontology Editor and Knowledge Acquisition Tool for the Web

PubMed Central

Tudorache, Tania; Nyulas, Csongor; Noy, Natalya F.; Musen, Mark A.

2012-01-01

In this paper, we present WebProtégé—a lightweight ontology editor and knowledge acquisition tool for the Web. With the wide adoption of Web 2.0 platforms and the gradual adoption of ontologies and Semantic Web technologies in the real world, we need ontology-development tools that are better suited for the novel ways of interacting, constructing and consuming knowledge. Users today take Web-based content creation and online collaboration for granted. WebProtégé integrates these features as part of the ontology development process itself. We tried to lower the entry barrier to ontology development by providing a tool that is accessible from any Web browser, has extensive support for collaboration, and a highly customizable and pluggable user interface that can be adapted to any level of user expertise. The declarative user interface enabled us to create custom knowledge-acquisition forms tailored for domain experts. We built WebProtégé using the existing Protégé infrastructure, which supports collaboration on the back end side, and the Google Web Toolkit for the front end. The generic and extensible infrastructure allowed us to easily deploy WebProtégé in production settings for several projects. We present the main features of WebProtégé and its architecture and describe briefly some of its uses for real-world projects. WebProtégé is free and open source. An online demo is available at http://webprotege.stanford.edu. PMID:23807872

Development of a telemedicine model for emerging countries: a case study on pediatric oncology in Brazil.

PubMed

Hira, A Y; Nebel de Mello, A; Faria, R A; Odone Filho, V; Lopes, R D; Zuffo, M K

2006-01-01

This article discusses a telemedicine model for emerging countries, through the description of ONCONET, a telemedicine initiative applied to pediatric oncology in Brazil. The ONCONET core technology is a Web-based system that offers health information and other services specialized in childhood cancer such as electronic medical records and cooperative protocols for complex treatments. All Web-based services are supported by the use of high performance computing infrastructure based on clusters of commodity computers. The system was fully implemented on an open-source and free-software approach. Aspects of modeling, implementation and integration are covered. A model, both technologically and economically viable, was created through the research and development of in-house solutions adapted to the emerging countries reality and with focus on scalability both in the total number of patients and in the national infrastructure.

SMARTe: A FREE Web-Based Tool To Help Communities Overcome Revitalization Obstacles

EPA Science Inventory

SMARTe (Sustainable Management Approaches and Revitalization Tools -electronic) is a web-based decision support tool developed by the Office of Research and Development (ORD) in partnership with the Office of Brownfields and Land Revitali...

A web-based clinical decision tool to support treatment decision-making in psychiatry: a pilot focus group study with clinicians, patients and carers.

PubMed

Henshall, Catherine; Marzano, Lisa; Smith, Katharine; Attenburrow, Mary-Jane; Puntis, Stephen; Zlodre, Jakov; Kelly, Kathleen; Broome, Matthew R; Shaw, Susan; Barrera, Alvaro; Molodynski, Andrew; Reid, Alastair; Geddes, John R; Cipriani, Andrea

2017-07-21

Treatment decision tools have been developed in many fields of medicine, including psychiatry, however benefits for patients have not been sustained once the support is withdrawn. We have developed a web-based computerised clinical decision support tool (CDST), which can provide patients and clinicians with continuous, up-to-date, personalised information about the efficacy and tolerability of competing interventions. To test the feasibility and acceptability of the CDST we conducted a focus group study, aimed to explore the views of clinicians, patients and carers. The CDST was developed in Oxford. To tailor treatments at an individual level, the CDST combines the best available evidence from the scientific literature with patient preferences and values, and with patient medical profile to generate personalised clinical recommendations. We conducted three focus groups comprising of three different participant types: consultant psychiatrists, participants with a mental health diagnosis and/or experience of caring for someone with a mental health diagnosis, and primary care practitioners and nurses. Each 1-h focus group started with a short visual demonstration of the CDST. To standardise the discussion during the focus groups, we used the same topic guide that covered themes relating to the acceptability and usability of the CDST. Focus groups were recorded and any identifying participant details were anonymised. Data were analysed thematically and managed using the Framework method and the constant comparative method. The focus groups took place in Oxford between October 2016 and January 2017. Overall 31 participants attended (12 consultants, 11 primary care practitioners and 8 patients or carers). The main themes that emerged related to CDST applications in clinical practice, communication, conflicting priorities, record keeping and data management. CDST was considered a useful clinical decision support, with recognised value in promoting clinician-patient collaboration and contributing to the development of personalised medicine. One major benefit of the CDST was perceived to be the open discussion about the possible side-effects of medications. Participants from all the three groups, however, universally commented that the terminology and language presented on the CDST were too medicalised, potentially leading to ethical issues around consent to treatment. The CDST can improve communication pathways between patients, carers and clinicians, identifying care priorities and providing an up-to-date platform for implementing evidence-based practice, with regard to prescribing practices.

Development of a Web-Based Registry to Support Diabetes Care in Free Medical Clinics

PubMed Central

McFadden, Norman; Daniel, Bryan; Hoyt, Robert; Snider, Dallas

2017-01-01

The United States has more than 1,000 free medical clinics. Because these clinics do not bill Medicare or Medicaid, they are not eligible for federal reimbursement for electronic health record (EHR) adoption. As a result, most do not have EHRs or electronic disease registries. A web-based diabetes registry was created with all open-source components for use in an urban free clinic to manage patients with type 2 diabetes and comorbidities. The registry was modeled after the Chronic Disease Electronic Management System and recommendations of the American Diabetes Association. The software was enhanced to include multiple other features, such as progress notes, so that it can function as a simple EHR. The configuration permits other free clinics to join securely, and the software can be shared. PMID:28566990

ShinyGPAS: interactive genomic prediction accuracy simulator based on deterministic formulas.

PubMed

Morota, Gota

2017-12-20

Deterministic formulas for the accuracy of genomic predictions highlight the relationships among prediction accuracy and potential factors influencing prediction accuracy prior to performing computationally intensive cross-validation. Visualizing such deterministic formulas in an interactive manner may lead to a better understanding of how genetic factors control prediction accuracy. The software to simulate deterministic formulas for genomic prediction accuracy was implemented in R and encapsulated as a web-based Shiny application. Shiny genomic prediction accuracy simulator (ShinyGPAS) simulates various deterministic formulas and delivers dynamic scatter plots of prediction accuracy versus genetic factors impacting prediction accuracy, while requiring only mouse navigation in a web browser. ShinyGPAS is available at: https://chikudaisei.shinyapps.io/shinygpas/ . ShinyGPAS is a shiny-based interactive genomic prediction accuracy simulator using deterministic formulas. It can be used for interactively exploring potential factors that influence prediction accuracy in genome-enabled prediction, simulating achievable prediction accuracy prior to genotyping individuals, or supporting in-class teaching. ShinyGPAS is open source software and it is hosted online as a freely available web-based resource with an intuitive graphical user interface.

Automation Hooks Architecture Trade Study for Flexible Test Orchestration

NASA Technical Reports Server (NTRS)

Lansdowne, Chatwin A.; Maclean, John R.; Graffagnino, Frank J.; McCartney, Patrick A.

2010-01-01

We describe the conclusions of a technology and communities survey supported by concurrent and follow-on proof-of-concept prototyping to evaluate feasibility of defining a durable, versatile, reliable, visible software interface to support strategic modularization of test software development. The objective is that test sets and support software with diverse origins, ages, and abilities can be reliably integrated into test configurations that assemble and tear down and reassemble with scalable complexity in order to conduct both parametric tests and monitored trial runs. The resulting approach is based on integration of three recognized technologies that are currently gaining acceptance within the test industry and when combined provide a simple, open and scalable test orchestration architecture that addresses the objectives of the Automation Hooks task. The technologies are automated discovery using multicast DNS Zero Configuration Networking (zeroconf), commanding and data retrieval using resource-oriented Restful Web Services, and XML data transfer formats based on Automatic Test Markup Language (ATML). This open-source standards-based approach provides direct integration with existing commercial off-the-shelf (COTS) analysis software tools.

An exploratory mixed-methods crossover study comparing DVD- vs. Web-based patient decision support in three conditions: The importance of patient perspectives.

PubMed

Halley, Meghan C; Rendle, Katharine A S; Gillespie, Katherine A; Stanley, Katherine M; Frosch, Dominick L

2015-12-01

The last 15 years have witnessed considerable progress in the development of decision support interventions (DESIs). However, fundamental questions about design and format of delivery remain. An exploratory, randomized mixed-method crossover study was conducted to compare a DVD- and Web-based DESI. Randomized participants used either the Web or the DVD first, followed by the alternative format. Participants completed a questionnaire to assess decision-specific knowledge at baseline and a questionnaire and structured qualitative interview after viewing each format. Tracking software was used to capture Web utilization. Transcripts were analyzed using integrated inductive and deductive approaches. Quantitative data were analyzed using exploratory bivariate and multivariate analyses. Exploratory knowledge analyses suggest that both formats increased knowledge, with limited evidence that the DVD increased knowledge more than the Web. Format preference varied across participants: 44% preferred the Web, 32% preferred the DVD and 24% preferred 'both'. Patient discussions of preferences for DESI information structure and the importance of a patients' stage of a given decision suggest these characteristics may be important factors underlying variation in utilization, format preferences and knowledge outcomes. Our results suggest that both DESI formats effectively increase knowledge. Patients' perceptions of these two formats further suggest that there may be no single 'best' format for all patients. These results have important implications for understanding why different DESI formats might be preferable to and more effective for different patients. Further research is needed to explore the relationship between these factors and DESI utilization outcomes across diverse patient populations. © 2014 John Wiley & Sons Ltd.

Application of a web-based Decision Support System in risk management

NASA Astrophysics Data System (ADS)

Aye, Zar Chi; Jaboyedoff, Michel; Derron, Marc-Henri

2013-04-01

Increasingly, risk information is widely available with the help of advanced technologies such as earth observation satellites, global positioning technologies, coupled with hazard modeling and analysis, and geographical information systems (GIS). Even though it exists, no effort will be put into action if it is not properly presented to the decision makers. These information need to be communicated clearly and show its usefulness so that people can make better informed decision. Therefore, communicating available risk information has become an important challenge and decision support systems have been one of the significant approaches which can help not only in presenting risk information to the decision makers but also in making efficient decisions while reducing human resources and time needed. In this study, the conceptual framework of an internet-based decision support system is presented to highlight its importance role in risk management framework and how it can be applied in case study areas chosen. The main purpose of the proposed system is to facilitate the available risk information in risk reduction by taking into account of the changes in climate, land use and socio-economic along with the risk scenarios. It allows the users to formulate, compare and select risk reduction scenarios (mainly for floods and landslides) through an enhanced participatory platform with diverse stakeholders' involvement in the decision making process. It is based on the three-tier (client-server) architecture which integrates web-GIS plus DSS functionalities together with cost benefit analysis and other supporting tools. Embedding web-GIS provides its end users to make better planning and informed decisions referenced to a geographical location, which is the one of the essential factors in disaster risk reduction programs. Different risk reduction measures of a specific area (local scale) will be evaluated using this web-GIS tool, available risk scenarios obtained from Probabilistic Risk Assessment (PRA) model and the knowledge collected from experts. The visualization of the risk reduction scenarios can also be shared among the users on the web to support the on-line participatory process. In addition, cost-benefit ratios of the different risk reduction scenarios can be prepared in order to serve as inputs for high-level decision makers. The most appropriate risk reduction scenarios will be chosen using Multi-Criteria Evaluation (MCE) method by weighting different parameters according to the preferences and criteria defined by the users. The role of public participation has been changing from one-way communication between authorities, experts, stakeholders and citizens towards more intensive two-way interaction. Involving the affected public and interest groups can enhance the level of legitimacy, transparency, and confidence in the decision making process. Due to its important part in decision making, online participatory tool is included in the DSS in order to allow the involved stakeholders interactively in risk reduction and be aware of the existing vulnerability conditions of the community. Moreover, it aims to achieve a more transparent and better informed decision-making process. The system is under in progress and the first tools implemented will be presented showing the wide possibilities of new web technologies which can have a great impact on the decision making process. It will be applied in four pilot areas in Europe: French Alps, North Eastern Italy, Romania and Poland. Nevertheless, the framework will be designed and implemented in a way to be applicable in any other regions.

A Web-Based Decision Support System for Assessing Regional Water-Quality Conditions and Management Actions

USGS Publications Warehouse

Booth, N.L.; Everman, E.J.; Kuo, I.-L.; Sprague, L.; Murphy, L.

2011-01-01

The U.S. Geological Survey National Water Quality Assessment Program has completed a number of water-quality prediction models for nitrogen and phosphorus for the conterminous United States as well as for regional areas of the nation. In addition to estimating water-quality conditions at unmonitored streams, the calibrated SPAtially Referenced Regressions On Watershed attributes (SPARROW) models can be used to produce estimates of yield, flow-weighted concentration, or load of constituents in water under various land-use condition, change, or resource management scenarios. A web-based decision support infrastructure has been developed to provide access to SPARROW simulation results on stream water-quality conditions and to offer sophisticated scenario testing capabilities for research and water-quality planning via a graphical user interface with familiar controls. The SPARROW decision support system (DSS) is delivered through a web browser over an Internet connection, making it widely accessible to the public in a format that allows users to easily display water-quality conditions and to describe, test, and share modeled scenarios of future conditions. SPARROW models currently supported by the DSS are based on the modified digital versions of the 1:500,000-scale River Reach File (RF1) and 1:100,000-scale National Hydrography Dataset (medium-resolution, NHDPlus) stream networks. ?? 2011 American Water Resources Association. This article is a U.S. Government work and is in the public domain in the USA.

WMS and WFS Standards Implementation of Weather Data

NASA Astrophysics Data System (ADS)

Armstrong, M.

2005-12-01

CustomWeather is private weather company that delivers global weather data products. CustomWeather has built a mapping platform according to OGC standards. Currently, both a Web Mapping Service (WMS) and Web Feature Service (WFS) are supported by CustomWeather. Supporting open geospatial standards has lead to number of positive changes internally to the processes of CustomWeather, along with those of the clients accessing the data. Quite a number of challenges surfaced during this process, particularly with respect to combining a wide variety of raw modeling and sensor data into a single delivery platform. Open standards have, however, made the delivery of very different data products rather seamless. The discussion will address the issues faced in building an OGC-based mapping platform along with the limitations encountered. While the availability of these data products through open standards is still very young, there have already been many adopters in the utility and navigation industries. The discussion will take a closer look at the different approach taken by these two industries as they utilize interoperability standards with existing data. Insight will be given in regards to applications already taking advantage of this new technology and how this is affecting decision-making processes. CustomWeather has observed considerable interest and potential benefit in this technology from developing countries. Weather data is a key element in disaster management. Interoperability is literally opening up a world of data and has the potential to quickly enable functionality that would otherwise take considerable time to implement. The discussion will briefly touch on our experience.

Managing and Integrating Open Environmental Data - Technological Requirements and Challenges

NASA Astrophysics Data System (ADS)

Devaraju, Anusuriya; Kunkel, Ralf; Jirka, Simon

2014-05-01

Understanding environment conditions and trends requires information. This information is usually generated from sensor observations. Today, several infrastructures (e.g., GEOSS, EarthScope, NEON, NETLAKE, OOI, TERENO, WASCAL, and PEER-EurAqua) have been deployed to promote full and open exchange of environmental data. Standards for interfaces as well as data models/formats (OGC, CUAHSI, INSPIRE, SEE Grid, ISO) and open source tools have been developed to support seamless data exchange between various domains and organizations. In spite of this growing interest, it remains a challenge to manage and integrate open environmental data on the fly due to the distributed and heterogeneous nature of the data. Intuitive tools and standardized interfaces are vital to hide the technical complexity of underlying data management infrastructures. Meaningful descriptions of raw sensor data are necessary to achieve interoperability among different sources. As raw sensor data sets usually goes through several layers of summarization and aggregation, metadata and quality measures associated with these should be captured. Further processing of sensor data sets requires that they should be made compatible with existing environmental models. We need data policies and management plans on how to handle and publish open sensor data coming from different institutions. Clearly, a better management and usability of open environmental data is crucial, not only to gather large amounts of data, but also to cater various aspects such as data integration, privacy and trust, uncertainty, quality control, visualization, and data management policies. The proposed talk presents several key findings in terms of requirements, ongoing developments and technical challenges concerning these aspects from our recent work. This includes two workshops on open observation data and supporting tools, as well as the long-term environmental monitoring initiatives such as TERENO and TERENO-MED. Workshops Details: Spin the Sensor Web: Sensor Web Workshop 2013, Muenster, 21st-22nd November 2013 (http://52north.org/news/spin-the-sensor-web-sensor-web-workshop-2013) Special Session on Management of Open Environmental Observation Data - MOEOD 2014, Lisbon, 8th January 2014 (http://www.sensornets.org/MOEOD.aspx?y=2014) Monitoring Networks: TERENO : http://teodoor.icg.kfa-juelich.de/ TERENO-MED : http://www.tereno-med.net/

An Offline-Online Android Application for Hazard Event Mapping Using WebGIS Open Source Technologies

NASA Astrophysics Data System (ADS)

Olyazadeh, Roya; Jaboyedoff, Michel; Sudmeier-Rieux, Karen; Derron, Marc-Henri; Devkota, Sanjaya

2016-04-01

Nowadays, Free and Open Source Software (FOSS) plays an important role in better understanding and managing disaster risk reduction around the world. National and local government, NGOs and other stakeholders are increasingly seeking and producing data on hazards. Most of the hazard event inventories and land use mapping are based on remote sensing data, with little ground truthing, creating difficulties depending on the terrain and accessibility. Open Source WebGIS tools offer an opportunity for quicker and easier ground truthing of critical areas in order to analyse hazard patterns and triggering factors. This study presents a secure mobile-map application for hazard event mapping using Open Source WebGIS technologies such as Postgres database, Postgis, Leaflet, Cordova and Phonegap. The objectives of this prototype are: 1. An Offline-Online android mobile application with advanced Geospatial visualisation; 2. Easy Collection and storage of events information applied services; 3. Centralized data storage with accessibility by all the service (smartphone, standard web browser); 4. Improving data management by using active participation in hazard event mapping and storage. This application has been implemented as a low-cost, rapid and participatory method for recording impacts from hazard events and includes geolocation (GPS data and Internet), visualizing maps with overlay of satellite images, viewing uploaded images and events as cluster points, drawing and adding event information. The data can be recorded in offline (Android device) or online version (all browsers) and consequently uploaded through the server whenever internet is available. All the events and records can be visualized by an administrator and made public after approval. Different user levels can be defined to access the data for communicating the information. This application was tested for landslides in post-earthquake Nepal but can be used for any other type of hazards such as flood, avalanche, etc. Keywords: Offline, Online, WebGIS Open source, Android, Hazard Event Mapping

A WebGIS platform for the monitoring of Farm Animal Genetic Resources (GENMON).

PubMed

Duruz, Solange; Flury, Christine; Matasci, Giona; Joerin, Florent; Widmer, Ivo; Joost, Stéphane

2017-01-01

In 2007, the Food and Agriculture Organization of the United Nations (FAO) initiated the Global plan of action for Farm Animal Genetic Resources (FAnGR). The main goal of this plan is to reduce further loss of genetic diversity in farm animals, so as to protect and promote the diversity of farm animal resources. An important step to reach this goal is to monitor and prioritize endangered breeds in the context of conservation programs. The GENMON WebGIS platform is able to monitor FAnGR and to evaluate the degree of endangerment of livestock breeds. The system takes into account pedigree and introgression information, the geographical concentration of animals, the cryo-conservation plan and the sustainability of breeding activities based on socio-economic data as well as present and future land use conditions. A multi-criteria decision tool supports the aggregation of the multi-thematic indices mentioned above using the MACBETH method, which is based on a weighted average using satisfaction thresholds. GENMON is a monitoring tool to reach subjective decisions made by a government agency. It relies on open source software and is available at http://lasigsrv2.epfl.ch/genmon-ch. GENMON allows users to upload pedigree-information (animal ID, parents, birthdate, sex, location and introgression) from a specific livestock breed and to define species and/or region-specific weighting parameters and thresholds. The program then completes a pedigree analysis and derives several indices that are used to calculate an integrated score of conservation prioritization for the breeds under investigation. The score can be visualized on a geographic map and allows a fast, intuitive and regional identification of breeds in danger. Appropriate conservation actions and breeding programs can thus be undertaken in order to promote the recovery of the genetic diversity in livestock breeds in need. The use of the platform is illustrated by means of an example based on three local livestock breeds from different species in Switzerland.

Open source marketing: Camel cigarette brand marketing in the "Web 2.0" world.

PubMed

Freeman, B; Chapman, S

2009-06-01

The international trend towards comprehensive bans on tobacco advertising has seen the tobacco industry become increasingly innovative in its approach to marketing. Further fuelling this innovation is the rapid evolution and accessibility of web-based technology. The internet, as a relatively unregulated marketing environment, provides many opportunities for tobacco companies to pursue their promotional ambitions. In this paper, "open source marketing" is considered as a vehicle that has been appropriated by the tobacco industry, through a case study of efforts to design the packaging for the Camel Signature Blends range of cigarettes. Four sources are used to explore this case study including a marketing literature search, a web-based content search via the Google search engine, interviews with advertising trade informants and an analysis of the Camel brand website. RJ Reynolds (RJR) has proven to be particularly innovative in designing cigarette packaging. RJR engaged with thousands of consumers through their Camel brand website to design four new cigarette flavours and packages. While the Camel Signature Blends packaging designs were subsequently modified for the retail market due to problems arising with their cartoon-like imagery, important lessons arise on how the internet blurs the line between marketing and market research. Open source marketing has the potential to exploit advertising ban loopholes and stretch legal definitions in order to generate positive word of mouth about tobacco products. There are also lessons in the open source marketing movement for more effective tobacco control measures including interactive social marketing campaigns and requiring plain packaging of tobacco products.

