HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis

PubMed Central

David, Fabrice P. A.; Delafontaine, Julien; Carat, Solenne; Ross, Frederick J.; Lefebvre, Gregory; Jarosz, Yohan; Sinclair, Lucas; Noordermeer, Daan; Rougemont, Jacques; Leleu, Marion

2014-01-01

The HTSstation analysis portal is a suite of simple web forms coupled to modular analysis pipelines for various applications of High-Throughput Sequencing including ChIP-seq, RNA-seq, 4C-seq and re-sequencing. HTSstation offers biologists the possibility to rapidly investigate their HTS data using an intuitive web application with heuristically pre-defined parameters. A number of open-source software components have been implemented and can be used to build, configure and run HTS analysis pipelines reactively. Besides, our programming framework empowers developers with the possibility to design their own workflows and integrate additional third-party software. The HTSstation web application is accessible at http://htsstation.epfl.ch. PMID:24475057

Introduction to geospatial semantics and technology workshop handbook

USGS Publications Warehouse

Varanka, Dalia E.

2012-01-01

The workshop is a tutorial on introductory geospatial semantics with hands-on exercises using standard Web browsers. The workshop is divided into two sections, general semantics on the Web and specific examples of geospatial semantics using data from The National Map of the U.S. Geological Survey and the Open Ontology Repository. The general semantics section includes information and access to publicly available semantic archives. The specific session includes information on geospatial semantics with access to semantically enhanced data for hydrography, transportation, boundaries, and names. The Open Ontology Repository offers open-source ontologies for public use.

OpenMSI: A High-Performance Web-Based Platform for Mass Spectrometry Imaging

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

Rubel, Oliver; Greiner, Annette; Cholia, Shreyas

Mass spectrometry imaging (MSI) enables researchers to directly probe endogenous molecules directly within the architecture of the biological matrix. Unfortunately, efficient access, management, and analysis of the data generated by MSI approaches remain major challenges to this rapidly developing field. Despite the availability of numerous dedicated file formats and software packages, it is a widely held viewpoint that the biggest challenge is simply opening, sharing, and analyzing a file without loss of information. Here we present OpenMSI, a software framework and platform that addresses these challenges via an advanced, high-performance, extensible file format and Web API for remote data accessmore » (http://openmsi.nersc.gov). The OpenMSI file format supports storage of raw MSI data, metadata, and derived analyses in a single, self-describing format based on HDF5 and is supported by a large range of analysis software (e.g., Matlab and R) and programming languages (e.g., C++, Fortran, and Python). Careful optimization of the storage layout of MSI data sets using chunking, compression, and data replication accelerates common, selective data access operations while minimizing data storage requirements and are critical enablers of rapid data I/O. The OpenMSI file format has shown to provide >2000-fold improvement for image access operations, enabling spectrum and image retrieval in less than 0.3 s across the Internet even for 50 GB MSI data sets. To make remote high-performance compute resources accessible for analysis and to facilitate data sharing and collaboration, we describe an easy-to-use yet powerful Web API, enabling fast and convenient access to MSI data, metadata, and derived analysis results stored remotely to facilitate high-performance data analysis and enable implementation of Web based data sharing, visualization, and analysis.« less

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.

Description of the U.S. Geological Survey Geo Data Portal data integration framework

USGS Publications Warehouse

Blodgett, David L.; Booth, Nathaniel L.; Kunicki, Thomas C.; Walker, Jordan I.; Lucido, Jessica M.

2012-01-01

The U.S. Geological Survey has developed an open-standard data integration framework for working efficiently and effectively with large collections of climate and other geoscience data. A web interface accesses catalog datasets to find data services. Data resources can then be rendered for mapping and dataset metadata are derived directly from these web services. Algorithm configuration and information needed to retrieve data for processing are passed to a server where all large-volume data access and manipulation takes place. The data integration strategy described here was implemented by leveraging existing free and open source software. Details of the software used are omitted; rather, emphasis is placed on how open-standard web services and data encodings can be used in an architecture that integrates common geographic and atmospheric data.

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.

Improving Land Cover Mapping: a Mobile Application Based on ESA Sentinel 2 Imagery

NASA Astrophysics Data System (ADS)

Melis, M. T.; Dessì, F.; Loddo, P.; La Mantia, C.; Da Pelo, S.; Deflorio, A. M.; Ghiglieri, G.; Hailu, B. T.; Kalegele, K.; Mwasi, B. N.

2018-04-01

The increasing availability of satellite data is a real value for the enhancement of environmental knowledge and land management. Possibilities to integrate different source of geo-data are growing and methodologies to create thematic database are becoming very sophisticated. Moreover, the access to internet services and, in particular, to web mapping services is well developed and spread either between expert users than the citizens. Web map services, like Google Maps or Open Street Maps, give the access to updated optical imagery or topographic maps but information on land cover/use - are not still provided. Therefore, there are many failings in the general utilization -non-specialized users- and access to those maps. This issue is particularly felt where the digital (web) maps could form the basis for land use management as they are more economic and accessible than the paper maps. These conditions are well known in many African countries where, while the internet access is becoming open to all, the local map agencies and their products are not widespread.

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.

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.

Opening Up Access to Open Access

ERIC Educational Resources Information Center

Singer, Ross

2008-01-01

As the corpus of gray literature grows and the price of serials rises, it becomes increasingly important to explore ways to integrate the free and open Web seamlessly into one's collections. Users, after all, are discovering these materials all the time via sites such as Google Scholar and Scirus or by searching arXiv.org or CiteSeer directly.…

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

Sketching Up New Geographies: Open Sourcing and Curriculum Development

ERIC Educational Resources Information Center

Boyd, William; Ellis, David

2013-01-01

The functionality of web 2.0 technologies has caused academics to rethink their development of teaching and learning methods and approaches. The editable, open access nature of web 2.0 encourages the innovative collaboration of ideas, the creation of equitable visual and tactile learning environments, and opportunity for academics to develop…

Accessing near real-time Antarctic meteorological data through an OGC Sensor Observation Service (SOS)

NASA Astrophysics Data System (ADS)

Kirsch, Peter; Breen, Paul

2013-04-01

We wish to highlight outputs of a project conceived from a science requirement to improve discovery and access to Antarctic meteorological data in near real-time. Given that the data was distributed in both spatial and temporal domains and is to be accessed across several science disciplines, the creation of an interoperable, OGC compliant web service was deemed the most appropriate approach. We will demonstrate an implementation of the OGC SOS Interface Standard to discover, browse, and access Antarctic meteorological data-sets. A selection of programmatic (R, Perl) and web client interfaces utilizing open technologies ( e.g. jQuery, Flot, openLayers ) will be demonstrated. In addition we will show how high level abstractions can be constructed to allow the users flexible and straightforward access to SOS retrieved data.

Cheminformatics and the Semantic Web: adding value with linked data and enhanced provenance

PubMed Central

Frey, Jeremy G; Bird, Colin L

2013-01-01

Cheminformatics is evolving from being a field of study associated primarily with drug discovery into a discipline that embraces the distribution, management, access, and sharing of chemical data. The relationship with the related subject of bioinformatics is becoming stronger and better defined, owing to the influence of Semantic Web technologies, which enable researchers to integrate heterogeneous sources of chemical, biochemical, biological, and medical information. These developments depend on a range of factors: the principles of chemical identifiers and their role in relationships between chemical and biological entities; the importance of preserving provenance and properly curated metadata; and an understanding of the contribution that the Semantic Web can make at all stages of the research lifecycle. The movements toward open access, open source, and open collaboration all contribute to progress toward the goals of integration. PMID:24432050

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.

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

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…

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…

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

Automatically exposing OpenLifeData via SADI semantic Web Services.

PubMed

González, Alejandro Rodríguez; Callahan, Alison; Cruz-Toledo, José; Garcia, Adrian; Egaña Aranguren, Mikel; Dumontier, Michel; Wilkinson, Mark D

2014-01-01

Two distinct trends are emerging with respect to how data is shared, collected, and analyzed within the bioinformatics community. First, Linked Data, exposed as SPARQL endpoints, promises to make data easier to collect and integrate by moving towards the harmonization of data syntax, descriptive vocabularies, and identifiers, as well as providing a standardized mechanism for data access. Second, Web Services, often linked together into workflows, normalize data access and create transparent, reproducible scientific methodologies that can, in principle, be re-used and customized to suit new scientific questions. Constructing queries that traverse semantically-rich Linked Data requires substantial expertise, yet traditional RESTful or SOAP Web Services cannot adequately describe the content of a SPARQL endpoint. We propose that content-driven Semantic Web Services can enable facile discovery of Linked Data, independent of their location. We use a well-curated Linked Dataset - OpenLifeData - and utilize its descriptive metadata to automatically configure a series of more than 22,000 Semantic Web Services that expose all of its content via the SADI set of design principles. The OpenLifeData SADI services are discoverable via queries to the SHARE registry and easy to integrate into new or existing bioinformatics workflows and analytical pipelines. We demonstrate the utility of this system through comparison of Web Service-mediated data access with traditional SPARQL, and note that this approach not only simplifies data retrieval, but simultaneously provides protection against resource-intensive queries. We show, through a variety of different clients and examples of varying complexity, that data from the myriad OpenLifeData can be recovered without any need for prior-knowledge of the content or structure of the SPARQL endpoints. We also demonstrate that, via clients such as SHARE, the complexity of federated SPARQL queries is dramatically reduced.

Balancing Ideology and Feasibility: A Case Study on Adopting and Evaluating Open Access Publishing Models for a Society Journal within Philosophy

ERIC Educational Resources Information Center

Neuman, Yrsa; Laakso, Mikael

2017-01-01

Introduction: Open access, the notion that research output, such as journal articles, should be freely accessible to readers on the Web, is arguably in the best interest of science. In this article, we (1) describe in-depth how a society-owned philosophy journal, "Nordic Wittgenstein Review," evaluated various publishing models and made…

MOOCs: When Opening Doors to Education, Institutions Must Ensure That People with Disabilities Have Equal Access

ERIC Educational Resources Information Center

Anastasopoulos, Nicholas; Baer, Amanda Marie

2013-01-01

Massive Open Online Courses ("MOOCs") are free online courses offered by institutions of higher education to individuals across the world, without any admissions criteria. Through web-based courses hosted by MOOC platforms, student-participants learn by accessing media, including documents, pictures and uploaded lectures on the course…

Measuring Link-Resolver Success: Comparing 360 Link with a Local Implementation of WebBridge

ERIC Educational Resources Information Center

Herrera, Gail

2011-01-01

This study reviewed link resolver success comparing 360 Link and a local implementation of WebBridge. Two methods were used: (1) comparing article-level access and (2) examining technical issues for 384 randomly sampled OpenURLs. Google Analytics was used to collect user-generated OpenURLs. For both methods, 360 Link out-performed the local…

Indexing the medical open access literature for textual and content-based visual retrieval.

PubMed

Eggel, Ivan; Müller, Henning

2010-01-01

Over the past few years an increasing amount of scientific journals have been created in an open access format. Particularly in the medical field the number of openly accessible journals is enormous making a wide body of knowledge available for analysis and retrieval. Part of the trend towards open access publications can be linked to funding bodies such as the NIH¹ (National Institutes of Health) and the Swiss National Science Foundation (SNF²) requiring funded projects to make all articles of funded research available publicly. This article describes an approach to make part of the knowledge of open access journals available for retrieval including the textual information but also the images contained in the articles. For this goal all articles of 24 journals related to medical informatics and medical imaging were crawled from the web pages of BioMed Central. Text and images of the PDF (Portable Document Format) files were indexed separately and a web-based retrieval interface allows for searching via keyword queries or by visual similarity queries. Starting point for a visual similarity query can be an image on the local hard disk that is uploaded or any image found via the textual search. Search for similar documents is also possible.

Exploring NASA GES DISC Data with Interoperable Services

NASA Technical Reports Server (NTRS)

Zhao, Peisheng; Yang, Wenli; Hegde, Mahabal; Wei, Jennifer C.; Kempler, Steven; Pham, Long; Teng, William; Savtchenko, Andrey

2015-01-01

Overview of NASA GES DISC (NASA Goddard Earth Science Data and Information Services Center) data with interoperable services: Open-standard and Interoperable Services Improve data discoverability, accessibility, and usability with metadata, catalogue and portal standards Achieve data, information and knowledge sharing across applications with standardized interfaces and protocols Open Geospatial Consortium (OGC) Data Services and Specifications Web Coverage Service (WCS) -- data Web Map Service (WMS) -- pictures of data Web Map Tile Service (WMTS) --- pictures of data tiles Styled Layer Descriptors (SLD) --- rendered styles.

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.

77 FR 32637 - Sunshine Act Meeting Notice

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-01

... 20551. Status: Open. On the day of the meeting, you will be able to view the meeting via Web cast from a link available on the Board's public Web site. You do not need to register to view the Web cast of the... start of the meeting. Both links may be accessed from the Board's public Web site at www.federalreserve...

Using a Web Site in an Elementary Science Methods Class: Are We Opening a Pandora's Box?

ERIC Educational Resources Information Center

Lewis, Scott P.; O'Brien, George E.

This paper describes the introduction and use of the World Wide Web (WWW) in an elementary science methods course at Florida International University (FIU). The goals of creating a web site include engaging conversations among educators, providing access to local resources for students, and examining student use of web sites and the Internet. The…

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)

PubMed Central

Dempsey, Donald M; Hendrickson, Robert Curtis; Orton, Richard J; Siddell, Stuart G; Smith, Donald B

2018-01-01

Abstract The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy. PMID:29040670

"Medical Education Online": A Case Study of an Open Access Journal in Health Professional Education

ERIC Educational Resources Information Center

Solomon, David J.

2007-01-01

Introduction: The development of the World Wide Web (WWW) has made it possible of small groups of colleagues or even single individuals to create peer-reviewed scholarly journals. This paper discusses the development of Medical Education Online (MEO) an open access peer-reviewed journal in health professional education. Description: MEO was first…

Post Graduations in Technologies and Computing Applied to Education: From F2F Classes to Multimedia Online Open Courses

ERIC Educational Resources Information Center

Marques, Bertil P.; Carvalho, Piedade; Escudeiro, Paula; Barata, Ana; Silva, Ana; Queiros, Sandra

2017-01-01

Promoted by the significant increase of large scale internet access, many audiences have turned to the web and to its resources for learning and inspiration, with diverse sets of skills and intents. In this context, Multimedia Online Open Courses (MOOC) consist in learning models supported on user-friendly web tools that allow anyone with minimum…

Web Map Apps using NASA's Earth Observing Fleet

NASA Technical Reports Server (NTRS)

Boller, R.; Baynes, K.; Pressley, N.; Thompson, C.; Cechini, M.; Schmaltz, J.; Alarcon, C.; De Cesare, C.; Gunnoe, T.; Wong, M.;

Web-based education in anesthesiology: a critical overview.

PubMed

Doyle, D John

2008-12-01

The purpose of this review is to discuss the rise of web-based educational resources available to the anesthesiology community. Recent developments of particular importance include the growth of 'Web 2.0' resources, the development of the concepts of 'open access' and 'information philanthropy', and the expansion of web-based medical simulation software products.In addition, peer review of online educational resources has now come of age. The worldwide web has made available a large variety of valuable medical information and education resources only dreamed of two decades ago. To a large extent,these developments represent a shift in the focus of medical education resources to emphasize free access to materials and to encourage collaborative development efforts.

SCHeMA web-based observation data information system

NASA Astrophysics Data System (ADS)

Novellino, Antonio; Benedetti, Giacomo; D'Angelo, Paolo; Confalonieri, Fabio; Massa, Francesco; Povero, Paolo; Tercier-Waeber, Marie-Louise

2016-04-01

It is well recognized that the need of sharing ocean data among non-specialized users is constantly increasing. Initiatives that are built upon international standards will contribute to simplify data processing and dissemination, improve user-accessibility also through web browsers, facilitate the sharing of information across the integrated network of ocean observing systems; and ultimately provide a better understanding of the ocean functioning. The SCHeMA (Integrated in Situ Chemical MApping probe) Project is developing an open and modular sensing solution for autonomous in situ high resolution mapping of a wide range of anthropogenic and natural chemical compounds coupled to master bio-physicochemical parameters (www.schema-ocean.eu). The SCHeMA web system is designed to ensure user-friendly data discovery, access and download as well as interoperability with other projects through a dedicated interface that implements the Global Earth Observation System of Systems - Common Infrastructure (GCI) recommendations and the international Open Geospatial Consortium - Sensor Web Enablement (OGC-SWE) standards. This approach will insure data accessibility in compliance with major European Directives and recommendations. Being modular, the system allows the plug-and-play of commercially available probes as well as new sensor probess under development within the project. The access to the network of monitoring probes is provided via a web-based system interface that, being implemented as a SOS (Sensor Observation Service), is providing standard interoperability and access tosensor observations systems through O&M standard - as well as sensor descriptions - encoded in Sensor Model Language (SensorML). The use of common vocabularies in all metadatabases and data formats, to describe data in an already harmonized and common standard is a prerequisite towards consistency and interoperability. Therefore, the SCHeMA SOS has adopted the SeaVox common vocabularies populated by SeaDataNet network of National Oceanographic Data Centres. The SCHeMA presentation layer, a fundamental part of the software architecture, offers to the user a bidirectional interaction with the integrated system allowing to manage and configure the sensor probes; view the stored observations and metadata, and handle alarms. The overall structure of the web portal developed within the SCHeMA initiative (Sensor Configuration, development of Core Profile interface for data access via OGC standard, external services such as web services, WMS, WFS; and Data download and query manager) will be presented and illustrated with examples of ongoing tests in costal and open sea.

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.

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.

Leveraging Open Standard Interfaces in Accessing and Processing NASA Data Model Outputs

NASA Astrophysics Data System (ADS)

Falke, S. R.; Alameh, N. S.; Hoijarvi, K.; de La Beaujardiere, J.; Bambacus, M. J.

2006-12-01

An objective of NASA's Earth Science Division is to develop advanced information technologies for processing, archiving, accessing, visualizing, and communicating Earth Science data. To this end, NASA and other federal agencies have collaborated with the Open Geospatial Consortium (OGC) to research, develop, and test interoperability specifications within projects and testbeds benefiting the government, industry, and the public. This paper summarizes the results of a recent effort under the auspices of the OGC Web Services testbed phase 4 (OWS-4) to explore standardization approaches for accessing and processing the outputs of NASA models of physical phenomena. Within the OWS-4 context, experiments were designed to leverage the emerging OGC Web Processing Service (WPS) and Web Coverage Service (WCS) specifications to access, filter and manipulate the outputs of the NASA Goddard Earth Observing System (GEOS) and Goddard Chemistry Aerosol Radiation and Transport (GOCART) forecast models. In OWS-4, the intent is to provide the users with more control over the subsets of data that they can extract from the model results as well as over the final portrayal of that data. To meet that goal, experiments have been designed to test the suitability of use of OGC's Web Processing Service (WPS) and Web Coverage Service (WCS) for filtering, processing and portraying the model results (including slices by height or by time), and to identify any enhancements to the specs to meet the desired objectives. This paper summarizes the findings of the experiments highlighting the value of the Web Processing Service in providing standard interfaces for accessing and manipulating model data within spatial and temporal frameworks. The paper also points out the key shortcomings of the WPS especially in terms in comparison with a SOAP/WSDL approach towards solving the same problem.

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.

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

78 FR 10613 - Proposed Agency Information Collection

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-14

.... The information collection requests a three-year approval of its Customer Electricity Data Access and... information about customer access to electricity usage data. The information will be shared on the DOE-supported OpenEI Web site where consumers can learn about the access offered by their electricity provider...

Web 2.0 Impact on Business Value at a Federal Government Housing Agency

ERIC Educational Resources Information Center

Lavender, Anthony L.

2013-01-01

The idea of Open Government is an extension of the Electronic Government Act of 2002 which addresses the accessibility, usability, and preservation of government information. The concept of Open Government has evolved into the open government directive that mandates Executive Departments and Agencies to become more open and transparent while…

Enhanced reproducibility of SADI web service workflows with Galaxy and Docker.

PubMed

Aranguren, Mikel Egaña; Wilkinson, Mark D

2015-01-01

Semantic Web technologies have been widely applied in the life sciences, for example by data providers such as OpenLifeData and through web services frameworks such as SADI. The recently reported OpenLifeData2SADI project offers access to the vast OpenLifeData data store through SADI services. This article describes how to merge data retrieved from OpenLifeData2SADI with other SADI services using the Galaxy bioinformatics analysis platform, thus making this semantic data more amenable to complex analyses. This is demonstrated using a working example, which is made distributable and reproducible through a Docker image that includes SADI tools, along with the data and workflows that constitute the demonstration. The combination of Galaxy and Docker offers a solution for faithfully reproducing and sharing complex data retrieval and analysis workflows based on the SADI Semantic web service design patterns.

Bridging the Gap in Global Advanced Radiation Oncology Training: Impact of a Web-Based Open-Access Interactive Three-Dimensional Contouring Atlas on Radiation Oncologist Practice in Russia.