The 2nd Generation Real Time Mission Monitor (RTMM) Development

NASA Technical Reports Server (NTRS)

Blakeslee, Richard; Goodman, Michael; Meyer, Paul; Hardin, Danny; Hall, John; He, Yubin; Regner, Kathryn; Conover, Helen; Smith, Tammy; Lu, Jessica;

OntoTrader: An Ontological Web Trading Agent Approach for Environmental Information Retrieval

PubMed Central

Iribarne, Luis; Padilla, Nicolás; Ayala, Rosa; Asensio, José A.; Criado, Javier

2014-01-01

Modern Web-based Information Systems (WIS) are becoming increasingly necessary to provide support for users who are in different places with different types of information, by facilitating their access to the information, decision making, workgroups, and so forth. Design of these systems requires the use of standardized methods and techniques that enable a common vocabulary to be defined to represent the underlying knowledge. Thus, mediation elements such as traders enrich the interoperability of web components in open distributed systems. These traders must operate with other third-party traders and/or agents in the system, which must also use a common vocabulary for communication between them. This paper presents the OntoTrader architecture, an Ontological Web Trading agent based on the OMG ODP trading standard. It also presents the ontology needed by some system agents to communicate with the trading agent and the behavioral framework for the SOLERES OntoTrader agent, an Environmental Management Information System (EMIS). This framework implements a “Query-Searching/Recovering-Response” information retrieval model using a trading service, SPARQL notation, and the JADE platform. The paper also presents reflection, delegation and, federation mediation models and describes formalization, an experimental testing environment in three scenarios, and a tool which allows our proposal to be evaluated and validated. PMID:24977211

OntoTrader: an ontological Web trading agent approach for environmental information retrieval.

PubMed

Iribarne, Luis; Padilla, Nicolás; Ayala, Rosa; Asensio, José A; Criado, Javier

2014-01-01

Modern Web-based Information Systems (WIS) are becoming increasingly necessary to provide support for users who are in different places with different types of information, by facilitating their access to the information, decision making, workgroups, and so forth. Design of these systems requires the use of standardized methods and techniques that enable a common vocabulary to be defined to represent the underlying knowledge. Thus, mediation elements such as traders enrich the interoperability of web components in open distributed systems. These traders must operate with other third-party traders and/or agents in the system, which must also use a common vocabulary for communication between them. This paper presents the OntoTrader architecture, an Ontological Web Trading agent based on the OMG ODP trading standard. It also presents the ontology needed by some system agents to communicate with the trading agent and the behavioral framework for the SOLERES OntoTrader agent, an Environmental Management Information System (EMIS). This framework implements a "Query-Searching/Recovering-Response" information retrieval model using a trading service, SPARQL notation, and the JADE platform. The paper also presents reflection, delegation and, federation mediation models and describes formalization, an experimental testing environment in three scenarios, and a tool which allows our proposal to be evaluated and validated.

The QuakeSim Project: Web Services for Managing Geophysical Data and Applications

NASA Astrophysics Data System (ADS)

Pierce, Marlon E.; Fox, Geoffrey C.; Aktas, Mehmet S.; Aydin, Galip; Gadgil, Harshawardhan; Qi, Zhigang; Sayar, Ahmet

2008-04-01

We describe our distributed systems research efforts to build the “cyberinfrastructure” components that constitute a geophysical Grid, or more accurately, a Grid of Grids. Service-oriented computing principles are used to build a distributed infrastructure of Web accessible components for accessing data and scientific applications. Our data services fall into two major categories: Archival, database-backed services based around Geographical Information System (GIS) standards from the Open Geospatial Consortium, and streaming services that can be used to filter and route real-time data sources such as Global Positioning System data streams. Execution support services include application execution management services and services for transferring remote files. These data and execution service families are bound together through metadata information and workflow services for service orchestration. Users may access the system through the QuakeSim scientific Web portal, which is built using a portlet component approach.

Sharing on Web 3d Models of Ancient Theatres. a Methodological Workflow

NASA Astrophysics Data System (ADS)

Scianna, A.; La Guardia, M.; Scaduto, M. L.

2016-06-01

In the last few years, the need to share on the Web the knowledge of Cultural Heritage (CH) through navigable 3D models has increased. This need requires the availability of Web-based virtual reality systems and 3D WEBGIS. In order to make the information available to all stakeholders, these instruments should be powerful and at the same time very user-friendly. However, research and experiments carried out so far show that a standardized methodology doesn't exist. All this is due both to complexity and dimensions of geometric models to be published, on the one hand, and to excessive costs of hardware and software tools, on the other. In light of this background, the paper describes a methodological approach for creating 3D models of CH, freely exportable on the Web, based on HTML5 and free and open source software. HTML5, supporting the WebGL standard, allows the exploration of 3D spatial models using most used Web browsers like Chrome, Firefox, Safari, Internet Explorer. The methodological workflow here described has been tested for the construction of a multimedia geo-spatial platform developed for three-dimensional exploration and documentation of the ancient theatres of Segesta and of Carthage, and the surrounding landscapes. The experimental application has allowed us to explore the potential and limitations of sharing on the Web of 3D CH models based on WebGL standard. Sharing capabilities could be extended defining suitable geospatial Web-services based on capabilities of HTML5 and WebGL technology.

A study on spatial decision support systems for HIV/AIDS prevention based on COM GIS technology

NASA Astrophysics Data System (ADS)

Yang, Kun; Luo, Huasong; Peng, Shungyun; Xu, Quanli

2007-06-01

Based on the deeply analysis of the current status and the existing problems of GIS technology applications in Epidemiology, this paper has proposed the method and process for establishing the spatial decision support systems of AIDS epidemic prevention by integrating the COM GIS, Spatial Database, GPS, Remote Sensing, and Communication technologies, as well as ASP and ActiveX software development technologies. One of the most important issues for constructing the spatial decision support systems of AIDS epidemic prevention is how to integrate the AIDS spreading models with GIS. The capabilities of GIS applications in the AIDS epidemic prevention have been described here in this paper firstly. Then some mature epidemic spreading models have also been discussed for extracting the computation parameters. Furthermore, a technical schema has been proposed for integrating the AIDS spreading models with GIS and relevant geospatial technologies, in which the GIS and model running platforms share a common spatial database and the computing results can be spatially visualized on Desktop or Web GIS clients. Finally, a complete solution for establishing the decision support systems of AIDS epidemic prevention has been offered in this paper based on the model integrating methods and ESRI COM GIS software packages. The general decision support systems are composed of data acquisition sub-systems, network communication sub-systems, model integrating sub-systems, AIDS epidemic information spatial database sub-systems, AIDS epidemic information querying and statistical analysis sub-systems, AIDS epidemic dynamic surveillance sub-systems, AIDS epidemic information spatial analysis and decision support sub-systems, as well as AIDS epidemic information publishing sub-systems based on Web GIS.

SMARTE: IMPROVING REVITALIZATION DECISIONS (BERLIN, GERMANY)

EPA Science Inventory

The U.S.-German Bilateral Working Group is developing Site-specific Management Approaches and Redevelopment Tools (SMART). In the U.S., the SMART compilation is housed in a web-based, decision support tool called SMARTe. All tools within SMARTe that are developed specifically for...

cPath: open source software for collecting, storing, and querying biological pathways.

PubMed

Cerami, Ethan G; Bader, Gary D; Gross, Benjamin E; Sander, Chris

2006-11-13

Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling.

A web-based library consult service for evidence-based medicine: Technical development.

PubMed

Schwartz, Alan; Millam, Gregory

2006-03-16

Incorporating evidence based medicine (EBM) into clinical practice requires clinicians to learn to efficiently gain access to clinical evidence and effectively appraise its validity. Even using current electronic systems, selecting literature-based data to solve a single patient-related problem can require more time than practicing physicians or residents can spare. Clinical librarians, as informationists, are uniquely suited to assist physicians in this endeavor. To improve support for evidence-based practice, we have developed a web-based EBM library consult service application (LCS). Librarians use the LCS system to provide full text evidence-based literature with critical appraisal in response to a clinical question asked by a remote physician. LCS uses an entirely Free/Open Source Software platform and will be released under a Free Software license. In the first year of the LCS project, the software was successfully developed and a reference implementation put into active use. Two years of evaluation of the clinical, educational, and attitudinal impact on physician-users and librarian staff are underway, and expected to lead to refinement and wide dissemination of the system. A web-based EBM library consult model may provide a useful way for informationists to assist clinicians, and is feasible to implement.

GIS embedded hydrological modeling: the SID&GRID project

NASA Astrophysics Data System (ADS)

Borsi, I.; Rossetto, R.; Schifani, C.

2012-04-01

The SID&GRID research project, started April 2010 and funded by Regione Toscana (Italy) under the POR FSE 2007-2013, aims to develop a Decision Support System (DSS) for water resource management and planning based on open source and public domain solutions. In order to quantitatively assess water availability in space and time and to support the planning decision processes, the SID&GRID solution consists of hydrological models (coupling 3D existing and newly developed surface- and ground-water and unsaturated zone modeling codes) embedded in a GIS interface, applications and library, where all the input and output data are managed by means of DataBase Management System (DBMS). A graphical user interface (GUI) to manage, analyze and run the SID&GRID hydrological models based on open source gvSIG GIS framework (Asociación gvSIG, 2011) and a Spatial Data Infrastructure to share and interoperate with distributed geographical data is being developed. Such a GUI is thought as a "master control panel" able to guide the user from pre-processing spatial and temporal data, running the hydrological models, and analyzing the outputs. To achieve the above-mentioned goals, the following codes have been selected and are being integrated: 1. Postgresql/PostGIS (PostGIS, 2011) for the Geo Data base Management System; 2. gvSIG with Sextante (Olaya, 2011) geo-algorithm library capabilities and Grass tools (GRASS Development Team, 2011) for the desktop GIS; 3. Geoserver and Geonetwork to share and discover spatial data on the web according to Open Geospatial Consortium; 4. new tools based on the Sextante GeoAlgorithm framework; 5. MODFLOW-2005 (Harbaugh, 2005) groundwater modeling code; 6. MODFLOW-LGR (Mehl and Hill 2005) for local grid refinement; 7. VSF (Thoms et al., 2006) for the variable saturated flow component; 8. new developed routines for overland flow; 9. new algorithms in Jython integrated in gvSIG to compute the net rainfall rate reaching the soil surface, as input for the unsaturated/saturated flow model. At this stage of the research (which will end April 2013), two primary components of the master control panel are being developed: i. a SID&GRID toolbar integrated into gvSIG map context; ii. a new Sextante set of geo-algorithm to pre- and post-process the spatial data to run the hydrological models. The groundwater part of the code has been fully integrated and tested and 3D visualization tools are being developed. The LGR capability has been extended to the 3D solution of the Richards' equation in order to solve in detail the unsaturated zone where required. To be updated about the project, please follow us at the website: http://ut11.isti.cnr.it/SIDGRID/

Web-based, GPU-accelerated, Monte Carlo simulation and visualization of indirect radiation imaging detector performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dong, Han; Sharma, Diksha; Badano, Aldo, E-mail: aldo.badano@fda.hhs.gov

2014-12-15

Purpose: Monte Carlo simulations play a vital role in the understanding of the fundamental limitations, design, and optimization of existing and emerging medical imaging systems. Efforts in this area have resulted in the development of a wide variety of open-source software packages. One such package, hybridMANTIS, uses a novel hybrid concept to model indirect scintillator detectors by balancing the computational load using dual CPU and graphics processing unit (GPU) processors, obtaining computational efficiency with reasonable accuracy. In this work, the authors describe two open-source visualization interfaces, webMANTIS and visualMANTIS to facilitate the setup of computational experiments via hybridMANTIS. Methods: Themore » visualization tools visualMANTIS and webMANTIS enable the user to control simulation properties through a user interface. In the case of webMANTIS, control via a web browser allows access through mobile devices such as smartphones or tablets. webMANTIS acts as a server back-end and communicates with an NVIDIA GPU computing cluster that can support multiuser environments where users can execute different experiments in parallel. Results: The output consists of point response and pulse-height spectrum, and optical transport statistics generated by hybridMANTIS. The users can download the output images and statistics through a zip file for future reference. In addition, webMANTIS provides a visualization window that displays a few selected optical photon path as they get transported through the detector columns and allows the user to trace the history of the optical photons. Conclusions: The visualization tools visualMANTIS and webMANTIS provide features such as on the fly generation of pulse-height spectra and response functions for microcolumnar x-ray imagers while allowing users to save simulation parameters and results from prior experiments. The graphical interfaces simplify the simulation setup and allow the user to go directly from specifying input parameters to receiving visual feedback for the model predictions.« less

Guiding Learners into Reengagement through the SCALE Environment: An Empirical Study

ERIC Educational Resources Information Center

Verginis, Ilias; Gouli, Evangelia; Gogoulou, Agoritsa; Grigoriadou, Maria

2011-01-01

The paper presents the facilities offered by the open learner model maintained in the web-based, adaptive, activity-oriented learning environment SCALE (Supporting Collaboration and Adaptation in a Learning Environment), in order to guide online students who become disengaged and support their reengagement. The open learner model (OLM_SCALE)…

Open-Source, Web-Based Dashboard Components for DICOM Connectivity.

PubMed

Bustamante, Catalina; Pineda, Julian; Rascovsky, Simon; Arango, Andres

2016-08-01

The administration of a DICOM network within an imaging healthcare institution requires tools that allow for monitoring of connectivity and availability for adequate uptime measurements and help guide technology management strategies. We present the implementation of an open-source widget for the Dashing framework that provides basic dashboard functionality allowing for monitoring of a DICOM network using network "ping" and DICOM "C-ECHO" operations.

Panorama: A Targeted Proteomics Knowledge Base

PubMed Central

2015-01-01

Panorama is a web application for storing, sharing, analyzing, and reusing targeted assays created and refined with Skyline,1 an increasingly popular Windows client software tool for targeted proteomics experiments. Panorama allows laboratories to store and organize curated results contained in Skyline documents with fine-grained permissions, which facilitates distributed collaboration and secure sharing of published and unpublished data via a web-browser interface. It is fully integrated with the Skyline workflow and supports publishing a document directly to a Panorama server from the Skyline user interface. Panorama captures the complete Skyline document information content in a relational database schema. Curated results published to Panorama can be aggregated and exported as chromatogram libraries. These libraries can be used in Skyline to pick optimal targets in new experiments and to validate peak identification of target peptides. Panorama is open-source and freely available. It is distributed as part of LabKey Server,2 an open source biomedical research data management system. Laboratories and organizations can set up Panorama locally by downloading and installing the software on their own servers. They can also request freely hosted projects on https://panoramaweb.org, a Panorama server maintained by the Department of Genome Sciences at the University of Washington. PMID:25102069

A comparison of web-based versus print-based decision AIDS for prostate cancer screening: participants' evaluation and utilization.

PubMed

Tomko, Catherine; Davis, Kimberly M; Luta, George; Krist, Alexander H; Woolf, Steven H; Taylor, Kathryn L

2015-01-01

Patient decision aids facilitate informed decision making for medical tests and procedures that have uncertain benefits. To describe participants' evaluation and utilization of print-based and web-based prostate cancer screening decision aids that were found to improve decisional outcomes in a prior randomized controlled trial. Men completed brief telephone interviews at baseline, one month, and 13 months post-randomization. Participants were primary care patients, 45-70 years old, who received the print-based (N = 628) or web-based decision aid (N = 625) and completed the follow-up assessments. We assessed men's baseline preference for web-based or print-based materials, time spent using the decision aids, comprehension of the overall message, and ratings of the content. Decision aid use was self-reported by 64.3 % (web) and 81.8 % (print) of participants. Significant predictors of decision aid use were race (white vs. non-white, OR = 2.43, 95 % CI: 1.77, 3.35), higher education (OR = 1.68, 95 % CI: 1.06, 2.70) and trial arm (print vs. web, OR = 2.78, 95 % CI: 2.03, 3.83). Multivariable analyses indicated that web-arm participants were more likely to use the website when they preferred web-based materials (OR: 1.91, CI: 1.17, 3.12), whereas use of the print materials was not significantly impacted by a preference for print-based materials (OR: 0.69, CI: 0.38, 1.25). Comprehension of the decision aid message (i.e., screening is an individual decision) did not significantly differ between arms in adjusted analyses (print: 61.9 % and web: 68.2 %, p = 0.42). Decision aid use was independently influenced by race, education, and the decision aid medium, findings consistent with the 'digital divide.' These results suggest that when it is not possible to provide this age cohort with their preferred decision aid medium, print materials will be more highly used than web-based materials. Although there are many advantages to web-based decision aids, providing an option for print-based decision aids should be considered.

Vulnerability Assessment of Open Source Wireshark and Chrome Browser

DTIC Science & Technology

2013-08-01

UNLIMITED 5 We spent much of the initial time learning about the logical model that modern HTML5 web browsers support, including how users interact with...are supposed to protect users of that site against cross-site scripting) and the new powerful an all-encompassing HTML5 standard. This vulnerability

T-Check in Technologies for Interoperability: Web Services and Security--Single Sign-On

DTIC Science & Technology

2007-12-01

following tools: • Apache Tomcat 6.0—a Java Servlet container to host the Web services and a simple Web client application [Apache 2007a] • Apache Axis...Eclipse. Eclipse – an open development platform. http://www.eclipse.org/ (2007) [Hunter 2001] Hunter, Jason. Java Servlet Programming, 2nd Edition...Citation SAML 1.1 Java Toolkit SAML Ping Identity’s SAML-1.1 implementation [SourceID 2006] OpenSAML SAML An open source implementation of SAML 1.1

Advancing the Implementation of Hydrologic Models as Web-based Applications

NASA Astrophysics Data System (ADS)

Dahal, P.; Tarboton, D. G.; Castronova, A. M.

2017-12-01

Advanced computer simulations are required to understand hydrologic phenomenon such as rainfall-runoff response, groundwater hydrology, snow hydrology, etc. Building a hydrologic model instance to simulate a watershed requires investment in data (diverse geospatial datasets such as terrain, soil) and computer resources, typically demands a wide skill set from the analyst, and the workflow involved is often difficult to reproduce. This work introduces a web-based prototype infrastructure in the form of a web application that provides researchers with easy to use access to complete hydrological modeling functionality. This includes creating the necessary geospatial and forcing data, preparing input files for a model by applying complex data preprocessing, running the model for a user defined watershed, and saving the results to a web repository. The open source Tethys Platform was used to develop the web app front-end Graphical User Interface (GUI). We used HydroDS, a webservice that provides data preparation processing capability to support backend computations used by the app. Results are saved in HydroShare, a hydrologic information system that supports the sharing of hydrologic data, model and analysis tools. The TOPographic Kinematic APproximation and Integration (TOPKAPI) model served as the example for which we developed a complete hydrologic modeling service to demonstrate the approach. The final product is a complete modeling system accessible through the web to create input files, and run the TOPKAPI hydrologic model for a watershed of interest. We are investigating similar functionality for the preparation of input to Regional Hydro-Ecological Simulation System (RHESSys). Key Words: hydrologic modeling, web services, hydrologic information system, HydroShare, HydroDS, Tethys Platform

SMARTe: A FREE Web-Based Tool To Help Communities Overcome Revitalization Obstacles - Detroit, MI, May 6, 2008

EPA Science Inventory

SMARTe (Sustainable Management Approaches and Revitalization Tools - electronic) is a web-based decision support tool being developed by the Office of Research and Development (ORD) in partnership with the Office of Brownfields and Land R...

Open Crowdsourcing: Leveraging Community Software Developers for IT Projects

ERIC Educational Resources Information Center

Phair, Derek

2012-01-01

This qualitative exploratory single-case study was designed to examine and understand the use of volunteer community participants as software developers and other project related roles, such as testers, in completing a web-based application project by a non-profit organization. This study analyzed the strategic decision to engage crowd…

Content Management Middleware for the Support of Distributed Teaching

ERIC Educational Resources Information Center

Tsalapatas, Hariklia; Stav, John B.; Kalantzis, Christos

2004-01-01

eCMS is a web-based federated content management system for the support of distributed teaching based on an open, distributed middleware architecture for the publication, discovery, retrieval, and integration of educational material. The infrastructure supports the management of both standalone material and structured courses, as well as the…

Datacube Services in Action, Using Open Source and Open Standards

NASA Astrophysics Data System (ADS)

Baumann, P.; Misev, D.

2016-12-01

Array Databases comprise novel, promising technology for massive spatio-temporal datacubes, extending the SQL paradigm of "any query, anytime" to n-D arrays. On server side, such queries can be optimized, parallelized, and distributed based on partitioned array storage. The rasdaman ("raster data manager") system, which has pioneered Array Databases, is available in open source on www.rasdaman.org. Its declarative query language extends SQL with array operators which are optimized and parallelized on server side. The rasdaman engine, which is part of OSGeo Live, is mature and in operational use databases individually holding dozens of Terabytes. Further, the rasdaman concepts have strongly impacted international Big Data standards in the field, including the forthcoming MDA ("Multi-Dimensional Array") extension to ISO SQL, the OGC Web Coverage Service (WCS) and Web Coverage Processing Service (WCPS) standards, and the forthcoming INSPIRE WCS/WCPS; in both OGC and INSPIRE, OGC is WCS Core Reference Implementation. In our talk we present concepts, architecture, operational services, and standardization impact of open-source rasdaman, as well as experiences made.

The Federal Geospatial Platform a shared infrastructure for publishing, discovering and exploiting public data and spatial applications.

NASA Astrophysics Data System (ADS)

Dabolt, T. O.

2016-12-01

The proliferation of open data and data services continues to thrive and is creating new challenges on how researchers, policy analysts and other decision makes can quickly discover and use relevant data. While traditional metadata catalog approaches used by applications such as data.gov prove to be useful starting points for data search they can quickly frustrate end users who are seeking ways to quickly find and then use data in machine to machine environs. The Geospatial Platform is overcoming these obstacles and providing end users and applications developers a richer more productive user experience. The Geospatial Platform leverages a collection of open source and commercial technology hosted on Amazon Web Services providing an ecosystem of services delivering trusted, consistent data in open formats to all users as well as a shared infrastructure for federal partners to serve their spatial data assets. It supports a diverse array of communities of practice ranging on topics from the 16 National Geospatial Data Assets Themes, to homeland security and climate adaptation. Come learn how you can contribute your data and leverage others or check it out on your own at https://www.geoplatform.gov/

In Pursuit of Alternatives in ELT Methodology: WebQuests

ERIC Educational Resources Information Center

Sen, Ayfer; Neufeld, Steve

2006-01-01

Although the Internet has opened up a vast new source of information for university students to use and explore, many students lack the skills to find, critically evaluate and intelligently exploit web-based resources. This problem is accentuated in English-medium universities where students learn and use English as a foreign language. In these…

System for selecting relevant information for decision support.