PubMed

McClelland, Shearwood; Chernykh, Marina; Dengina, Natalia; Gillespie, Erin F; Likhacheva, Anna; Usychkin, Sergey; Pankratov, Alexandr; Kharitonova, Ekaterina; Egorova, Yulia; Tsimafeyeu, Ilya; Tjulandin, Sergei; Thomas, Charles R; Mitin, Timur

2018-06-25

Radiation oncologists in Russia face a number of unique professional difficulties including lack of standardized training and continuing medical education. To combat this, under the auspices of the Russian Society of Clinical Oncology (RUSSCO), our group has developed a series of ongoing in-person interactive contouring workshops that are held during the major Russian oncology conferences in Moscow, Russia. Since November 2016 during each workshop, we utilized a web-based open-access interactive three-dimensional contouring atlas as part of our didactics. We sought to determine the impact of this resource on radiation oncology practice in Russia. We distributed an IRB-approved web-based survey to 172 practicing radiation oncologists in Russia. We inquired about practice demographics, RUSSCO contouring workshop attendance, and the clinical use of open-access English language interactive contouring atlas (eContour). The survey remained open for 2 months until November 2017. Eighty radiation oncologists completed the survey with a 46.5% response rate. Mean number of years in practice was 13.7. Sixty respondents (75%) attended at least one RUSSCO contouring workshop. Of those who were aware of eContour, 76% were introduced during a RUSSCO contouring workshop, and 81% continue to use it in their daily practice. The greatest obstacles to using the program were language barrier (51%) and internet access (38%). Nearly 90% reported their contouring practices changed since they started using the program, particularly for delineation of clinical target volumes (57%) and/or organs at risk (46%). More than 97% found the clinical pearls/links to cooperative group protocols in the software helpful in their daily practice. The majority used the contouring program several times per month (43%) or several times per week (41%). Face-to-face contouring instruction in combination with open-access web-based interactive contouring resource had a meaningful impact on perceived quality of radiation oncology contours among Russian practitioners and has the potential to have applications worldwide.

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV).

PubMed

Lefkowitz, Elliot J; Dempsey, Donald M; Hendrickson, Robert Curtis; Orton, Richard J; Siddell, Stuart G; Smith, Donald B

2018-01-04

The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.

PubMed

Whetzel, Patricia L; Noy, Natalya F; Shah, Nigam H; Alexander, Paul R; Nyulas, Csongor; Tudorache, Tania; Musen, Mark A

2011-07-01

The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computing funded under the NIH Roadmap Initiative. Contributing to the national computing infrastructure, NCBO has developed BioPortal, a web portal that provides access to a library of biomedical ontologies and terminologies (http://bioportal.bioontology.org) via the NCBO Web services. BioPortal enables community participation in the evaluation and evolution of ontology content by providing features to add mappings between terms, to add comments linked to specific ontology terms and to provide ontology reviews. The NCBO Web services (http://www.bioontology.org/wiki/index.php/NCBO_REST_services) enable this functionality and provide a uniform mechanism to access ontologies from a variety of knowledge representation formats, such as Web Ontology Language (OWL) and Open Biological and Biomedical Ontologies (OBO) format. The Web services provide multi-layered access to the ontology content, from getting all terms in an ontology to retrieving metadata about a term. Users can easily incorporate the NCBO Web services into software applications to generate semantically aware applications and to facilitate structured data collection.

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.

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…

Using the STOQS Web Application for Access to in situ Oceanographic Data

NASA Astrophysics Data System (ADS)

McCann, M. P.

2012-12-01

Using the STOQS Web Application for Access to in situ Oceanographic Data Mike McCann 7 August 2012 With increasing measurement and sampling capabilities of autonomous oceanographic platforms (e.g. Gliders, Autonomous Underwater Vehicles, Wavegliders), the need to efficiently access and visualize the data they collect is growing. The Monterey Bay Aquarium Research Institute has designed and built the Spatial Temporal Oceanographic Query System (STOQS) specifically to address this issue. The need for STOQS arises from inefficiencies discovered from using CF-NetCDF point observation conventions for these data. The problem is that access efficiency decreases with decreasing dimension of CF-NetCDF data. For example, the Trajectory Common Data Model feature type has only one coordinate dimension, usually Time - positions of the trajectory (Depth, Latitude, Longitude) are stored as non-indexed record variables within the NetCDF file. If client software needs to access data between two depth values or from a bounded geographic area, then the whole data set must be read and the selection made within the client software. This is very inefficient. What is needed is a way to easily select data of interest from an archive given any number of spatial, temporal, or other constraints. Geospatial relational database technology provides this capability. The full STOQS application consists of a Postgres/PostGIS database, Mapserver, and Python-Django running on a server and Web 2.0 technology (jQuery, OpenLayers, Twitter Bootstrap) running in a modern web browser. The web application provides faceted search capabilities allowing a user to quickly drill into the data of interest. Data selection can be constrained by spatial, temporal, and depth selections as well as by parameter value and platform name. The web application layer also provides a REST (Representational State Transfer) Application Programming Interface allowing tools such as the Matlab stoqstoolbox to retrieve data directly from the database. STOQS is an open source software project built upon a framework of free and open source software and is available for anyone to use for making their data more accessible and usable. For more information please see: http://code.google.com/p/stoqs/.; In the above screen grab a user has selected the "mass_concentrtion_of_chlorophyll_in_sea_water" parameter and a time depth range that includes three weeks of AUV missions of just the upper 5 meters.

OpenSearch technology for geospatial resources discovery

NASA Astrophysics Data System (ADS)

Papeschi, Fabrizio; Enrico, Boldrini; Mazzetti, Paolo

2010-05-01

In 2005, the term Web 2.0 has been coined by Tim O'Reilly to describe a quickly growing set of Web-based applications that share a common philosophy of "mutually maximizing collective intelligence and added value for each participant by formalized and dynamic information sharing". Around this same period, OpenSearch a new Web 2.0 technology, was developed. More properly, OpenSearch is a collection of technologies that allow publishing of search results in a format suitable for syndication and aggregation. It is a way for websites and search engines to publish search results in a standard and accessible format. Due to its strong impact on the way the Web is perceived by users and also due its relevance for businesses, Web 2.0 has attracted the attention of both mass media and the scientific community. This explosive growth in popularity of Web 2.0 technologies like OpenSearch, and practical applications of Service Oriented Architecture (SOA) resulted in an increased interest in similarities, convergence, and a potential synergy of these two concepts. SOA is considered as the philosophy of encapsulating application logic in services with a uniformly defined interface and making these publicly available via discovery mechanisms. Service consumers may then retrieve these services, compose and use them according to their current needs. A great degree of similarity between SOA and Web 2.0 may be leading to a convergence between the two paradigms. They also expose divergent elements, such as the Web 2.0 support to the human interaction in opposition to the typical SOA machine-to-machine interaction. According to these considerations, the Geospatial Information (GI) domain, is also moving first steps towards a new approach of data publishing and discovering, in particular taking advantage of the OpenSearch technology. A specific GI niche is represented by the OGC Catalog Service for Web (CSW) that is part of the OGC Web Services (OWS) specifications suite, which provides a set of services for discovery, access, and processing of geospatial resources in a SOA framework. GI-cat is a distributed CSW framework implementation developed by the ESSI Lab of the Italian National Research Council (CNR-IMAA) and the University of Florence. It provides brokering and mediation functionalities towards heterogeneous resources and inventories, exposing several standard interfaces for query distribution. This work focuses on a new GI-cat interface which allows the catalog to be queried according to the OpenSearch syntax specification, thus filling the gap between the SOA architectural design of the CSW and the Web 2.0. At the moment, there is no OGC standard specification about this topic, but an official change request has been proposed in order to enable the OGC catalogues to support OpenSearch queries. In this change request, an OpenSearch extension is proposed providing a standard mechanism to query a resource based on temporal and geographic extents. Two new catalog operations are also proposed, in order to publish a suitable OpenSearch interface. This extended interface is implemented by the modular GI-cat architecture adding a new profiling module called "OpenSearch profiler". Since GI-cat also acts as a clearinghouse catalog, another component called "OpenSearch accessor" is added in order to access OpenSearch compliant services. An important role in the GI-cat extension, is played by the adopted mapping strategy. Two different kind of mappings are required: query, and response elements mapping. Query mapping is provided in order to fit the simple OpenSearch query syntax to the complex CSW query expressed by the OGC Filter syntax. GI-cat internal data model is based on the ISO-19115 profile, that is more complex than the simple XML syndication formats, such as RSS 2.0 and Atom 1.0, suggested by OpenSearch. Once response elements are available, in order to be presented, they need to be translated from the GI-cat internal data model, to the above mentioned syndication formats; the mapping processing, is bidirectional. When GI-cat is used to access OpenSearch compliant services, the CSW query must be mapped to the OpenSearch query, and the response elements, must be translated according to the GI-cat internal data model. As results of such extensions, GI-cat provides a user friendly facade to the complex CSW interface, thus enabling it to be queried, for example, using a browser toolbar.

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.

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.

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.

Wood Utilization Research Dissemination on the World Wide Web: A Case Study

Treesearch

Daniel L. Schmoldt; Matthew F. Winn; Philip A. Araman

1997-01-01

Because many research products are informational rather than tangible, emerging information technologies, such as the multi-media format of the World Wide Web, provide an open and easily accessible mechanism for transferring research to user groups. We have found steady, increasing use of our Web site over the first 6-1/2 months of operation; almost one-third of the...

Connecting long-tail scientists with big data centers using SaaS

NASA Astrophysics Data System (ADS)

Percivall, G. S.; Bermudez, L. E.

2012-12-01

Big data centers and long tail scientists represent two extremes in the geoscience research community. Interoperability and inter-use based on software-as-a-service (SaaS) increases access to big data holdings by this underserved community of scientists. Large, institutional data centers have long been recognized as vital resources in the geoscience community. Permanent data archiving and dissemination centers provide "access to the data and (are) a critical source of people who have experience in the use of the data and can provide advice and counsel for new applications." [NRC] The "long-tail of science" is the geoscience researchers that work separate from institutional data centers [Heidorn]. Long-tail scientists need to be efficient consumers of data from large, institutional data centers. Discussions in NSF EarthCube capture the challenges: "Like the vast majority of NSF-funded researchers, Alice (a long-tail scientist) works with limited resources. In the absence of suitable expertise and infrastructure, the apparently simple task that she assigns to her graduate student becomes an information discovery and management nightmare. Downloading and transforming datasets takes weeks." [Foster, et.al.] The long-tail metaphor points to methods to bridge the gap, i.e., the Web. A decade ago, OGC began building a geospatial information space using open, web standards for geoprocessing [ORM]. Recently, [Foster, et.al.] accurately observed that "by adopting, adapting, and applying semantic web and SaaS technologies, we can make the use of geoscience data as easy and convenient as consumption of online media." SaaS places web services into Cloud Computing. SaaS for geospatial is emerging rapidly building on the first-generation geospatial web, e.g., OGC Web Coverage Service [WCS] and the Data Access Protocol [DAP]. Several recent examples show progress in applying SaaS to geosciences: - NASA's Earth Data Coherent Web has a goal to improve science user experience using Web Services (e.g. W*S, SOAP, RESTful) to reduce barriers to using EOSDIS data [ECW]. - NASA's LANCE provides direct access to vast amounts of satellite data using the OGC Web Map Tile Service (WMTS). - NOAA's Unified Access Framework for Gridded Data (UAF Grid) is a web service based capability for direct access to a variety of datasets using netCDF, OPeNDAP, THREDDS, WMS and WCS. [UAF] Tools to access SaaS's are many and varied: some proprietary, others open source; some run in browsers, others are stand-alone applications. What's required is interoperability using web interfaces offered by the data centers. NOAA's UAF service stack supports Matlab, ArcGIS, Ferret, GrADS, Google Earth, IDV, LAS. Any SaaS that offers OGC Web Services (WMS, WFS, WCS) can be accessed by scores of clients [OGC]. While there has been much progress in the recent year toward offering web services for the long-tail of scientists, more needs to be done. Web services offer data access but more than access is needed for inter-use of data, e.g. defining data schemas that allow for data fusion, addressing coordinate systems, spatial geometry, and semantics for observations. Connecting long-tail scientists with large, data centers using SaaS and, in the future, semantic web, will address this large and currently underserved user community.

CovalentDock Cloud: a web server for automated covalent docking.

PubMed

Ouyang, Xuchang; Zhou, Shuo; Ge, Zemei; Li, Runtao; Kwoh, Chee Keong

2013-07-01

Covalent binding is an important mechanism for many drugs to gain its function. We developed a computational algorithm to model this chemical event and extended it to a web server, the CovalentDock Cloud, to make it accessible directly online without any local installation and configuration. It provides a simple yet user-friendly web interface to perform covalent docking experiments and analysis online. The web server accepts the structures of both the ligand and the receptor uploaded by the user or retrieved from online databases with valid access id. It identifies the potential covalent binding patterns, carries out the covalent docking experiments and provides visualization of the result for user analysis. This web server is free and open to all users at http://docking.sce.ntu.edu.sg/.

CovalentDock Cloud: a web server for automated covalent docking

PubMed Central

Ouyang, Xuchang; Zhou, Shuo; Ge, Zemei; Li, Runtao; Kwoh, Chee Keong

2013-01-01

Covalent binding is an important mechanism for many drugs to gain its function. We developed a computational algorithm to model this chemical event and extended it to a web server, the CovalentDock Cloud, to make it accessible directly online without any local installation and configuration. It provides a simple yet user-friendly web interface to perform covalent docking experiments and analysis online. The web server accepts the structures of both the ligand and the receptor uploaded by the user or retrieved from online databases with valid access id. It identifies the potential covalent binding patterns, carries out the covalent docking experiments and provides visualization of the result for user analysis. This web server is free and open to all users at http://docking.sce.ntu.edu.sg/. PMID:23677616

Do Web 2.0 Tools Really Open the Door to Learning? Practices, Perceptions and Profiles of 11-16-Year-Old Students

ERIC Educational Resources Information Center

Luckin, Rosemary; Clark, Wilma; Graber, Rebecca; Logan, Kit; Mee, Adrian; Oliver, Martin

2009-01-01

In this paper, we report on survey and focus group data relating to the activities and perceptions of learning with Web 2.0 technologies of students aged between 11 and 16 years in 27 UK secondary schools. The study confirms that these learners had high levels of access to Web 2.0 technologies and that Web 2.0 activities were prolific. However,…

Open Access Journal Policies: A Systematic Analysis of Radiology Journals.

PubMed

Narayan, Anand; Lobner, Katie; Fritz, Jan

2018-02-01

The open access movement has pushed for greater access to scientific knowledge by expanding access to scientific journal articles. There is limited information about the extent to which open access policies have been adopted by radiology journals. We performed a systematic analysis to ascertain the proportion of radiology journals with open access options. A search was performed with the assistance of a clinical informationist. Full and mixed English-language diagnostic and interventional radiology Web of Science journals (impact factors > 1.0) were included. Nuclear medicine, radiation oncology, physics, and solicitation-only journals were excluded. Primary outcome was open access option (yes or no) with additional outcomes including presence or absence of embargo, complete or partial copyright transfer, publication fees, and self-archiving policies. Secondary outcomes included journal citations, journal impact factors, immediacy, Eigenfactor, and article influence scores. Independent double readings were performed with differences resolved by consensus, supplemented by contacting editorial staff at each journal. In all, 125 journals were identified; review yielded 49 journals (39%, mean impact factor of 2.61). Thirty-six of the journals had open access options (73.4%), and four journals were exclusively open access (8.2%). Twelve-month embargoes were most commonly cited (90.6%) with 28.6% of journals stating that they did not require a complete transfer of copyright. Prices for open access options ranged from $750 to $4,000 (median $3,000). No statistically significant differences were found in journal impact measures comparing journals with open access options to journals without open access options. Diagnostic and interventional radiology journals have widely adopted open access options with a few radiology journals being exclusively open access. Copyright © 2017 American College of Radiology. Published by Elsevier Inc. All rights reserved.

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.

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).

Breaking and Fixing Origin-Based Access Control in Hybrid Web/Mobile Application Frameworks.

PubMed

Georgiev, Martin; Jana, Suman; Shmatikov, Vitaly

2014-02-01

Hybrid mobile applications (apps) combine the features of Web applications and "native" mobile apps. Like Web applications, they are implemented in portable, platform-independent languages such as HTML and JavaScript. Like native apps, they have direct access to local device resources-file system, location, camera, contacts, etc. Hybrid apps are typically developed using hybrid application frameworks such as PhoneGap. The purpose of the framework is twofold. First, it provides an embedded Web browser (for example, WebView on Android) that executes the app's Web code. Second, it supplies "bridges" that allow Web code to escape the browser and access local resources on the device. We analyze the software stack created by hybrid frameworks and demonstrate that it does not properly compose the access-control policies governing Web code and local code, respectively. Web code is governed by the same origin policy, whereas local code is governed by the access-control policy of the operating system (for example, user-granted permissions in Android). The bridges added by the framework to the browser have the same local access rights as the entire application, but are not correctly protected by the same origin policy. This opens the door to fracking attacks, which allow foreign-origin Web content included into a hybrid app (e.g., ads confined in iframes) to drill through the layers and directly access device resources. Fracking vulnerabilities are generic: they affect all hybrid frameworks, all embedded Web browsers, all bridge mechanisms, and all platforms on which these frameworks are deployed. We study the prevalence of fracking vulnerabilities in free Android apps based on the PhoneGap framework. Each vulnerability exposes sensitive local resources-the ability to read and write contacts list, local files, etc.-to dozens of potentially malicious Web domains. We also analyze the defenses deployed by hybrid frameworks to prevent resource access by foreign-origin Web content and explain why they are ineffectual. We then present NoFrak, a capability-based defense against fracking attacks. NoFrak is platform-independent, compatible with any framework and embedded browser, requires no changes to the code of the existing hybrid apps, and does not break their advertising-supported business model.

Open Data, Jupyter Notebooks and Geospatial Data Standards Combined - Opening up large volumes of marine and climate data to other communities

NASA Astrophysics Data System (ADS)

Clements, O.; Siemen, S.; Wagemann, J.

2017-12-01

The EU-funded Earthserver-2 project aims to offer on-demand access to large volumes of environmental data (Earth Observation, Marine, Climate data and Planetary data) via the interface standard Web Coverage Service defined by the Open Geospatial Consortium. Providing access to data via OGC web services (e.g. WCS and WMS) has the potential to open up services to a wider audience, especially to users outside the respective communities. Especially WCS 2.0 with its processing extension Web Coverage Processing Service (WCPS) is highly beneficial to make large volumes accessible to non-expert communities. Users do not have to deal with custom community data formats, such as GRIB for the meteorological community, but can directly access the data in a format they are more familiar with, such as NetCDF, JSON or CSV. Data requests can further directly be integrated into custom processing routines and users are not required to download Gigabytes of data anymore. WCS supports trim (reduction of data extent) and slice (reduction of data dimension) operations on multi-dimensional data, providing users a very flexible on-demand access to the data. WCPS allows the user to craft queries to run on the data using a text-based query language, similar to SQL. These queries can be very powerful, e.g. condensing a three-dimensional data cube into its two-dimensional mean. However, the more processing-intensive the more complex the query. As part of the EarthServer-2 project, we developed a python library that helps users to generate complex WCPS queries with Python, a programming language they are more familiar with. The interactive presentation aims to give practical examples how users can benefit from two specific WCS services from the Marine and Climate community. Use-cases from the two communities will show different approaches to take advantage of a Web Coverage (Processing) Service. The entire content is available with Jupyter Notebooks, as they prove to be a highly beneficial tool to generate reproducible workflows for environmental data analysis.

Pathview Web: user friendly pathway visualization and data integration

PubMed Central

Pant, Gaurav; Bhavnasi, Yeshvant K.; Blanchard, Steven G.; Brouwer, Cory

2017-01-01

Abstract Pathway analysis is widely used in omics studies. Pathway-based data integration and visualization is a critical component of the analysis. To address this need, we recently developed a novel R package called Pathview. Pathview maps, integrates and renders a large variety of biological data onto molecular pathway graphs. Here we developed the Pathview Web server, as to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources. Pathview Web features an intuitive graphical web interface and a user centered design. The server not only expands the core functions of Pathview, but also provides many useful features not available in the offline R package. Importantly, the server presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data. In addition, the server also provides a RESTful API for programmatic access and conveniently integration in third-party software or workflows. Pathview Web is openly and freely accessible at https://pathview.uncc.edu/. PMID:28482075

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.

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.

42 CFR 423.128 - Dissemination of Part D plan information.

Code of Federal Regulations, 2011 CFR

2011-10-01

... plan sponsor's toll free customer service line or by accessing the plan sponsor's internet Web site. (8... redetermination processes via an Internet Web site; and (iii) A system that transmits codes to network pharmacies...— (1) A toll-free customer call center that— (i) Is open during usual business hours. (ii) Provides...

An Open-Source and Java-Technologies Approach to Web Applications

DTIC Science & Technology

2003-09-01

program for any purpose (Freedom 0). • The freedom to study how the program works, and adapt it to individual needs (Freedom 1). Access to the source...manage information for many purposes. Today a key technology that allows developers to make Web applications is server-side programming to generate a

Places to Go: Sakai|http://www.sakaiproject.org/

ERIC Educational Resources Information Center

Downes, Stephen

2006-01-01

Stephen Downes continues his examination of open source learning management systems (LMSs) with a visit to Sakai's Web site. While Sakai's Web site is not particularly easy to navigate, it provides access to a large community and constellation of related online learning products and initiatives. Visitors can visit discussion forums to ask…

Options and Functions of the Revised IVS Combination Web Site

NASA Astrophysics Data System (ADS)

Messerschmitt, Linda; Bachmann, Sabine; Thaller, Daniela

2016-12-01

The World Wide Web is one of the most important communication and information exchange platforms today. Because of the high amount of users and the global accessibility, every business is interested in the Internet. It opens up new possibilities of international cooperation. In geodesy, this aspect of international cooperation is of prime importance.

Access Control of Web and Java Based Applications

NASA Technical Reports Server (NTRS)

Tso, Kam S.; Pajevski, Michael J.; Johnson, Bryan

2011-01-01

Cyber security has gained national and international attention as a result of near continuous headlines from financial institutions, retail stores, government offices and universities reporting compromised systems and stolen data. Concerns continue to rise as threats of service interruption, and spreading of viruses become ever more prevalent and serious. Controlling access to application layer resources is a critical component in a layered security solution that includes encryption, firewalls, virtual private networks, antivirus, and intrusion detection. In this paper we discuss the development of an application-level access control solution, based on an open-source access manager augmented with custom software components, to provide protection to both Web-based and Java-based client and server applications.