PubMed

Kalina, Jan; Seidl, Libor; Zvára, Karel; Grünfeldová, Hana; Slovák, Dalibor; Zvárová, Jana

2013-01-01

We implemented a prototype of a decision support system called SIR which has a form of a web-based classification service for diagnostic decision support. The system has the ability to select the most relevant variables and to learn a classification rule, which is guaranteed to be suitable also for high-dimensional measurements. The classification system can be useful for clinicians in primary care to support their decision-making tasks with relevant information extracted from any available clinical study. The implemented prototype was tested on a sample of patients in a cardiological study and performs an information extraction from a high-dimensional set containing both clinical and gene expression data.

Web catalog of oceanographic data using GeoNetwork

NASA Astrophysics Data System (ADS)

Marinova, Veselka; Stefanov, Asen

2017-04-01

Most of the data collected, analyzed and used by Bulgarian oceanographic data center (BgODC) from scientific cruises, argo floats, ferry boxes and real time operating systems are spatially oriented and need to be displayed on the map. The challenge is to make spatial information more accessible to users, decision makers and scientists. In order to meet this challenge, BgODC concentrate its efforts on improving dynamic and standardized access to their geospatial data as well as those from various related organizations and institutions. BgODC currently is implementing a project to create a geospatial portal for distributing metadata and search, exchange and harvesting spatial data. There are many open source software solutions able to create such spatial data infrastructure (SDI). Finally, the GeoNetwork open source is chosen, as it is already widespread. This software is free, effective and "cheap" solution for implementing SDI at organization level. It is platform independent and runs under many operating systems. Filling of the catalog goes through these practical steps: • Managing and storing data reliably within MS SQL spatial data base; • Registration of maps and data of various formats and sources in GeoServer (most popular open source geospatial server embedded with GeoNetwork) ; • Filling added meta data and publishing geospatial data at the desktop of GeoNetwork. GeoServer and GeoNetwork are based on Java so they require installing of a servlet engine like Tomcat. The experience gained from the use of GeoNetwork Open Source confirms that the catalog meets the requirements for data management and is flexible enough to customize. Building the catalog facilitates sustainable data exchange between end users. The catalog is a big step towards implementation of the INSPIRE directive due to availability of many features necessary for producing "INSPIRE compliant" metadata records. The catalog now contains all available GIS data provided by BgODC for Internet access. Searching data within the catalog is based upon geographic extent, theme type and free text search.

Design and evaluation of a web-based decision support tool for district-level disease surveillance in a low-resource setting

PubMed Central

Pore, Meenal; Sengeh, David M.; Mugambi, Purity; Purswani, Nuri V.; Sesay, Tom; Arnold, Anna Lena; Tran, Anh-Minh A.; Myers, Ralph

2017-01-01

During the 2014 West African Ebola Virus outbreak it became apparent that the initial response to the outbreak was hampered by limitations in the collection, aggregation, analysis and use of data for intervention planning. As part of the post-Ebola recovery phase, IBM Research Africa partnered with the Port Loko District Health Management Team (DHMT) in Sierra Leone and GOAL Global, to design, implement and deploy a web-based decision support tool for district-level disease surveillance. This paper discusses the design process and the functionality of the first version of the system. The paper presents evaluation results prior to a pilot deployment and identifies features for future iterations. A qualitative assessment of the tool prior to pilot deployment indicates that it improves the timeliness and ease of using data for making decisions at the DHMT level. PMID:29854209

Data near processing support for climate data analysis

NASA Astrophysics Data System (ADS)

Kindermann, Stephan; Ehbrecht, Carsten; Hempelmann, Nils

2016-04-01

Climate data repositories grow in size exponentially. Scalable data near processing capabilities are required to meet future data analysis requirements and to replace current "data download and process at home" workflows and approaches. On one hand side, these processing capabilities should be accessible via standardized interfaces (e.g. OGC WPS), on the other side a large variety of processing tools, toolboxes and deployment alternatives have to be supported and maintained at the data/processing center. We present a community approach of a modular and flexible system supporting the development, deployment and maintenace of OGC-WPS based web processing services. This approach is organized in an open source github project (called "bird-house") supporting individual processing services ("birds", e.g. climate index calculations, model data ensemble calculations), which rely on basic common infrastructural components (e.g. installation and deployment recipes, analysis code dependencies management). To support easy deployment at data centers as well as home institutes (e.g. for testing and development) the system supports the management of the often very complex package dependency chain of climate data analysis packages as well as docker based packaging and installation. We present a concrete deployment scenario at the German Climate Computing Center (DKRZ). The DKRZ one hand side hosts a multi-petabyte climate archive which is integrated e.g. into the european ENES and worldwide ESGF data infrastructure, and on the other hand hosts an HPC center supporting (model) data production and data analysis. The deployment scenario also includes openstack based data cloud services to support data import and data distribution for bird-house based WPS web processing services. Current challenges for inter-institutionnal deployments of web processing services supporting the european and international climate modeling community as well as the climate impact community are highlighted. Also aspects supporting future WPS based cross community usage scenarios supporting data reuse and data provenance aspects are reflected.

Accessibility, usability, and usefulness of a Web-based clinical decision support tool to enhance provider-patient communication around Self-management TO Prevent (STOP) Stroke.

PubMed

Anderson, Jane A; Godwin, Kyler M; Saleem, Jason J; Russell, Scott; Robinson, Joshua J; Kimmel, Barbara

2014-12-01

This article reports redesign strategies identified to create a Web-based user-interface for the Self-management TO Prevent (STOP) Stroke Tool. Members of a Stroke Quality Improvement Network (N = 12) viewed a visualization video of a proposed prototype and provided feedback on implementation barriers/facilitators. Stroke-care providers (N = 10) tested the Web-based prototype in think-aloud sessions of simulated clinic visits. Participants' dialogues were coded into themes. Access to comprehensive information and the automated features/systematized processes were the primary accessibility and usability facilitator themes. The need for training, time to complete the tool, and computer-centric care were identified as possible usability barriers. Patient accountability, reminders for best practice, goal-focused care, and communication/counseling themes indicate that the STOP Stroke Tool supports the paradigm of patient-centered care. The STOP Stroke Tool was found to prompt clinicians on secondary stroke-prevention clinical-practice guidelines, facilitate comprehensive documentation of evidence-based care, and support clinicians in providing patient-centered care through the shared decision-making process that occurred while using the action-planning/goal-setting feature of the tool. © The Author(s) 2013.

Harvest: an open platform for developing web-based biomedical data discovery and reporting applications.

PubMed

Pennington, Jeffrey W; Ruth, Byron; Italia, Michael J; Miller, Jeffrey; Wrazien, Stacey; Loutrel, Jennifer G; Crenshaw, E Bryan; White, Peter S

2014-01-01

Biomedical researchers share a common challenge of making complex data understandable and accessible as they seek inherent relationships between attributes in disparate data types. Data discovery in this context is limited by a lack of query systems that efficiently show relationships between individual variables, but without the need to navigate underlying data models. We have addressed this need by developing Harvest, an open-source framework of modular components, and using it for the rapid development and deployment of custom data discovery software applications. Harvest incorporates visualizations of highly dimensional data in a web-based interface that promotes rapid exploration and export of any type of biomedical information, without exposing researchers to underlying data models. We evaluated Harvest with two cases: clinical data from pediatric cardiology and demonstration data from the OpenMRS project. Harvest's architecture and public open-source code offer a set of rapid application development tools to build data discovery applications for domain-specific biomedical data repositories. All resources, including the OpenMRS demonstration, can be found at http://harvest.research.chop.edu.

Harvest: an open platform for developing web-based biomedical data discovery and reporting applications

PubMed Central

Pennington, Jeffrey W; Ruth, Byron; Italia, Michael J; Miller, Jeffrey; Wrazien, Stacey; Loutrel, Jennifer G; Crenshaw, E Bryan; White, Peter S

2014-01-01

Biomedical researchers share a common challenge of making complex data understandable and accessible as they seek inherent relationships between attributes in disparate data types. Data discovery in this context is limited by a lack of query systems that efficiently show relationships between individual variables, but without the need to navigate underlying data models. We have addressed this need by developing Harvest, an open-source framework of modular components, and using it for the rapid development and deployment of custom data discovery software applications. Harvest incorporates visualizations of highly dimensional data in a web-based interface that promotes rapid exploration and export of any type of biomedical information, without exposing researchers to underlying data models. We evaluated Harvest with two cases: clinical data from pediatric cardiology and demonstration data from the OpenMRS project. Harvest's architecture and public open-source code offer a set of rapid application development tools to build data discovery applications for domain-specific biomedical data repositories. All resources, including the OpenMRS demonstration, can be found at http://harvest.research.chop.edu PMID:24131510

Implementation of workflow engine technology to deliver basic clinical decision support functionality

PubMed Central

2011-01-01

Background Workflow engine technology represents a new class of software with the ability to graphically model step-based knowledge. We present application of this novel technology to the domain of clinical decision support. Successful implementation of decision support within an electronic health record (EHR) remains an unsolved research challenge. Previous research efforts were mostly based on healthcare-specific representation standards and execution engines and did not reach wide adoption. We focus on two challenges in decision support systems: the ability to test decision logic on retrospective data prior prospective deployment and the challenge of user-friendly representation of clinical logic. Results We present our implementation of a workflow engine technology that addresses the two above-described challenges in delivering clinical decision support. Our system is based on a cross-industry standard of XML (extensible markup language) process definition language (XPDL). The core components of the system are a workflow editor for modeling clinical scenarios and a workflow engine for execution of those scenarios. We demonstrate, with an open-source and publicly available workflow suite, that clinical decision support logic can be executed on retrospective data. The same flowchart-based representation can also function in a prospective mode where the system can be integrated with an EHR system and respond to real-time clinical events. We limit the scope of our implementation to decision support content generation (which can be EHR system vendor independent). We do not focus on supporting complex decision support content delivery mechanisms due to lack of standardization of EHR systems in this area. We present results of our evaluation of the flowchart-based graphical notation as well as architectural evaluation of our implementation using an established evaluation framework for clinical decision support architecture. Conclusions We describe an implementation of a free workflow technology software suite (available at http://code.google.com/p/healthflow) and its application in the domain of clinical decision support. Our implementation seamlessly supports clinical logic testing on retrospective data and offers a user-friendly knowledge representation paradigm. With the presented software implementation, we demonstrate that workflow engine technology can provide a decision support platform which evaluates well against an established clinical decision support architecture evaluation framework. Due to cross-industry usage of workflow engine technology, we can expect significant future functionality enhancements that will further improve the technology's capacity to serve as a clinical decision support platform. PMID:21477364

NOAA's Data Catalog and the Federal Open Data Policy

NASA Astrophysics Data System (ADS)

Wengren, M. J.; de la Beaujardiere, J.

2014-12-01

The 2013 Open Data Policy Presidential Directive requires Federal agencies to create and maintain a 'public data listing' that includes all agency data that is currently or will be made publicly-available in the future. The directive requires the use of machine-readable and open formats that make use of 'common core' and extensible metadata formats according to the best practices published in an online repository called 'Project Open Data', to use open licenses where possible, and to adhere to existing metadata and other technology standards to promote interoperability. In order to meet the requirements of the Open Data Policy, the National Oceanic and Atmospheric Administration (NOAA) has implemented an online data catalog that combines metadata from all subsidiary NOAA metadata catalogs into a single master inventory. The NOAA Data Catalog is available to the public for search and discovery, providing access to the NOAA master data inventory through multiple means, including web-based text search, OGC CS-W endpoint, as well as a native Application Programming Interface (API) for programmatic query. It generates on a daily basis the Project Open Data JavaScript Object Notation (JSON) file required for compliance with the Presidential directive. The Data Catalog is based on the open source Comprehensive Knowledge Archive Network (CKAN) software and runs on the Amazon Federal GeoCloud. This presentation will cover topics including mappings of existing metadata in standard formats (FGDC-CSDGM and ISO 19115 XML ) to the Project Open Data JSON metadata schema, representation of metadata elements within the catalog, and compatible metadata sources used to feed the catalog to include Web Accessible Folder (WAF), Catalog Services for the Web (CS-W), and Esri ArcGIS.com. It will also discuss related open source technologies that can be used together to build a spatial data infrastructure compliant with the Open Data Policy.

Endeavour update: a web resource for gene prioritization in multiple species

PubMed Central

Tranchevent, Léon-Charles; Barriot, Roland; Yu, Shi; Van Vooren, Steven; Van Loo, Peter; Coessens, Bert; De Moor, Bart; Aerts, Stein; Moreau, Yves

2008-01-01

Endeavour (http://www.esat.kuleuven.be/endeavourweb; this web site is free and open to all users and there is no login requirement) is a web resource for the prioritization of candidate genes. Using a training set of genes known to be involved in a biological process of interest, our approach consists of (i) inferring several models (based on various genomic data sources), (ii) applying each model to the candidate genes to rank those candidates against the profile of the known genes and (iii) merging the several rankings into a global ranking of the candidate genes. In the present article, we describe the latest developments of Endeavour. First, we provide a web-based user interface, besides our Java client, to make Endeavour more universally accessible. Second, we support multiple species: in addition to Homo sapiens, we now provide gene prioritization for three major model organisms: Mus musculus, Rattus norvegicus and Caenorhabditis elegans. Third, Endeavour makes use of additional data sources and is now including numerous databases: ontologies and annotations, protein–protein interactions, cis-regulatory information, gene expression data sets, sequence information and text-mining data. We tested the novel version of Endeavour on 32 recent disease gene associations from the literature. Additionally, we describe a number of recent independent studies that made use of Endeavour to prioritize candidate genes for obesity and Type II diabetes, cleft lip and cleft palate, and pulmonary fibrosis. PMID:18508807

An Open-source Community Web Site To Support Ground-Water Model Testing

NASA Astrophysics Data System (ADS)

Kraemer, S. R.; Bakker, M.; Craig, J. R.

2007-12-01

A community wiki wiki web site has been created as a resource to support ground-water model development and testing. The Groundwater Gourmet wiki is a repository for user supplied analytical and numerical recipes, howtos, and examples. Members are encouraged to submit analytical solutions, including source code and documentation. A diversity of code snippets are sought in a variety of languages, including Fortran, C, C++, Matlab, Python. In the spirit of a wiki, all contributions may be edited and altered by other users, and open source licensing is promoted. Community accepted contributions are graduated into the library of analytic solutions and organized into either a Strack (Groundwater Mechanics, 1989) or Bruggeman (Analytical Solutions of Geohydrological Problems, 1999) classification. The examples section of the wiki are meant to include laboratory experiments (e.g., Hele Shaw), classical benchmark problems (e.g., Henry Problem), and controlled field experiments (e.g., Borden landfill and Cape Cod tracer tests). Although this work was reviewed by EPA and approved for publication, it may not necessarily reflect official Agency policy. Mention of trade names or commercial products does not constitute endorsement or recommendation for use.

Distributed Hydrologic Modeling Apps for Decision Support in the Cloud

NASA Astrophysics Data System (ADS)

Swain, N. R.; Latu, K.; Christiensen, S.; Jones, N.; Nelson, J.

2013-12-01

Advances in computation resources and greater availability of water resources data represent an untapped resource for addressing hydrologic uncertainties in water resources decision-making. The current practice of water authorities relies on empirical, lumped hydrologic models to estimate watershed response. These models are not capable of taking advantage of many of the spatial datasets that are now available. Physically-based, distributed hydrologic models are capable of using these data resources and providing better predictions through stochastic analysis. However, there exists a digital divide that discourages many science-minded decision makers from using distributed models. This divide can be spanned using a combination of existing web technologies. The purpose of this presentation is to present a cloud-based environment that will offer hydrologic modeling tools or 'apps' for decision support and the web technologies that have been selected to aid in its implementation. Compared to the more commonly used lumped-parameter models, distributed models, while being more intuitive, are still data intensive, computationally expensive, and difficult to modify for scenario exploration. However, web technologies such as web GIS, web services, and cloud computing have made the data more accessible, provided an inexpensive means of high-performance computing, and created an environment for developing user-friendly apps for distributed modeling. Since many water authorities are primarily interested in the scenario exploration exercises with hydrologic models, we are creating a toolkit that facilitates the development of a series of apps for manipulating existing distributed models. There are a number of hurdles that cloud-based hydrologic modeling developers face. One of these is how to work with the geospatial data inherent with this class of models in a web environment. Supporting geospatial data in a website is beyond the capabilities of standard web frameworks and it requires the use of additional software. In particular, there are at least three elements that are needed: a geospatially enabled database, a map server, and geoprocessing toolbox. We recommend a software stack for geospatial web application development comprising: MapServer, PostGIS, and 52 North with Python as the scripting language to tie them together. Another hurdle that must be cleared is managing the cloud-computing load. We are using HTCondor as a solution to this end. Finally, we are creating a scripting environment wherein developers will be able to create apps that use existing hydrologic models in our system with minimal effort. This capability will be accomplished by creating a plugin for a Python content management system called CKAN. We are currently developing cyberinfrastructure that utilizes this stack and greatly lowers the investment required to deploy cloud-based modeling apps. This material is based upon work supported by the National Science Foundation under Grant No. 1135482

Resurrecting Legacy Code Using Ontosoft Knowledge-Sharing and Digital Object Management to Revitalize and Reproduce Software for Groundwater Management Research

NASA Astrophysics Data System (ADS)

Kwon, N.; Gentle, J.; Pierce, S. A.

2015-12-01

Software code developed for research is often used for a relatively short period of time before it is abandoned, lost, or becomes outdated. This unintentional abandonment of code is a valid problem in the 21st century scientific process, hindering widespread reusability and increasing the effort needed to develop research software. Potentially important assets, these legacy codes may be resurrected and documented digitally for long-term reuse, often with modest effort. Furthermore, the revived code may be openly accessible in a public repository for researchers to reuse or improve. For this study, the research team has begun to revive the codebase for Groundwater Decision Support System (GWDSS), originally developed for participatory decision making to aid urban planning and groundwater management, though it may serve multiple use cases beyond those originally envisioned. GWDSS was designed as a java-based wrapper with loosely federated commercial and open source components. If successfully revitalized, GWDSS will be useful for both practical applications as a teaching tool and case study for groundwater management, as well as informing theoretical research. Using the knowledge-sharing approaches documented by the NSF-funded Ontosoft project, digital documentation of GWDSS is underway, from conception to development, deployment, characterization, integration, composition, and dissemination through open source communities and geosciences modeling frameworks. Information assets, documentation, and examples are shared using open platforms for data sharing and assigned digital object identifiers. Two instances of GWDSS version 3.0 are being created: 1) a virtual machine instance for the original case study to serve as a live demonstration of the decision support tool, assuring the original version is usable, and 2) an open version of the codebase, executable installation files, and developer guide available via an open repository, assuring the source for the application is accessible with version control and potential for new branch developments. Finally, metadata about the software has been completed within the OntoSoft portal to provide descriptive curation, make GWDSS searchable, and complete documentation of the scientific software lifecycle.

An Interactive Web-Based Analysis Framework for Remote Sensing Cloud Computing

NASA Astrophysics Data System (ADS)

Wang, X. Z.; Zhang, H. M.; Zhao, J. H.; Lin, Q. H.; Zhou, Y. C.; Li, J. H.

2015-07-01

Spatiotemporal data, especially remote sensing data, are widely used in ecological, geographical, agriculture, and military research and applications. With the development of remote sensing technology, more and more remote sensing data are accumulated and stored in the cloud. An effective way for cloud users to access and analyse these massive spatiotemporal data in the web clients becomes an urgent issue. In this paper, we proposed a new scalable, interactive and web-based cloud computing solution for massive remote sensing data analysis. We build a spatiotemporal analysis platform to provide the end-user with a safe and convenient way to access massive remote sensing data stored in the cloud. The lightweight cloud storage system used to store public data and users' private data is constructed based on open source distributed file system. In it, massive remote sensing data are stored as public data, while the intermediate and input data are stored as private data. The elastic, scalable, and flexible cloud computing environment is built using Docker, which is a technology of open-source lightweight cloud computing container in the Linux operating system. In the Docker container, open-source software such as IPython, NumPy, GDAL, and Grass GIS etc., are deployed. Users can write scripts in the IPython Notebook web page through the web browser to process data, and the scripts will be submitted to IPython kernel to be executed. By comparing the performance of remote sensing data analysis tasks executed in Docker container, KVM virtual machines and physical machines respectively, we can conclude that the cloud computing environment built by Docker makes the greatest use of the host system resources, and can handle more concurrent spatial-temporal computing tasks. Docker technology provides resource isolation mechanism in aspects of IO, CPU, and memory etc., which offers security guarantee when processing remote sensing data in the IPython Notebook. Users can write complex data processing code on the web directly, so they can design their own data processing algorithm.

Advanced Computational Framework for Environmental Management ZEM, Version 1.x

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vesselinov, Velimir V.; O'Malley, Daniel; Pandey, Sachin

2016-11-04

Typically environmental management problems require analysis of large and complex data sets originating from concurrent data streams with different data collection frequencies and pedigree. These big data sets require on-the-fly integration into a series of models with different complexity for various types of model analyses where the data are applied as soft and hard model constraints. This is needed to provide fast iterative model analyses based on the latest available data to guide decision-making. Furthermore, the data and model are associated with uncertainties. The uncertainties are probabilistic (e.g. measurement errors) and non-probabilistic (unknowns, e.g. alternative conceptual models characterizing site conditions).more » To address all of these issues, we have developed an integrated framework for real-time data and model analyses for environmental decision-making called ZEM. The framework allows for seamless and on-the-fly integration of data and modeling results for robust and scientifically-defensible decision-making applying advanced decision analyses tools such as Bayesian- Information-Gap Decision Theory (BIG-DT). The framework also includes advanced methods for optimization that are capable of dealing with a large number of unknown model parameters, and surrogate (reduced order) modeling capabilities based on support vector regression techniques. The framework is coded in Julia, a state-of-the-art high-performance programing language (http://julialang.org). The ZEM framework is open-source and can be applied to any environmental management site. The framework will be open-source and released under GPL V3 license.« less

E-DECIDER Disaster Response and Decision Support Cyberinfrastructure: Technology and Challenges

NASA Astrophysics Data System (ADS)

Glasscoe, M. T.; Parker, J. W.; Pierce, M. E.; Wang, J.; Eguchi, R. T.; Huyck, C. K.; Hu, Z.; Chen, Z.; Yoder, M. R.; Rundle, J. B.; Rosinski, A.