78 FR 20422 - Boards and Committees

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-05

... be accessed on the Agency's open Government Web site at http://www.nasa.gov/open/ . DATES: This... NATIONAL AERONAUTICS AND SPACE ADMINISTRATION 14 CFR Part 1209 [Docket No. NASA-2013-0001] RIN... referenced in NASA's Contract Adjustment Board rule. The revision to this rule is part of NASA's...

What Can OpenEI Do For You?

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

None

2010-12-10

Open Energy Information (OpenEI) is an open source web platform—similar to the one used by Wikipedia—developed by the US Department of Energy (DOE) and the National Renewable Energy Laboratory (NREL) to make the large amounts of energy-related data and information more easily searched, accessed, and used both by people and automated machine processes. Built utilizing the standards and practices of the Linked Open Data community, the OpenEI platform is much more robust and powerful than typical web sites and databases. As an open platform, all users can search, edit, add, and access data in OpenEI for free. The user communitymore » contributes the content and ensures its accuracy and relevance; as the community expands, so does the content's comprehensiveness and quality. The data are structured and tagged with descriptors to enable cross-linking among related data sets, advanced search functionality, and consistent, usable formatting. Data input protocols and quality standards help ensure the content is structured and described properly and derived from a credible source. Although DOE/NREL is developing OpenEI and seeding it with initial data, it is designed to become a true community model with millions of users, a large core of active contributors, and numerous sponsors.« less

What Can OpenEI Do For You?

ScienceCinema

None

2018-02-06

Open Energy Information (OpenEI) is an open source web platform—similar to the one used by Wikipedia—developed by the US Department of Energy (DOE) and the National Renewable Energy Laboratory (NREL) to make the large amounts of energy-related data and information more easily searched, accessed, and used both by people and automated machine processes. Built utilizing the standards and practices of the Linked Open Data community, the OpenEI platform is much more robust and powerful than typical web sites and databases. As an open platform, all users can search, edit, add, and access data in OpenEI for free. The user community contributes the content and ensures its accuracy and relevance; as the community expands, so does the content's comprehensiveness and quality. The data are structured and tagged with descriptors to enable cross-linking among related data sets, advanced search functionality, and consistent, usable formatting. Data input protocols and quality standards help ensure the content is structured and described properly and derived from a credible source. Although DOE/NREL is developing OpenEI and seeding it with initial data, it is designed to become a true community model with millions of users, a large core of active contributors, and numerous sponsors.

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

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.

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.

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.

Cloud-based Web Services for Near-Real-Time Web access to NPP Satellite Imagery and other Data

NASA Astrophysics Data System (ADS)

Evans, J. D.; Valente, E. G.

2010-12-01

We are building a scalable, cloud computing-based infrastructure for Web access to near-real-time data products synthesized from the U.S. National Polar-Orbiting Environmental Satellite System (NPOESS) Preparatory Project (NPP) and other geospatial and meteorological data. Given recent and ongoing changes in the the NPP and NPOESS programs (now Joint Polar Satellite System), the need for timely delivery of NPP data is urgent. We propose an alternative to a traditional, centralized ground segment, using distributed Direct Broadcast facilities linked to industry-standard Web services by a streamlined processing chain running in a scalable cloud computing environment. Our processing chain, currently implemented on Amazon.com's Elastic Compute Cloud (EC2), retrieves raw data from NASA's Moderate Resolution Imaging Spectroradiometer (MODIS) and synthesizes data products such as Sea-Surface Temperature, Vegetation Indices, etc. The cloud computing approach lets us grow and shrink computing resources to meet large and rapid fluctuations (twice daily) in both end-user demand and data availability from polar-orbiting sensors. Early prototypes have delivered various data products to end-users with latencies between 6 and 32 minutes. We have begun to replicate machine instances in the cloud, so as to reduce latency and maintain near-real time data access regardless of increased data input rates or user demand -- all at quite moderate monthly costs. Our service-based approach (in which users invoke software processes on a Web-accessible server) facilitates access into datasets of arbitrary size and resolution, and allows users to request and receive tailored and composite (e.g., false-color multiband) products on demand. To facilitate broad impact and adoption of our technology, we have emphasized open, industry-standard software interfaces and open source software. Through our work, we envision the widespread establishment of similar, derived, or interoperable systems for processing and serving near-real-time data from NPP and other sensors. A scalable architecture based on cloud computing ensures cost-effective, real-time processing and delivery of NPP and other data. Access via standard Web services maximizes its interoperability and usefulness.

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.

77 FR 60620 - Update of Existing Privacy Act-NASA Regulations

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-04

... be accessed on the Agency's open Government Web site at http://www.nasa.gov/open/ . DATES: This rule... NATIONAL AERONAUTICS AND SPACE ADMINISTRATION 14 CFR Part 1212 [Document No. NASA--NASA-2012-0005] RIN 2700-AD86 Update of Existing Privacy Act--NASA Regulations AGENCY: National Aeronautics and Space...

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.

Open Educational Resources: Tools to Help 21st Century Students Achieve Their Postsecondary Education Goals and Keep America Competitive

ERIC Educational Resources Information Center

Center for American Progress, 2012

2012-01-01

Open courseware and other open educational resources are beginning to draw the attention of higher education policymakers and other leaders. These web-based educational tools hold the promise of both reducing the cost of higher education and helping learners to complete their degrees by providing access to top quality course materials and…

Open Access Publishing in the Field of Medical Informatics.

PubMed

Kuballa, Stefanie

2017-05-01

The open access paradigm has become an important approach in today's information and communication society. Funders and governments in different countries stipulate open access publications of funded research results. Medical informatics as part of the science, technology and medicine disciplines benefits from many research funds, such as National Institutes of Health in the US, Wellcome Trust in UK, German Research Foundation in Germany and many more. In this study an overview of the current open access programs and conditions of major journals in the field of medical informatics is presented. It was investigated whether there are suitable options and how they are shaped. Therefore all journals in Thomson Reuters Web of Science that were listed in the subject category "Medical Informatics" in 2014 were examined. An Internet research was conducted by investigating the journals' websites. It was reviewed whether journals offer an open access option with a subsequent check of conditions as for example the type of open access, the fees and the licensing. As a result all journals in the field of medical informatics that had an impact factor in 2014 offer an open access option. A predominantly consistent pricing range was determined with an average fee of 2.248 € and a median fee of 2.207 €. The height of a journals' open access fee did not correlate with the height of its Impact Factor. Hence, medical informatics journals have recognized the trend of open access publishing, though the vast majority of them are working with the hybrid method. Hybrid open access may however lead to problems in questions of double dipping and the often stipulated gold open access.

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.

ICT and Web Technology Based Innovations in Education Sector

ERIC Educational Resources Information Center

Sangeeta Namdev, Dhamdhere

2012-01-01

ICT made real magic and drastic changes in all service sectors along with higher education and library practices and services. The academic environment is changing from formal education to distance and online learning mode because of ICT. Web technology and mobile technology has made great impact on education sector. The role of Open Access,…

76 FR 5148 - Loveland Area Projects-Western Area Colorado Missouri Balancing Authority-Rate Order No. WAPA-155

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-28

... (RMR) Open Access Same Time Information System Web site. Transmission Losses are assessed for all real... post information about the rate process, as well as comments received via letter and e-mail, on its Web... hourly load coincident with the LAP monthly transmission system peak. See discussion below on the...

Unipept web services for metaproteomics analysis.

PubMed

Mesuere, Bart; Willems, Toon; Van der Jeugt, Felix; Devreese, Bart; Vandamme, Peter; Dawyndt, Peter

2016-06-01

Unipept is an open source web application that is designed for metaproteomics analysis with a focus on interactive datavisualization. It is underpinned by a fast index built from UniProtKB and the NCBI taxonomy that enables quick retrieval of all UniProt entries in which a given tryptic peptide occurs. Unipept version 2.4 introduced web services that provide programmatic access to the metaproteomics analysis features. This enables integration of Unipept functionality in custom applications and data processing pipelines. The web services are freely available at http://api.unipept.ugent.be and are open sourced under the MIT license. Unipept@ugent.be Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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.

Breaking and Fixing Origin-Based Access Control in Hybrid Web/Mobile Application Frameworks

PubMed Central

Georgiev, Martin; Jana, Suman; Shmatikov, Vitaly

2014-01-01

Hybrid mobile applications (apps) combine the features of Web applications and “native” mobile apps. Like Web applications, they are implemented in portable, platform-independent languages such as HTML and JavaScript. Like native apps, they have direct access to local device resources—file system, location, camera, contacts, etc. Hybrid apps are typically developed using hybrid application frameworks such as PhoneGap. The purpose of the framework is twofold. First, it provides an embedded Web browser (for example, WebView on Android) that executes the app's Web code. Second, it supplies “bridges” that allow Web code to escape the browser and access local resources on the device. We analyze the software stack created by hybrid frameworks and demonstrate that it does not properly compose the access-control policies governing Web code and local code, respectively. Web code is governed by the same origin policy, whereas local code is governed by the access-control policy of the operating system (for example, user-granted permissions in Android). The bridges added by the framework to the browser have the same local access rights as the entire application, but are not correctly protected by the same origin policy. This opens the door to fracking attacks, which allow foreign-origin Web content included into a hybrid app (e.g., ads confined in iframes) to drill through the layers and directly access device resources. Fracking vulnerabilities are generic: they affect all hybrid frameworks, all embedded Web browsers, all bridge mechanisms, and all platforms on which these frameworks are deployed. We study the prevalence of fracking vulnerabilities in free Android apps based on the PhoneGap framework. Each vulnerability exposes sensitive local resources—the ability to read and write contacts list, local files, etc.—to dozens of potentially malicious Web domains. We also analyze the defenses deployed by hybrid frameworks to prevent resource access by foreign-origin Web content and explain why they are ineffectual. We then present NoFrak, a capability-based defense against fracking attacks. NoFrak is platform-independent, compatible with any framework and embedded browser, requires no changes to the code of the existing hybrid apps, and does not break their advertising-supported business model. PMID:25485311

National Utility Rate Database: Preprint

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

Ong, S.; McKeel, R.

2012-08-01

When modeling solar energy technologies and other distributed energy systems, using high-quality expansive electricity rates is essential. The National Renewable Energy Laboratory (NREL) developed a utility rate platform for entering, storing, updating, and accessing a large collection of utility rates from around the United States. This utility rate platform lives on the Open Energy Information (OpenEI) website, OpenEI.org, allowing the data to be programmatically accessed from a web browser, using an application programming interface (API). The semantic-based utility rate platform currently has record of 1,885 utility rates and covers over 85% of the electricity consumption in the United States.

Remote Sensing Information Gateway: A free application and web service for fast, convenient, interoperable access to large repositories of atmospheric data

NASA Astrophysics Data System (ADS)

Plessel, T.; Szykman, J.; Freeman, M.

2012-12-01

EPA's Remote Sensing Information Gateway (RSIG) is a widely used free applet and web service for quickly and easily retrieving, visualizing and saving user-specified subsets of atmospheric data - by variable, geographic domain and time range. Petabytes of available data include thousands of variables from a set of NASA and NOAA satellites, aircraft, ground stations and EPA air-quality models. The RSIG applet is used by atmospheric researchers and uses the rsigserver web service to obtain data and images. The rsigserver web service is compliant with the Open Geospatial Consortium Web Coverage Service (OGC-WCS) standard to facilitate data discovery and interoperability. Since rsigserver is publicly accessible, it can be (and is) used by other applications. This presentation describes the architecture and technical implementation details of this successful system with an emphasis on achieving convenience, high-performance, data integrity and security.

Pathview Web: user friendly pathway visualization and data integration.

PubMed

Luo, Weijun; Pant, Gaurav; Bhavnasi, Yeshvant K; Blanchard, Steven G; Brouwer, Cory

2017-07-03

Pathway analysis is widely used in omics studies. Pathway-based data integration and visualization is a critical component of the analysis. To address this need, we recently developed a novel R package called Pathview. Pathview maps, integrates and renders a large variety of biological data onto molecular pathway graphs. Here we developed the Pathview Web server, as to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources. Pathview Web features an intuitive graphical web interface and a user centered design. The server not only expands the core functions of Pathview, but also provides many useful features not available in the offline R package. Importantly, the server presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data. In addition, the server also provides a RESTful API for programmatic access and conveniently integration in third-party software or workflows. Pathview Web is openly and freely accessible at https://pathview.uncc.edu/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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.

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

DTIC Science & Technology

2016-03-01

distribution is unlimited. 13. SUPPLEMENTARY NOTES 14. ABSTRACT This document serves as the quick-start guide for GIFT Cloud, the web -based...to users with a GIFT Account at no cost. GIFT Cloud is a new implementation of GIFT. This web -based application allows learners, authors, and...distribution is unlimited. 3 3. Requirements for GIFT Cloud GIFT Cloud is accessed via a web browser. Officially, GIFT Cloud has been tested to work on

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.

Easy access to geophysical data sets at the IRIS Data Management Center

NASA Astrophysics Data System (ADS)

Trabant, C.; Ahern, T.; Suleiman, Y.; Karstens, R.; Weertman, B.

2012-04-01

At the IRIS Data Management Center (DMC) we primarily manage seismological data but also have other geophysical data sets for related fields including atmospheric pressure and gravity measurements and higher level data products derived from raw data. With a few exceptions all data managed by the IRIS DMC are openly available and we serve an international research audience. These data are available via a number of different mechanisms from batch requests submitted through email, web interfaces, near real time streams and more recently web services. Our initial suite of web services offer access to almost all of the raw data and associated metadata managed at the DMC. In addition, we offer services that apply processing to the data before it is sent to the user. Web service technologies are ubiquitous with support available in nearly every programming language and operating system. By their nature web services are programmatic interfaces, but by choosing a simple subset of web service methods we make our data available to a very broad user base. These interfaces will be usable by professional developers as well as non-programmers. Whenever possible we chose open and recognized standards. The data returned to the user is in a variety of formats depending on type, including FDSN SEED, QuakeML, StationXML, ASCII, PNG images and in some cases where no appropriate standard could be found a customized XML format. To promote easy access to seismological data for all researchers we are coordinating with international partners to define web service interfaces standards. Additionally we are working with key partners in Europe to complete the initial implementation of these services. Once a standard has been adopted and implemented at multiple data centers researchers will be able to use the same request tools to access data across multiple data centers. The web services that apply on-demand processing to requested data include the capability to apply instrument corrections and format translations which ultimately allows more researchers to use the data without knowledge of specific data and metadata formats. In addition to serving as a new platform on top of which research scientists will build advanced processing tools we anticipate that they will result in more data being accessible by more users.

Facilitating Scientific Collaboration and Education with Easy Access Web Maps Using the AGAP Antarctic Geophysical Data

NASA Astrophysics Data System (ADS)

Abdi, A.

2012-12-01

Science and science education benefit from easy access to data yet often geophysical data sets are large, complex and difficult to share. The difficulty in sharing data and imagery easily inhibits both collaboration and the use of real data in educational applications. The dissemination of data products through web maps serves a very efficient and user-friendly method for students, the public and the science community to gain insights and understanding from data. Few research groups provide direct access to their data, let alone map-based visualizations. By building upon current GIS infrastructure with web mapping technologies, like ArcGIS Server, scientific groups, institutions and agencies can enhance the value of their GIS investments. The advantages of web maps to serve data products are many; existing web-mapping technology allows complex GIS analysis to be shared across the Internet, and can be easily scaled from a few users to millions. This poster highlights the features of an interactive web map developed at the Polar Geophysics Group at the Lamont-Doherty Earth Observatory of Columbia University that provides a visual representation of, and access to, data products that resulted from the group's recently concluded AGAP project (http://pgg.ldeo.columbia.edu). The AGAP project collected more than 120,000 line km of new aerogeophysical data using two Twin Otter aircrafts. Data included ice penetrating radar, magnetometer, gravimeter and laser altimeter measurements. The web map is based upon ArcGIS Viewer for Flex, which is a configurable client application built on the ArcGIS API for Flex that works seamlessly with ArcGIS Server 10. The application can serve a variety of raster and vector file formats through the Data Interoperability for Server, which eliminates data sharing barriers across numerous file formats. The ability of the application to serve large datasets is only hindered by the availability of appropriate hardware. ArcGIS is a proprietary product, but there are a few data portals in the earth sciences that have a map interface using open access products such as MapServer and OpenLayers, the most notable being the NASA IceBridge Data Portal. Indeed, with the widespread availability of web mapping technology, the scientific community should advance towards this direction when disseminating their data.

Web-GIS visualisation of permafrost-related Remote Sensing products for ESA GlobPermafrost

NASA Astrophysics Data System (ADS)

Haas, A.; Heim, B.; Schaefer-Neth, C.; Laboor, S.; Nitze, I.; Grosse, G.; Bartsch, A.; Kaab, A.; Strozzi, T.; Wiesmann, A.; Seifert, F. M.

2016-12-01

The ESA GlobPermafrost (www.globpermafrost.info) provides a remote sensing service for permafrost research and applications. The service comprises of data product generation for various sites and regions as well as specific infrastructure allowing overview and access to datasets. Based on an online user survey conducted within the project, the user community extensively applies GIS software to handle remote sensing-derived datasets and requires preview functionalities before accessing them. In response, we develop the Permafrost Information System PerSys which is conceptualized as an open access geospatial data dissemination and visualization portal. PerSys will allow visualisation of GlobPermafrost raster and vector products such as land cover classifications, Landsat multispectral index trend datasets, lake and wetland extents, InSAR-based land surface deformation maps, rock glacier velocity fields, spatially distributed permafrost model outputs, and land surface temperature datasets. The datasets will be published as WebGIS services relying on OGC-standardized Web Mapping Service (WMS) and Web Feature Service (WFS) technologies for data display and visualization. The WebGIS environment will be hosted at the AWI computing centre where a geodata infrastructure has been implemented comprising of ArcGIS for Server 10.4, PostgreSQL 9.2 and a browser-driven data viewer based on Leaflet (http://leafletjs.com). Independently, we will provide an `Access - Restricted Data Dissemination Service', which will be available to registered users for testing frequently updated versions of project datasets. PerSys will become a core project of the Arctic Permafrost Geospatial Centre (APGC) within the ERC-funded PETA-CARB project (www.awi.de/petacarb). The APGC Data Catalogue will contain all final products of GlobPermafrost, allow in-depth dataset search via keywords, spatial and temporal coverage, data type, etc., and will provide DOI-based links to the datasets archived in the long-term, open access PANGAEA data repository.

Is open access sufficient? A review of the quality of open-access nursing journals.

PubMed

Crowe, Marie; Carlyle, Dave

2015-02-01

The present study aims to review the quality of open-access nursing journals listed in the Directory of Open Access Journals that published papers in 2013 with a nursing focus, written in English, and were freely accessible. Each journal was reviewed in relation to their publisher, year of commencement, number of papers published in 2013, fee for publication, indexing, impact factor, and evidence of requirements for ethics and disclosure statements. The quality of the journals was assessed by impact factors and the requirements for indexing in PubMed. A total of 552 were published in 2013 in the 19 open-access nursing journals that met the inclusion criteria. No journals had impact factors listed in Web of Knowledge, but three had low Scopus impact factors. Only five journals were indexed with PubMed. The quality of the 19 journals included in the review was evaluated as inferior to most subscription-fee journals. Mental health nursing has some responsibility to the general public, and in particular, consumers of mental health services and their families, for the quality of papers published in open-access journals. The way forward might involve dual-platform publication or a process that enables assessment of how research has improved clinical outcomes. © 2014 Australian College of Mental Health Nurses Inc.

Clinical Interpretation of Variants in Cancer (CIViC) Knowledgebase | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer. Our goal is to enable precision medicine by providing an educational forum for dissemination of knowledge and active discussion of the clinical significance of cancer genome alterations.

Survey of Learning Experiences and Influence of Learning Style Preferences on User Intentions Regarding MOOCs

ERIC Educational Resources Information Center

Chang, Ray I.; Hung, Yu Hsin; Lin, Chun Fu

2015-01-01

With the rapid development of web techniques, information and communication technology is being increasingly used in curricula, and learning portfolios can be automatically retrieved and maintained as learners interact through e-learning platforms. Further, massive open online courses (MOOCs), which apply such technology to provide open access to…

76 FR 31884 - Reducing Regulatory Burden; Retrospective Review Under E.O. 13563

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-02

...: Submit comments to http://www.regulations.gov , or e-mail comments to [email protected]nasa.gov . FOR FURTHER INFORMATION CONTACT: Nanette Jennings, 202-358-0819, [email protected]nasa.gov.... NASA's plan is accessible on its Open Government Web site at http://www.nasa.gov/open/ . Submit...

A Systematic Review of the Socio-Ethical Aspects of Massive Online Open Courses

ERIC Educational Resources Information Center

Rolfe, Vivien

2015-01-01

Massive open online courses (MOOCs) offer learners across the globe unprecedented access to education. Through sophisticated e-learning technologies and web approaches, MOOCs attract massive scale participation and global interest. Some commercial ventures place social equality at the heart of their missions, claiming to empower communities by…

Scientific Journal Publishing: Yearly Volume and Open Access Availability

ERIC Educational Resources Information Center

Bjork, Bo-Christer; Roos, Annikki; Lauri, Mari

2009-01-01

Introduction: We estimate the total yearly volume of peer-reviewed scientific journal articles published world-wide as well as the share of these articles available openly on the Web either directly or as copies in e-print repositories. Method: We rely on data from two commercial databases (ISI and Ulrich's Periodicals Directory) supplemented by…

Learning in Virtual Forest: A Forest Ecosystem in the Web-Based Learning Environment

ERIC Educational Resources Information Center

Jussila, Terttu; Virtanen, Viivi

2014-01-01

Virtual Forest is a web-based, open-access learning environment about forests designed for primary-school pupils between the ages of 10 and 13 years. It is pedagogically designed to develop an understanding of ecology, to enhance conceptual development and to give a holistic view of forest ecosystems. Various learning tools, such as concept maps,…

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.

Web-based spatial analysis with the ILWIS open source GIS software and satellite images from GEONETCast

NASA Astrophysics Data System (ADS)

Lemmens, R.; Maathuis, B.; Mannaerts, C.; Foerster, T.; Schaeffer, B.; Wytzisk, A.

2009-12-01

This paper involves easy accessible integrated web-based analysis of satellite images with a plug-in based open source software. The paper is targeted to both users and developers of geospatial software. Guided by a use case scenario, we describe the ILWIS software and its toolbox to access satellite images through the GEONETCast broadcasting system. The last two decades have shown a major shift from stand-alone software systems to networked ones, often client/server applications using distributed geo-(web-)services. This allows organisations to combine without much effort their own data with remotely available data and processing functionality. Key to this integrated spatial data analysis is a low-cost access to data from within a user-friendly and flexible software. Web-based open source software solutions are more often a powerful option for developing countries. The Integrated Land and Water Information System (ILWIS) is a PC-based GIS & Remote Sensing software, comprising a complete package of image processing, spatial analysis and digital mapping and was developed as commercial software from the early nineties onwards. Recent project efforts have migrated ILWIS into a modular, plug-in-based open source software, and provide web-service support for OGC-based web mapping and processing. The core objective of the ILWIS Open source project is to provide a maintainable framework for researchers and software developers to implement training components, scientific toolboxes and (web-) services. The latest plug-ins have been developed for multi-criteria decision making, water resources analysis and spatial statistics analysis. The development of this framework is done since 2007 in the context of 52°North, which is an open initiative that advances the development of cutting edge open source geospatial software, using the GPL license. GEONETCast, as part of the emerging Global Earth Observation System of Systems (GEOSS), puts essential environmental data at the fingertips of users around the globe. This user-friendly and low-cost information dissemination provides global information as a basis for decision-making in a number of critical areas, including public health, energy, agriculture, weather, water, climate, natural disasters and ecosystems. GEONETCast makes available satellite images via Digital Video Broadcast (DVB) technology. An OGC WMS interface and plug-ins which convert GEONETCast data streams allow an ILWIS user to integrate various distributed data sources with data locally stored on his machine. Our paper describes a use case in which ILWIS is used with GEONETCast satellite imagery for decision making processes in Ghana. We also explain how the ILWIS software can be extended with additional functionality by means of building plug-ins and unfold our plans to implement other OGC standards, such as WCS and WPS in the same context. Especially, the latter one can be seen as a major step forward in terms of moving well-proven desktop based processing functionality to the web. This enables the embedding of ILWIS functionality in Spatial Data Infrastructures or even the execution in scalable and on-demand cloud computing environments.

Trends in scientific publishing: Dark clouds loom large.

PubMed

Vinny, Pulikottil Wilson; Vishnu, Venugopalan Y; Lal, Vivek

2016-04-15

The world wide web has brought about a paradigm shift in the way medical research is published and accessed. The ease with which a new journal can be started/hosted by publishing start-ups is unprecedented. The tremendous capabilities of the world wide web and the open access revolution when combined with a highly profitable business have attracted unscrupulous fraudulent operators to the publishing industry. The intent of these fraudulent publishers is solely driven by profit with utter disregard to scientific content, peer reviews and ethics. This phenomenon has been referred to as "predatory publishing". The "international" tag of such journals often betrays their true origins. The gold open access model of publishing, where the author pays the publisher, when coupled with a non-existent peer review threatens to blur the distinction between science and pseudoscience. The average researcher needs to be made more aware of this clear and present danger to the scientific community. Prevention is better than cure. Copyright © 2016 Elsevier B.V. All rights reserved.

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.

Public health, GIS, and the internet.

PubMed

Croner, Charles M

2003-01-01

Internet access and use of georeferenced public health information for GIS application will be an important and exciting development for the nation's Department of Health and Human Services and other health agencies in this new millennium. Technological progress toward public health geospatial data integration, analysis, and visualization of space-time events using the Web portends eventual robust use of GIS by public health and other sectors of the economy. Increasing Web resources from distributed spatial data portals and global geospatial libraries, and a growing suite of Web integration tools, will provide new opportunities to advance disease surveillance, control, and prevention, and insure public access and community empowerment in public health decision making. Emerging supercomputing, data mining, compression, and transmission technologies will play increasingly critical roles in national emergency, catastrophic planning and response, and risk management. Web-enabled public health GIS will be guided by Federal Geographic Data Committee spatial metadata, OpenGIS Web interoperability, and GML/XML geospatial Web content standards. Public health will become a responsive and integral part of the National Spatial Data Infrastructure.

49 CFR 601.42 - Emergency relief docket.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Emergency Relief Docket in the publicly accessible DOT Docket Management System (DMS) (http://dms.dot.gov... message on its web page (http://www.fta.dot.gov) indicating the Emergency Relief Docket has been opened...

49 CFR 601.42 - Emergency relief docket.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Emergency Relief Docket in the publicly accessible DOT Docket Management System (DMS) (http://dms.dot.gov... message on its web page (http://www.fta.dot.gov) indicating the Emergency Relief Docket has been opened...

49 CFR 601.42 - Emergency relief docket.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Emergency Relief Docket in the publicly accessible DOT Docket Management System (DMS) (http://dms.dot.gov... message on its web page (http://www.fta.dot.gov) indicating the Emergency Relief Docket has been opened...

49 CFR 601.42 - Emergency relief docket.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Emergency Relief Docket in the publicly accessible DOT Docket Management System (DMS) (http://dms.dot.gov... message on its web page (http://www.fta.dot.gov) indicating the Emergency Relief Docket has been opened...

49 CFR 601.42 - Emergency relief docket.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Emergency Relief Docket in the publicly accessible DOT Docket Management System (DMS) (http://dms.dot.gov... message on its web page (http://www.fta.dot.gov) indicating the Emergency Relief Docket has been opened...

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.

Using Open and Interoperable Ways to Publish and Access LANCE AIRS Near-Real Time Data

NASA Astrophysics Data System (ADS)

Zhao, P.; Lynnes, C.; Vollmer, B.; Savtchenko, A. K.; Yang, W.

2011-12-01

Atmospheric Infrared Sounder (AIRS) Near-Real Time (NRT) data from the Land Atmosphere Near real time Capability for EOS (LANCE) provide the information on the global and regional atmospheric state with very low latency. An open and interoperable platform is useful to facilitate access to and integration of LANCE AIRS NRT data. This paper discusses the use of open-source software components to build Web services for publishing and accessing AIRS NRT data in the context of Service Oriented Architecture (SOA). The AIRS NRT data have also been made available through an OPeNDAP server. OPeNDAP allows several open-source netCDF-based tools such as Integrated Data Viewer, Ferret and Panoply to directly display the Level 2 data over the network. To enable users to locate swath data files in the OPeNDAP server that lie within a certain geographical area, graphical "granule maps" are being added to show the outline of each file on a map of the Earth. The metadata of AIRS NRT data and services is then explored to implement information advertisement and discovery in catalogue systems. Datacasting, an RSS-based technology for accessing Earth Science data and information to facilitate the subscriptions to AIRS NRT data availability, filtering, downloading and viewing data, is also discussed. To provide an easy entry point to AIRS NRT data and services, a Web portal designed for customized data downloading and visualization is introduced.

From Web accessibility to Web adaptability.

PubMed

Kelly, Brian; Nevile, Liddy; Sloan, David; Fanou, Sotiris; Ellison, Ruth; Herrod, Lisa

2009-07-01

This article asserts that current approaches to enhance the accessibility of Web resources fail to provide a solid foundation for the development of a robust and future-proofed framework. In particular, they fail to take advantage of new technologies and technological practices. The article introduces a framework for Web adaptability, which encourages the development of Web-based services that can be resilient to the diversity of uses of such services, the target audience, available resources, technical innovations, organisational policies and relevant definitions of 'accessibility'. The article refers to a series of author-focussed approaches to accessibility through which the authors and others have struggled to find ways to promote accessibility for people with disabilities. These approaches depend upon the resource author's determination of the anticipated users' needs and their provision. Through approaches labelled as 1.0, 2.0 and 3.0, the authors have widened their focus to account for contexts and individual differences in target audiences. Now, the authors want to recognise the role of users in determining their engagement with resources (including services). To distinguish this new approach, the term 'adaptability' has been used to replace 'accessibility'; new definitions of accessibility have been adopted, and the authors have reviewed their previous work to clarify how it is relevant to the new approach. Accessibility 1.0 is here characterised as a technical approach in which authors are told how to construct resources for a broadly defined audience. This is known as universal design. Accessibility 2.0 was introduced to point to the need to account for the context in which resources would be used, to help overcome inadequacies identified in the purely technical approach. Accessibility 3.0 moved the focus on users from a homogenised universal definition to recognition of the idiosyncratic needs and preferences of individuals and to cater for them. All of these approaches placed responsibility within the authoring/publishing domain without recognising the role the user might want to play, or the roles that other users in social networks, or even Web services might play. Adaptability shifts the emphasis and calls for greater freedom for the users to facilitate individual accessibility in the open Web environment.

The Water SWITCH-ON Spatial Information Platform (SIP)

NASA Astrophysics Data System (ADS)

Sala Calero, J., Sr.; Boot, G., Sr.; Dihé, P., Sr.; Arheimer, B.

2017-12-01

The amount of hydrological open data is continually growing and providing opportunities to the scientific community. Although the existing data portals (GEOSS Portal, INSPIRE community geoportal and others) enable access to open data, many users still find browsing through them difficult. Moreover, the time spent on gathering and preparing data usually is more significant than the time spent on the experiment itself. Thus, any improvement on searching, understanding, accessing or using open data is greatly beneficial. The Spatial Information Platform (SIP) has been developed to tackle these issues within the SWITCH-ON European Commission funded FP7 project. The SIP has been designed as a set of tools based on open standards that provide to the user all the necessary functionalities as described in the Publish-Find-Bind (PFB) pattern. In other words, this means that the SIP helps users to locate relevant and suitable data for their experiments analysis, to access and transform it (filtering, extraction, selection, conversion, aggregation). Moreover, the SIP can be used to provide descriptive information about the data and to publish it so others can find and use it. The SIP is based on existing open data protocols such as the OGC/CSW, OGC/WMS, OpenDAP and open-source components like PostgreSQL/PostGIS, GeoServer and pyCSW. The SIP is divided in three main user interfaces: the BYOD (Browse your open dataset) web interface, the Expert GUI tool and the Upload Data and Metadata web interface. The BYOD HTML5 client is the main entry point for users that want to browse through open data in the SIP. The BYOD has a map interface based on Leaflet JavaScript libraries so that the users can search more efficiently. The web-based Open Data Registration Tool is a user-friendly upload and metadata description interface (geographical extent, license, DOI generation). The Expert GUI is a desktop application that provides full metadata editing capabilities for the metadata moderators of the project. In conclusion, the Spatial Information Platform (SIP) provides to its community a set of tools for better understanding and ease of use of hydrological open-data. Moreover, the SIP has been based on well-known OGC standards that will allow the connection and data harvesting from popular open data portals such as the GEOSS system of systems.

A grid-enabled web service for low-resolution crystal structure refinement.

PubMed

O'Donovan, Daniel J; Stokes-Rees, Ian; Nam, Yunsun; Blacklow, Stephen C; Schröder, Gunnar F; Brunger, Axel T; Sliz, Piotr

2012-03-01

Deformable elastic network (DEN) restraints have proved to be a powerful tool for refining structures from low-resolution X-ray crystallographic data sets. Unfortunately, optimal refinement using DEN restraints requires extensive calculations and is often hindered by a lack of access to sufficient computational resources. The DEN web service presented here intends to provide structural biologists with access to resources for running computationally intensive DEN refinements in parallel on the Open Science Grid, the US cyberinfrastructure. Access to the grid is provided through a simple and intuitive web interface integrated into the SBGrid Science Portal. Using this portal, refinements combined with full parameter optimization that would take many thousands of hours on standard computational resources can now be completed in several hours. An example of the successful application of DEN restraints to the human Notch1 transcriptional complex using the grid resource, and summaries of all submitted refinements, are presented as justification.

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.

U.S. Geological Survey (USGS) Earthquake Web Applications

NASA Astrophysics Data System (ADS)

Fee, J.; Martinez, E.

2015-12-01

USGS Earthquake web applications provide access to earthquake information from USGS and other Advanced National Seismic System (ANSS) contributors. One of the primary goals of these applications is to provide a consistent experience for accessing both near-real time information as soon as it is available and historic information after it is thoroughly reviewed. Millions of people use these applications every month including people who feel an earthquake, emergency responders looking for the latest information about a recent event, and scientists researching historic earthquakes and their effects. Information from multiple catalogs and contributors is combined by the ANSS Comprehensive Catalog into one composite catalog, identifying the most preferred information from any source for each event. A web service and near-real time feeds provide access to all contributed data, and are used by a number of users and software packages. The Latest Earthquakes application displays summaries of many events, either near-real time feeds or custom searches, and the Event Page application shows detailed information for each event. Because all data is accessed through the web service, it can also be downloaded by users. The applications are maintained as open source projects on github, and use mobile-first and responsive-web-design approaches to work well on both mobile devices and desktop computers. http://earthquake.usgs.gov/earthquakes/map/

On-line access to geoscience bibliographic citations

USGS Publications Warehouse

Wild, Emily C.

2012-01-01

On-line geoscience bibliographic citations and access points to citations are exponentially increasing as commercial, non-profit, and government agencies worldwide publish materials electronically. On-line bibliographic tools capture cited works, and open access content allows for freely obtained citations and documents. For this newsletter, citations from the numerous journals and books listed in the "Recent Papers" section of the EXPLORE newsletters from 2008-2011 were used to provide freely-accessible web sites to determine the availability of bibliographic information.

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.

Behind the Scenes with OpenLearn: The Challenges of Researching the Provision of Open Educational Resources

ERIC Educational Resources Information Center

Godwin, Stephen; McAndrew, Patrick; Santos, Andreia

2008-01-01

Web-enabled technology is now being applied on a large scale. In this paper we look at open access provision of teaching and learning leading to many users with varying patterns and motivations for use. This has provided us with a research challenge to find methods that help us understand and explain such initiatives. We describe ways to model the…

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.

NOBAI: a web server for character coding of geometrical and statistical features in RNA structure

PubMed Central

Knudsen, Vegeir; Caetano-Anollés, Gustavo

2008-01-01

The Numeration of Objects in Biology: Alignment Inferences (NOBAI) web server provides a web interface to the applications in the NOBAI software package. This software codes topological and thermodynamic information related to the secondary structure of RNA molecules as multi-state phylogenetic characters, builds character matrices directly in NEXUS format and provides sequence randomization options. The web server is an effective tool that facilitates the search for evolutionary history embedded in the structure of functional RNA molecules. The NOBAI web server is accessible at ‘http://www.manet.uiuc.edu/nobai/nobai.php’. This web site is free and open to all users and there is no login requirement. PMID:18448469

Unifying Access to National Hydrologic Data Repositories via Web Services

NASA Astrophysics Data System (ADS)

Valentine, D. W.; Jennings, B.; Zaslavsky, I.; Maidment, D. R.

2006-12-01

The CUAHSI hydrologic information system (HIS) is designed to be a live, multiscale web portal system for accessing, querying, visualizing, and publishing distributed hydrologic observation data and models for any location or region in the United States. The HIS design follows the principles of open service oriented architecture, i.e. system components are represented as web services with well defined standard service APIs. WaterOneFlow web services are the main component of the design. The currently available services have been completely re-written compared to the previous version, and provide programmatic access to USGS NWIS. (steam flow, groundwater and water quality repositories), DAYMET daily observations, NASA MODIS, and Unidata NAM streams, with several additional web service wrappers being added (EPA STORET, NCDC and others.). Different repositories of hydrologic data use different vocabularies, and support different types of query access. Resolving semantic and structural heterogeneities across different hydrologic observation archives and distilling a generic set of service signatures is one of the main scalability challenges in this project, and a requirement in our web service design. To accomplish the uniformity of the web services API, data repositories are modeled following the CUAHSI Observation Data Model. The web service responses are document-based, and use an XML schema to express the semantics in a standard format. Access to station metadata is provided via web service methods, GetSites, GetSiteInfo and GetVariableInfo. The methdods form the foundation of CUAHSI HIS discovery interface and may execute over locally-stored metadata or request the information from remote repositories directly. Observation values are retrieved via a generic GetValues method which is executed against national data repositories. The service is implemented in ASP.Net, and other providers are implementing WaterOneFlow services in java. Reference implementation of WaterOneFlow web services is available. More information about the ongoing development of CUAHSI HIS is available from http://www.cuahsi.org/his/.

Towards exergaming commons: composing the exergame ontology for publishing open game data.

PubMed

Bamparopoulos, Giorgos; Konstantinidis, Evdokimos; Bratsas, Charalampos; Bamidis, Panagiotis D

2016-01-01

It has been shown that exergames have multiple benefits for physical, mental and cognitive health. Only recently, however, researchers have started considering them as health monitoring tools, through collection and analysis of game metrics data. In light of this and initiatives like the Quantified Self, there is an emerging need to open the data produced by health games and their associated metrics in order for them to be evaluated by the research community in an attempt to quantify their potential health, cognitive and physiological benefits. We have developed an ontology that describes exergames using the Web Ontology Language (OWL); it is available at http://purl.org/net/exergame/ns#. After an investigation of key components of exergames, relevant ontologies were incorporated, while necessary classes and properties were defined to model these components. A JavaScript framework was also developed in order to apply the ontology to online exergames. Finally, a SPARQL Endpoint is provided to enable open data access to potential clients through the web. Exergame components include details for players, game sessions, as well as, data produced during these game-playing sessions. The description of the game includes elements such as goals, game controllers and presentation hardware used; what is more, concepts from already existing ontologies are reused/repurposed. Game sessions include information related to the player, the date and venue where the game was played, as well as, the results/scores that were produced/achieved. These games are subsequently played by 14 users in multiple game sessions and the results derived from these sessions are published in a triplestore as open data. We model concepts related to exergames by providing a standardized structure for reference and comparison. This is the first work that publishes data from actual exergame sessions on the web, facilitating the integration and analysis of the data, while allowing open data access through the web in an effort to enable the concept of Open Trials for Active and Healthy Ageing.

Web Based Data Access to the World Data Center for Climate

NASA Astrophysics Data System (ADS)

Toussaint, F.; Lautenschlager, M.

2006-12-01

The World Data Center for Climate (WDC-Climate, www.wdc-climate.de) is hosted by the Model &Data Group (M&D) of the Max Planck Institute for Meteorology. The M&D department is financed by the German government and uses the computers and mass storage facilities of the German Climate Computing Centre (Deutsches Klimarechenzentrum, DKRZ). The WDC-Climate provides web access to 200 Terabytes of climate data; the total mass storage archive contains nearly 4 Petabytes. Although the majority of the datasets concern model output data, some satellite and observational data are accessible as well. The underlying relational database is distributed on five servers. The CERA relational data model is used to integrate catalogue data and mass data. The flexibility of the model allows to store and access very different types of data and metadata. The CERA metadata catalogue provides easy access to the content of the CERA database as well as to other data in the web. Visit ceramodel.wdc-climate.de for additional information on the CERA data model. The majority of the users access data via the CERA metadata catalogue, which is open without registration. However, prior to retrieving data user are required to check in and apply for a userid and password. The CERA metadata catalogue is servlet based. So it is accessible worldwide through any web browser at cera.wdc-climate.de. In addition to data and metadata access by the web catalogue, WDC-Climate offers a number of other forms of web based data access. All metadata are available via http request as xml files in various metadata formats (ISO, DC, etc., see wini.wdc-climate.de) which allows for easy data interchange with other catalogues. Model data can be retrieved in GRIB, ASCII, NetCDF, and binary (IEEE) format. WDC-Climate serves as data centre for various projects. Since xml files are accessible by http, the integration of data into applications of different projects is very easy. Projects supported by WDC-Climate are e.g. CEOP, IPCC, and CARIBIC. A script tool for data download (jblob) is offered on the web page, to make retrieval of huge data quantities more comfortable.

Using open-source programs to create a web-based portal for hydrologic information

NASA Astrophysics Data System (ADS)

Kim, H.

2013-12-01

Some hydrologic data sets, such as basin climatology, precipitation, and terrestrial water storage, are not easily obtainable and distributable due to their size and complexity. We present a Hydrologic Information Portal (HIP) that has been implemented at the University of California for Hydrologic Modeling (UCCHM) and that has been organized around the large river basins of North America. This portal can be easily accessed through a modern web browser that enables easy access and visualization of such hydrologic data sets. Some of the main features of our HIP include a set of data visualization features so that users can search, retrieve, analyze, integrate, organize, and map data within large river basins. Recent information technologies such as Google Maps, Tornado (Python asynchronous web server), NumPy/SciPy (Scientific Library for Python) and d3.js (Visualization library for JavaScript) were incorporated into the HIP to create ease in navigating large data sets. With such open source libraries, HIP can give public users a way to combine and explore various data sets by generating multiple chart types (Line, Bar, Pie, Scatter plot) directly from the Google Maps viewport. Every rendered object such as a basin shape on the viewport is clickable, and this is the first step to access the visualization of data sets.

Effectiveness of a Web-Supplemented Astronomy Survey Course

NASA Astrophysics Data System (ADS)

Hufnagel, B.

1997-12-01

An astronomy survey course for \\ 200 non-science majors, offered in spring 1997 at Michigan State University, was supplemented with an internet site. Web access was voluntary, with the exception of about 10% of the homework problems. In addition, all of the answers to homeworks, in-class activities, and tests were available only on the website. The website included web versions of all the usual hard-copy handouts, as well as lecture notes, links to other astronomy URLs, and a frequently-asked question (FAQ) site taken from student email to the professors. MSU students can access the Web through \\ 30 PC labs on and off campus, and through private PCs in the dorms where most of the MSU students live. A mid-semester open-ended feedback form (for class credit) was administered in-class to the students, with 151 respondents. Their responses to the question ``About how frequently do you access the course website?'' will be correlated to their grade at that point in the course, their gender, and their purpose for accessing the website. These results will be interesting to astronomy teachers who would like to offer additional resources and more lines of communication to their students at low cost and without abandoning traditional methods.