2014-12-01

Timely delivery of critical information to decision makers during a disaster is essential to response and damage assessment. Key issues to an efficient emergency response after a natural disaster include rapidly processing and delivering this critical information to emergency responders and reducing human intervention as much as possible. Essential elements of information necessary to achieve situational awareness are often generated by a wide array of organizations and disciplines, using any number of geospatial and non-geospatial technologies. A key challenge is the current state of practice does not easily support information sharing and technology interoperability. NASA E-DECIDER (Emergency Data Enhanced Cyber-Infrastructure for Disaster Evaluation and Response) has worked with the California Earthquake Clearinghouse and its partners to address these issues and challenges by adopting the XChangeCore Web Service Data Orchestration technology and participating in several earthquake response exercises. The E-DECIDER decision support system provides rapid delivery of advanced situational awareness data products to operations centers and emergency responders in the field. Remote sensing and hazard data, model-based map products, information from simulations, damage detection, and crowdsourcing is integrated into a single geospatial view and delivered through a service oriented architecture for improved decision-making and then directly to mobile devices of responders. By adopting a Service Oriented Architecture based on Open Geospatial Consortium standards, the system provides an extensible, comprehensive framework for geospatial data processing and distribution on Cloud platforms and other distributed environments. While the Clearinghouse and its partners are not first responders, they do support the emergency response community by providing information about the damaging effects earthquakes. It is critical for decision makers to maintain a situational awareness that is knowledgeable of potential and current conditions, possible impacts on populations and infrastructure, and other key information. E-DECIDER and the Clearinghouse have worked together to address many of these issues and challenges to deliver interoperable, authoritative decision support products.

The S-Web Model for the Sources of the Slow Solar Wind

NASA Technical Reports Server (NTRS)

Antiochos, Spiro K.; Karpen, Judith T.; DeVore, C. Richard

2012-01-01

Models for the origin of the slow solar wind must account for two seemingly contradictory observations: The slow wind has the composition of the closed-field corona, implying that it originates from the continuous opening and closing of flux at the boundary between open and closed field. On the other hand, the slow wind has large angular width, up to 60 degrees, suggesting that its source extends far from the open-closed boundary. We describe a model that can explain both observations. The key idea is that the source of the slow wind at the Sun is a network of narrow (possibly singular) open-field corridors that map to a web of separatrices (the S-Web) and quasi-separatrix layers in the heliosphere. We discuss the dynamics of the S-Web model and its implications for present observations and for the upcoming observations from Solar Orbiter and Solar Probe Plus.

Web-Based Learning Materials for Higher Education: The MERLOT Repository

ERIC Educational Resources Information Center

Orhun, Emrah

2004-01-01

MERLOT (Multimedia Educational Resource for Learning and Online Teaching) is a web-based open resource designed primarily for faculty and students in higher education. The resources in MERLOT include over 8,000 learning materials and support materials from a wide variety of disciplines that can be integrated within the context of a larger course.…

Software Agents to Assist in Distance Learning Environments

ERIC Educational Resources Information Center

Choy, Sheung-On; Ng, Sin-Chun; Tsang, Yiu-Chung

2005-01-01

The Open University of Hong Kong (OUHK) is a distance education university with about 22,500 students. In fulfilling its mission, the university has adopted various Web-based and electronic means to support distance learning. For instance, OUHK uses a Web-based course management system (CMS) to provide students with a flexible way to obtain course…

Helping Italian science teachers to make earth and climate active lessons. Results of 3 years support with the ICLEEN project

NASA Astrophysics Data System (ADS)

Cattadori, M.

2013-12-01

It has been demonstrated that in Italy Earth and Climate System Sciences Education (ESS) is one of the scientific disciplines where science teachers show a greatest need in terms of professional support. Among the causes that have been reported we should mention: the predominance of science teachers with a degree in biological disciplines rather then geo-logical or physical topics, and the high interdisciplinarity of certain topics, in particular those related to the climate system. Furthermore, it was found that ESS topics are predominant in the science curricula of those grades in which have been reported the major students dropout rates during the whole italian school cycle . In this context, in 2010, the MUSE, the Museum of Science of Trento (Italy), created a web-based service named I-Cleen (Inquring on Climate and Energy www.icleen.muse.it). This is a tool aimed at promoting the collaboration among science teachers in order to share resources and enhance the professional collaboration by means of participatory methods and models belonging to the world of open source and open content. The main instrument of the I-CLEEN project is an online repository (with metadata compliant with the DCMI and LOM international standards) of teaching resources focused on Earth and Climate Sciences all published under the Creative Commons license Attribution 3.0 and therefore, belonging to the model of OER (Open Educational Resources). The service has been designed, developed and managed by a team consisting of very experiencing science teachers and scientists from the Museum and other partners research institutions. The editorial work is carried out online utilizing a specific platform made with LifeRay, a CMS (Content Management System) software that is open source and manageable in a single Java-frameworked environment using the dbase, the website, the editorial process and several web 2.0 services. The project has been subjected to two distinct testing activities in collaboration with the University of Trento dealing with the effectiveness of the service as well as the usability of the graphic user interface (GUI). The present work aims to illustrate the essential features of the service I-cleen and the results achieved during the last three years of operation. It will be display and interpret for the first time data with web traffic, and other data from downloading and publishing documents of the teaching resources and the main outcomes of the above mentioned tests. The purpose of this contribution is to highlight strengths and weaknesses of this experience and potentially able to provide valuable information on the role of today's web based services and online communities to help support teachers in earth and climate sciences subjects.

Survey of Non-Rigid Registration Tools in Medicine.

PubMed

Keszei, András P; Berkels, Benjamin; Deserno, Thomas M

2017-02-01

We catalogue available software solutions for non-rigid image registration to support scientists in selecting suitable tools for specific medical registration purposes. Registration tools were identified using non-systematic search in Pubmed, Web of Science, IEEE Xplore® Digital Library, Google Scholar, and through references in identified sources (n = 22). Exclusions are due to unavailability or inappropriateness. The remaining (n = 18) tools were classified by (i) access and technology, (ii) interfaces and application, (iii) living community, (iv) supported file formats, and (v) types of registration methodologies emphasizing the similarity measures implemented. Out of the 18 tools, (i) 12 are open source, 8 are released under a permissive free license, which imposes the least restrictions on the use and further development of the tool, 8 provide graphical processing unit (GPU) support; (ii) 7 are built on software platforms, 5 were developed for brain image registration; (iii) 6 are under active development but only 3 have had their last update in 2015 or 2016; (iv) 16 support the Analyze format, while 7 file formats can be read with only one of the tools; and (v) 6 provide multiple registration methods and 6 provide landmark-based registration methods. Based on open source, licensing, GPU support, active community, several file formats, algorithms, and similarity measures, the tools Elastics and Plastimatch are chosen for the platform ITK and without platform requirements, respectively. Researchers in medical image analysis already have a large choice of registration tools freely available. However, the most recently published algorithms may not be included in the tools, yet.

Model My Watershed and BiG CZ Data Portal: Interactive geospatial analysis and hydrological modeling web applications that leverage the Amazon cloud for scientists, resource managers and students

NASA Astrophysics Data System (ADS)

Aufdenkampe, A. K.; Mayorga, E.; Tarboton, D. G.; Sazib, N. S.; Horsburgh, J. S.; Cheetham, R.

2016-12-01

The Model My Watershed Web app (http://wikiwatershed.org/model/) was designed to enable citizens, conservation practitioners, municipal decision-makers, educators, and students to interactively select any area of interest anywhere in the continental USA to: (1) analyze real land use and soil data for that area; (2) model stormwater runoff and water-quality outcomes; and (3) compare how different conservation or development scenarios could modify runoff and water quality. The BiG CZ Data Portal is a web application for scientists for intuitive, high-performance map-based discovery, visualization, access and publication of diverse earth and environmental science data via a map-based interface that simultaneously performs geospatial analysis of selected GIS and satellite raster data for a selected area of interest. The two web applications share a common codebase (https://github.com/WikiWatershed and https://github.com/big-cz), high performance geospatial analysis engine (http://geotrellis.io/ and https://github.com/geotrellis) and deployment on the Amazon Web Services (AWS) cloud cyberinfrastructure. Users can use "on-the-fly" rapid watershed delineation over the national elevation model to select their watershed or catchment of interest. The two web applications also share the goal of enabling the scientists, resource managers and students alike to share data, analyses and model results. We will present these functioning web applications and their potential to substantially lower the bar for studying and understanding our water resources. We will also present work in progress, including a prototype system for enabling citizen-scientists to register open-source sensor stations (http://envirodiy.org/mayfly/) to stream data into these systems, so that they can be reshared using Water One Flow web services.

Planning and Management of Real-Time Geospatialuas Missions Within a Virtual Globe Environment

NASA Astrophysics Data System (ADS)

Nebiker, S.; Eugster, H.; Flückiger, K.; Christen, M.

2011-09-01

This paper presents the design and development of a hardware and software framework supporting all phases of typical monitoring and mapping missions with mini and micro UAVs (unmanned aerial vehicles). The developed solution combines state-of-the art collaborative virtual globe technologies with advanced geospatial imaging techniques and wireless data link technologies supporting the combined and highly reliable transmission of digital video, high-resolution still imagery and mission control data over extended operational ranges. The framework enables the planning, simulation, control and real-time monitoring of UAS missions in application areas such as monitoring of forest fires, agronomical research, border patrol or pipeline inspection. The geospatial components of the project are based on the Virtual Globe Technology i3D OpenWebGlobe of the Institute of Geomatics Engineering at the University of Applied Sciences Northwestern Switzerland (FHNW). i3D OpenWebGlobe is a high-performance 3D geovisualisation engine supporting the web-based streaming of very large amounts of terrain and POI data.

Modular Architecture for Integrated Model-Based Decision Support.

PubMed

Gaebel, Jan; Schreiber, Erik; Oeser, Alexander; Oeltze-Jafra, Steffen

2018-01-01

Model-based decision support systems promise to be a valuable addition to oncological treatments and the implementation of personalized therapies. For the integration and sharing of decision models, the involved systems must be able to communicate with each other. In this paper, we propose a modularized architecture of dedicated systems for the integration of probabilistic decision models into existing hospital environments. These systems interconnect via web services and provide model sharing and processing capabilities for clinical information systems. Along the lines of IHE integration profiles from other disciplines and the meaningful reuse of routinely recorded patient data, our approach aims for the seamless integration of decision models into hospital infrastructure and the physicians' daily work.

An optimized web-based approach for collaborative stereoscopic medical visualization

PubMed Central

Kaspar, Mathias; Parsad, Nigel M; Silverstein, Jonathan C

2013-01-01

Objective Medical visualization tools have traditionally been constrained to tethered imaging workstations or proprietary client viewers, typically part of hospital radiology systems. To improve accessibility to real-time, remote, interactive, stereoscopic visualization and to enable collaboration among multiple viewing locations, we developed an open source approach requiring only a standard web browser with no added client-side software. Materials and Methods Our collaborative, web-based, stereoscopic, visualization system, CoWebViz, has been used successfully for the past 2 years at the University of Chicago to teach immersive virtual anatomy classes. It is a server application that streams server-side visualization applications to client front-ends, comprised solely of a standard web browser with no added software. Results We describe optimization considerations, usability, and performance results, which make CoWebViz practical for broad clinical use. We clarify technical advances including: enhanced threaded architecture, optimized visualization distribution algorithms, a wide range of supported stereoscopic presentation technologies, and the salient theoretical and empirical network parameters that affect our web-based visualization approach. Discussion The implementations demonstrate usability and performance benefits of a simple web-based approach for complex clinical visualization scenarios. Using this approach overcomes technical challenges that require third-party web browser plug-ins, resulting in the most lightweight client. Conclusions Compared to special software and hardware deployments, unmodified web browsers enhance remote user accessibility to interactive medical visualization. Whereas local hardware and software deployments may provide better interactivity than remote applications, our implementation demonstrates that a simplified, stable, client approach using standard web browsers is sufficient for high quality three-dimensional, stereoscopic, collaborative and interactive visualization. PMID:23048008

Increasing Open Source Software Integration on the Department of Defense Unclassified Desktop

DTIC Science & Technology

2008-06-01

free and legal access to the source code grants the user or operating agency considerable power and control . Commercial, off-the-shelf (COTS...COMMAND, CONTROL AND COMMUNICATIONS (C-3)) from the NAVAL POSTGRADUATE SCHOOL June 2008 Author: Steven A. Schearer Approved...Network. This fee also entitles users to unlimited web support with a two-business-day turnaround time. The retail price for a one year, basic

DEVELOPMENT PLAN FOR THE CAUSAL ANALYSIS / DIAGNOSIS DECISION INFORMATION SYSTEM (CADDIS) 2001-2004

EPA Science Inventory

The Causal Analysis/Diagnosis Decision Information System (CADDIS) is a web-based system that provides technical support for states, tribes and other users of the Office of Water's Stressor Identification Guidance. The Stressor Identific...

The evaluation of web-based data collection for enhanced surveillance of cryptosporidiosis.

PubMed

Viney, Kerri A; McAnulty, Jeremy M

2008-01-01

Following an increase in the number of people diagnosed with cryptosporidiosis in November 2005, the Communicable Diseases Branch initiated enhanced surveillance using a developmental version of NetEpi Collection, an open-source, web-based data collection tool. We evaluated the usefulness of NetEpi Collection for enhanced surveillance, using the Centers for Disease Control and Prevention's Updated Guidelines for Evaluating Public Health Surveillance Systems as a guide. Most staff (73 per cent) who used NetEpi Collection found it easy to use. Although ongoing support was thought to be adequate by 82 per cent of respondents who used NetEpi Collection, 36 per cent reported that training was limited and 27 per cent reported technical problems such as internet, server and password problems. In order to improve its usefulness in enhanced surveillance, training in NetEpi Collection should be enhanced and the stability of the system improved.

WriteSim TCExam - An open source text simulation environment for training novice researchers in scientific writing

PubMed Central

2010-01-01

Background The ability to write clearly and effectively is of central importance to the scientific enterprise. Encouraged by the success of simulation environments in other biomedical sciences, we developed WriteSim TCExam, an open-source, Web-based, textual simulation environment for teaching effective writing techniques to novice researchers. We shortlisted and modified an existing open source application - TCExam to serve as a textual simulation environment. After testing usability internally in our team, we conducted formal field usability studies with novice researchers. These were followed by formal surveys with researchers fitting the role of administrators and users (novice researchers) Results The development process was guided by feedback from usability tests within our research team. Online surveys and formal studies, involving members of the Research on Research group and selected novice researchers, show that the application is user-friendly. Additionally it has been used to train 25 novice researchers in scientific writing to date and has generated encouraging results. Conclusion WriteSim TCExam is the first Web-based, open-source textual simulation environment designed to complement traditional scientific writing instruction. While initial reviews by students and educators have been positive, a formal study is needed to measure its benefits in comparison to standard instructional methods. PMID:20509946

Coordinated Technology-Delivered Treatment to Prevent Rehospitalization in Schizophrenia: A Novel Model of Care.

PubMed

Brunette, Mary F; Rotondi, Armando J; Ben-Zeev, Dror; Gottlieb, Jennifer D; Mueser, Kim T; Robinson, Delbert G; Achtyes, Eric D; Gingerich, Susan; Marcy, Patricia; Schooler, Nina R; Meyer-Kalos, Piper; Kane, John M

2016-04-01

Despite advances in schizophrenia treatment, symptom relapses and rehospitalizations impede recovery for many people and are a principal driver of the high cost of care. Technology-delivered or technology-enhanced treatment may be a cost-effective way to provide flexible, personalized evidence-based treatments directly to people in their homes and communities. However, evidence for the safety, acceptability, and efficacy of such interventions is only now being established. The authors of this Open Forum describe a novel, technology-based approach to prevent relapse after a hospitalization for psychosis, the Health Technology Program (HTP), which they developed. HTP provides in-person relapse prevention planning that directs use of tailored, technology-based treatment based on cognitive-behavioral therapy for psychosis, family psychoeducation for schizophrenia, and prescriber decision support through a Web-based program that solicits information from clients at every visit. Technology-based treatments are delivered through smartphones and computers.

Implementing a low-cost web-based clinical trial management system for community studies: a case study.

PubMed

Geyer, John; Myers, Kathleen; Vander Stoep, Ann; McCarty, Carolyn; Palmer, Nancy; DeSalvo, Amy

2011-10-01

Clinical trials with multiple intervention locations and a single research coordinating center can be logistically difficult to implement. Increasingly, web-based systems are used to provide clinical trial support with many commercial, open source, and proprietary systems in use. New web-based tools are available which can be customized without programming expertise to deliver web-based clinical trial management and data collection functions. To demonstrate the feasibility of utilizing low-cost configurable applications to create a customized web-based data collection and study management system for a five intervention site randomized clinical trial establishing the efficacy of providing evidence-based treatment via teleconferencing to children with attention-deficit hyperactivity disorder. The sites are small communities that would not usually be included in traditional randomized trials. A major goal was to develop database that participants could access from computers in their home communities for direct data entry. Discussed is the selection process leading to the identification and utilization of a cost-effective and user-friendly set of tools capable of customization for data collection and study management tasks. An online assessment collection application, template-based web portal creation application, and web-accessible Access 2007 database were selected and customized to provide the following features: schedule appointments, administer and monitor online secure assessments, issue subject incentives, and securely transmit electronic documents between sites. Each tool was configured by users with limited programming expertise. As of June 2011, the system has successfully been used with 125 participants in 5 communities, who have completed 536 sets of assessment questionnaires, 8 community therapists, and 11 research staff at the research coordinating center. Total automation of processes is not possible with the current set of tools as each is loosely affiliated, creating some inefficiency. This system is best suited to investigations with a single data source e.g., psychosocial questionnaires. New web-based applications can be used by investigators with limited programming experience to implement user-friendly, efficient, and cost-effective tools for multi-site clinical trials with small distant communities. Such systems allow the inclusion in research of populations that are not usually involved in clinical trials.

US-German Cooperation For Further Development Of Decision Support Systems For Sustainable Contaminated Site Revitalization - Berlin, Germany, Sept. 24, 2008.

EPA Science Inventory

SMARTe (Sustainable Management Approaches and Revitalization Tools - electronic) is a web-based decision support tool developed by the Office of Research and Development (ORD) in partnership with the Office of Brownfields and Land Revital...

DECISION SUPPORT FOR REVITALIZATION PRACTITIONERS: SUSTAINABLE MANAGEMENT APPROACHES AND REVITALIZATION TOOLS-ELECTRONIC (SMARTE-TRAINING FOR OH EPA - APRIL 13, 2006

EPA Science Inventory

SMARTe (Sustainable Management Approaches and Revitalization Tools-electronic) is a web-based decision support tool being developed by the Office of Research and Development (ORD) in partnership with the Office of Brownfields Cleanup and ...

A Model for the Sources of the Slow Solar Wind

NASA Astrophysics Data System (ADS)

Antiochos, Spiro K.; Mikic, Z.; Lionello, R.; Titov, V.; Linker, J.

2010-05-01

Models for the origin of the slow solar wind must account for two seemingly contradictory observations: The slow wind has the composition of the closed-field corona, implying that it originates at the open-closed field boundary layer, but it also has large angular width, up to 40 degrees. We propose a model that can explain both observations. The key idea is that the source of the slow wind at the Sun is a network of narrow (possibly singular) open-field corridors that map to a web of separatrices and quasi-separatrix layers in the heliosphere. We calculate with high numerical resolution, the quasi-steady solar wind and magnetic field for a Carrington rotation centered about the August 1, 2008 total solar eclipse. Our numerical results demonstrate that, at least for this time period, a web of separatrices (S-web) forms with sufficient density and extent in the heliosphere to account for the observed properties of the slow wind. We discuss the implications of our S-web model for the structure and dynamics of the corona and heliosphere, and propose further tests of the model. This work was supported, in part, by the NASA HTP, TR&T and SR&T programs.

Phylesystem: a git-based data store for community-curated phylogenetic estimates.

PubMed

McTavish, Emily Jane; Hinchliff, Cody E; Allman, James F; Brown, Joseph W; Cranston, Karen A; Holder, Mark T; Rees, Jonathan A; Smith, Stephen A

2015-09-01

Phylogenetic estimates from published studies can be archived using general platforms like Dryad (Vision, 2010) or TreeBASE (Sanderson et al., 1994). Such services fulfill a crucial role in ensuring transparency and reproducibility in phylogenetic research. However, digital tree data files often require some editing (e.g. rerooting) to improve the accuracy and reusability of the phylogenetic statements. Furthermore, establishing the mapping between tip labels used in a tree and taxa in a single common taxonomy dramatically improves the ability of other researchers to reuse phylogenetic estimates. As the process of curating a published phylogenetic estimate is not error-free, retaining a full record of the provenance of edits to a tree is crucial for openness, allowing editors to receive credit for their work and making errors introduced during curation easier to correct. Here, we report the development of software infrastructure to support the open curation of phylogenetic data by the community of biologists. The backend of the system provides an interface for the standard database operations of creating, reading, updating and deleting records by making commits to a git repository. The record of the history of edits to a tree is preserved by git's version control features. Hosting this data store on GitHub (http://github.com/) provides open access to the data store using tools familiar to many developers. We have deployed a server running the 'phylesystem-api', which wraps the interactions with git and GitHub. The Open Tree of Life project has also developed and deployed a JavaScript application that uses the phylesystem-api and other web services to enable input and curation of published phylogenetic statements. Source code for the web service layer is available at https://github.com/OpenTreeOfLife/phylesystem-api. The data store can be cloned from: https://github.com/OpenTreeOfLife/phylesystem. A web application that uses the phylesystem web services is deployed at http://tree.opentreeoflife.org/curator. Code for that tool is available from https://github.com/OpenTreeOfLife/opentree. mtholder@gmail.com. © The Author 2015. Published by Oxford University Press.

An open source, web based, simple solution for seismic data dissemination and collaborative research

NASA Astrophysics Data System (ADS)

Diviacco, Paolo

2005-06-01

Collaborative research and data dissemination in the field of geophysical exploration need network tools that can access large amounts of data from anywhere using any PC or workstation. Simple solutions based on a combination of Open Source software can be developed to address such requests, exploiting the possibilities offered by the web technologies, and at the same time avoiding the costs and inflexibility of commercial systems. A viable solution consists of MySQL for data storage and retrieval, CWP/SU and GMT for data visualisation and a scripting layer driven by PHP that allows users to access the system via an Apache web server. In the light of the experience building the on-line archive of seismic data of the Istituto Nazionale di Oceanografia e di Geofisica Sperimentale (OGS), we describe the solutions and the methods adopted, with a view to stimulate both the attitude of network collaborative research of other institutions similar to ours, and the development of different applications.

Readability Levels of Health-Based Websites: From Content to Comprehension

ERIC Educational Resources Information Center

Schutten, Mary; McFarland, Allison

2009-01-01

Three of the national health education standards include decision-making, accessing information and analyzing influences. WebQuests are a popular inquiry-oriented method used by secondary teachers to help students achieve these content standards. While WebQuests support higher level thinking skills, the readability level of the information on the…

Advancements in Open Geospatial Standards for Photogrammetry and Remote Sensing from Ogc

NASA Astrophysics Data System (ADS)

Percivall, George; Simonis, Ingo

2016-06-01

The necessity of open standards for effective sharing and use of remote sensing continues to receive increasing emphasis in policies of agencies and projects around the world. Coordination on the development of open standards for geospatial information is a vital step to insure that the technical standards are ready to support the policy objectives. The mission of the Open Geospatial Consortium (OGC) is to advance development and use of international standards and supporting services that promote geospatial interoperability. To accomplish this mission, OGC serves as the global forum for the collaboration of geospatial data / solution providers and users. Photogrammetry and remote sensing are sources of the largest and most complex geospatial information. Some of the most mature OGC standards for remote sensing include the Sensor Web Enablement (SWE) standards, the Web Coverage Service (WCS) suite of standards, encodings such as NetCDF, GMLJP2 and GeoPackage, and the soon to be approved Discrete Global Grid Systems (DGGS) standard. In collaboration with ISPRS, OGC working with government, research and industrial organizations continue to advance the state of geospatial standards for full use of photogrammetry and remote sensing.

Web Based GIS System For Monitoring the Implementation of County Integrated Development Plan a Case Study of Nandi County, Kenya.

NASA Astrophysics Data System (ADS)

Kurui, P. K.; Mutua, F.

2016-12-01

The paper seek to propose a conceptual framework of a way of monitoring and evaluating the implementation of the projects listed in the county integrated development plan by applying the use of the geospatial technologies with the focus being developing a web based GIS system in which the public can be able to track and monitor the progress of implementation of the projects in various parts of the county , although the guidelines developed by the ministry of devolution provides for the inclusion of the implementation monitoring and evaluation framework specifying projects to be implemented during the plan period and specification of veriable indicators it does not provide mechanisms for public participation during implementation and monitoring stage. This calls for a system that the public can interact with. The web based GIS system has been developed using the free open source softwares. Development projects have been categorized into; ongoing, completed and planned It can also be shown that a web based GIS system can be used as an important tool for monitoring the implementation of the CIDP due to its easy to use nature and supported by the fact that internet is easily accessed by the majority of the public making it a powerful tool for public participation.

Development of a Web-Based Clinical Decision Support System for Drug Prescription: Non-Interventional Naturalistic Description of the Antipsychotic Prescription Patterns in 4345 Outpatients and Future Applications.

PubMed

Berrouiguet, Sofian; Barrigón, Maria Luisa; Brandt, Sara A; Ovejero-García, Santiago; Álvarez-García, Raquel; Carballo, Juan Jose; Lenca, Philippe; Courtet, Philippe; Baca-García, Enrique

2016-01-01

The emergence of electronic prescribing devices with clinical decision support systems (CDSS) is able to significantly improve management pharmacological treatments. We developed a web application available on smartphones in order to help clinicians monitor prescription and further propose CDSS. A web application (www.MEmind.net) was developed to assess patients and collect data regarding gender, age, diagnosis and treatment. We analyzed antipsychotic prescriptions in 4345 patients attended in five Psychiatric Community Mental Health Centers from June 2014 to October 2014. The web-application reported average daily dose prescribed for antipsychotics, prescribed daily dose (PDD), and the PDD to defined daily dose (DDD) ratio. The MEmind web-application reported that antipsychotics were used in 1116 patients out of the total sample, mostly in 486 (44%) patients with schizophrenia related disorders but also in other diagnoses. Second generation antipsychotics (quetiapine, aripiprazole and long-acting paliperidone) were preferably employed. Low doses were more frequently used than high doses. Long acting paliperidone and ziprasidone however, were the only two antipsychotics used at excessive dosing. Antipsychotic polypharmacy was used in 287 (26%) patients with classic depot drugs, clotiapine, amisulpride and clozapine. In this study we describe the first step of the development of a web application that is able to make polypharmacy, high dose usage and off label usage of antipsychotics visible to clinicians. Current development of the MEmind web application may help to improve prescription security via momentary feedback of prescription and clinical decision support system.

Development of a Web-Based Clinical Decision Support System for Drug Prescription: Non-Interventional Naturalistic Description of the Antipsychotic Prescription Patterns in 4345 Outpatients and Future Applications

PubMed Central

Berrouiguet, Sofian; Barrigón, Maria Luisa; Brandt, Sara A.; Ovejero-García, Santiago; Álvarez-García, Raquel; Carballo, Juan Jose; Lenca, Philippe; Courtet, Philippe; Baca-García, Enrique

2016-01-01

Purpose The emergence of electronic prescribing devices with clinical decision support systems (CDSS) is able to significantly improve management pharmacological treatments. We developed a web application available on smartphones in order to help clinicians monitor prescription and further propose CDSS. Method A web application (www.MEmind.net) was developed to assess patients and collect data regarding gender, age, diagnosis and treatment. We analyzed antipsychotic prescriptions in 4345 patients attended in five Psychiatric Community Mental Health Centers from June 2014 to October 2014. The web-application reported average daily dose prescribed for antipsychotics, prescribed daily dose (PDD), and the PDD to defined daily dose (DDD) ratio. Results The MEmind web-application reported that antipsychotics were used in 1116 patients out of the total sample, mostly in 486 (44%) patients with schizophrenia related disorders but also in other diagnoses. Second generation antipsychotics (quetiapine, aripiprazole and long-acting paliperidone) were preferably employed. Low doses were more frequently used than high doses. Long acting paliperidone and ziprasidone however, were the only two antipsychotics used at excessive dosing. Antipsychotic polypharmacy was used in 287 (26%) patients with classic depot drugs, clotiapine, amisulpride and clozapine. Conclusions In this study we describe the first step of the development of a web application that is able to make polypharmacy, high dose usage and off label usage of antipsychotics visible to clinicians. Current development of the MEmind web application may help to improve prescription security via momentary feedback of prescription and clinical decision support system. PMID:27764107

Teaching Undergraduate Software Engineering Using Open Source Development Tools

DTIC Science & Technology

2012-01-01

ware. Some example appliances are: a LAMP stack, Redmine, MySQL database, Moodle, Tom- cat on Apache, and Bugzilla. Some of the important features...Ada, C, C++, PHP , Py- thon, etc., and also supports a wide range of SDKs such as Google’s Android SDK and the Google Web Toolkit SDK. Additionally

Acquire: an open-source comprehensive cancer biobanking system.

PubMed

Dowst, Heidi; Pew, Benjamin; Watkins, Chris; McOwiti, Apollo; Barney, Jonathan; Qu, Shijing; Becnel, Lauren B

2015-05-15

The probability of effective treatment of cancer with a targeted therapeutic can be improved for patients with defined genotypes containing actionable mutations. To this end, many human cancer biobanks are integrating more tightly with genomic sequencing facilities and with those creating and maintaining patient-derived xenografts (PDX) and cell lines to provide renewable resources for translational research. To support the complex data management needs and workflows of several such biobanks, we developed Acquire. It is a robust, secure, web-based, database-backed open-source system that supports all major needs of a modern cancer biobank. Its modules allow for i) up-to-the-minute 'scoreboard' and graphical reporting of collections; ii) end user roles and permissions; iii) specimen inventory through caTissue Suite; iv) shipping forms for distribution of specimens to pathology, genomic analysis and PDX/cell line creation facilities; v) robust ad hoc querying; vi) molecular and cellular quality control metrics to track specimens' progress and quality; vii) public researcher request; viii) resource allocation committee distribution request review and oversight and ix) linkage to available derivatives of specimen. © The Author 2015. Published by Oxford University Press.

The GLIMS Glacier Database

NASA Astrophysics Data System (ADS)

Raup, B. H.; Khalsa, S. S.; Armstrong, R.

2007-12-01

The Global Land Ice Measurements from Space (GLIMS) project has built a geospatial and temporal database of glacier data, composed of glacier outlines and various scalar attributes. These data are being derived primarily from satellite imagery, such as from ASTER and Landsat. Each "snapshot" of a glacier is from a specific time, and the database is designed to store multiple snapshots representative of different times. We have implemented two web-based interfaces to the database; one enables exploration of the data via interactive maps (web map server), while the other allows searches based on text-field constraints. The web map server is an Open Geospatial Consortium (OGC) compliant Web Map Server (WMS) and Web Feature Server (WFS). This means that other web sites can display glacier layers from our site over the Internet, or retrieve glacier features in vector format. All components of the system are implemented using Open Source software: Linux, PostgreSQL, PostGIS (geospatial extensions to the database), MapServer (WMS and WFS), and several supporting components such as Proj.4 (a geographic projection library) and PHP. These tools are robust and provide a flexible and powerful framework for web mapping applications. As a service to the GLIMS community, the database contains metadata on all ASTER imagery acquired over glacierized terrain. Reduced-resolution of the images (browse imagery) can be viewed either as a layer in the MapServer application, or overlaid on the virtual globe within Google Earth. The interactive map application allows the user to constrain by time what data appear on the map. For example, ASTER or glacier outlines from 2002 only, or from Autumn in any year, can be displayed. The system allows users to download their selected glacier data in a choice of formats. The results of a query based on spatial selection (using a mouse) or text-field constraints can be downloaded in any of these formats: ESRI shapefiles, KML (Google Earth), MapInfo, GML (Geography Markup Language) and GMT (Generic Mapping Tools). This "clip-and-ship" function allows users to download only the data they are interested in. Our flexible web interfaces to the database, which includes various support layers (e.g. a layer to help collaborators identify satellite imagery over their region of expertise) will facilitate enhanced analysis to be undertaken on glacier systems, their distribution, and their impacts on other Earth systems.

Application of OpenStreetMap (OSM) to Support the Mapping Village in Indonesia

NASA Astrophysics Data System (ADS)

Swasti Kanthi, Nurin; Hery Purwanto, Taufik

2016-11-01

Geospatial Information is a important thing in this era, because the need for location information is needed to know the condition of a region. In 2015 the Indonesian government release detailed mapping in village level and their Parent maps Indonesian state regulatory standards set forth in Rule form Norm Standards, Procedures and Criteria for Mapping Village (NSPK). Over time Web and Mobile GIS was developed with a wide range of applications. The merger between detailed mapping and Web GIS is still rarely performed and not used optimally. OpenStreetMap (OSM) is a WebGIS which can be utilized as Mobile GIS providing sufficient information to the representative levels of the building and can be used for mapping the village.Mapping Village using OSM was conducted using remote sensing approach and Geographical Information Systems (GIS), which's to interpret remote sensing imagery from OSM. The study was conducted to analyzed how far the role of OSM to support the mapping of the village, it's done by entering the house number data, administrative boundaries, public facilities and land use into OSM with reference data and data image Village Plan. The results of the mapping portion villages in OSM as a reference map-making village and analyzed in accordance with NSPK for detailed mapping Rukun Warga (RW) is part of the village mapping. The use of OSM greatly assists the process of mapping the details of the region with data sources in the form of images and can be accessed for Open Source. But still need their care and updating the data source to maintain the validity of the data.

SMARTE: IMPROVING REVITALIZATION DECISIONS (CINCINNATI, OHIO)

EPA Science Inventory

SMARTe (Sustainable Management Approaches and Revitalization Tools-electronic) is a web-based decision support tool being developed by the Office of Research and Development (ORD) in partnership with the Office of Brownfields Cleanup and ...

Leveraging the geospatial advantage

Treesearch

Ben Butler; Andrew Bailey

2013-01-01

The Wildland Fire Decision Support System (WFDSS) web-based application leverages geospatial data to inform strategic decisions on wildland fires. A specialized data team, working within the Wildland Fire Management Research Development and Application group (WFM RD&A), assembles authoritative national-level data sets defining values to be protected. The use of...

Open Data, Open Specifications and Free and Open Source Software: A powerful mix to create distributed Web-based water information systems

NASA Astrophysics Data System (ADS)

Arias, Carolina; Brovelli, Maria Antonia; Moreno, Rafael

2015-04-01

We are in an age when water resources are increasingly scarce and the impacts of human activities on them are ubiquitous. These problems don't respect administrative or political boundaries and they must be addressed integrating information from multiple sources at multiple spatial and temporal scales. Communication, coordination and data sharing are critical for addressing the water conservation and management issues of the 21st century. However, different countries, provinces, local authorities and agencies dealing with water resources have diverse organizational, socio-cultural, economic, environmental and information technology (IT) contexts that raise challenges to the creation of information systems capable of integrating and distributing information across their areas of responsibility in an efficient and timely manner. Tight and disparate financial resources, and dissimilar IT infrastructures (data, hardware, software and personnel expertise) further complicate the creation of these systems. There is a pressing need for distributed interoperable water information systems that are user friendly, easily accessible and capable of managing and sharing large volumes of spatial and non-spatial data. In a distributed system, data and processes are created and maintained in different locations each with competitive advantages to carry out specific activities. Open Data (data that can be freely distributed) is available in the water domain, and it should be further promoted across countries and organizations. Compliance with Open Specifications for data collection, storage and distribution is the first step toward the creation of systems that are capable of interacting and exchanging data in a seamlessly (interoperable) way. The features of Free and Open Source Software (FOSS) offer low access cost that facilitate scalability and long-term viability of information systems. The World Wide Web (the Web) will be the platform of choice to deploy and access these systems. Geospatial capabilities for mapping, visualization, and spatial analysis will be important components of these new generation of Web-based interoperable information systems in the water domain. The purpose of this presentation is to increase the awareness of scientists, IT personnel and agency managers about the advantages offered by the combined use of Open Data, Open Specifications for geospatial and water-related data collection, storage and sharing, as well as mature FOSS projects for the creation of interoperable Web-based information systems in the water domain. A case study is used to illustrate how these principles and technologies can be integrated to create a system with the previously mentioned characteristics for managing and responding to flood events.

Primary Care Provider Views About Usefulness and Dissemination of a Web-Based Depression Treatment Information Decision Aid.

PubMed

Beaulac, Julie; Westmacott, Robin; Walker, John R; Vardanyan, Gohar

2016-06-08

Decisions related to mental health are often complex, problems often remain undetected and untreated, information unavailable or not used, and treatment decisions frequently not informed by best practice or patient preferences. The objective of this paper was to obtain the opinions of health professionals working in primary health care settings about a Web-based information decision aid (IDA) for patients concerning treatment options for depression and the dissemination of the resources in primary care settings. Participants were recruited from primary care clinics in Winnipeg and Ottawa, Canada, and included 48 family physicians, nurses, and primary care staff. The study design was a qualitative framework analytic approach of 5 focus groups. Focus groups were conducted during regular staff meetings, were digitally recorded, and transcripts created. Analysis involved a content and theme analysis. Seven key themes emerged including the key role of the primary care provider, common questions about treatments, treatment barriers, sources of patient information, concern about quality and quantity of available information, positive opinions about the IDA, and disseminating the IDA. The most common questions mentioned were about medication and side effects and alternatives to medication. Patients have limited access to alternative treatment options owing to cost and availability. Practitioners evaluated the IDA positively. The resources were described as useful, supportive of providers' messages, and accessible for patients. There was unanimous consensus that information needs to be available electronically through the Internet.

Canto: an online tool for community literature curation.

PubMed

Rutherford, Kim M; Harris, Midori A; Lock, Antonia; Oliver, Stephen G; Wood, Valerie

2014-06-15

Detailed curation of published molecular data is essential for any model organism database. Community curation enables researchers to contribute data from their papers directly to databases, supplementing the activity of professional curators and improving coverage of a growing body of literature. We have developed Canto, a web-based tool that provides an intuitive curation interface for both curators and researchers, to support community curation in the fission yeast database, PomBase. Canto supports curation using OBO ontologies, and can be easily configured for use with any species. Canto code and documentation are available under an Open Source license from http://curation.pombase.org/. Canto is a component of the Generic Model Organism Database (GMOD) project (http://www.gmod.org/). © The Author 2014. Published by Oxford University Press.

Using Open and Interoperable Ways to Publish and Access LANCE AIRS Near-Real Time Data

NASA Technical Reports Server (NTRS)

Zhao, Peisheng; Lynnes, Christopher; Vollmer, Bruce; Savtchenko, Andrey; Theobald, Michael; Yang, Wenli

2011-01-01

The Atmospheric Infrared Sounder (AIRS) Near-Real Time (NRT) data from the Land Atmosphere Near real-time Capability for EOS (LANCE) element at the Goddard Earth Sciences Data and Information Services Center (GES DISC) provides information on the global and regional atmospheric state, with very low temporal latency, to support climate research and improve weather forecasting. An open and interoperable platform is useful to facilitate access to, and integration of, LANCE AIRS NRT data. As Web services technology has matured in recent years, a new scalable Service-Oriented Architecture (SOA) is emerging as the basic platform for distributed computing and large networks of interoperable applications. Following the provide-register-discover-consume SOA paradigm, this presentation discusses how to use open-source geospatial software components to build Web services for publishing and accessing AIRS NRT data, explore the metadata relevant to registering and discovering data and services in the catalogue systems, and implement a Web portal to facilitate users' consumption of the data and services.

Sustainable Software Decisions for Long-term Projects (Invited)

NASA Astrophysics Data System (ADS)

Shepherd, A.; Groman, R. C.; Chandler, C. L.; Gaylord, D.; Sun, M.

2013-12-01

Adopting new, emerging technologies can be difficult for established projects that are positioned to exist for years to come. In some cases the challenge lies in the pre-existing software architecture. In others, the challenge lies in the fluctuation of resources like people, time and funding. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) was created in late 2006 by combining the data management offices for the U.S. GLOBEC and U.S. JGOFS programs to publish data for researchers funded by the National Science Foundation (NSF). Since its inception, BCO-DMO has been supporting access and discovery of these data through web-accessible software systems, and the office has worked through many of the challenges of incorporating new technologies into its software systems. From migrating human readable, flat file metadata storage into a relational database, and now, into a content management system (Drupal) to incorporating controlled vocabularies, new technologies can radically affect the existing software architecture. However, through the use of science-driven use cases, effective resource management, and loosely coupled software components, BCO-DMO has been able to adapt its existing software architecture to adopt new technologies. One of the latest efforts at BCO-DMO revolves around applying metadata semantics for publishing linked data in support of data discovery. This effort primarily affects the metadata web interface software at http://bco-dmo.org and the geospatial interface software at http://mapservice.bco-dmo.org/. With guidance from science-driven use cases and consideration of our resources, implementation decisions are made using a strategy to loosely couple the existing software systems to the new technologies. The results of this process led to the use of REST web services and a combination of contributed and custom Drupal modules for publishing BCO-DMO's content using the Resource Description Framework (RDF) via an instance of the Virtuoso Open-Source triplestore.

cPath: open source software for collecting, storing, and querying biological pathways

PubMed Central

Cerami, Ethan G; Bader, Gary D; Gross, Benjamin E; Sander, Chris

2006-01-01

Background Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. Results We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. Conclusion cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling. PMID:17101041

Medical knowledge packages and their integration into health-care information systems and the World Wide Web.

PubMed

Adlassnig, Klaus-Peter; Rappelsberger, Andrea

2008-01-01

Software-based medical knowledge packages (MKPs) are packages of highly structured medical knowledge that can be integrated into various health-care information systems or the World Wide Web. They have been established to provide different forms of clinical decision support such as textual interpretation of combinations of laboratory rest results, generating diagnostic hypotheses as well as confirmed and excluded diagnoses to support differential diagnosis in internal medicine, or for early identification and automatic monitoring of hospital-acquired infections. Technically, an MKP may consist of a number of inter-connected Arden Medical Logic Modules. Several MKPs have been integrated thus far into hospital, laboratory, and departmental information systems. This has resulted in useful and widely accepted software-based clinical decision support for the benefit of the patient, the physician, and the organization funding the health care system.

Evaluation and selection of open-source EMR software packages based on integrated AHP and TOPSIS.

PubMed

Zaidan, A A; Zaidan, B B; Al-Haiqi, Ahmed; Kiah, M L M; Hussain, Muzammil; Abdulnabi, Mohamed

2015-02-01

Evaluating and selecting software packages that meet the requirements of an organization are difficult aspects of software engineering process. Selecting the wrong open-source EMR software package can be costly and may adversely affect business processes and functioning of the organization. This study aims to evaluate and select open-source EMR software packages based on multi-criteria decision-making. A hands-on study was performed and a set of open-source EMR software packages were implemented locally on separate virtual machines to examine the systems more closely. Several measures as evaluation basis were specified, and the systems were selected based a set of metric outcomes using Integrated Analytic Hierarchy Process (AHP) and TOPSIS. The experimental results showed that GNUmed and OpenEMR software can provide better basis on ranking score records than other open-source EMR software packages. Copyright © 2014 Elsevier Inc. All rights reserved.