Accessing and managing open medical resources in Africa over the Internet

NASA Astrophysics Data System (ADS)

Hussein, Rada; Khalifa, Aly; Jimenez-Castellanos, Ana; de la Calle, Guillermo; Ramirez-Robles, Maximo; Crespo, Jose; Perez-Rey, David; Garcia-Remesal, Miguel; Anguita, Alberto; Alonso-Calvo, Raul; de la Iglesia, Diana; Barreiro, Jose M.; Maojo, Victor

2014-10-01

Recent commentaries have proposed the advantages of using open exchange of data and informatics resources for improving health-related policies and patient care in Africa. Yet, in many African regions, both private medical and public health information systems are still unaffordable. Open exchange over the social Web 2.0 could encourage more altruistic support of medical initiatives. We have carried out some experiments to demonstrate the feasibility of using this approach to disseminate open data and informatics resources in Africa. After the experiments we developed the AFRICA BUILD Portal, the first Social Network for African biomedical researchers. Through the AFRICA BUILD Portal users can access in a transparent way to several resources. Currently, over 600 researchers are using distributed and open resources through this platform committed to low connections.

Spatial Data Services for Interdisciplinary Applications from the NASA Socioeconomic Data and Applications Center

NASA Astrophysics Data System (ADS)

Chen, R. S.; MacManus, K.; Vinay, S.; Yetman, G.

2016-12-01

The Socioeconomic Data and Applications Center (SEDAC), one of 12 Distributed Active Archive Centers (DAACs) in the NASA Earth Observing System Data and Information System (EOSDIS), has developed a variety of operational spatial data services aimed at providing online access, visualization, and analytic functions for geospatial socioeconomic and environmental data. These services include: open web services that implement Open Geospatial Consortium (OGC) specifications such as Web Map Service (WMS), Web Feature Service (WFS), and Web Coverage Service (WCS); spatial query services that support Web Processing Service (WPS) and Representation State Transfer (REST); and web map clients and a mobile app that utilize SEDAC and other open web services. These services may be accessed from a variety of external map clients and visualization tools such as NASA's WorldView, NOAA's Climate Explorer, and ArcGIS Online. More than 200 data layers related to population, settlements, infrastructure, agriculture, environmental pollution, land use, health, hazards, climate change and other aspects of sustainable development are available through WMS, WFS, and/or WCS. Version 2 of the SEDAC Population Estimation Service (PES) supports spatial queries through WPS and REST in the form of a user-defined polygon or circle. The PES returns an estimate of the population residing in the defined area for a specific year (2000, 2005, 2010, 2015, or 2020) based on SEDAC's Gridded Population of the World version 4 (GPWv4) dataset, together with measures of accuracy. The SEDAC Hazards Mapper and the recently released HazPop iOS mobile app enable users to easily submit spatial queries to the PES and see the results. SEDAC has developed an operational virtualized backend infrastructure to manage these services and support their continual improvement as standards change, new data and services become available, and user needs evolve. An ongoing challenge is to improve the reliability and performance of the infrastructure, in conjunction with external services, to meet both research and operational needs.

Operational Marine Data Acquisition and Delivery Powered by Web and Geospatial Standards

NASA Astrophysics Data System (ADS)

Thomas, R.; Buck, J. J. H.

2015-12-01

As novel sensor types and new platforms are deployed to monitor the global oceans, the volumes of scientific and environmental data collected in the marine context are rapidly growing. In order to use these data in both the traditional operational modes and in innovative "Big Data" applications the data must be readily understood by software agents. One approach to achieving this is the application of both World Wide Web and Open Geospatial Consortium standards: namely Linked Data1 and Sensor Web Enablement2 (SWE). The British Oceanographic Data Centre (BODC) is adopting this strategy in a number of European Commission funded projects (NETMAR; SenseOCEAN; Ocean Data Interoperability Platform - ODIP; and AtlantOS) to combine its existing data archiving architecture with SWE components (such as Sensor Observation Services) and a Linked Data interface. These will evolve the data management and data transfer from a process that requires significant manual intervention to an automated operational process enabling the rapid, standards-based, ingestion and delivery of data. This poster will show the current capabilities of BODC and the status of on-going implementation of this strategy. References1. World Wide Web Consortium. (2013). Linked Data. Available:http://www.w3.org/standards/semanticweb/data. Last accessed 7th April 20152. Open Geospatial Consortium. (2014). Sensor Web Enablement (SWE). Available:http://www.opengeospatial.org/ogc/markets-technologies/swe. Last accessed 8th October 2014

Born semantic: linking data from sensors to users and balancing hardware limitations with data standards

NASA Astrophysics Data System (ADS)

Buck, Justin; Leadbetter, Adam

2015-04-01

New users for the growing volume of ocean data for purposes such as 'big data' data products and operational data assimilation/ingestion require data to be readily ingestible. This can be achieved via the application of World Wide Web Consortium (W3C) Linked Data and Open Geospatial Consortium (OGC) Sensor Web Enablement (SWE) standards to data management. As part of several Horizons 2020 European projects (SenseOCEAN, ODIP, AtlantOS) the British Oceanographic Data Centre (BODC) are working on combining existing data centre architecture and SWE software such as Sensor Observation Services with a Linked Data front end. The standards to enable data delivery are proven and well documented1,2 There are practical difficulties when SWE standards are applied to real time data because of internal hardware bandwidth restrictions and a requirement to constrain data transmission costs. A pragmatic approach is proposed where sensor metadata and data output in OGC standards are implemented "shore-side" with sensors and instruments transmitting unique resolvable web linkages to persistent OGC SensorML records published at the BODC. References: 1. World Wide Web Consortium. (2013). Linked Data. Available: http://www.w3.org/standards/semanticweb/data. Last accessed 8th October 2014. 2. Open Geospatial Consortium. (2014). Sensor Web Enablement (SWE). Available: http://www.opengeospatial.org/ogc/markets-technologies/swe. Last accessed 8th October 2014.

Design of a High Resolution Open Access Global Snow Cover Web Map Service Using Ground and Satellite Observations

NASA Astrophysics Data System (ADS)

Kadlec, J.; Ames, D. P.

2014-12-01

The aim of the presented work is creating a freely accessible, dynamic and re-usable snow cover map of the world by combining snow extent and snow depth datasets from multiple sources. The examined data sources are: remote sensing datasets (MODIS, CryoLand), weather forecasting model outputs (OpenWeatherMap, forecast.io), ground observation networks (CUAHSI HIS, GSOD, GHCN, and selected national networks), and user-contributed snow reports on social networks (cross-country and backcountry skiing trip reports). For adding each type of dataset, an interface and an adapter is created. Each adapter supports queries by area, time range, or combination of area and time range. The combined dataset is published as an online snow cover mapping service. This web service lowers the learning curve that is required to view, access, and analyze snow depth maps and snow time-series. All data published by this service are licensed as open data; encouraging the re-use of the data in customized applications in climatology, hydrology, sports and other disciplines. The initial version of the interactive snow map is on the website snow.hydrodata.org. This website supports the view by time and view by site. In view by time, the spatial distribution of snow for a selected area and time period is shown. In view by site, the time-series charts of snow depth at a selected location is displayed. All snow extent and snow depth map layers and time series are accessible and discoverable through internationally approved protocols including WMS, WFS, WCS, WaterOneFlow and WaterML. Therefore they can also be easily added to GIS software or 3rd-party web map applications. The central hypothesis driving this research is that the integration of user contributed data and/or social-network derived snow data together with other open access data sources will result in more accurate and higher resolution - and hence more useful snow cover maps than satellite data or government agency produced data by itself.

Growing a National Learning Environments and Resources Network for Science, Mathematics, Engineering, and Technology Education: Current Issues and Opportunities for the NSDL Program; Open Linking in the Scholarly Information Environment Using the OpenURL Framework; The HeadLine Personal Information Environment: Evaluation Phase One.

ERIC Educational Resources Information Center

Zia, Lee L.; Van de Sompel, Herbert; Beit-Arie, Oren; Gambles, Anne

2001-01-01

Includes three articles that discuss the National Science Foundation's National Science, Mathematics, Engineering, and Technology Education Digital Library (NSDL) program; the OpenURL framework for open reference linking in the Web-based scholarly information environment; and HeadLine (Hybrid Electronic Access and Delivery in the Library Networked…

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.

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

Distributed data discovery, access and visualization services to Improve Data Interoperability across different data holdings

NASA Astrophysics Data System (ADS)

Palanisamy, G.; Krassovski, M.; Devarakonda, R.; Santhana Vannan, S.

2012-12-01

The current climate debate is highlighting the importance of free, open, and authoritative sources of high quality climate data that are available for peer review and for collaborative purposes. It is increasingly important to allow various organizations around the world to share climate data in an open manner, and to enable them to perform dynamic processing of climate data. This advanced access to data can be enabled via Web-based services, using common "community agreed" standards without having to change their internal structure used to describe the data. The modern scientific community has become diverse and increasingly complex in nature. To meet the demands of such diverse user community, the modern data supplier has to provide data and other related information through searchable, data and process oriented tool. This can be accomplished by setting up on-line, Web-based system with a relational database as a back end. The following common features of the web data access/search systems will be outlined in the proposed presentation: - A flexible data discovery - Data in commonly used format (e.g., CSV, NetCDF) - Preparing metadata in standard formats (FGDC, ISO19115, EML, DIF etc.) - Data subseting capabilities and ability to narrow down to individual data elements - Standards based data access protocols and mechanisms (SOAP, REST, OpenDAP, OGC etc.) - Integration of services across different data systems (discovery to access, visualizations and subseting) This presentation will also include specific examples of integration of various data systems that are developed by Oak Ridge National Laboratory's - Climate Change Science Institute, their ability to communicate between each other to enable better data interoperability and data integration. References: [1] Devarakonda, Ranjeet, and Harold Shanafield. "Drupal: Collaborative framework for science research." Collaboration Technologies and Systems (CTS), 2011 International Conference on. IEEE, 2011. [2]Devarakonda, R., Shrestha, B., Palanisamy, G., Hook, L. A., Killeffer, T. S., Boden, T. A., ... & Lazer, K. (2014). THE NEW ONLINE METADATA EDITOR FOR GENERATING STRUCTURED METADATA. Oak Ridge National Laboratory (ORNL).

Improving data discoverability, accessibility, and interoperability with the Esri ArcGIS Platform at the NASA Atmospheric Science Data Center (ASDC).

NASA Astrophysics Data System (ADS)

Tisdale, M.

2017-12-01

NASA's Atmospheric Science Data Center (ASDC) is operationally using the Esri ArcGIS Platform to improve data discoverability, accessibility and interoperability to meet the diversifying user requirements from government, private, public and academic communities. The ASDC is actively working to provide their mission essential datasets as ArcGIS Image Services, Open Geospatial Consortium (OGC) Web Mapping Services (WMS), and OGC Web Coverage Services (WCS) while leveraging the ArcGIS multidimensional mosaic dataset structure. Science teams at ASDC are utilizing these services through the development of applications using the Web AppBuilder for ArcGIS and the ArcGIS API for Javascript. These services provide greater exposure of ASDC data holdings to the GIS community and allow for broader sharing and distribution to various end users. These capabilities provide interactive visualization tools and improved geospatial analytical tools for a mission critical understanding in the areas of the earth's radiation budget, clouds, aerosols, and tropospheric chemistry. The presentation will cover how the ASDC is developing geospatial web services and applications to improve data discoverability, accessibility, and interoperability.

Development and Use of an Adaptive Learning Environment to Research Online Study Behaviour

ERIC Educational Resources Information Center

Jonsdottir, Anna Helga; Jakobsdottir, Audbjorg; Stefansson, Gunnar

2015-01-01

This paper describes a system for research on the behaviour of students taking online drills. The system is accessible and free to use for anyone with web access. Based on open source software, the teaching material is licensed under a Creative Commons License. The system has been used for computer-assisted education in statistics, mathematics and…

Enhancing the AliEn Web Service Authentication

NASA Astrophysics Data System (ADS)

Zhu, Jianlin; Saiz, Pablo; Carminati, Federico; Betev, Latchezar; Zhou, Daicui; Mendez Lorenzo, Patricia; Grigoras, Alina Gabriela; Grigoras, Costin; Furano, Fabrizio; Schreiner, Steffen; Vladimirovna Datskova, Olga; Sankar Banerjee, Subho; Zhang, Guoping

2011-12-01

Web Services are an XML based technology that allow applications to communicate with each other across disparate systems. Web Services are becoming the de facto standard that enable inter operability between heterogeneous processes and systems. AliEn2 is a grid environment based on web services. The AliEn2 services can be divided in three categories: Central services, deployed once per organization; Site services, deployed on each of the participating centers; Job Agents running on the worker nodes automatically. A security model to protect these services is essential for the whole system. Current implementations of web server, such as Apache, are not suitable to be used within the grid environment. Apache with the mod_ssl and OpenSSL only supports the X.509 certificates. But in the grid environment, the common credential is the proxy certificate for the purpose of providing restricted proxy and delegation. An Authentication framework was taken for AliEn2 web services to add the ability to accept X.509 certificates and proxy certificates from client-side to Apache Web Server. The authentication framework could also allow the generation of access control policies to limit access to the AliEn2 web services.

The Neotoma Paleoecology Database

NASA Astrophysics Data System (ADS)

Grimm, E. C.; Ashworth, A. C.; Barnosky, A. D.; Betancourt, J. L.; Bills, B.; Booth, R.; Blois, J.; Charles, D. F.; Graham, R. W.; Goring, S. J.; Hausmann, S.; Smith, A. J.; Williams, J. W.; Buckland, P.

2015-12-01

The Neotoma Paleoecology Database (www.neotomadb.org) is a multiproxy, open-access, relational database that includes fossil data for the past 5 million years (the late Neogene and Quaternary Periods). Modern distributional data for various organisms are also being made available for calibration and paleoecological analyses. The project is a collaborative effort among individuals from more than 20 institutions worldwide, including domain scientists representing a spectrum of Pliocene-Quaternary fossil data types, as well as experts in information technology. Working groups are active for diatoms, insects, ostracodes, pollen and plant macroscopic remains, testate amoebae, rodent middens, vertebrates, age models, geochemistry and taphonomy. Groups are also active in developing online tools for data analyses and for developing modules for teaching at different levels. A key design concept of NeotomaDB is that stewards for various data types are able to remotely upload and manage data. Cooperatives for different kinds of paleo data, or from different regions, can appoint their own stewards. Over the past year, much progress has been made on development of the steward software-interface that will enable this capability. The steward interface uses web services that provide access to the database. More generally, these web services enable remote programmatic access to the database, which both desktop and web applications can use and which provide real-time access to the most current data. Use of these services can alleviate the need to download the entire database, which can be out-of-date as soon as new data are entered. In general, the Neotoma web services deliver data either from an entire table or from the results of a view. Upon request, new web services can be quickly generated. Future developments will likely expand the spatial and temporal dimensions of the database. NeotomaDB is open to receiving new datasets and stewards from the global Quaternary community. Research is supported by NSF EAR-0622349.

The Ecological Model Web Concept: A Consultative Infrastructure for Decision Makers and Researchers

NASA Astrophysics Data System (ADS)

Geller, G.; Nativi, S.

2011-12-01

Rapid climate and socioeconomic changes may be outrunning society's ability to understand, predict, and respond to change effectively. Decision makers want better information about what these changes will be and how various resources will be affected, while researchers want better understanding of the components and processes of ecological systems, how they interact, and how they respond to change. Although there are many excellent models in ecology and related disciplines, there is only limited coordination among them, and accessible, openly shared models or model systems that can be consulted to gain insight on important ecological questions or assist with decision-making are rare. A "consultative infrastructure" that increased access to and sharing of models and model outputs would benefit decision makers, researchers, as well as modelers. Of course, envisioning such an ambitious system is much easier than building it, but several complementary approaches exist that could contribute. The one discussed here is called the Model Web. This is a concept for an open-ended system of interoperable computer models and databases based on making models and their outputs available as services ("model as a service"). Initially, it might consist of a core of several models from which it could grow gradually as new models or databases were added. However, a model web would not be a monolithic, rigidly planned and built system--instead, like the World Wide Web, it would grow largely organically, with limited central control, within a framework of broad goals and data exchange standards. One difference from the WWW is that a model web is much harder to create, and has more pitfalls, and thus is a long term vision. However, technology, science, observations, and models have advanced enough so that parts of an ecological model web can be built and utilized now, forming a framework for gradual growth as well as a broadly accessible infrastructure. Ultimately, the value of a model web lies in the increase in access to and sharing of both models and model outputs. By lowering access barriers to models and their outputs there is less reinvention, more efficient use of resources, greater interaction among researchers and across disciplines, as well as other benefits. The growth of such a system of models fits well with the concept and architecture of the Global Earth Observing System of Systems (GEOSS) as well as the Semantic Web. And, while framed here in the context of ecological forecasting, the same concept can be applied to any discipline utilizing models.

The BioExtract Server: a web-based bioinformatic workflow platform

PubMed Central

Lushbough, Carol M.; Jennewein, Douglas M.; Brendel, Volker P.

2011-01-01

The BioExtract Server (bioextract.org) is an open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet. PMID:21546552

PlanetServer: Innovative approaches for the online analysis of hyperspectral satellite data from Mars

NASA Astrophysics Data System (ADS)

Oosthoek, J. H. P.; Flahaut, J.; Rossi, A. P.; Baumann, P.; Misev, D.; Campalani, P.; Unnithan, V.

2014-06-01

PlanetServer is a WebGIS system, currently under development, enabling the online analysis of Compact Reconnaissance Imaging Spectrometer (CRISM) hyperspectral data from Mars. It is part of the EarthServer project which builds infrastructure for online access and analysis of huge Earth Science datasets. Core functionality consists of the rasdaman Array Database Management System (DBMS) for storage, and the Open Geospatial Consortium (OGC) Web Coverage Processing Service (WCPS) for data querying. Various WCPS queries have been designed to access spatial and spectral subsets of the CRISM data. The client WebGIS, consisting mainly of the OpenLayers javascript library, uses these queries to enable online spatial and spectral analysis. Currently the PlanetServer demonstration consists of two CRISM Full Resolution Target (FRT) observations, surrounding the NASA Curiosity rover landing site. A detailed analysis of one of these observations is performed in the Case Study section. The current PlanetServer functionality is described step by step, and is tested by focusing on detecting mineralogical evidence described in earlier Gale crater studies. Both the PlanetServer methodology and its possible use for mineralogical studies will be further discussed. Future work includes batch ingestion of CRISM data and further development of the WebGIS and analysis tools.

A National Crop Progress Monitoring System Based on NASA Earth Science Results

NASA Astrophysics Data System (ADS)

Di, L.; Yu, G.; Zhang, B.; Deng, M.; Yang, Z.

2011-12-01

Crop progress is an important piece of information for food security and agricultural commodities. Timely monitoring and reporting are mandated for the operation of agricultural statistical agencies. Traditionally, the weekly reporting issued by the National Agricultural Statistics Service (NASS) of the United States Department of Agriculture (USDA) is based on reports from the knowledgeable state and county agricultural officials and farmers. The results are spatially coarse and subjective. In this project, a remote-sensing-supported crop progress monitoring system is being developed intensively using the data and derived products from NASA Earth Observing satellites. Moderate Resolution Imaging Spectroradiometer (MODIS) Level 3 product - MOD09 (Surface Reflectance) is used for deriving daily normalized vegetation index (NDVI), vegetation condition index (VCI), and mean vegetation condition index (MVCI). Ratio change to previous year and multiple year mean can be also produced on demand. The time-series vegetation condition indices are further combined with the NASS' remote-sensing-derived Cropland Data Layer (CDL) to estimate crop condition and progress crop by crop. To facilitate the operational requirement and increase the accessibility of data and products by different users, each component of the system has being developed and implemented following open specifications under the Web Service reference model of Open Geospatial Consortium Inc. Sensor observations and data are accessed through Web Coverage Service (WCS), Web Feature Service (WFS), or Sensor Observation Service (SOS) if available. Products are also served through such open-specification-compliant services. For rendering and presentation, Web Map Service (WMS) is used. A Web-service based system is set up and deployed at dss.csiss.gmu.edu/NDVIDownload. Further development will adopt crop growth models, feed the models with remotely sensed precipitation and soil moisture information, and incorporate the model results with vegetation-index time series for crop progress stage estimation.

Cafe Variome: general-purpose software for making genotype-phenotype data discoverable in restricted or open access contexts.

PubMed

Lancaster, Owen; Beck, Tim; Atlan, David; Swertz, Morris; Thangavelu, Dhiwagaran; Veal, Colin; Dalgleish, Raymond; Brookes, Anthony J

2015-10-01

Biomedical data sharing is desirable, but problematic. Data "discovery" approaches-which establish the existence rather than the substance of data-precisely connect data owners with data seekers, and thereby promote data sharing. Cafe Variome (http://www.cafevariome.org) was therefore designed to provide a general-purpose, Web-based, data discovery tool that can be quickly installed by any genotype-phenotype data owner, or network of data owners, to make safe or sensitive content appropriately discoverable. Data fields or content of any type can be accommodated, from simple ID and label fields through to extensive genotype and phenotype details based on ontologies. The system provides a "shop window" in front of data, with main interfaces being a simple search box and a powerful "query-builder" that enable very elaborate queries to be formulated. After a successful search, counts of records are reported grouped by "openAccess" (data may be directly accessed), "linkedAccess" (a source link is provided), and "restrictedAccess" (facilitated data requests and subsequent provision of approved records). An administrator interface provides a wide range of options for system configuration, enabling highly customized single-site or federated networks to be established. Current uses include rare disease data discovery, patient matchmaking, and a Beacon Web service. © 2015 WILEY PERIODICALS, INC.