Creating a spatial multi-criteria decision support system for energy related integrated environmental impact assessment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wanderer, Thomas, E-mail: thomas.wanderer@dlr.de; Herle, Stefan, E-mail: stefan.herle@rwth-aachen.de

2015-04-15

By their spatially very distributed nature, profitability and impacts of renewable energy resources are highly correlated with the geographic locations of power plant deployments. A web-based Spatial Decision Support System (SDSS) based on a Multi-Criteria Decision Analysis (MCDA) approach has been implemented for identifying preferable locations for solar power plants based on user preferences. The designated areas found serve for the input scenario development for a subsequent integrated Environmental Impact Assessment. The capabilities of the SDSS service get showcased for Concentrated Solar Power (CSP) plants in the region of Andalusia, Spain. The resulting spatial patterns of possible power plant sitesmore » are an important input to the procedural chain of assessing impacts of renewable energies in an integrated effort. The applied methodology and the implemented SDSS are applicable for other renewable technologies as well. - Highlights: • The proposed tool facilitates well-founded CSP plant siting decisions. • Spatial MCDA methods are implemented in a WebGIS environment. • GIS-based SDSS can contribute to a modern integrated impact assessment workflow. • The conducted case study proves the suitability of the methodology.« less

S3DB core: a framework for RDF generation and management in bioinformatics infrastructures

PubMed Central

2010-01-01

Background Biomedical research is set to greatly benefit from the use of semantic web technologies in the design of computational infrastructure. However, beyond well defined research initiatives, substantial issues of data heterogeneity, source distribution, and privacy currently stand in the way towards the personalization of Medicine. Results A computational framework for bioinformatic infrastructure was designed to deal with the heterogeneous data sources and the sensitive mixture of public and private data that characterizes the biomedical domain. This framework consists of a logical model build with semantic web tools, coupled with a Markov process that propagates user operator states. An accompanying open source prototype was developed to meet a series of applications that range from collaborative multi-institution data acquisition efforts to data analysis applications that need to quickly traverse complex data structures. This report describes the two abstractions underlying the S3DB-based infrastructure, logical and numerical, and discusses its generality beyond the immediate confines of existing implementations. Conclusions The emergence of the "web as a computer" requires a formal model for the different functionalities involved in reading and writing to it. The S3DB core model proposed was found to address the design criteria of biomedical computational infrastructure, such as those supporting large scale multi-investigator research, clinical trials, and molecular epidemiology. PMID:20646315

An Open Source Software and Web-GIS Based Platform for Airborne SAR Remote Sensing Data Management, Distribution and Sharing

NASA Astrophysics Data System (ADS)

Changyong, Dou; Huadong, Guo; Chunming, Han; Ming, Liu

2014-03-01

With more and more Earth observation data available to the community, how to manage and sharing these valuable remote sensing datasets is becoming an urgent issue to be solved. The web based Geographical Information Systems (GIS) technology provides a convenient way for the users in different locations to share and make use of the same dataset. In order to efficiently use the airborne Synthetic Aperture Radar (SAR) remote sensing data acquired in the Airborne Remote Sensing Center of the Institute of Remote Sensing and Digital Earth (RADI), Chinese Academy of Sciences (CAS), a Web-GIS based platform for airborne SAR data management, distribution and sharing was designed and developed. The major features of the system include map based navigation search interface, full resolution imagery shown overlaid the map, and all the software adopted in the platform are Open Source Software (OSS). The functions of the platform include browsing the imagery on the map navigation based interface, ordering and downloading data online, image dataset and user management, etc. At present, the system is under testing in RADI and will come to regular operation soon.

Food webs of two intermittently open estuaries receiving 15N-enriched sewage effluent

NASA Astrophysics Data System (ADS)

Hadwen, Wade L.; Arthington, Angela H.

2007-01-01

Carbon and nitrogen stable isotope signatures were used to assess the response of food webs to sewage effluent discharged into two small intermittently open estuaries in northern New South Wales, Australia. One of these systems, Tallows Creek, has a history of direct sewage inputs, whilst the other, Belongil Creek, receives wastewater via an extensive wetland treatment system. The food webs of both systems were driven by algal sources of carbon, reflecting high autotrophic productivity in response to the nutrients entering the system from sewage effluent. All aquatic biota collected from Tallows Creek had significantly enriched δ15N signatures relative to their conspecifics from Belongil Creek, indicating that sewage nitrogen had been assimilated and transferred throughout the Tallows Creek food web. These δ15N values were higher than those reported from studies in permanently open estuaries receiving sewage effluent. We suggest that these enriched signatures and the transfer of nitrogen throughout the entire food web reflect differences in hydrology and associated nitrogen cycling processes between permanently open and intermittently open estuaries. Although all organisms in Tallows Creek were generally 15N-enriched, isotopically light (less 15N-enriched) individuals of estuary perchlet ( Ambassis marianus) and sea mullet ( Mugil cephalus) were also collected. These individuals were most likely recent immigrants into Tallows Creek, as this system had only recently been opened to the ocean. This isotopic discrimination between resident (enriched) and immigrant (significantly less enriched) individuals can provide information on fish movement patterns and the role of heavily polluted intermittently open estuaries in supporting commercially and recreationally valuable estuarine species.

Real-time Internet connections: implications for surgical decision making in laparoscopy.

PubMed

Broderick, T J; Harnett, B M; Doarn, C R; Rodas, E B; Merrell, R C

2001-08-01

To determine whether a low-bandwidth Internet connection can provide adequate image quality to support remote real-time surgical consultation. Telemedicine has been used to support care at a distance through the use of expensive equipment and broadband communication links. In the past, the operating room has been an isolated environment that has been relatively inaccessible for real-time consultation. Recent technological advances have permitted videoconferencing over low-bandwidth, inexpensive Internet connections. If these connections are shown to provide adequate video quality for surgical applications, low-bandwidth telemedicine will open the operating room environment to remote real-time surgical consultation. Surgeons performing a laparoscopic cholecystectomy in Ecuador or the Dominican Republic shared real-time laparoscopic images with a panel of surgeons at the parent university through a dial-up Internet account. The connection permitted video and audio teleconferencing to support real-time consultation as well as the transmission of real-time images and store-and-forward images for observation by the consultant panel. A total of six live consultations were analyzed. In addition, paired local and remote images were "grabbed" from the video feed during these laparoscopic cholecystectomies. Nine of these paired images were then placed into a Web-based tool designed to evaluate the effect of transmission on image quality. The authors showed for the first time the ability to identify critical anatomic structures in laparoscopy over a low-bandwidth connection via the Internet. The consultant panel of surgeons correctly remotely identified biliary and arterial anatomy during six laparoscopic cholecystectomies. Within the Web-based questionnaire, 15 surgeons could not blindly distinguish the quality of local and remote laparoscopic images. Low-bandwidth, Internet-based telemedicine is inexpensive, effective, and almost ubiquitous. Use of these inexpensive, portable technologies will allow sharing of surgical procedures and decisions regardless of location. Internet telemedicine consistently supported real-time intraoperative consultation in laparoscopic surgery. The implications are broad with respect to quality improvement and diffusion of knowledge as well as for basic consultation.

Integrated web system of geospatial data services for climate research

NASA Astrophysics Data System (ADS)

Okladnikov, Igor; Gordov, Evgeny; Titov, Alexander

2016-04-01

Georeferenced datasets are currently actively used for modeling, interpretation and forecasting of climatic and ecosystem changes on different spatial and temporal scales. Due to inherent heterogeneity of environmental datasets as well as their huge size (up to tens terabytes for a single dataset) a special software supporting studies in the climate and environmental change areas is required. An approach for integrated analysis of georefernced climatological data sets based on combination of web and GIS technologies in the framework of spatial data infrastructure paradigm is presented. According to this approach a dedicated data-processing web system for integrated analysis of heterogeneous georeferenced climatological and meteorological data is being developed. It is based on Open Geospatial Consortium (OGC) standards and involves many modern solutions such as object-oriented programming model, modular composition, and JavaScript libraries based on GeoExt library, ExtJS Framework and OpenLayers software. This work is supported by the Ministry of Education and Science of the Russian Federation, Agreement #14.613.21.0037.

DOE Office of Scientific and Technical Information (OSTI.GOV)

O'Malley, Daniel; Vesselinov, Velimir V.

MADSpython (Model analysis and decision support tools in Python) is a code in Python that streamlines the process of using data and models for analysis and decision support using the code MADS. MADS is open-source code developed at LANL and written in C/C++ (MADS; http://mads.lanl.gov; LA-CC-11-035). MADS can work with external models of arbitrary complexity as well as built-in models of flow and transport in porous media. The Python scripts in MADSpython facilitate the generation of input and output file needed by MADS as wells as the external simulators which include FEHM and PFLOTRAN. MADSpython enables a number of data-more » and model-based analyses including model calibration, sensitivity analysis, uncertainty quantification, and decision analysis. MADSpython will be released under GPL V3 license. MADSpython will be distributed as a Git repo at gitlab.com and github.com. MADSpython manual and documentation will be posted at http://madspy.lanl.gov.« less

EPA MODELING TOOLS FOR CAPTURE ZONE DELINEATION

EPA Science Inventory

The EPA Office of Research and Development supports a step-wise modeling approach for design of wellhead protection areas for water supply wells. A web-based WellHEDSS (wellhead decision support system) is under development for determining when simple capture zones (e.g., centri...

Chemotion ELN: an Open Source electronic lab notebook for chemists in academia.

PubMed

Tremouilhac, Pierre; Nguyen, An; Huang, Yu-Chieh; Kotov, Serhii; Lütjohann, Dominic Sebastian; Hübsch, Florian; Jung, Nicole; Bräse, Stefan

2017-09-25

The development of an electronic lab notebook (ELN) for researchers working in the field of chemical sciences is presented. The web based application is available as an Open Source software that offers modern solutions for chemical researchers. The Chemotion ELN is equipped with the basic functionalities necessary for the acquisition and processing of chemical data, in particular the work with molecular structures and calculations based on molecular properties. The ELN supports planning, description, storage, and management for the routine work of organic chemists. It also provides tools for communicating and sharing the recorded research data among colleagues. Meeting the requirements of a state of the art research infrastructure, the ELN allows the search for molecules and reactions not only within the user's data but also in conventional external sources as provided by SciFinder and PubChem. The presented development makes allowance for the growing dependency of scientific activity on the availability of digital information by providing Open Source instruments to record and reuse research data. The current version of the ELN has been using for over half of a year in our chemistry research group, serves as a common infrastructure for chemistry research and enables chemistry researchers to build their own databases of digital information as a prerequisite for the detailed, systematic investigation and evaluation of chemical reactions and mechanisms.

Data Model for Multi Hazard Risk Assessment Spatial Support Decision System

NASA Astrophysics Data System (ADS)

Andrejchenko, Vera; Bakker, Wim; van Westen, Cees

2014-05-01

The goal of the CHANGES Spatial Decision Support System is to support end-users in making decisions related to risk reduction measures for areas at risk from multiple hydro-meteorological hazards. The crucial parts in the design of the system are the user requirements, the data model, the data storage and management, and the relationships between the objects in the system. The implementation of the data model is carried out entirely with an open source database management system with a spatial extension. The web application is implemented using open source geospatial technologies with PostGIS as the database, Python for scripting, and Geoserver and javascript libraries for visualization and the client-side user-interface. The model can handle information from different study areas (currently, study areas from France, Romania, Italia and Poland are considered). Furthermore, the data model handles information about administrative units, projects accessible by different types of users, user-defined hazard types (floods, snow avalanches, debris flows, etc.), hazard intensity maps of different return periods, spatial probability maps, elements at risk maps (buildings, land parcels, linear features etc.), economic and population vulnerability information dependent on the hazard type and the type of the element at risk, in the form of vulnerability curves. The system has an inbuilt database of vulnerability curves, but users can also add their own ones. Included in the model is the management of a combination of different scenarios (e.g. related to climate change, land use change or population change) and alternatives (possible risk-reduction measures), as well as data-structures for saving the calculated economic or population loss or exposure per element at risk, aggregation of the loss and exposure using the administrative unit maps, and finally, producing the risk maps. The risk data can be used for cost-benefit analysis (CBA) and multi-criteria evaluation (SMCE). The data model includes data-structures for CBA and SMCE. The model is at the stage where risk and cost-benefit calculations can be stored but the remaining part is currently under development. Multi-criteria information, user management and the relation of these with the rest of the model is our next step. Having a carefully designed data model plays a crucial role in the development of the whole system for rapid development, keeping the data consistent, and in the end, support the end-user in making good decisions in risk-reduction measures related to multiple natural hazards. This work is part of the EU FP7 Marie Curie ITN "CHANGES"project (www.changes-itn.edu)

Database Organisation in a Web-Enabled Free and Open-Source Software (foss) Environment for Spatio-Temporal Landslide Modelling

NASA Astrophysics Data System (ADS)

Das, I.; Oberai, K.; Sarathi Roy, P.

2012-07-01

Landslides exhibit themselves in different mass movement processes and are considered among the most complex natural hazards occurring on the earth surface. Making landslide database available online via WWW (World Wide Web) promotes the spreading and reaching out of the landslide information to all the stakeholders. The aim of this research is to present a comprehensive database for generating landslide hazard scenario with the help of available historic records of landslides and geo-environmental factors and make them available over the Web using geospatial Free & Open Source Software (FOSS). FOSS reduces the cost of the project drastically as proprietary software's are very costly. Landslide data generated for the period 1982 to 2009 were compiled along the national highway road corridor in Indian Himalayas. All the geo-environmental datasets along with the landslide susceptibility map were served through WEBGIS client interface. Open source University of Minnesota (UMN) mapserver was used as GIS server software for developing web enabled landslide geospatial database. PHP/Mapscript server-side application serve as a front-end application and PostgreSQL with PostGIS extension serve as a backend application for the web enabled landslide spatio-temporal databases. This dynamic virtual visualization process through a web platform brings an insight into the understanding of the landslides and the resulting damage closer to the affected people and user community. The landslide susceptibility dataset is also made available as an Open Geospatial Consortium (OGC) Web Feature Service (WFS) which can be accessed through any OGC compliant open source or proprietary GIS Software.

Enhancements to TauDEM to support Rapid Watershed Delineation Services

NASA Astrophysics Data System (ADS)

Sazib, N. S.; Tarboton, D. G.

2015-12-01

Watersheds are widely recognized as the basic functional unit for water resources management studies and are important for a variety of problems in hydrology, ecology, and geomorphology. Nevertheless, delineating a watershed spread across a large region is still cumbersome due to the processing burden of working with large Digital Elevation Model. Terrain Analysis Using Digital Elevation Models (TauDEM) software supports the delineation of watersheds and stream networks from within desktop Geographic Information Systems. A rich set of watershed and stream network attributes are computed. However limitations of the TauDEM desktop tools are (1) it supports only one type of raster (tiff format) data (2) requires installation of software for parallel processing, and (3) data have to be in projected coordinate system. This paper presents enhancements to TauDEM that have been developed to extend its generality and support web based watershed delineation services. The enhancements of TauDEM include (1) reading and writing raster data with the open-source geospatial data abstraction library (GDAL) not limited to the tiff data format and (2) support for both geographic and projected coordinates. To support web services for rapid watershed delineation a procedure has been developed for sub setting the domain based on sub-catchments, with preprocessed data prepared for each catchment stored. This allows the watershed delineation to function locally, while extending to the full extent of watersheds using preprocessed information. Additional capabilities of this program includes computation of average watershed properties and geomorphic and channel network variables such as drainage density, shape factor, relief ratio and stream ordering. The updated version of TauDEM increases the practical applicability of it in terms of raster data type, size and coordinate system. The watershed delineation web service functionality is useful for web based software as service deployments that alleviate the need for users to install and work with desktop GIS software.

Publically accessible decision support system of the spatially referenced regressions on watershed attributes (SPARROW) model and model enhancements in South Carolina

Treesearch

Celeste Journey; Anne B. Hoos; David E. Ladd; John W. brakebill; Richard A. Smith

2016-01-01

The U.S. Geological Survey (USGS) National Water Quality Assessment program has developed a web-based decision support system (DSS) to provide free public access to the steady-stateSPAtially Referenced Regressions On Watershed attributes (SPARROW) model simulation results on nutrient conditions in streams and rivers and to offer scenario testing capabilities for...

Virtual Patients on the Semantic Web: A Proof-of-Application Study

PubMed Central

Dafli, Eleni; Antoniou, Panagiotis; Ioannidis, Lazaros; Dombros, Nicholas; Topps, David

2015-01-01

Background Virtual patients are interactive computer simulations that are increasingly used as learning activities in modern health care education, especially in teaching clinical decision making. A key challenge is how to retrieve and repurpose virtual patients as unique types of educational resources between different platforms because of the lack of standardized content-retrieving and repurposing mechanisms. Semantic Web technologies provide the capability, through structured information, for easy retrieval, reuse, repurposing, and exchange of virtual patients between different systems. Objective An attempt to address this challenge has been made through the mEducator Best Practice Network, which provisioned frameworks for the discovery, retrieval, sharing, and reuse of medical educational resources. We have extended the OpenLabyrinth virtual patient authoring and deployment platform to facilitate the repurposing and retrieval of existing virtual patient material. Methods A standalone Web distribution and Web interface, which contains an extension for the OpenLabyrinth virtual patient authoring system, was implemented. This extension was designed to semantically annotate virtual patients to facilitate intelligent searches, complex queries, and easy exchange between institutions. The OpenLabyrinth extension enables OpenLabyrinth authors to integrate and share virtual patient case metadata within the mEducator3.0 network. Evaluation included 3 successive steps: (1) expert reviews; (2) evaluation of the ability of health care professionals and medical students to create, share, and exchange virtual patients through specific scenarios in extended OpenLabyrinth (OLabX); and (3) evaluation of the repurposed learning objects that emerged from the procedure. Results We evaluated 30 repurposed virtual patient cases. The evaluation, with a total of 98 participants, demonstrated the system’s main strength: the core repurposing capacity. The extensive metadata schema presentation facilitated user exploration and filtering of resources. Usability weaknesses were primarily related to standard computer applications’ ease of use provisions. Most evaluators provided positive feedback regarding educational experiences on both content and system usability. Evaluation results replicated across several independent evaluation events. Conclusions The OpenLabyrinth extension, as part of the semantic mEducator3.0 approach, is a virtual patient sharing approach that builds on a collection of Semantic Web services and federates existing sources of clinical and educational data. It is an effective sharing tool for virtual patients and has been merged into the next version of the app (OpenLabyrinth 3.3). Such tool extensions may enhance the medical education arsenal with capacities of creating simulation/game-based learning episodes, massive open online courses, curricular transformations, and a future robust infrastructure for enabling mobile learning. PMID:25616272

Virtual patients on the semantic Web: a proof-of-application study.

PubMed

Dafli, Eleni; Antoniou, Panagiotis; Ioannidis, Lazaros; Dombros, Nicholas; Topps, David; Bamidis, Panagiotis D

2015-01-22

Virtual patients are interactive computer simulations that are increasingly used as learning activities in modern health care education, especially in teaching clinical decision making. A key challenge is how to retrieve and repurpose virtual patients as unique types of educational resources between different platforms because of the lack of standardized content-retrieving and repurposing mechanisms. Semantic Web technologies provide the capability, through structured information, for easy retrieval, reuse, repurposing, and exchange of virtual patients between different systems. An attempt to address this challenge has been made through the mEducator Best Practice Network, which provisioned frameworks for the discovery, retrieval, sharing, and reuse of medical educational resources. We have extended the OpenLabyrinth virtual patient authoring and deployment platform to facilitate the repurposing and retrieval of existing virtual patient material. A standalone Web distribution and Web interface, which contains an extension for the OpenLabyrinth virtual patient authoring system, was implemented. This extension was designed to semantically annotate virtual patients to facilitate intelligent searches, complex queries, and easy exchange between institutions. The OpenLabyrinth extension enables OpenLabyrinth authors to integrate and share virtual patient case metadata within the mEducator3.0 network. Evaluation included 3 successive steps: (1) expert reviews; (2) evaluation of the ability of health care professionals and medical students to create, share, and exchange virtual patients through specific scenarios in extended OpenLabyrinth (OLabX); and (3) evaluation of the repurposed learning objects that emerged from the procedure. We evaluated 30 repurposed virtual patient cases. The evaluation, with a total of 98 participants, demonstrated the system's main strength: the core repurposing capacity. The extensive metadata schema presentation facilitated user exploration and filtering of resources. Usability weaknesses were primarily related to standard computer applications' ease of use provisions. Most evaluators provided positive feedback regarding educational experiences on both content and system usability. Evaluation results replicated across several independent evaluation events. The OpenLabyrinth extension, as part of the semantic mEducator3.0 approach, is a virtual patient sharing approach that builds on a collection of Semantic Web services and federates existing sources of clinical and educational data. It is an effective sharing tool for virtual patients and has been merged into the next version of the app (OpenLabyrinth 3.3). Such tool extensions may enhance the medical education arsenal with capacities of creating simulation/game-based learning episodes, massive open online courses, curricular transformations, and a future robust infrastructure for enabling mobile learning.