2B-Alert Web: An Open-Access Tool for Predicting the Effects of Sleep/Wake Schedules and Caffeine Consumption on Neurobehavioral Performance.

PubMed

Reifman, Jaques; Kumar, Kamal; Wesensten, Nancy J; Tountas, Nikolaos A; Balkin, Thomas J; Ramakrishnan, Sridhar

2016-12-01

Computational tools that predict the effects of daily sleep/wake amounts on neurobehavioral performance are critical components of fatigue management systems, allowing for the identification of periods during which individuals are at increased risk for performance errors. However, none of the existing computational tools is publicly available, and the commercially available tools do not account for the beneficial effects of caffeine on performance, limiting their practical utility. Here, we introduce 2B-Alert Web, an open-access tool for predicting neurobehavioral performance, which accounts for the effects of sleep/wake schedules, time of day, and caffeine consumption, while incorporating the latest scientific findings in sleep restriction, sleep extension, and recovery sleep. We combined our validated Unified Model of Performance and our validated caffeine model to form a single, integrated modeling framework instantiated as a Web-enabled tool. 2B-Alert Web allows users to input daily sleep/wake schedules and caffeine consumption (dosage and time) to obtain group-average predictions of neurobehavioral performance based on psychomotor vigilance tasks. 2B-Alert Web is accessible at: https://2b-alert-web.bhsai.org. The 2B-Alert Web tool allows users to obtain predictions for mean response time, mean reciprocal response time, and number of lapses. The graphing tool allows for simultaneous display of up to seven different sleep/wake and caffeine schedules. The schedules and corresponding predicted outputs can be saved as a Microsoft Excel file; the corresponding plots can be saved as an image file. The schedules and predictions are erased when the user logs off, thereby maintaining privacy and confidentiality. The publicly accessible 2B-Alert Web tool is available for operators, schedulers, and neurobehavioral scientists as well as the general public to determine the impact of any given sleep/wake schedule, caffeine consumption, and time of day on performance of a group of individuals. This evidence-based tool can be used as a decision aid to design effective work schedules, guide the design of future sleep restriction and caffeine studies, and increase public awareness of the effects of sleep amounts, time of day, and caffeine on alertness. © 2016 Associated Professional Sleep Societies, LLC.

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.

Introducing the PRIDE Archive RESTful web services.

PubMed

Reisinger, Florian; del-Toro, Noemi; Ternent, Tobias; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-07-01

The PRIDE (PRoteomics IDEntifications) database is one of the world-leading public repositories of mass spectrometry (MS)-based proteomics data and it is a founding member of the ProteomeXchange Consortium of proteomics resources. In the original PRIDE database system, users could access data programmatically by accessing the web services provided by the PRIDE BioMart interface. New REST (REpresentational State Transfer) web services have been developed to serve the most popular functionality provided by BioMart (now discontinued due to data scalability issues) and address the data access requirements of the newly developed PRIDE Archive. Using the API (Application Programming Interface) it is now possible to programmatically query for and retrieve peptide and protein identifications, project and assay metadata and the originally submitted files. Searching and filtering is also possible by metadata information, such as sample details (e.g. species and tissues), instrumentation (mass spectrometer), keywords and other provided annotations. The PRIDE Archive web services were first made available in April 2014. The API has already been adopted by a few applications and standalone tools such as PeptideShaker, PRIDE Inspector, the Unipept web application and the Python-based BioServices package. This application is free and open to all users with no login requirement and can be accessed at http://www.ebi.ac.uk/pride/ws/archive/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Comparative Case Studies on Indonesian Higher Education Rankings

NASA Astrophysics Data System (ADS)

Kurniasih, Nuning; Hasyim, C.; Wulandari, A.; Setiawan, M. I.; Ahmar, A. S.

2018-01-01

The quality of the higher education is the result of a continuous process. There are many indicators that can be used to assess the quality of a higher education. The existence of different indicators makes the different result of university rankings. This research aims to find variables that can connect ranking indicators that are used by Indonesian Ministry of Research, Technology, and Higher Education with indicators that are used by international rankings by taking two kind of ranking systems i.e. Webometrics and 4icu. This research uses qualitative research method with comparative case studies approach. The result of the research shows that to bridge the indicators that are used by Indonesian Ministry or Research, Technology, and Higher Education with web-based ranking system like Webometrics and 4icu so that the Indonesian higher education institutions need to open access towards either scientific or non-scientific that are publicly used into web-based environment. One of the strategies that can be used to improve the openness and access towards scientific work of a university is by involving in open science and collaboration.

21st Century Senior Leader Education: Ubiquitous Open Access Learning Environment

DTIC Science & Technology

2011-02-22

Failures: It‘s the content, stupid ‖22 because agencies focus on systems rather than substance and access to the content is critical. The access to Army...Resource Capabilities. 18 As an example to demonstrate how a civilian capability provides learning value to the PLE, the ― Google Alerts‖ ® web...technology pushed content to the author for review in the development of this paper. The technology consists of a user creating a Google account, logging

Addressing Open Water Data Challenges in the Bureau of Reclamation

NASA Astrophysics Data System (ADS)

Brekke, L. D.; Danner, A.; Nagode, J.; Rocha, J.; Poulton, S.; Anderson, A.

2017-12-01

The Bureau of Reclamation is largest wholesaler of water in the United States. Located in the 17 western states, Reclamation serves water to 31 million people, provides irrigated water to 20 percent of Western farmers, and is the second largest producer of hydroelectric power in the United States. Through these activities, Reclamation generates large amounts of water and water-related data, describing reservoirs and river system conditions, hydropower, environmental compliance activities, infrastructure assets, and other aspects of Reclamation's mission activities. Reclamation aims to make water and water-related data sets more easily found, accessed, and used in decision-making activities in order to benefit the public, private sector, and research communities. Historically, there has not been an integrated, bureau-wide system to store data in machine-readable formats; nor a system to permit centralized browsing, open access, and web-services. Reclamation began addressing these limitations by developing the Reclamation Water Information System (RWIS), released in Spring 2017 (https://water.usbr.gov/). A bureau-wide team contributed to RWIS development, including water data stewards, database administrators, and information technology (IT) specialists. The first RWIS release publishes reservoir time series data from Reclamation's five regions and includes a map interface for sites identification, a query interface for data discovery and access, and web-services for automated retrieval. As RWIS enhancement continues, the development team is developing a companion system - the Reclamation Information Sharing Environment (RISE) - to provide access to the other data subjects and types (geospatial, documents). While RWIS and RISE are promising starts, Reclamation continues to face challenges in addressing open water data goals: making data consolidation and open publishing a value-added activity for programs that publish data locally, going beyond providing open access to also providing decision-support, and scaling up IT solutions for future success - where Reclamation programs increasingly elect to more and more data through RWIS/RISE, thereby creating a big data challenge. This presentation will highlight activities status, lessons learned, and future directions.

Participating in the Geospatial Web: Collaborative Mapping, Social Networks and Participatory GIS

NASA Astrophysics Data System (ADS)

Rouse, L. Jesse; Bergeron, Susan J.; Harris, Trevor M.

In 2005, Google, Microsoft and Yahoo! released free Web mapping applications that opened up digital mapping to mainstream Internet users. Importantly, these companies also released free APIs for their platforms, allowing users to geo-locate and map their own data. These initiatives have spurred the growth of the Geospatial Web and represent spatially aware online communities and new ways of enabling communities to share information from the bottom up. This chapter explores how the emerging Geospatial Web can meet some of the fundamental needs of Participatory GIS projects to incorporate local knowledge into GIS, as well as promote public access and collaborative mapping.

Providing Web Interfaces to the NSF EarthScope USArray Transportable Array

NASA Astrophysics Data System (ADS)

Vernon, Frank; Newman, Robert; Lindquist, Kent

2010-05-01

Since April 2004 the EarthScope USArray seismic network has grown to over 850 broadband stations that stream multi-channel data in near real-time to the Array Network Facility in San Diego. Providing secure, yet open, access to real-time and archived data for a broad range of audiences is best served by a series of platform agnostic low-latency web-based applications. We present a framework of tools that mediate between the world wide web and Boulder Real Time Technologies Antelope Environmental Monitoring System data acquisition and archival software. These tools provide comprehensive information to audiences ranging from network operators and geoscience researchers, to funding agencies and the general public. This ranges from network-wide to station-specific metadata, state-of-health metrics, event detection rates, archival data and dynamic report generation over a station's two year life span. Leveraging open source web-site development frameworks for both the server side (Perl, Python and PHP) and client-side (Flickr, Google Maps/Earth and jQuery) facilitates the development of a robust extensible architecture that can be tailored on a per-user basis, with rapid prototyping and development that adheres to web-standards. Typical seismic data warehouses allow online users to query and download data collected from regional networks, without the scientist directly visually assessing data coverage and/or quality. Using a suite of web-based protocols, we have recently developed an online seismic waveform interface that directly queries and displays data from a relational database through a web-browser. Using the Python interface to Datascope and the Python-based Twisted network package on the server side, and the jQuery Javascript framework on the client side to send and receive asynchronous waveform queries, we display broadband seismic data using the HTML Canvas element that is globally accessible by anyone using a modern web-browser. We are currently creating additional interface tools to create a rich-client interface for accessing and displaying seismic data that can be deployed to any system running the Antelope Real Time System. The software is freely available from the Antelope contributed code Git repository (http://www.antelopeusersgroup.org).

Exploring the SCOAP3 Research Contributions of the United States

NASA Astrophysics Data System (ADS)

Marsteller, Matthew

2016-03-01

The Sponsoring Consortium for Open Access Publishing in Particle Physics (SCOAP3) is a successful global partnership of libraries, funding agencies and research centers. This presentation will inform the audience about SCOAP3 and also delve into descriptive statistics of the United States' intellectual contribution to particle physics via these open access journals. Exploration of the SCOAP3 particle physics literature using a variety of metrics tools such as Web of Science™, InCites™, Scopus® and SciVal will be shared. ORA or Sci2 will be used to visualize author collaboration networks.

45 CFR 159.120 - Data submission for the individual and small group markets.

Code of Federal Regulations, 2012 CFR

2012-10-01

... RELATING TO HEALTH CARE ACCESS HEALTH CARE REFORM INSURANCE WEB PORTAL § 159.120 Data submission for the... reopened for enrollment within 30 days of opening for enrollment. (e) Issuers must annually verify the data...

45 CFR 159.120 - Data submission for the individual and small group markets.

Code of Federal Regulations, 2013 CFR

2013-10-01

... RELATING TO HEALTH CARE ACCESS HEALTH CARE REFORM INSURANCE WEB PORTAL § 159.120 Data submission for the... reopened for enrollment within 30 days of opening for enrollment. (e) Issuers must annually verify the data...

45 CFR 159.120 - Data submission for the individual and small group markets.

Code of Federal Regulations, 2014 CFR

2014-10-01

... RELATING TO HEALTH CARE ACCESS HEALTH CARE REFORM INSURANCE WEB PORTAL § 159.120 Data submission for the... reopened for enrollment within 30 days of opening for enrollment. (e) Issuers must annually verify the data...

Development of a Web-Based Visualization Platform for Climate Research Using Google Earth

NASA Technical Reports Server (NTRS)

Sun, Xiaojuan; Shen, Suhung; Leptoukh, Gregory G.; Wang, Panxing; Di, Liping; Lu, Mingyue

2011-01-01

Recently, it has become easier to access climate data from satellites, ground measurements, and models from various data centers, However, searching. accessing, and prc(essing heterogeneous data from different sources are very tim -consuming tasks. There is lack of a comprehensive visual platform to acquire distributed and heterogeneous scientific data and to render processed images from a single accessing point for climate studies. This paper. documents the design and implementation of a Web-based visual, interoperable, and scalable platform that is able to access climatological fields from models, satellites, and ground stations from a number of data sources using Google Earth (GE) as a common graphical interface. The development is based on the TCP/IP protocol and various data sharing open sources, such as OPeNDAP, GDS, Web Processing Service (WPS), and Web Mapping Service (WMS). The visualization capability of integrating various measurements into cE extends dramatically the awareness and visibility of scientific results. Using embedded geographic information in the GE, the designed system improves our understanding of the relationships of different elements in a four dimensional domain. The system enables easy and convenient synergistic research on a virtual platform for professionals and the general public, gr$tly advancing global data sharing and scientific research collaboration.

Data visualization in interactive maps and time series

NASA Astrophysics Data System (ADS)

Maigne, Vanessa; Evano, Pascal; Brockmann, Patrick; Peylin, Philippe; Ciais, Philippe

2014-05-01

State-of-the-art data visualization has nothing to do with plots and maps we used few years ago. Many opensource tools are now available to provide access to scientific data and implement accessible, interactive, and flexible web applications. Here we will present a web site opened November 2013 to create custom global and regional maps and time series from research models and datasets. For maps, we explore and get access to data sources from a THREDDS Data Server (TDS) with the OGC WMS protocol (using the ncWMS implementation) then create interactive maps with the OpenLayers javascript library and extra information layers from a GeoServer. Maps become dynamic, zoomable, synchroneaously connected to each other, and exportable to Google Earth. For time series, we extract data from a TDS with the Netcdf Subset Service (NCSS) then display interactive graphs with a custom library based on the Data Driven Documents javascript library (D3.js). This time series application provides dynamic functionalities such as interpolation, interactive zoom on different axes, display of point values, and export to different formats. These tools were implemented for the Global Carbon Atlas (http://www.globalcarbonatlas.org): a web portal to explore, visualize, and interpret global and regional carbon fluxes from various model simulations arising from both human activities and natural processes, a work led by the Global Carbon Project.

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.

The Colima Volcano WebGIS: system acquisition, application and database development in an open-source environment

NASA Astrophysics Data System (ADS)

Manea, M.; Norini, G.; Capra, L.; Manea, V. C.

2009-04-01

The Colima Volcano is currently the most active Mexican volcano. After the 1913 plinian activity the volcano presented several eruptive phases that lasted few years, but since 1991 its activity became more persistent with vulcanian eruptions, lava and dome extrusions. During the last 15 years the volcano suffered several eruptive episodes as in 1991, 1994, 1998-1999, 2001-2003, 2004 and 2005 with the emplacement of pyroclastic flows. During rain seasons lahars are frequent affecting several infrastructures such as bridges and electric towers. Researchers from different institutions (Mexico, USA, Germany, Italy, and Spain) are currently working on several aspects of the volcano, from remote sensing, field data of old and recent deposits, structural framework, monitoring (rain, seismicity, deformation and visual observations) and laboratory experiments (analogue models and numerical simulations). Each investigation is focused to explain a single process, but it is fundamental to visualize the global status of the volcano in order to understand its behavior and to mitigate future hazards. The Colima Volcano WebGIS represents an initiative aimed to collect and store on a systematic basis all the data obtained so far for the volcano and to continuously update the database with new information. The Colima Volcano WebGIS is hosted on the Computational Geodynamics Laboratory web server and it is based entirely on Open Source software. The web pages, written in php/html will extract information from a mysql relational database, which will host the information needed for the MapBender application. There will be two types of intended users: 1) researchers working on the Colima Volcano, interested in this project and collaborating in common projects will be provided with open access to the database and will be able to introduce their own data, results, interpretation or recommendations; 2) general users, interested in accessing information on Colima Volcano will be provided with restricted access and will be able to visualize maps, images, diagrams, and current activity. The website can be visited at: http://www.geociencias.unam.mx/colima

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.

In an Age of Open Access to Research Policies: Physician and Public Health NGO Staff Research Use and Policy Awareness.

PubMed

Moorhead, Laura L; Holzmeyer, Cheryl; Maggio, Lauren A; Steinberg, Ryan M; Willinsky, John

2015-01-01

Through funding agency and publisher policies, an increasing proportion of the health sciences literature is being made open access. Such an increase in access raises questions about the awareness and potential utilization of this literature by those working in health fields. A sample of physicians (N=336) and public health non-governmental organization (NGO) staff (N=92) were provided with relatively complete access to the research literature indexed in PubMed, as well as access to the point-of-care service UpToDate, for up to one year, with their usage monitored through the tracking of web-log data. The physicians also participated in a one-month trial of relatively complete or limited access. The study found that participants' research interests were not satisfied by article abstracts alone nor, in the case of the physicians, by a clinical summary service such as UpToDate. On average, a third of the physicians viewed research a little more frequently than once a week, while two-thirds of the public health NGO staff viewed more than three articles a week. Those articles were published since the 2008 adoption of the NIH Public Access Policy, as well as prior to 2008 and during the maximum 12-month embargo period. A portion of the articles in each period was already open access, but complete access encouraged a viewing of more research articles. Those working in health fields will utilize more research in the course of their work as a result of (a) increasing open access to research, (b) improving awareness of and preparation for this access, and (c) adjusting public and open access policies to maximize the extent of potential access, through reduction in embargo periods and access to pre-policy literature.

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.

Open courses: one view of the future of online education.

PubMed

Alemi, Farrokh; Maddox, P J

2008-01-01

Open courses provide the entire course (lectures, assignments, syllabus, student's discussions, and student's projects) online without revealing student's personal information. We report on our experience in managing 8 open online courses at http://nhs.georgetown.edu/open. Open courses have several advantages over password protected courses: (1) they are available through search engines and thus reduce the program's marketing cost, (2) continuous feedback from the web enables rapid improvements to the course, (3) customer relationship tools, tied to open courses, radically reduce faculty time spent on one-on-one emails while increasing student/faculty interaction. We provide details of one course. In 15 weeks, 803 emails were received by and 1181 sent by the faculty (all within 6% of a working week and 82% savings of faculty time). We show how open courses can be accessed through search engines, how students questions are answered on the web and how student projects, in popular sites such as You Tube and Face Book, improve course marketing. The paper reports that student satisfaction with three open online courses delivered overall several semesters was high.

Open Access Could Transform Drug Discovery: A Case Study of JQ1.

PubMed

Arshad, Zeeshaan; Smith, James; Roberts, Mackenna; Lee, Wen Hwa; Davies, Ben; Bure, Kim; Hollander, Georg A; Dopson, Sue; Bountra, Chas; Brindley, David

2016-01-01

The cost to develop a new drug from target discovery to market is a staggering $1.8 billion, largely due to the very high attrition rate of drug candidates and the lengthy transition times during development. Open access is an emerging model of open innovation that places no restriction on the use of information and has the potential to accelerate the development of new drugs. To date, no quantitative assessment has yet taken place to determine the effects and viability of open access on the process of drug translation. This need is addressed within this study. The literature and intellectual property landscapes of the drug candidate JQ1, which was made available on an open access basis when discovered, and conventionally developed equivalents that were not are compared using the Web of Science and Thomson Innovation software, respectively. Results demonstrate that openly sharing the JQ1 molecule led to a greater uptake by a wider and more multi-disciplinary research community. A comparative analysis of the patent landscapes for each candidate also found that the broader scientific diaspora of the publically released JQ1 data enhanced innovation, evidenced by a greater number of downstream patents filed in relation to JQ1. The authors' findings counter the notion that open access drug discovery would leak commercial intellectual property. On the contrary, JQ1 serves as a test case to evidence that open access drug discovery can be an economic model that potentially improves efficiency and cost of drug discovery and its subsequent commercialization.

PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation

PubMed Central

Portales-Casamar, Elodie; Kirov, Stefan; Lim, Jonathan; Lithwick, Stuart; Swanson, Magdalena I; Ticoll, Amy; Snoddy, Jay; Wasserman, Wyeth W

2007-01-01

PAZAR is an open-access and open-source database of transcription factor and regulatory sequence annotation with associated web interface and programming tools for data submission and extraction. Curated boutique data collections can be maintained and disseminated through the unified schema of the mall-like PAZAR repository. The Pleiades Promoter Project collection of brain-linked regulatory sequences is introduced to demonstrate the depth of annotation possible within PAZAR. PAZAR, located at , is open for business. PMID:17916232

PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation.

PubMed

Portales-Casamar, Elodie; Kirov, Stefan; Lim, Jonathan; Lithwick, Stuart; Swanson, Magdalena I; Ticoll, Amy; Snoddy, Jay; Wasserman, Wyeth W

2007-01-01

PAZAR is an open-access and open-source database of transcription factor and regulatory sequence annotation with associated web interface and programming tools for data submission and extraction. Curated boutique data collections can be maintained and disseminated through the unified schema of the mall-like PAZAR repository. The Pleiades Promoter Project collection of brain-linked regulatory sequences is introduced to demonstrate the depth of annotation possible within PAZAR. PAZAR, located at http://www.pazar.info, is open for business.

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.

The DOI Is Coming.

ERIC Educational Resources Information Center

Scharf, Davida

2002-01-01

Discussion of improving accessibility to copyrighted electronic content focuses on the Digital Object Identifier (DOI) and the Open URL standard and linking software. Highlights include work of the World Wide Web consortium; URI (Uniform Resource Identifier); URL (Uniform Resource Locator); URN (Uniform Resource Name); OCLC's (Online Computer…

Restrictions impeding web-based courses: a survey of publishers' variation in authorising access to high quality on-line literature.

PubMed

Langlois, Michele; Heller, Richard F; Edwards, Richard; Lyratzopoulos, Georgios; Sandars, John

2004-04-07

Web-based delivery of educational programmes is becoming increasingly popular and is expected to expand, especially in medicine. The successful implementation of these programmes is reliant on their ability to provide access to web based materials, including high quality published work. Publishers' responses to requests to access health literature in the context of developing an electronic Master's degree course are described. Two different permission requests were submitted to publishers. The first was to store an electronic version of a journal article, to which we subscribe, on a secure password protected server. The second was to reproduce extracts of published material on password protected web pages and CD Rom. Eight of 16 publishers were willing to grant permission to store electronic versions of articles without levying charges additional to the subscription. Twenty of 35 publishers gave permission to reproduce extracts of published work at no fee. Publishers' responses were highly variable to the requests for access to published material. This may be influenced by vague terminology within the 'fair dealing' provision in the copyright legislation, which seems to leave it open to individual interpretation. Considerable resource costs were incurred by the exercise. Time expended included those incurred by us: research to identify informed representatives within the publishing organisation, request 'chase-ups' and alternative examples being sought if publishers were uncooperative; and the publisher when dealing with numerous permission requests. Financial costs were also incurred by both parties through additional staffing and paperwork generated by the permission process, the latter including those purely borne by educators due to the necessary provision of photocopy 'course packs' when no suitably alternative material could be found if publishers were uncooperative. Finally we discuss the resultant bias in material towards readily available electronic resources as a result of publisher's uncooperative stance and encourage initiatives that aim to improve open electronic access. The permission request process has been expensive and has resulted in reduced access for students to the relevant literature. Variations in the responses from publishers suggest that for educational purposes common policies could be agreed and unnecessary restrictions removed in the future.

Persistent Identifiers for Improved Accessibility for Linked Data Querying

NASA Astrophysics Data System (ADS)

Shepherd, A.; Chandler, C. L.; Arko, R. A.; Fils, D.; Jones, M. B.; Krisnadhi, A.; Mecum, B.

2016-12-01

The adoption of linked open data principles within the geosciences has increased the amount of accessible information available on the Web. However, this data is difficult to consume for those who are unfamiliar with Semantic Web technologies such as Web Ontology Language (OWL), Resource Description Framework (RDF) and SPARQL - the RDF query language. Consumers would need to understand the structure of the data and how to efficiently query it. Furthermore, understanding how to query doesn't solve problems of poor precision and recall in search results. For consumers unfamiliar with the data, full-text searches are most accessible, but not ideal as they arrest the advantages of data disambiguation and co-reference resolution efforts. Conversely, URI searches across linked data can deliver improved search results, but knowledge of these exact URIs may remain difficult to obtain. The increased adoption of Persistent Identifiers (PIDs) can lead to improved linked data querying by a wide variety of consumers. Because PIDs resolve to a single entity, they are an excellent data point for disambiguating content. At the same time, PIDs are more accessible and prominent than a single data provider's linked data URI. When present in linked open datasets, PIDs provide balance between the technical and social hurdles of linked data querying as evidenced by the NSF EarthCube GeoLink project. The GeoLink project, funded by NSF's EarthCube initiative, have brought together data repositories include content from field expeditions, laboratory analyses, journal publications, conference presentations, theses/reports, and funding awards that span scientific studies from marine geology to marine ecosystems and biogeochemistry to paleoclimatology.

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.

Detection and Monitoring of Improvised Explosive Device Education Networks through the World Wide Web

DTIC Science & Technology

2009-06-01

search engines are not up to this task, as they have been optimized to catalog information quickly and efficiently for user ease of access while promoting retail commerce at the same time. This thesis presents a performance analysis of a new search engine algorithm designed to help find IED education networks using the Nutch open-source search engine architecture. It reveals which web pages are more important via references from other web pages regardless of domain. In addition, this thesis discusses potential evaluation and monitoring techniques to be used in conjunction

OpenFDA: an innovative platform providing access to a wealth of FDA's publicly available data.

PubMed

Kass-Hout, Taha A; Xu, Zhiheng; Mohebbi, Matthew; Nelsen, Hans; Baker, Adam; Levine, Jonathan; Johanson, Elaine; Bright, Roselie A

2016-05-01

The objective of openFDA is to facilitate access and use of big important Food and Drug Administration public datasets by developers, researchers, and the public through harmonization of data across disparate FDA datasets provided via application programming interfaces (APIs). Using cutting-edge technologies deployed on FDA's new public cloud computing infrastructure, openFDA provides open data for easier, faster (over 300 requests per second per process), and better access to FDA datasets; open source code and documentation shared on GitHub for open community contributions of examples, apps and ideas; and infrastructure that can be adopted for other public health big data challenges. Since its launch on June 2, 2014, openFDA has developed four APIs for drug and device adverse events, recall information for all FDA-regulated products, and drug labeling. There have been more than 20 million API calls (more than half from outside the United States), 6000 registered users, 20,000 connected Internet Protocol addresses, and dozens of new software (mobile or web) apps developed. A case study demonstrates a use of openFDA data to understand an apparent association of a drug with an adverse event. With easier and faster access to these datasets, consumers worldwide can learn more about FDA-regulated products. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved.

OpenFDA: an innovative platform providing access to a wealth of FDA’s publicly available data

PubMed Central

Kass-Hout, Taha A; Mohebbi, Matthew; Nelsen, Hans; Baker, Adam; Levine, Jonathan; Johanson, Elaine; Bright, Roselie A

2016-01-01

Objective The objective of openFDA is to facilitate access and use of big important Food and Drug Administration public datasets by developers, researchers, and the public through harmonization of data across disparate FDA datasets provided via application programming interfaces (APIs). Materials and Methods Using cutting-edge technologies deployed on FDA’s new public cloud computing infrastructure, openFDA provides open data for easier, faster (over 300 requests per second per process), and better access to FDA datasets; open source code and documentation shared on GitHub for open community contributions of examples, apps and ideas; and infrastructure that can be adopted for other public health big data challenges. Results Since its launch on June 2, 2014, openFDA has developed four APIs for drug and device adverse events, recall information for all FDA-regulated products, and drug labeling. There have been more than 20 million API calls (more than half from outside the United States), 6000 registered users, 20,000 connected Internet Protocol addresses, and dozens of new software (mobile or web) apps developed. A case study demonstrates a use of openFDA data to understand an apparent association of a drug with an adverse event. Conclusion With easier and faster access to these datasets, consumers worldwide can learn more about FDA-regulated products. PMID:26644398

Connecting geoscience systems and data using Linked Open Data in the Web of Data

NASA Astrophysics Data System (ADS)

Ritschel, Bernd; Neher, Günther; Iyemori, Toshihiko; Koyama, Yukinobu; Yatagai, Akiyo; Murayama, Yasuhiro; Galkin, Ivan; King, Todd; Fung, Shing F.; Hughes, Steve; Habermann, Ted; Hapgood, Mike; Belehaki, Anna

2014-05-01

Linked Data or Linked Open Data (LOD) in the realm of free and publically accessible data is one of the most promising and most used semantic Web frameworks connecting various types of data and vocabularies including geoscience and related domains. The semantic Web extension to the commonly existing and used World Wide Web is based on the meaning of entities and relationships or in different words classes and properties used for data in a global data and information space, the Web of Data. LOD data is referenced and mash-uped by URIs and is retrievable using simple parameter controlled HTTP-requests leading to a result which is human-understandable or machine-readable. Furthermore the publishing and mash-up of data in the semantic Web realm is realized by specific Web standards, such as RDF, RDFS, OWL and SPARQL defined for the Web of Data. Semantic Web based mash-up is the Web method to aggregate and reuse various contents from different sources, such as e.g. using FOAF as a model and vocabulary for the description of persons and organizations -in our case- related to geoscience projects, instruments, observations, data and so on. On the example of three different geoscience data and information management systems, such as ESPAS, IUGONET and GFZ ISDC and the associated science data and related metadata or better called context data, the concept of the mash-up of systems and data using the semantic Web approach and the Linked Open Data framework is described in this publication. Because the three systems are based on different data models, data storage structures and technical implementations an extra semantic Web layer upon the existing interfaces is used for mash-up solutions. In order to satisfy the semantic Web standards, data transition processes, such as the transfer of content stored in relational databases or mapped in XML documents into SPARQL capable databases or endpoints using D2R or XSLT is necessary. In addition, the use of mapped and/or merged domain specific and cross-domain vocabularies in the sense of terminological ontologies are the foundation for a virtually unified data retrieval and access in IUGONET, ESPAS and GFZ ISDC data management systems. SPARQL endpoints realized either by originally RDF databases, e.g. Virtuoso or by virtual SPARQL endpoints, e.g. D2R services enable an only upon Web standard-based mash-up of domain-specific systems and data, such as in this case the space weather and geomagnetic domain but also cross-domain connection to data and vocabularies, e.g. related to NASA's VxOs, particularly VWO or NASA's PDS data system within LOD. LOD - Linked Open Data RDF - Resource Description Framework RDFS - RDF Schema OWL - Ontology Web Language SPARQL - SPARQL Protocol and RDF Query Language FOAF - Friends of a Friend ontology ESPAS - Near Earth Space Data Infrastructure for e-Science (Project) IUGONET - Inter-university Upper Atmosphere Global Observation Network (Project) GFZ ISDC - German Research Centre for Geosciences Information System and Data Center XML - Extensible Mark-up Language D2R - (Relational) Database to RDF (Transformation) XSLT - Extensible Stylesheet Language Transformation Virtuoso - OpenLink Virtuoso Universal Server (including RDF data management) NASA - National Aeronautics and Space Administration VOx - Virtual Observatories VWO - Virtual Wave Observatory PDS - Planetary Data System

Harmonizing the Interests of Free Speech, Obscenity and Child Pornography on Cyberspace: The New Roles of Parents, Technology and Legislation for Internet Safety

ERIC Educational Resources Information Center

Olagunju, Amos O.

2008-01-01

Incorrect access to Web site addresses and spam e-mails are continuing to make pornography rampant on the Internet at schools, homes and libraries. Collectively, parents, teachers and members of communities must become more aware of the risks and consequences of open access to the Internet, and the distinction between censorship and Internet…

Secure Web-based Ground System User Interfaces over the Open Internet

NASA Technical Reports Server (NTRS)

Langston, James H.; Murray, Henry L.; Hunt, Gary R.

1998-01-01

A prototype has been developed which makes use of commercially available products in conjunction with the Java programming language to provide a secure user interface for command and control over the open Internet. This paper reports successful demonstration of: (1) Security over the Internet, including encryption and certification; (2) Integration of Java applets with a COTS command and control product; (3) Remote spacecraft commanding using the Internet. The Java-based Spacecraft Web Interface to Telemetry and Command Handling (Jswitch) ground system prototype provides these capabilities. This activity demonstrates the use and integration of current technologies to enable a spacecraft engineer or flight operator to monitor and control a spacecraft from a user interface communicating over the open Internet using standard World Wide Web (WWW) protocols and commercial off-the-shelf (COTS) products. The core command and control functions are provided by the COTS Epoch 2000 product. The standard WWW tools and browsers are used in conjunction with the Java programming technology. Security is provided with the current encryption and certification technology. This system prototype is a step in the direction of giving scientist and flight operators Web-based access to instrument, payload, and spacecraft data.

NASA SensorWeb and OGC Standards for Disaster Management

NASA Technical Reports Server (NTRS)

Mandl, Dan

2010-01-01

I. Goal: Enable user to cost-effectively find and create customized data products to help manage disasters; a) On-demand; b) Low cost and non-specialized tools such as Google Earth and browsers; c) Access via open network but with sufficient security. II. Use standards to interface various sensors and resultant data: a) Wrap sensors in Open Geospatial Consortium (OGC) standards; b) Wrap data processing algorithms and servers with OGC standards c) Use standardized workflows to orchestrate and script the creation of these data; products. III. Target Web 2.0 mass market: a) Make it simple and easy to use; b) Leverage new capabilities and tools that are emerging; c) Improve speed and responsiveness.

PIQMIe: a web server for semi-quantitative proteomics data management and analysis

PubMed Central

Kuzniar, Arnold; Kanaar, Roland

2014-01-01

We present the Proteomics Identifications and Quantitations Data Management and Integration Service or PIQMIe that aids in reliable and scalable data management, analysis and visualization of semi-quantitative mass spectrometry based proteomics experiments. PIQMIe readily integrates peptide and (non-redundant) protein identifications and quantitations from multiple experiments with additional biological information on the protein entries, and makes the linked data available in the form of a light-weight relational database, which enables dedicated data analyses (e.g. in R) and user-driven queries. Using the web interface, users are presented with a concise summary of their proteomics experiments in numerical and graphical forms, as well as with a searchable protein grid and interactive visualization tools to aid in the rapid assessment of the experiments and in the identification of proteins of interest. The web server not only provides data access through a web interface but also supports programmatic access through RESTful web service. The web server is available at http://piqmie.semiqprot-emc.cloudlet.sara.nl or http://www.bioinformatics.nl/piqmie. This website is free and open to all users and there is no login requirement. PMID:24861615

PIQMIe: a web server for semi-quantitative proteomics data management and analysis.

PubMed

Kuzniar, Arnold; Kanaar, Roland

2014-07-01

We present the Proteomics Identifications and Quantitations Data Management and Integration Service or PIQMIe that aids in reliable and scalable data management, analysis and visualization of semi-quantitative mass spectrometry based proteomics experiments. PIQMIe readily integrates peptide and (non-redundant) protein identifications and quantitations from multiple experiments with additional biological information on the protein entries, and makes the linked data available in the form of a light-weight relational database, which enables dedicated data analyses (e.g. in R) and user-driven queries. Using the web interface, users are presented with a concise summary of their proteomics experiments in numerical and graphical forms, as well as with a searchable protein grid and interactive visualization tools to aid in the rapid assessment of the experiments and in the identification of proteins of interest. The web server not only provides data access through a web interface but also supports programmatic access through RESTful web service. The web server is available at http://piqmie.semiqprot-emc.cloudlet.sara.nl or http://www.bioinformatics.nl/piqmie. This website is free and open to all users and there is no login requirement. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

A Security Architecture for Grid-enabling OGC Web Services

NASA Astrophysics Data System (ADS)

Angelini, Valerio; Petronzio, Luca

2010-05-01

In the proposed presentation we describe an architectural solution for enabling a secure access to Grids and possibly other large scale on-demand processing infrastructures through OGC (Open Geospatial Consortium) Web Services (OWS). This work has been carried out in the context of the security thread of the G-OWS Working Group. G-OWS (gLite enablement of OGC Web Services) is an international open initiative started in 2008 by the European CYCLOPS , GENESI-DR, and DORII Project Consortia in order to collect/coordinate experiences in the enablement of OWS's on top of the gLite Grid middleware. G-OWS investigates the problem of the development of Spatial Data and Information Infrastructures (SDI and SII) based on the Grid/Cloud capacity in order to enable Earth Science applications and tools. Concerning security issues, the integration of OWS compliant infrastructures and gLite Grids needs to address relevant challenges, due to their respective design principles. In fact OWS's are part of a Web based architecture that demands security aspects to other specifications, whereas the gLite middleware implements the Grid paradigm with a strong security model (the gLite Grid Security Infrastructure: GSI). In our work we propose a Security Architectural Framework allowing the seamless use of Grid-enabled OGC Web Services through the federation of existing security systems (mostly web based) with the gLite GSI. This is made possible mediating between different security realms, whose mutual trust is established in advance during the deployment of the system itself. Our architecture is composed of three different security tiers: the user's security system, a specific G-OWS security system, and the gLite Grid Security Infrastructure. Applying the separation-of-concerns principle, each of these tiers is responsible for controlling the access to a well-defined resource set, respectively: the user's organization resources, the geospatial resources and services, and the Grid resources. While the gLite middleware is tied to a consolidated security approach based on X.509 certificates, our system is able to support different kinds of user's security infrastructures. Our central component, the G-OWS Security Framework, is based on the OASIS WS-Trust specifications and on the OGC GeoRM architectural framework. This allows to satisfy advanced requirements such as the enforcement of specific geospatial policies and complex secure web service chained requests. The typical use case is represented by a scientist belonging to a given organization who issues a request to a G-OWS Grid-enabled Web Service. The system initially asks the user to authenticate to his/her organization's security system and, after verification of the user's security credentials, it translates the user's digital identity into a G-OWS identity. This identity is linked to a set of attributes describing the user's access rights to the G-OWS services and resources. Inside the G-OWS Security system, access restrictions are applied making use of the enhanced Geospatial capabilities specified by the OGC GeoXACML. If the required action needs to make use of the Grid environment the system checks if the user is entitled to access a Grid infrastructure. In that case his/her identity is translated to a temporary Grid security token using the Short Lived Credential Services (IGTF Standard). In our case, for the specific gLite Grid infrastructure, some information (VOMS Attributes) is plugged into the Grid Security Token to grant the access to the user's Virtual Organization Grid resources. The resulting token is used to submit the request to the Grid and also by the various gLite middleware elements to verify the user's grants. Basing on the presented framework, the G-OWS Security Working Group developed a prototype, enabling the execution of OGC Web Services on the EGEE Production Grid through the federation with a Shibboleth based security infrastructure. Future plans aim to integrate other Web authentication services such as OpenID, Kerberos and WS-Federation.

Hydrocarbon Spectral Database

National Institute of Standards and Technology Data Gateway

SRD 115 Hydrocarbon Spectral Database (Web, free access)   All of the rotational spectral lines observed and reported in the open literature for 91 hydrocarbon molecules have been tabulated. The isotopic molecular species, assigned quantum numbers, observed frequency, estimated measurement uncertainty and reference are given for each transition reported.

Diatomic Spectral Database

National Institute of Standards and Technology Data Gateway

SRD 114 Diatomic Spectral Database (Web, free access)   All of the rotational spectral lines observed and reported in the open literature for 121 diatomic molecules have been tabulated. The isotopic molecular species, assigned quantum numbers, observed frequency, estimated measurement uncertainty, and reference are given for each transition reported.

Triatomic Spectral Database

National Institute of Standards and Technology Data Gateway

SRD 117 Triatomic Spectral Database (Web, free access)   All of the rotational spectral lines observed and reported in the open literature for 55 triatomic molecules have been tabulated. The isotopic molecular species, assigned quantum numbers, observed frequency, estimated measurement uncertainty and reference are given for each transition reported.

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.

Macroscopic characterisations of Web accessibility

NASA Astrophysics Data System (ADS)

Lopes, Rui; Carriço, Luis

2010-12-01

The Web Science framework poses fundamental questions on the analysis of the Web, by focusing on how microscopic properties (e.g. at the level of a Web page or Web site) emerge into macroscopic properties and phenomena. One research topic on the analysis of the Web is Web accessibility evaluation, which centres on understanding how accessible a Web page is for people with disabilities. However, when framing Web accessibility evaluation on Web Science, we have found that existing research stays at the microscopic level. This article presents an experimental study on framing Web accessibility evaluation into Web Science's goals. This study resulted in novel accessibility properties of the Web not found at microscopic levels, as well as of Web accessibility evaluation processes themselves. We observed at large scale some of the empirical knowledge on how accessibility is perceived by designers and developers, such as the disparity of interpretations of accessibility evaluation tools warnings. We also found a direct relation between accessibility quality and Web page complexity. We provide a set of guidelines for designing Web pages, education on Web accessibility, as well as on the computational limits of large-scale Web accessibility evaluations.

ZeBase: an open-source relational database for zebrafish laboratories.

PubMed

Hensley, Monica R; Hassenplug, Eric; McPhail, Rodney; Leung, Yuk Fai

2012-03-01

Abstract ZeBase is an open-source relational database for zebrafish inventory. It is designed for the recording of genetic, breeding, and survival information of fish lines maintained in a single- or multi-laboratory environment. Users can easily access ZeBase through standard web-browsers anywhere on a network. Convenient search and reporting functions are available to facilitate routine inventory work; such functions can also be automated by simple scripting. Optional barcode generation and scanning are also built-in for easy access to the information related to any fish. Further information of the database and an example implementation can be found at http://zebase.bio.purdue.edu.

Open access behaviours and perceptions of health sciences faculty and roles of information professionals.

PubMed

Lwoga, Edda T; Questier, Frederik

2015-03-01

This study sought to investigate the faculty's awareness, attitudes and use of open access, and the role of information professionals in supporting open access (OA) scholarly communication in Tanzanian health sciences universities. A cross-sectional survey was conducted. Semi-structured interviews were conducted with 16 librarians, while questionnaires were physically distributed to 415 faculty members in all eight Tanzanian health sciences universities, with a response rate of 71.1%. The study found that most faculty members were aware about OA issues. However, the high level of OA awareness among faculty members did not translate into actual dissemination of faculty's research outputs through OA web avenues. A small proportion of faculty's research materials was made available as OA. Faculty were more engaged with OA journal publishing than with self-archiving practices. Senior faculty with proficient technical skills were more likely to use open access than junior faculty. Major barriers to OA usage were related to ICT infrastructure, awareness, skills, author-pay model, and copyright and plagiarism concerns. Interviews with librarians revealed that there was a strong support for promoting OA issues on campus; however, this positive support with various open access-related tasks did not translate into actual action. It is thus important for librarians and OA administrators to consider all these factors for effective implementation of OA projects in research and academic institutions. This is the first comprehensive and detailed study focusing on the health sciences faculty's and librarians' behaviours and perceptions of open access initiatives in Tanzania and reveals findings that are useful for planning and implementing open access initiatives in other institutions with similar conditions. © 2015 Health Libraries Journal.

Enabling Web-Based GIS Tools for Internet and Mobile Devices To Improve and Expand NASA Data Accessibility and Analysis Functionality for the Renewable Energy and Agricultural Applications

NASA Astrophysics Data System (ADS)

Ross, A.; Stackhouse, P. W.; Tisdale, B.; Tisdale, M.; Chandler, W.; Hoell, J. M., Jr.; Kusterer, J.