Clinical software development for the Web: lessons learned from the BOADICEA project

PubMed Central

2012-01-01

Background In the past 20 years, society has witnessed the following landmark scientific advances: (i) the sequencing of the human genome, (ii) the distribution of software by the open source movement, and (iii) the invention of the World Wide Web. Together, these advances have provided a new impetus for clinical software development: developers now translate the products of human genomic research into clinical software tools; they use open-source programs to build them; and they use the Web to deliver them. Whilst this open-source component-based approach has undoubtedly made clinical software development easier, clinical software projects are still hampered by problems that traditionally accompany the software process. This study describes the development of the BOADICEA Web Application, a computer program used by clinical geneticists to assess risks to patients with a family history of breast and ovarian cancer. The key challenge of the BOADICEA Web Application project was to deliver a program that was safe, secure and easy for healthcare professionals to use. We focus on the software process, problems faced, and lessons learned. Our key objectives are: (i) to highlight key clinical software development issues; (ii) to demonstrate how software engineering tools and techniques can facilitate clinical software development for the benefit of individuals who lack software engineering expertise; and (iii) to provide a clinical software development case report that can be used as a basis for discussion at the start of future projects. Results We developed the BOADICEA Web Application using an evolutionary software process. Our approach to Web implementation was conservative and we used conventional software engineering tools and techniques. The principal software development activities were: requirements, design, implementation, testing, documentation and maintenance. The BOADICEA Web Application has now been widely adopted by clinical geneticists and researchers. BOADICEA Web Application version 1 was released for general use in November 2007. By May 2010, we had > 1200 registered users based in the UK, USA, Canada, South America, Europe, Africa, Middle East, SE Asia, Australia and New Zealand. Conclusions We found that an evolutionary software process was effective when we developed the BOADICEA Web Application. The key clinical software development issues identified during the BOADICEA Web Application project were: software reliability, Web security, clinical data protection and user feedback. PMID:22490389

Clinical software development for the Web: lessons learned from the BOADICEA project.

PubMed

Cunningham, Alex P; Antoniou, Antonis C; Easton, Douglas F

2012-04-10

In the past 20 years, society has witnessed the following landmark scientific advances: (i) the sequencing of the human genome, (ii) the distribution of software by the open source movement, and (iii) the invention of the World Wide Web. Together, these advances have provided a new impetus for clinical software development: developers now translate the products of human genomic research into clinical software tools; they use open-source programs to build them; and they use the Web to deliver them. Whilst this open-source component-based approach has undoubtedly made clinical software development easier, clinical software projects are still hampered by problems that traditionally accompany the software process. This study describes the development of the BOADICEA Web Application, a computer program used by clinical geneticists to assess risks to patients with a family history of breast and ovarian cancer. The key challenge of the BOADICEA Web Application project was to deliver a program that was safe, secure and easy for healthcare professionals to use. We focus on the software process, problems faced, and lessons learned. Our key objectives are: (i) to highlight key clinical software development issues; (ii) to demonstrate how software engineering tools and techniques can facilitate clinical software development for the benefit of individuals who lack software engineering expertise; and (iii) to provide a clinical software development case report that can be used as a basis for discussion at the start of future projects. We developed the BOADICEA Web Application using an evolutionary software process. Our approach to Web implementation was conservative and we used conventional software engineering tools and techniques. The principal software development activities were: requirements, design, implementation, testing, documentation and maintenance. The BOADICEA Web Application has now been widely adopted by clinical geneticists and researchers. BOADICEA Web Application version 1 was released for general use in November 2007. By May 2010, we had > 1200 registered users based in the UK, USA, Canada, South America, Europe, Africa, Middle East, SE Asia, Australia and New Zealand. We found that an evolutionary software process was effective when we developed the BOADICEA Web Application. The key clinical software development issues identified during the BOADICEA Web Application project were: software reliability, Web security, clinical data protection and user feedback.

Standards-Based Procedural Phenotyping: The Arden Syntax on i2b2.

PubMed

Mate, Sebastian; Castellanos, Ixchel; Ganslandt, Thomas; Prokosch, Hans-Ulrich; Kraus, Stefan

2017-01-01

Phenotyping, or the identification of patient cohorts, is a recurring challenge in medical informatics. While there are open source tools such as i2b2 that address this problem by providing user-friendly querying interfaces, these platforms lack semantic expressiveness to model complex phenotyping algorithms. The Arden Syntax provides procedural programming language construct, designed specifically for medical decision support and knowledge transfer. In this work, we investigate how language constructs of the Arden Syntax can be used for generic phenotyping. We implemented a prototypical tool to integrate i2b2 with an open source Arden execution environment. To demonstrate the applicability of our approach, we used the tool together with an Arden-based phenotyping algorithm to derive statistics about ICU-acquired hypernatremia. Finally, we discuss how the combination of i2b2's user-friendly cohort pre-selection and Arden's procedural expressiveness could benefit phenotyping.

RECOVER - An Automated Burned Area Emergency Response Decision Support System for Post-fire Rehabilitation Management of Savanna Ecosystems in the Western US

NASA Astrophysics Data System (ADS)

Weber, K.; Schnase, J. L.; Carroll, M.; Brown, M. E.; Gill, R.; Haskett, G.; Gardner, T.

2013-12-01

In partnership with the Department of Interior's Bureau of Land Management (BLM) and the Idaho Department of Lands (IDL), we are building and evaluating the RECOVER decision support system. RECOVER - which stands for Rehabilitation Capability Convergence for Ecosystem Recovery - is an automatically deployable, context-aware decision support system for savanna wildfires that brings together in a single application the information necessary for post-fire rehabilitation decision-making and long-term ecosystem monitoring. RECOVER uses state-of-the-art cloud-based data management technologies to improve performance, reduce cost, and provide site-specific flexibility for each fire. The RECOVER Server uses Integrated Rule-Oriented Data System (iRODS) data grid technology deployed in the Amazon Elastic Compute Cloud (EC2). The RECOVER Client is an Adobe Flex web map application that is able to provide a suite of convenient GIS analytical capabilities. In a typical use scenario, the RECOVER Server is provided a wildfire name and geospatial extent. The Server then automatically gathers Earth observational data and other relevant products from various geographically distributed data sources. The Server creates a database in the cloud where all relevant information about the wildfire is stored. This information is made available to the RECOVER Client and ultimately to fire managers through their choice of web browser. The Server refreshes the data throughout the burn and subsequent recovery period (3-5 years) with each refresh requiring two minutes to complete. Since remediation plans must be completed within 14 days of a fire's containment, RECOVER has the potential to significantly improve the decision-making process. RECOVER adds an important new dimension to post-fire decision-making by focusing on ecosystem rehabilitation in semiarid savannas. A novel aspect of RECOVER's approach involves the use of soil moisture estimates, which are an important but difficult-to-obtain element of post-fire rehabilitation planning. We will use downscaled soil moisture data from three primary observational sources to begin evaluation of soil moisture products and build the technology needed for RECOVER to use future SMAP products. As a result, RECOVER, BLM, and the fire applications community will be ready customers for data flowing out of new NASA missions, such as NPP, LDCM, and SMAP.

Advanced Clinical Decision Support for Vaccine Adverse Event Detection and Reporting.

PubMed

Baker, Meghan A; Kaelber, David C; Bar-Shain, David S; Moro, Pedro L; Zambarano, Bob; Mazza, Megan; Garcia, Crystal; Henry, Adam; Platt, Richard; Klompas, Michael

2015-09-15

Reporting of adverse events (AEs) following vaccination can help identify rare or unexpected complications of immunizations and aid in characterizing potential vaccine safety signals. We developed an open-source, generalizable clinical decision support system called Electronic Support for Public Health-Vaccine Adverse Event Reporting System (ESP-VAERS) to assist clinicians with AE detection and reporting. ESP-VAERS monitors patients' electronic health records for new diagnoses, changes in laboratory values, and new allergies following vaccinations. When suggestive events are found, ESP-VAERS sends the patient's clinician a secure electronic message with an invitation to affirm or refute the message, add comments, and submit an automated, prepopulated electronic report to VAERS. High-probability AEs are reported automatically if the clinician does not respond. We implemented ESP-VAERS in December 2012 throughout the MetroHealth System, an integrated healthcare system in Ohio. We queried the VAERS database to determine MetroHealth's baseline reporting rates from January 2009 to March 2012 and then assessed changes in reporting rates with ESP-VAERS. In the 8 months following implementation, 91 622 vaccinations were given. ESP-VAERS sent 1385 messages to responsible clinicians describing potential AEs. Clinicians opened 1304 (94.2%) messages, responded to 209 (15.1%), and confirmed 16 for transmission to VAERS. An additional 16 high-probability AEs were sent automatically. Reported events included seizure, pleural effusion, and lymphocytopenia. The odds of a VAERS report submission during the implementation period were 30.2 (95% confidence interval, 9.52-95.5) times greater than the odds during the comparable preimplementation period. An open-source, electronic health record-based clinical decision support system can increase AE detection and reporting rates in VAERS. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Web-Based Portfolio Assessment: Validation of an Open Source Platform

ERIC Educational Resources Information Center

Collins, Regina; Elliot, Norbert; Klobucar, Andrew; Deek, Fadi P.

2013-01-01

Assessment of educational outcomes through purchased tests is commonplace in the evaluation of individual student ability and of educational programs. Focusing on the assessment of writing performance in a longitudinal study of first-time, full-time students (n = 598), this research describes the design, use, and assessment of an open-source…

Low Cost, Open-Source, and Low-Power: But What to Do with the Data?

NASA Astrophysics Data System (ADS)

Horsburgh, J. S.; Aufdenkampe, A. K.; Arscott, D.; Damiano, S. G.; Hicks, S. D.

2017-12-01

There are now many ongoing efforts to develop low-cost, open-source, low-power sensors and datalogging solutions for environmental applications. Many of these have advanced to the point that high quality scientific measurements can be made using relatively inexpensive and increasingly off-the-shelf components. With the development of these innovative systems, however, comes the ability to generate large volumes of high-frequency monitoring data and the challenge of how to log, transmit, store, and share the resulting data. This presentation will focus on a new, web-based system http://data.envirodiy.org that was designed to enable citizen scientists to stream sensor data from a network of EnviroDIY Mayfly Arduino-based dataloggers. This system enables registration of new sensor nodes through a website. Once registered, any Internet connected device (e.g., cellular or WIFI) can then post data to the data.envirodiy.org website through a web service programming interface. Data are stored in a back-end data store that implements Version 2 of the Observations Data Model (ODM2). Live data can then be viewed and downloaded from the data.envirodiy.org website in a simple text format. While this system was purpose built to support an emerging network of Arduino-based sensor nodes deployed by citizen scientists in the Delaware River Basin, the architecture and components are generic and could be used by any Internet connected device capable of making measurements and formulating an HTTP POST request to send them to data.envirodiy.org.

Access Control of Web- and Java-Based Applications

NASA Technical Reports Server (NTRS)

Tso, Kam S.; Pajevski, Michael J.

2013-01-01

Cybersecurity has become a great concern as threats of service interruption, unauthorized access, stealing and altering of information, and spreading of viruses have become more prevalent and serious. Application layer access control of applications is a critical component in the overall security solution that also includes encryption, firewalls, virtual private networks, antivirus, and intrusion detection. An access control solution, based on an open-source access manager augmented with custom software components, was developed to provide protection to both Web-based and Javabased client and server applications. The DISA Security Service (DISA-SS) provides common access control capabilities for AMMOS software applications through a set of application programming interfaces (APIs) and network- accessible security services for authentication, single sign-on, authorization checking, and authorization policy management. The OpenAM access management technology designed for Web applications can be extended to meet the needs of Java thick clients and stand alone servers that are commonly used in the JPL AMMOS environment. The DISA-SS reusable components have greatly reduced the effort for each AMMOS subsystem to develop its own access control strategy. The novelty of this work is that it leverages an open-source access management product that was designed for Webbased applications to provide access control for Java thick clients and Java standalone servers. Thick clients and standalone servers are still commonly used in businesses and government, especially for applications that require rich graphical user interfaces and high-performance visualization that cannot be met by thin clients running on Web browsers

Providing Global Change Information for Decision-Making: Capturing and Presenting Provenance

NASA Technical Reports Server (NTRS)

Ma, Xiaogang; Fox, Peter; Tilmes, Curt; Jacobs, Katherine; Waple, Anne

2014-01-01

Global change information demands access to data sources and well-documented provenance to provide evidence needed to build confidence in scientific conclusions and, in specific applications, to ensure the information's suitability for use in decision-making. A new generation of Web technology, the Semantic Web, provides tools for that purpose. The topic of global change covers changes in the global environment (including alterations in climate, land productivity, oceans or other water resources, atmospheric composition and or chemistry, and ecological systems) that may alter the capacity of the Earth to sustain life and support human systems. Data and findings associated with global change research are of great public, government, and academic concern and are used in policy and decision-making, which makes the provenance of global change information especially important. In addition, since different types of decisions benefit from different types of information, understanding how to capture and present the provenance of global change information is becoming more of an imperative in adaptive planning.

A web-based Decision Support System for the optimal management of construction and demolition waste.

PubMed

Banias, G; Achillas, Ch; Vlachokostas, Ch; Moussiopoulos, N; Papaioannou, I

2011-12-01

Wastes from construction activities constitute nowadays the largest by quantity fraction of solid wastes in urban areas. In addition, it is widely accepted that the particular waste stream contains hazardous materials, such as insulating materials, plastic frames of doors, windows, etc. Their uncontrolled disposal result to long-term pollution costs, resource overuse and wasted energy. Within the framework of the DEWAM project, a web-based Decision Support System (DSS) application - namely DeconRCM - has been developed, aiming towards the identification of the optimal construction and demolition waste (CDW) management strategy that minimises end-of-life costs and maximises the recovery of salvaged building materials. This paper addresses both technical and functional structure of the developed web-based application. The web-based DSS provides an accurate estimation of the generated CDW quantities of twenty-one different waste streams (e.g. concrete, bricks, glass, etc.) for four different types of buildings (residential, office, commercial and industrial). With the use of mathematical programming, the DeconRCM provides also the user with the optimal end-of-life management alternative, taking into consideration both economic and environmental criteria. The DSS's capabilities are illustrated through a real world case study of a typical five floor apartment building in Thessaloniki, Greece. Copyright © 2011 Elsevier Ltd. All rights reserved.

Towards Web-based representation and processing of health information

PubMed Central

Gao, Sheng; Mioc, Darka; Yi, Xiaolun; Anton, Francois; Oldfield, Eddie; Coleman, David J

2009-01-01

Background There is great concern within health surveillance, on how to grapple with environmental degradation, rapid urbanization, population mobility and growth. The Internet has emerged as an efficient way to share health information, enabling users to access and understand data at their fingertips. Increasingly complex problems in the health field require increasingly sophisticated computer software, distributed computing power, and standardized data sharing. To address this need, Web-based mapping is now emerging as an important tool to enable health practitioners, policy makers, and the public to understand spatial health risks, population health trends and vulnerabilities. Today several web-based health applications generate dynamic maps; however, for people to fully interpret the maps they need data source description and the method used in the data analysis or statistical modeling. For the representation of health information through Web-mapping applications, there still lacks a standard format to accommodate all fixed (such as location) and variable (such as age, gender, health outcome, etc) indicators in the representation of health information. Furthermore, net-centric computing has not been adequately applied to support flexible health data processing and mapping online. Results The authors of this study designed a HEalth Representation XML (HERXML) schema that consists of the semantic (e.g., health activity description, the data sources description, the statistical methodology used for analysis), geometric, and cartographical representations of health data. A case study has been carried on the development of web application and services within the Canadian Geospatial Data Infrastructure (CGDI) framework for community health programs of the New Brunswick Lung Association. This study facilitated the online processing, mapping and sharing of health information, with the use of HERXML and Open Geospatial Consortium (OGC) services. It brought a new solution in better health data representation and initial exploration of the Web-based processing of health information. Conclusion The designed HERXML has been proven to be an appropriate solution in supporting the Web representation of health information. It can be used by health practitioners, policy makers, and the public in disease etiology, health planning, health resource management, health promotion and health education. The utilization of Web-based processing services in this study provides a flexible way for users to select and use certain processing functions for health data processing and mapping via the Web. This research provides easy access to geospatial and health data in understanding the trends of diseases, and promotes the growth and enrichment of the CGDI in the public health sector. PMID:19159445

Nessi: An EEG-Controlled Web Browser for Severely Paralyzed Patients

PubMed Central

Bensch, Michael; Karim, Ahmed A.; Mellinger, Jürgen; Hinterberger, Thilo; Tangermann, Michael; Bogdan, Martin; Rosenstiel, Wolfgang; Birbaumer, Niels

2007-01-01

We have previously demonstrated that an EEG-controlled web browser based on self-regulation of slow cortical potentials (SCPs) enables severely paralyzed patients to browse the internet independently of any voluntary muscle control. However, this system had several shortcomings, among them that patients could only browse within a limited number of web pages and had to select links from an alphabetical list, causing problems if the link names were identical or if they were unknown to the user (as in graphical links). Here we describe a new EEG-controlled web browser, called Nessi, which overcomes these shortcomings. In Nessi, the open source browser, Mozilla, was extended by graphical in-place markers, whereby different brain responses correspond to different frame colors placed around selectable items, enabling the user to select any link on a web page. Besides links, other interactive elements are accessible to the user, such as e-mail and virtual keyboards, opening up a wide range of hypertext-based applications. PMID:18350132

A WebGL Tool for Visualizing the Topology of the Sun's Coronal Magnetic Field

NASA Astrophysics Data System (ADS)

Duffy, A.; Cheung, C.; DeRosa, M. L.

2012-12-01

We present a web-based, topology-viewing tool that allows users to visualize the geometry and topology of the Sun's 3D coronal magnetic field in an interactive manner. The tool is implemented using, open-source, mature, modern web technologies including WebGL, jQuery, HTML 5, and CSS 3, which are compatible with nearly all modern web browsers. As opposed to the traditional method of visualization, which involves the downloading and setup of various software packages-proprietary and otherwise-the tool presents a clean interface that allows the user to easily load and manipulate the model, while also offering great power to choose which topological features are displayed. The tool accepts data encoded in the JSON open format that has libraries available for nearly every major programming language, making it simple to generate the data.

A Web Application for Cotton Irrigation Management on The US Southern High Plains. Part I: Crop Yield Modeling and Profit Analysis

USDA-ARS?s Scientific Manuscript database

Irrigated cotton (Gossypium Hirsutum L.) production is a central part of west Texas agriculture that depends on the essentially non-renewable water resource of the Ogallala aquifer. Web-based decision support tools that estimate the profit effects of irrigation for cotton under varying lint price, p...

Tracking the fate of watershed nitrogen: The “N-Sink” Web Tool and Two Case Studies

EPA Science Inventory

This product describes the application of a web-based decision support tool, N-Sink, in two case study watersheds. N-Sink is a customized ArcMap© program that provides maps of N sourcesand sinks within a watershed, and estimates the delivery efficiency of N movement from sou...

Measuring agreement between decision support reminders: the cloud vs. the local expert.

PubMed

Dixon, Brian Edward; Simonaitis, Linas; Perkins, Susan M; Wright, Adam; Middleton, Blackford

2014-04-10

A cloud-based clinical decision support system (CDSS) was implemented to remotely provide evidence-based guideline reminders in support of preventative health. Following implementation, we measured the agreement between preventive care reminders generated by an existing, local CDSS and the new, cloud-based CDSS operating on the same patient visit data. Electronic health record data for the same set of patients seen in primary care were sent to both the cloud-based web service and local CDSS. The clinical reminders returned by both services were captured for analysis. Cohen's Kappa coefficient was calculated to compare the two sets of reminders. Kappa statistics were further adjusted for prevalence and bias due to the potential effects of bias in the CDS logic and prevalence in the relative small sample of patients. The cloud-based CDSS generated 965 clinical reminders for 405 patient visits over 3 months. The local CDSS returned 889 reminders for the same patient visit data. When adjusted for prevalence and bias, observed agreement varied by reminder from 0.33 (95% CI 0.24 - 0.42) to 0.99 (95% CI 0.97 - 1.00) and demonstrated almost perfect agreement for 7 of the 11 reminders. Preventive care reminders delivered by two disparate CDS systems show substantial agreement. Subtle differences in rule logic and terminology mapping appear to account for much of the discordance. Cloud-based CDSS therefore show promise, opening the door for future development and implementation in support of health care providers with limited resources for knowledge management of complex logic and rules.

Measuring agreement between decision support reminders: the cloud vs. the local expert

PubMed Central

2014-01-01

Background A cloud-based clinical decision support system (CDSS) was implemented to remotely provide evidence-based guideline reminders in support of preventative health. Following implementation, we measured the agreement between preventive care reminders generated by an existing, local CDSS and the new, cloud-based CDSS operating on the same patient visit data. Methods Electronic health record data for the same set of patients seen in primary care were sent to both the cloud-based web service and local CDSS. The clinical reminders returned by both services were captured for analysis. Cohen’s Kappa coefficient was calculated to compare the two sets of reminders. Kappa statistics were further adjusted for prevalence and bias due to the potential effects of bias in the CDS logic and prevalence in the relative small sample of patients. Results The cloud-based CDSS generated 965 clinical reminders for 405 patient visits over 3 months. The local CDSS returned 889 reminders for the same patient visit data. When adjusted for prevalence and bias, observed agreement varied by reminder from 0.33 (95% CI 0.24 – 0.42) to 0.99 (95% CI 0.97 – 1.00) and demonstrated almost perfect agreement for 7 of the 11 reminders. Conclusions Preventive care reminders delivered by two disparate CDS systems show substantial agreement. Subtle differences in rule logic and terminology mapping appear to account for much of the discordance. Cloud-based CDSS therefore show promise, opening the door for future development and implementation in support of health care providers with limited resources for knowledge management of complex logic and rules. PMID:24720863

A framework for air quality monitoring based on free public data and open source tools

NASA Astrophysics Data System (ADS)

Nikolov, Hristo; Borisova, Denitsa

2014-10-01

In the recent years more and more widely accepted by the Space agencies (e.g. NASA, ESA) is the policy toward provision of Earth observation (EO) data and end products concerning air quality especially in large urban areas without cost to researchers and SMEs. Those EO data are complemented by increasing amount of in-situ data also provided at no cost either from national authorities or having crowdsourced origin. This accessibility together with the increased processing capabilities of the free and open source software is a prerequisite for creation of solid framework for air modeling in support of decision making at medium and large scale. Essential part of this framework is web-based GIS mapping tool responsible for dissemination of the output generated. In this research an attempt is made to establish a running framework based solely on openly accessible data on air quality and on set of freely available software tools for processing and modeling taking into account the present status quo in Bulgaria. Among the primary sources of data, especially for bigger urban areas, for different types of gases and dust particles, noted should be the National Institute of Meteorology and Hydrology of Bulgaria (NIMH) and National System for Environmental Monitoring managed by Bulgarian Executive Environmental Agency (ExEA). Both authorities provide data for concentration of several gases just to mention CO, CO2, NO2, SO2, and fine suspended dust (PM10, PM2.5) on monthly (for some data on daily) basis. In the framework proposed these data will complement the data from satellite-based sensors such as OMI instrument aboard EOS-Aura satellite and from TROPOMI instrument payload for future ESA Sentinel-5P mission. Integral part of the framework is the modern map for the land use/land cover which is provided from EEA by initiative GIO Land CORINE. This map is also a product from EO data distributed at European level. First and above all, our effort is focused on provision to the wider public living in urbanized areas with one reliable source of information on the present conditions concerning the air quality. Also this information might be used as indicator for presence of acid rains in agriculture areas close to industrial or electricity plants. Its availability at regular basis makes such information valuable source in case of manmade industrial disasters or incidents such as forest fires. Key issue in developing this framework is to ensure the delivery of reliable data products related to air quality at larger scale that those available at the moment.

A web-based library consult service for evidence-based medicine: Technical development

PubMed Central

Schwartz, Alan; Millam, Gregory

2006-01-01

Background Incorporating evidence based medicine (EBM) into clinical practice requires clinicians to learn to efficiently gain access to clinical evidence and effectively appraise its validity. Even using current electronic systems, selecting literature-based data to solve a single patient-related problem can require more time than practicing physicians or residents can spare. Clinical librarians, as informationists, are uniquely suited to assist physicians in this endeavor. Results To improve support for evidence-based practice, we have developed a web-based EBM library consult service application (LCS). Librarians use the LCS system to provide full text evidence-based literature with critical appraisal in response to a clinical question asked by a remote physician. LCS uses an entirely Free/Open Source Software platform and will be released under a Free Software license. In the first year of the LCS project, the software was successfully developed and a reference implementation put into active use. Two years of evaluation of the clinical, educational, and attitudinal impact on physician-users and librarian staff are underway, and expected to lead to refinement and wide dissemination of the system. Conclusion A web-based EBM library consult model may provide a useful way for informationists to assist clinicians, and is feasible to implement. PMID:16542453

jSPyDB, an open source database-independent tool for data management

NASA Astrophysics Data System (ADS)

Pierro, Giuseppe Antonio; Cavallari, Francesca; Di Guida, Salvatore; Innocente, Vincenzo

2011-12-01

Nowadays, the number of commercial tools available for accessing Databases, built on Java or .Net, is increasing. However, many of these applications have several drawbacks: usually they are not open-source, they provide interfaces only with a specific kind of database, they are platform-dependent and very CPU and memory consuming. jSPyDB is a free web-based tool written using Python and Javascript. It relies on jQuery and python libraries, and is intended to provide a simple handler to different database technologies inside a local web browser. Such a tool, exploiting fast access libraries such as SQLAlchemy, is easy to install, and to configure. The design of this tool envisages three layers. The front-end client side in the local web browser communicates with a backend server. Only the server is able to connect to the different databases for the purposes of performing data definition and manipulation. The server makes the data available to the client, so that the user can display and handle them safely. Moreover, thanks to jQuery libraries, this tool supports export of data in different formats, such as XML and JSON. Finally, by using a set of pre-defined functions, users are allowed to create their customized views for a better data visualization. In this way, we optimize the performance of database servers by avoiding short connections and concurrent sessions. In addition, security is enforced since we do not provide users the possibility to directly execute any SQL statement.

A decision support system and rule-based algorithm to augment the human interpretation of the 12-lead electrocardiogram.

PubMed

Cairns, Andrew W; Bond, Raymond R; Finlay, Dewar D; Guldenring, Daniel; Badilini, Fabio; Libretti, Guido; Peace, Aaron J; Leslie, Stephen J

The 12-lead Electrocardiogram (ECG) has been used to detect cardiac abnormalities in the same format for more than 70years. However, due to the complex nature of 12-lead ECG interpretation, there is a significant cognitive workload required from the interpreter. This complexity in ECG interpretation often leads to errors in diagnosis and subsequent treatment. We have previously reported on the development of an ECG interpretation support system designed to augment the human interpretation process. This computerised decision support system has been named 'Interactive Progressive based Interpretation' (IPI). In this study, a decision support algorithm was built into the IPI system to suggest potential diagnoses based on the interpreter's annotations of the 12-lead ECG. We hypothesise semi-automatic interpretation using a digital assistant can be an optimal man-machine model for ECG interpretation. To improve interpretation accuracy and reduce missed co-abnormalities. The Differential Diagnoses Algorithm (DDA) was developed using web technologies where diagnostic ECG criteria are defined in an open storage format, Javascript Object Notation (JSON), which is queried using a rule-based reasoning algorithm to suggest diagnoses. To test our hypothesis, a counterbalanced trial was designed where subjects interpreted ECGs using the conventional approach and using the IPI+DDA approach. A total of 375 interpretations were collected. The IPI+DDA approach was shown to improve diagnostic accuracy by 8.7% (although not statistically significant, p-value=0.1852), the IPI+DDA suggested the correct interpretation more often than the human interpreter in 7/10 cases (varying statistical significance). Human interpretation accuracy increased to 70% when seven suggestions were generated. Although results were not found to be statistically significant, we found; 1) our decision support tool increased the number of correct interpretations, 2) the DDA algorithm suggested the correct interpretation more often than humans, and 3) as many as 7 computerised diagnostic suggestions augmented human decision making in ECG interpretation. Statistical significance may be achieved by expanding sample size. Copyright © 2017 Elsevier Inc. All rights reserved.

TOPSAN: a dynamic web database for structural genomics.

PubMed

Ellrott, Kyle; Zmasek, Christian M; Weekes, Dana; Sri Krishna, S; Bakolitsa, Constantina; Godzik, Adam; Wooley, John

2011-01-01

The Open Protein Structure Annotation Network (TOPSAN) is a web-based collaboration platform for exploring and annotating structures determined by structural genomics efforts. Characterization of those structures presents a challenge since the majority of the proteins themselves have not yet been characterized. Responding to this challenge, the TOPSAN platform facilitates collaborative annotation and investigation via a user-friendly web-based interface pre-populated with automatically generated information. Semantic web technologies expand and enrich TOPSAN's content through links to larger sets of related databases, and thus, enable data integration from disparate sources and data mining via conventional query languages. TOPSAN can be found at http://www.topsan.org.

Molecular property diagnostic suite (MPDS): Development of disease-specific open source web portals for drug discovery.

PubMed

Nagamani, S; Gaur, A S; Tanneeru, K; Muneeswaran, G; Madugula, S S; Consortium, Mpds; Druzhilovskiy, D; Poroikov, V V; Sastry, G N

2017-11-01

Molecular property diagnostic suite (MPDS) is a Galaxy-based open source drug discovery and development platform. MPDS web portals are designed for several diseases, such as tuberculosis, diabetes mellitus, and other metabolic disorders, specifically aimed to evaluate and estimate the drug-likeness of a given molecule. MPDS consists of three modules, namely data libraries, data processing, and data analysis tools which are configured and interconnected to assist drug discovery for specific diseases. The data library module encompasses vast information on chemical space, wherein the MPDS compound library comprises 110.31 million unique molecules generated from public domain databases. Every molecule is assigned with a unique ID and card, which provides complete information for the molecule. Some of the modules in the MPDS are specific to the diseases, while others are non-specific. Importantly, a suitably altered protocol can be effectively generated for another disease-specific MPDS web portal by modifying some of the modules. Thus, the MPDS suite of web portals shows great promise to emerge as disease-specific portals of great value, integrating chemoinformatics, bioinformatics, molecular modelling, and structure- and analogue-based drug discovery approaches.

Data-mining to build a knowledge representation store for clinical decision support. Studies on curation and validation based on machine performance in multiple choice medical licensing examinations.

PubMed

Robson, Barry; Boray, Srinidhi

2016-06-01

Extracting medical knowledge by structured data mining of many medical records and from unstructured data mining of natural language source text on the Internet will become increasingly important for clinical decision support. Output from these sources can be transformed into large numbers of elements of knowledge in a Knowledge Representation Store (KRS), here using the notation and to some extent the algebraic principles of the Q-UEL Web-based universal exchange and inference language described previously, rooted in Dirac notation from quantum mechanics and linguistic theory. In a KRS, semantic structures or statements about the world of interest to medicine are analogous to natural language sentences seen as formed from noun phrases separated by verbs, prepositions and other descriptions of relationships. A convenient method of testing and better curating these elements of knowledge is by having the computer use them to take the test of a multiple choice medical licensing examination. It is a venture which perhaps tells us almost as much about the reasoning of students and examiners as it does about the requirements for Artificial Intelligence as employed in clinical decision making. It emphasizes the role of context and of contextual probabilities as opposed to the more familiar intrinsic probabilities, and of a preliminary form of logic that we call presyllogistic reasoning. Copyright © 2016 Elsevier Ltd. All rights reserved.

Development of a coastal information system for the management of Jeddah coastal waters in Saudi Arabia

NASA Astrophysics Data System (ADS)

Mayerle, R.; Al-Subhi, A.; Fernández Jaramillo, J.; Salama, A.; Bruss, G.; Zubier, K.; Runte, K.; Turki, A.; Hesse, K.; Jastania, H.; Ladwig, N.; Mudarris, M.

2016-04-01

This paper presents results of the development and application of a web-based information system, Jeddah CIS, for assisting decision makers in the management of Jeddah coastal waters, in Saudi Arabia. The system will support coastal planning, management of navigation and tackle pollution due to accidents. The system was developed primarily to nowcast in quasi-real time and to deliver short-term forecasts of water levels, current velocities and waves with high spatial and temporal resolution for the area near Jeddah. Therefor it will hasten response when adverse weather conditions prevail. The Jeddah-CIS integrates sensors transmitting in real time, meteorological, oceanographic and water quality parameters and operational models for flow and waves. It also provides interactive tools using advanced visualization techniques to facilitate dissemination of information. The system relies on open source software and has been designed to facilitate the integration of additional components for enhanced information processing, data evaluation and generation of higher water level, current velocity and wave for the general public. Jeddah-CIS has been operational since 2013. Extensions of the system to speed operations and improving the accuracy of the predictions to the public are currently underway.

quantGenius: implementation of a decision support system for qPCR-based gene quantification.

PubMed

Baebler, Špela; Svalina, Miha; Petek, Marko; Stare, Katja; Rotter, Ana; Pompe-Novak, Maruša; Gruden, Kristina

2017-05-25

Quantitative molecular biology remains a challenge for researchers due to inconsistent approaches for control of errors in the final results. Due to several factors that can influence the final result, quantitative analysis and interpretation of qPCR data are still not trivial. Together with the development of high-throughput qPCR platforms, there is a need for a tool allowing for robust, reliable and fast nucleic acid quantification. We have developed "quantGenius" ( http://quantgenius.nib.si ), an open-access web application for a reliable qPCR-based quantification of nucleic acids. The quantGenius workflow interactively guides the user through data import, quality control (QC) and calculation steps. The input is machine- and chemistry-independent. Quantification is performed using the standard curve approach, with normalization to one or several reference genes. The special feature of the application is the implementation of user-guided QC-based decision support system, based on qPCR standards, that takes into account pipetting errors, assay amplification efficiencies, limits of detection and quantification of the assays as well as the control of PCR inhibition in individual samples. The intermediate calculations and final results are exportable in a data matrix suitable for further statistical analysis or visualization. We additionally compare the most important features of quantGenius with similar advanced software tools and illustrate the importance of proper QC system in the analysis of qPCR data in two use cases. To our knowledge, quantGenius is the only qPCR data analysis tool that integrates QC-based decision support and will help scientists to obtain reliable results which are the basis for biologically meaningful data interpretation.

Implementing information technology to improve workplace health: a web-based information needs assessment of managers in Fraser Health, British Columbia.

PubMed

Sandhu, Jag S; Anderson, Keith; Keen, Dave; Yassi, Annalee

2005-01-01

A web-based questionnaire-survey was administered primarily to determine what information is useful to managers in Fraser Health, of British Columbia to support decision-making for workplace health and safety. The results indicated that managers prefer electronic quarterly reports, with targets, goals, and historical trends rated as "very important." Over 85.7% "agree" that if information was readily available in the "most beneficial" format, they would be able to improve workplace health. Recommendations include that managers be presented with clear and concise workplace health reports that facilitate analysis for decision-making.

Structured data entry for narrative data in a broad specialty: patient history and physical examination in pediatrics

PubMed Central

Bleeker, Sacha E; Derksen-Lubsen, Gerarda; van Ginneken, Astrid M; van der Lei, Johan; Moll, Henriëtte A

2006-01-01

Background Whereas an electronic medical record (EMR) system can partly address the limitations, of paper-based documentation, such as fragmentation of patient data, physical paper records missing and poor legibility, structured data entry (SDE, i.e. data entry based on selection of predefined medical concepts) is essential for uniformity of data, easier reporting, decision support, quality assessment, and patient-oriented clinical research. The aim of this project was to explore whether a previously developed generic (i.e. content independent) SDE application to support the structured documentation of narrative data (called OpenSDE) can be used to model data obtained at history taking and physical examination of a broad specialty. Methods OpenSDE was customized for the broad domain of general pediatrics: medical concepts and its descriptors from history taking and physical examination were modeled into a tree structure. Results An EMR system allowing structured recording (OpenSDE) of pediatric narrative data was developed. Patient history is described by 20 main concepts and physical examination by 11. In total, the thesaurus consists of about 1800 items, used in 8648 nodes in the tree with a maximum depth of 9 levels. Patient history contained 6312 nodes, and physical examination 2336. User-defined entry forms can be composed according to individual needs, without affecting the underlying data representation. The content of the tree can be adjusted easily and sharing records among different disciplines is possible. Data that are relevant in more than one context can be accessed from multiple branches of the tree without duplication or ambiguity of data entry via "shortcuts". Conclusion An expandable EMR system with structured data entry (OpenSDE) for pediatrics was developed, allowing structured documentation of patient history and physical examination. For further evaluation in other environments, the tree structure for general pediatrics is available at the Erasmus MC Web site (in Dutch, translation into English in progress) [1]. The generic OpenSDE application is available at the OpenSDE Web site [2]. PMID:16839414

AI based HealthCare Platform for Real Time, Predictive and Prescriptive Analytics using Reactive Programming

NASA Astrophysics Data System (ADS)

Kaur, Jagreet; Singh Mann, Kulwinder, Dr.

2018-01-01

AI in Healthcare needed to bring real, actionable insights and Individualized insights in real time for patients and Doctors to support treatment decisions., We need a Patient Centred Platform for integrating EHR Data, Patient Data, Prescriptions, Monitoring, Clinical research and Data. This paper proposes a generic architecture for enabling AI based healthcare analytics Platform by using open sources Technologies Apache beam, Apache Flink Apache Spark, Apache NiFi, Kafka, Tachyon, Gluster FS, NoSQL- Elasticsearch, Cassandra. This paper will show the importance of applying AI based predictive and prescriptive analytics techniques in Health sector. The system will be able to extract useful knowledge that helps in decision making and medical monitoring in real-time through an intelligent process analysis and big data processing.

A web-based multicriteria evaluation of spatial trade-offs between environmental and economic implications from hydraulic fracturing in a shale gas region in Ohio.

PubMed

Liu, X; Gorsevski, P V; Yacobucci, M M; Onasch, C M

2016-06-01

Planning of shale gas infrastructure and drilling sites for hydraulic fracturing has important spatial implications. The evaluation of conflicting and competing objectives requires an explicit consideration of multiple criteria as they have important environmental and economic implications. This study presents a web-based multicriteria spatial decision support system (SDSS) prototype with a flexible and user-friendly interface that could provide educational or decision-making capabilities with respect to hydraulic fracturing site selection in eastern Ohio. One of the main features of this SDSS is to emphasize potential trade-offs between important factors of environmental and economic ramifications from hydraulic fracturing activities using a weighted linear combination (WLC) method. In the prototype, the GIS-enabled analytical components allow spontaneous visualization of available alternatives on maps which provide value-added features for decision support processes and derivation of final decision maps. The SDSS prototype also facilitates nonexpert participation capabilities using a mapping module, decision-making tool, group decision module, and social media sharing tools. The logical flow of successively presented forms and standardized criteria maps is used to generate visualization of trade-off scenarios and alternative solutions tailored to individual user's preferences that are graphed for subsequent decision-making.

Unifying Water Data Sources: How the CUAHSI Water Data Center is Enabling and Improving Access to a Growing Catalog of over 100 Data Providers

NASA Astrophysics Data System (ADS)

Pollak, J.; Berry, K.; Couch, A.; Arrigo, J.; Hooper, R. P.

2013-12-01

Scientific data about water are collected and distributed by numerous sources which can differ tremendously in scale. As competition for water resources increases, increasing access to and understanding of information about water will be critical. The mission of the new CUAHSI Water Data Center (WDC) is to provide those researchers who collect data a medium to publish their datasets and give those wanting to discover data the proper tools to efficiently find the data that they seek. These tools include standards-based data publication, data discovery tools based upon faceted and telescoping search, and a data analysis tool HydroDesktop that downloads and unifies data in standardized formats. The CUAHSI Hydrologic Information System (HIS) is a community developed and open source system for sharing water data. As a federated, web service oriented system it enables data publication for a diverse user population including scientific investigators (Research Coordination Networks, Critical Zone Observatories), government agencies (USGS, NASA, EPA), and citizen scientists (watershed associations). HydroDesktop is an end user application for data consumption in this system that the WDC supports. This application can be used for finding, downloading, and analyzing data from the HIS. It provides a GIS interface that allows users to incorporate spatial data that are not accessible via HIS, simple analysis tools to facilitate graphing and visualization, tools to export data to common file types, and provides an extensible architecture that developers can build upon. HydroDesktop, however, is just one example of a data access client for HIS. The web service oriented architecture enables data access by an unlimited number of clients provided they can consume the web services used in HIS. One such example developed at the WDC is the 'Faceted Search Client', which capitalizes upon exploratory search concepts to improve accuracy and precision during search. We highlight such features of the CUAHSI-HIS which make it particularly appropriate for providing unified access to several sources of water data. A growing community of researchers and educators are employing these tools for education; including sharing best practices around creating modules, supporting researchers and educators in accessing the services, and cataloging and sharing modules. The CUAHSI WDC is a community governed organization. Our agenda is driven by the community's voice through a Board of Directors and committees that decide strategic direction (new products), tactical decisions (product improvement), and evaluation of usability. By providing the aforementioned services within a community driven framework, we believe the WDC is providing critical services that include improving water data discoverability, accessibility and usability within a sustainable governance structure.

An Environment for Guideline-based Decision Support Systems for Outpatients Monitoring.

PubMed

Zini, Elisa M; Lanzola, Giordano; Bossi, Paolo; Quaglini, Silvana

2017-08-11

We propose an architecture for monitoring outpatients that relies on mobile technologies for acquiring data. The goal is to better control the onset of possible side effects between the scheduled visits at the clinic. We analyze the architectural components required to ensure a high level of abstraction from data. Clinical practice guidelines were formalized with Alium, an authoring tool based on the PROforma language, using SNOMED-CT as a terminology standard. The Alium engine is accessible through a set of APIs that may be leveraged for implementing an application based on standard web technologies to be used by doctors at the clinic. Data sent by patients using mobile devices need to be complemented with those already available in the Electronic Health Record to generate personalized recommendations. Thus a middleware pursuing data abstraction is required. To comply with current standards, we adopted the HL7 Virtual Medical Record for Clinical Decision Support Logical Model, Release 2. The developed architecture for monitoring outpatients includes: (1) a guideline-based Decision Support System accessible through a web application that helps the doctors with prevention, diagnosis and treatment of therapy side effects; (2) an application for mobile devices, which allows patients to regularly send data to the clinic. In order to tailor the monitoring procedures to the specific patient, the Decision Support System also helps physicians with the configuration of the mobile application, suggesting the data to be collected and the associated collection frequency that may change over time, according to the individual patient's conditions. A proof of concept has been developed with a system for monitoring the side effects of chemo-radiotherapy in head and neck cancer patients. Our environment introduces two main innovation elements with respect to similar works available in the literature. First, in order to meet the specific patients' needs, in our work the Decision Support System also helps the physicians in properly configuring the mobile application. Then the Decision Support System is also continuously fed by patient-reported outcomes.

An Unexpected Ally: Using Microsoft's SharePoint to Create a Departmental Intranet

ERIC Educational Resources Information Center

Dahl, David

2010-01-01

In September 2008, the Albert S. Cook Library at Towson University implemented an intranet to support the various functions of the library's Reference Department. This intranet is called the RefPortal. After exploring open source options and other Web 2.0 tools, the department (under the guidance of the library technology coordinator) chose…

Design and Implementation of Surrounding Transaction Plotting and Management System Based on Google Map API

NASA Astrophysics Data System (ADS)

Cao, Y. B.; Hua, Y. X.; Zhao, J. X.; Guo, S. M.

2013-11-01

With China's rapid economic development and comprehensive national strength growing, Border work has become a long-term and important task in China's diplomatic work. How to implement rapid plotting, real-time sharing and mapping surrounding affairs has taken great significance for government policy makers and diplomatic staff. However, at present the already exists Boundary information system are mainly have problems of Geospatial data update is heavily workload, plotting tools are in a state of serious lack of, Geographic events are difficult to share, this phenomenon has seriously hampered the smooth development of the border task. The development and progress of Geographic information system technology especially the development of Web GIS offers the possibility to solve the above problems, this paper adopts four layers of B/S architecture, with the support of Google maps service, uses the free API which is offered by Google maps and its features of openness, ease of use, sharing characteristics, highresolution images to design and implement the surrounding transaction plotting and management system based on the web development technology of ASP.NET, C#, Ajax. The system can provide decision support for government policy makers as well as diplomatic staff's real-time plotting and sharing of surrounding information. The practice has proved that the system has good usability and strong real-time.