2014-12-01

The NASA Langley Research Center Science Directorate and Atmospheric Science Data Center have initiated a pilot program to utilize Geographic Information System (GIS) tools that enable, generate and store climatological averages using spatial queries and calculations in a spatial database resulting in greater accessibility of data for government agencies, industry and private sector individuals. The major objectives of this effort include the 1) Processing and reformulation of current data to be consistent with ESRI and openGIS tools, 2) Develop functions to improve capability and analysis that produce "on-the-fly" data products, extending these past the single location to regional and global scales. 3) Update the current web sites to enable both web-based and mobile application displays for optimization on mobile platforms, 4) Interact with user communities in government and industry to test formats and usage of optimization, and 5) develop a series of metrics that allow for monitoring of progressive performance. Significant project results will include the the development of Open Geospatial Consortium (OGC) compliant web services (WMS, WCS, WFS, WPS) that serve renewable energy and agricultural application products to users using GIS software and tools. Each data product and OGC service will be registered within ECHO, the Common Metadata Repository, the Geospatial Platform, and Data.gov to ensure the data are easily discoverable and provide data users with enhanced access to SSE data, parameters, services, and applications. This effort supports cross agency, cross organization, and interoperability of SSE data products and services by collaborating with DOI, NRCan, NREL, NCAR, and HOMER for requirements vetting and test bed users before making available to the wider public.

The Creative task Creator: a tool for the generation of customized, Web-based creativity tasks.

PubMed

Pretz, Jean E; Link, John A

2008-11-01

This article presents a Web-based tool for the creation of divergent-thinking and open-ended creativity tasks. A Java program generates HTML forms with PHP scripting that run an Alternate Uses Task and/or open-ended response items. Researchers may specify their own instructions, objects, and time limits, or use default settings. Participants can also be prompted to select their best responses to the Alternate Uses Task (Silvia et al., 2008). Minimal programming knowledge is required. The program runs on any server, and responses are recorded in a standard MySQL database. Responses can be scored using the consensual assessment technique (Amabile, 1996) or Torrance's (1998) traditional scoring method. Adoption of this Web-based tool should facilitate creativity research across cultures and access to eminent creators. The Creative Task Creator may be downloaded from the Psychonomic Society's Archive of Norms, Stimuli, and Data, www.psychonomic.org/archive.

ABrowse--a customizable next-generation genome browser framework.

PubMed

Kong, Lei; Wang, Jun; Zhao, Shuqi; Gu, Xiaocheng; Luo, Jingchu; Gao, Ge

2012-01-05

With the rapid growth of genome sequencing projects, genome browser is becoming indispensable, not only as a visualization system but also as an interactive platform to support open data access and collaborative work. Thus a customizable genome browser framework with rich functions and flexible configuration is needed to facilitate various genome research projects. Based on next-generation web technologies, we have developed a general-purpose genome browser framework ABrowse which provides interactive browsing experience, open data access and collaborative work support. By supporting Google-map-like smooth navigation, ABrowse offers end users highly interactive browsing experience. To facilitate further data analysis, multiple data access approaches are supported for external platforms to retrieve data from ABrowse. To promote collaborative work, an online user-space is provided for end users to create, store and share comments, annotations and landmarks. For data providers, ABrowse is highly customizable and configurable. The framework provides a set of utilities to import annotation data conveniently. To build ABrowse on existing annotation databases, data providers could specify SQL statements according to database schema. And customized pages for detailed information display of annotation entries could be easily plugged in. For developers, new drawing strategies could be integrated into ABrowse for new types of annotation data. In addition, standard web service is provided for data retrieval remotely, providing underlying machine-oriented programming interface for open data access. ABrowse framework is valuable for end users, data providers and developers by providing rich user functions and flexible customization approaches. The source code is published under GNU Lesser General Public License v3.0 and is accessible at http://www.abrowse.org/. To demonstrate all the features of ABrowse, a live demo for Arabidopsis thaliana genome has been built at http://arabidopsis.cbi.edu.cn/.

Towards a virtual hub approach for landscape assessment and multimedia ecomuseum using multitemporal-maps

NASA Astrophysics Data System (ADS)

Brumana, R.; Santana Quintero, M.; Barazzetti, L.; Previtali, M.; Banfi, F.; Oreni, D.; Roels, D.; Roncoroni, F.

2015-08-01

Landscapes are dynamic entities, stretching and transforming across space and time, and need to be safeguarded as living places for the future, with interaction of human, social and economic dimensions. To have a comprehensive landscape evaluation several open data are needed, each one characterized by its own protocol, service interface, limiting or impeding this way interoperability and their integration. Indeed, nowadays the development of websites targeted to landscape assessment and touristic purposes requires many resources in terms of time, cost and IT skills to be implemented at different scales. For this reason these applications are limited to few cases mainly focusing on worldwide known touristic sites. The capability to spread the development of web-based multimedia virtual museum based on geospatial data relies for the future being on the possibility to discover the needed geo-spatial data through a single point of access in an homogenous way. In this paper the proposed innovative approach may facilitate the access to open data in a homogeneous way by means of specific components (the brokers) performing interoperability actions required to interconnect heterogeneous data sources. In the specific case study here analysed it has been implemented an interface to migrate a geo-swat chart based on local and regional geographic information into an user friendly Google Earth©-based infrastructure, integrating ancient cadastres and modern cartography, accessible by professionals and tourists via web and also via portable devices like tables and smartphones. The general aim of this work on the case study on the Lake of Como (Tremezzina municipality), is to boost the integration of assessment methodologies with digital geo-based technologies of map correlation for the multimedia ecomuseum system accessible via web. The developed WebGIS system integrates multi-scale and multi-temporal maps with different information (cultural, historical, landscape levels) represented by thematic icons allowing to transfer the richness of the landscape value to both tourists and professionals.

Sensor Webs in Digital Earth

NASA Astrophysics Data System (ADS)

Heavner, M. J.; Fatland, D. R.; Moeller, H.; Hood, E.; Schultz, M.

2007-12-01

The University of Alaska Southeast is currently implementing a sensor web identified as the SouthEast Alaska MOnitoring Network for Science, Telecommunications, Education, and Research (SEAMONSTER). From power systems and instrumentation through data management, visualization, education, and public outreach, SEAMONSTER is designed with modularity in mind. We are utilizing virtual earth infrastructures to enhance both sensor web management and data access. We will describe how the design philosophy of using open, modular components contributes to the exploration of different virtual earth environments. We will also describe the sensor web physical implementation and how the many components have corresponding virtual earth representations. This presentation will provide an example of the integration of sensor webs into a virtual earth. We suggest that IPY sensor networks and sensor webs may integrate into virtual earth systems and provide an IPY legacy easily accessible to both scientists and the public. SEAMONSTER utilizes geobrowsers for education and public outreach, sensor web management, data dissemination, and enabling collaboration. We generate near-real-time auto-updating geobrowser files of the data. In this presentation we will describe how we have implemented these technologies to date, the lessons learned, and our efforts towards greater OGC standard implementation. A major focus will be on demonstrating how geobrowsers have made this project possible.

77 FR 46444 - Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-03

... meeting by accessing the SAMHSA Committee Web site, http://nac.samhsa.gov/ , or by contacting Crystal C... Services National Advisory Council. Date/Time/Type: August 16, 2012, 8:30-5:00 (OPEN). Place: Live meeting webcast. Contact: Crystal C. Saunders, Acting Designated Federal Official, SAMHSA, Center for Mental...

Chemical Mahjong

ERIC Educational Resources Information Center

Cossairt, Travis J.; Grubbs, W. Tandy

2011-01-01

An open-access, Web-based mnemonic game is described whereby introductory chemistry knowledge is tested using mahjong solitaire game play. Several tile sets and board layouts are included that are themed upon different chemical topics. Introductory tile sets can be selected that prompt the player to match element names to symbols and metric…

Investigation Of Integrating Three-Dimensional (3-D) Geometry Into The Visual Anatomical Injury Descriptor (Visual AID) Using WebGL

DTIC Science & Technology

2011-08-01

generated using the Zygote Human Anatomy 3-D model (3). Use of a reference anatomy independent of personal identification, such as Zygote, allows Visual...Zygote Human Anatomy 3D Model, 2010. http://www.zygote.com/ (accessed July 26, 2011). 4. Khronos Group Web site. Khronos to Create New Open Standard for...understanding of the information at hand. In order to fulfill the medical illustration track, I completed a concentration in science, focusing on human

Tactical Web Services: Using XML and Java Web Services to Conduct Real-Time Net-Centric Sonar Visualization

DTIC Science & Technology

2004-09-01

Rosetti USN U.S. Navy Chesterton, IN 6. Erik Chaum NUWC Newport, RI 7. David Bellino NPRI Newport, RI 8. Dick Nadolink NUWC Newport, RI...found at (http://www.parallelgraphics.com/products/cortona). G. JFREECHART JFreeChart is an open source Java API created by David Gilbert and...www.xj3d.org/. Accessed 3 September 2004. Hunter, David , Kurt Cagle, and Chris Dix, eds. Beginning XML, Second Edition. Indianapolis, IN

Brave New World: Data Intensive Science with SDSS and the VO

NASA Astrophysics Data System (ADS)

Thakar, A. R.; Szalay, A. S.; O'Mullane, W.; Nieto-Santisteban, M.; Budavari, T.; Li, N.; Carliles, S.; Haridas, V.; Malik, T.; Gray, J.

2004-12-01

With the advent of digital archives and the VO, astronomy is quickly changing from a data-hungry to a data-intensive science. Local and specialized access to data will remain the most direct and efficient way to get data out of individual archives, especially if you know what you are looking for. However, the enormous sizes of the upcoming archives will preclude this type of access for most institutions, and will not allow researchers to tap the vast potential for discovery in cross-matching and comparing data between different archives. The VO makes this type of interoperability and distributed data access possible by adopting industry standards for data access (SQL) and data interchange (SOAP/XML) with platform independence (Web services). As a sneak preview of this brave new world where astronomers may need to become SQL warriors, we present a look at VO-enabled access to catalog data in the SDSS Catalog Archive Server (CAS): CasJobs - a workbench environment that allows arbitrarily complex SQL queries and your own personal database (MyDB) that you can share with collaborators; OpenSkyQuery - an IVOA (International Virtual Observatory Alliance) compliant federation of multiple archives (OpenSkyNodes) that currently links nearly 20 catalogs and allows cross-match queries (in ADQL - Astronomical Data Query Language) between them; Spectrum and Filter Profile Web services that provide access to an open database of spectra (registered users may add their own spectra); and VO-enabled Mirage - a Java visualizatiion tool developed at Bell Labs and enhanced at JHU that allows side-by-side comparison of SDSS catalog and FITS image data. Anticipating the next generation of Petabyte archives like LSST by the end of the decade, we are developing a parallel cross-match engine for all-sky cross-matches between large surveys, along with a 100-Terabyte data intensive science laboratory with high-speed parallel data access.

elevatr: Access Elevation Data from Various APIs | Science ...

EPA Pesticide Factsheets

Several web services are available that provide access to elevation data. This package provides access to several of those services and returns elevation data either as a SpatialPointsDataFrame from point elevation services or as a raster object from raster elevation services. Currently, the package supports access to the Mapzen Elevation Service, Mapzen Terrain Service, and the USGS Elevation Point Query Service. The R language for statistical computing is increasingly used for spatial data analysis . This R package, elevatr, is in response to this and provides access to elevation data from various sources directly in R. The impact of `elevatr` is that it will 1) facilitate spatial analysis in R by providing access to foundational dataset for many types of analyses (e.g. hydrology, limnology) 2) open up a new set of users and uses for APIs widely used outside of R, and 3) provide an excellent example federal open source development as promoted by the Federal Source Code Policy (https://sourcecode.cio.gov/).

Weaving a knowledge network for Deep Carbon Science

NASA Astrophysics Data System (ADS)

Ma, Xiaogang; West, Patrick; Zednik, Stephan; Erickson, John; Eleish, Ahmed; Chen, Yu; Wang, Han; Zhong, Hao; Fox, Peter

2017-05-01

Geoscience researchers are increasingly dependent on informatics and the Web to conduct their research. Geoscience is one of the first domains that take lead in initiatives such as open data, open code, open access, and open collections, which comprise key topics of Open Science in academia. The meaning of being open can be understood at two levels. The lower level is to make data, code, sample collections and publications, etc. freely accessible online and allow reuse, modification and sharing. The higher level is the annotation and connection between those resources to establish a network for collaborative scientific research. In the data science component of the Deep Carbon Observatory (DCO), we have leveraged state-of-the-art information technologies and existing online resources to deploy a web portal for the over 1000 researchers in the DCO community. An initial aim of the portal is to keep track of all research and outputs related to the DCO community. Further, we intend for the portal to establish a knowledge network, which supports various stages of an open scientific process within and beyond the DCO community. Annotation and linking are the key characteristics of the knowledge network. Not only are key assets, including DCO data and methods, published in an open and inter-linked fashion, but the people, organizations, groups, grants, projects, samples, field sites, instruments, software programs, activities, meetings, etc. are recorded and connected to each other through relationships based on well-defined, formal conceptual models. The network promotes collaboration among DCO participants, improves the openness and reproducibility of carbon-related research, facilitates accreditation to resource contributors, and eventually stimulates new ideas and findings in deep carbon-related studies.

Recent advances in the Lesser Antilles observatories Part 2 : WebObs - an integrated web-based system for monitoring and networks management

NASA Astrophysics Data System (ADS)

Beauducel, François; Bosson, Alexis; Randriamora, Frédéric; Anténor-Habazac, Christian; Lemarchand, Arnaud; Saurel, Jean-Marie; Nercessian, Alexandre; Bouin, Marie-Paule; de Chabalier, Jean-Bernard; Clouard, Valérie

2010-05-01

Seismological and Volcanological observatories have common needs and often common practical problems for multi disciplinary data monitoring applications. In fact, access to integrated data in real-time and estimation of measurements uncertainties are keys for an efficient interpretation, but instruments variety, heterogeneity of data sampling and acquisition systems lead to difficulties that may hinder crisis management. In Guadeloupe observatory, we have developed in the last years an operational system that attempts to answer the questions in the context of a pluri-instrumental observatory. Based on a single computer server, open source scripts (Matlab, Perl, Bash, Nagios) and a Web interface, the system proposes: an extended database for networks management, stations and sensors (maps, station file with log history, technical characteristics, meta-data, photos and associated documents); a web-form interfaces for manual data input/editing and export (like geochemical analysis, some of the deformation measurements, ...); routine data processing with dedicated automatic scripts for each technique, production of validated data outputs, static graphs on preset moving time intervals, and possible e-mail alarms; computers, acquisition processes, stations and individual sensors status automatic check with simple criteria (files update and signal quality), displayed as synthetic pages for technical control. In the special case of seismology, WebObs includes a digital stripchart multichannel continuous seismogram associated with EarthWorm acquisition chain (see companion paper Part 1), event classification database, location scripts, automatic shakemaps and regional catalog with associated hypocenter maps accessed through a user request form. This system leads to a real-time Internet access for integrated monitoring and becomes a strong support for scientists and technicians exchange, and is widely open to interdisciplinary real-time modeling. It has been set up at Martinique observatory and installation is planned this year at Montserrat Volcanological Observatory. It also in production at the geomagnetic observatory of Addis Abeba in Ethiopia.

How NASA's Atmospheric Science Data Center (ASDC) is operationally using the Esri ArcGIS Platform to improve data discoverability, accessibility and interoperability to meet the diversifying government, private, public and academic communities' driven requirements.

NASA Astrophysics Data System (ADS)

Tisdale, M.

2016-12-01

NASA's Atmospheric Science Data Center (ASDC) is operationally using the Esri ArcGIS Platform to improve data discoverability, accessibility and interoperability to meet the diversifying government, private, public and academic communities' driven requirements. The ASDC is actively working to provide their mission essential datasets as ArcGIS Image Services, Open Geospatial Consortium (OGC) Web Mapping Services (WMS), OGC Web Coverage Services (WCS) and leveraging the ArcGIS multidimensional mosaic dataset structure. Science teams and ASDC are utilizing these services, developing applications using the Web AppBuilder for ArcGIS and ArcGIS API for Javascript, and evaluating restructuring their data production and access scripts within the ArcGIS Python Toolbox framework and Geoprocessing service environment. These capabilities yield a greater usage and exposure of ASDC data holdings and provide improved geospatial analytical tools for a mission critical understanding in the areas of the earth's radiation budget, clouds, aerosols, and tropospheric chemistry.

Technical Note: Harmonizing met-ocean model data via standard web services within small research groups

USGS Publications Warehouse

Signell, Richard; Camossi, E.

2016-01-01

Work over the last decade has resulted in standardised web services and tools that can significantly improve the efficiency and effectiveness of working with meteorological and ocean model data. While many operational modelling centres have enabled query and access to data via common web services, most small research groups have not. The penetration of this approach into the research community, where IT resources are limited, can be dramatically improved by (1) making it simple for providers to enable web service access to existing output files; (2) using free technologies that are easy to deploy and configure; and (3) providing standardised, service-based tools that work in existing research environments. We present a simple, local brokering approach that lets modellers continue to use their existing files and tools, while serving virtual data sets that can be used with standardised tools. The goal of this paper is to convince modellers that a standardised framework is not only useful but can be implemented with modest effort using free software components. We use NetCDF Markup language for data aggregation and standardisation, the THREDDS Data Server for data delivery, pycsw for data search, NCTOOLBOX (MATLAB®) and Iris (Python) for data access, and Open Geospatial Consortium Web Map Service for data preview. We illustrate the effectiveness of this approach with two use cases involving small research modelling groups at NATO and USGS.

Technical note: Harmonising metocean model data via standard web services within small research groups

NASA Astrophysics Data System (ADS)

Signell, Richard P.; Camossi, Elena

2016-05-01

Work over the last decade has resulted in standardised web services and tools that can significantly improve the efficiency and effectiveness of working with meteorological and ocean model data. While many operational modelling centres have enabled query and access to data via common web services, most small research groups have not. The penetration of this approach into the research community, where IT resources are limited, can be dramatically improved by (1) making it simple for providers to enable web service access to existing output files; (2) using free technologies that are easy to deploy and configure; and (3) providing standardised, service-based tools that work in existing research environments. We present a simple, local brokering approach that lets modellers continue to use their existing files and tools, while serving virtual data sets that can be used with standardised tools. The goal of this paper is to convince modellers that a standardised framework is not only useful but can be implemented with modest effort using free software components. We use NetCDF Markup language for data aggregation and standardisation, the THREDDS Data Server for data delivery, pycsw for data search, NCTOOLBOX (MATLAB®) and Iris (Python) for data access, and Open Geospatial Consortium Web Map Service for data preview. We illustrate the effectiveness of this approach with two use cases involving small research modelling groups at NATO and USGS.

OpenFIRE - A Web GIS Service for Distributing the Finnish Reflection Experiment Datasets

NASA Astrophysics Data System (ADS)

Väkevä, Sakari; Aalto, Aleksi; Heinonen, Aku; Heikkinen, Pekka; Korja, Annakaisa

2017-04-01

The Finnish Reflection Experiment (FIRE) is a land-based deep seismic reflection survey conducted between 2001 and 2003 by a research consortium of the Universities of Helsinki and Oulu, the Geological Survey of Finland, and a Russian state-owned enterprise SpetsGeofysika. The dataset consists of 2100 kilometers of high-resolution profiles across the Archaean and Proterozoic nuclei of the Fennoscandian Shield. Although FIRE data have been available on request since 2009, the data have remained underused outside the original research consortium. The original FIRE data have been quality-controlled. The shot gathers have been cross-checked and comprehensive errata has been created. The brute stacks provided by the Russian seismic contractor have been reprocessed into seismic sections and replotted. A complete documentation of the intermediate processing steps is provided together with guidelines for setting up a computing environment and plotting the data. An open access web service "OpenFIRE" for the visualization and the downloading of FIRE data has been created. The service includes a mobile-responsive map application capable of enriching seismic sections with data from other sources such as open data from the National Land Survey and the Geological Survey of Finland. The AVAA team of the Finnish Open Science and Research Initiative has provided a tailored Liferay portal with necessary web components such as an API (Application Programming Interface) for download requests. INSPIRE (Infrastructure for Spatial Information in Europe) -compliant discovery metadata have been produced and geospatial data will be exposed as Open Geospatial Consortium standard services. The technical guidelines of the European Plate Observing System have been followed and the service could be considered as a reference application for sharing reflection seismic data. The OpenFIRE web service is available at www.seismo.helsinki.fi/openfire

Do It Yourself (DIY) Earth Science Collaboratories Using Best Practices and Breakthrough Technologies

NASA Astrophysics Data System (ADS)

Stephan, E.

2017-12-01

The objective of published earth science study data results and literature on the Web should be to provide a means to integrate discoverable science resources through an open collaborative-Web. At the core of any open science collaborative infrastructure is the ability to discover, manage and ultimately use relevant data accessible to the collaboration. Equally important are the relationships between people, applications, services, and publications, which capture critical contextual knowledge that enable their effective use. While contributions of either irreproducible or costly data can be a great asset the inability of users being able to use the data intelligently or make sense of it, makes these investments not usable. An ability to describe ad-hoc discoverable usage methodologies, provide feedback to data producers, and identify and cite data in a systematic way by leveraging existing Web-enabled off the shelf technology is needed. Fortunately many break-through advancements in data publication best practices and government, open source, and commercial investments support consumers who can provide feedback, share experiences, and contribute back to the earth science ecosystem.

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.

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy.

PubMed

Letunic, Ivica; Bork, Peer

2011-07-01

Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. In addition to classical tree viewer functions, iTOL offers many novel ways of annotating trees with various additional data. Current version introduces numerous new features and greatly expands the number of supported data set types. Trees can be interactively manipulated and edited. A free personal account system is available, providing management and sharing of trees in user defined workspaces and projects. Export to various bitmap and vector graphics formats is supported. Batch access interface is available for programmatic access or inclusion of interactive trees into other web services.

Java Web Simulation (JWS); a web based database of kinetic models.

PubMed

Snoep, J L; Olivier, B G

2002-01-01

Software to make a database of kinetic models accessible via the internet has been developed and a core database has been set up at http://jjj.biochem.sun.ac.za/. This repository of models, available to everyone with internet access, opens a whole new way in which we can make our models public. Via the database, a user can change enzyme parameters and run time simulations or steady state analyses. The interface is user friendly and no additional software is necessary. The database currently contains 10 models, but since the generation of the program code to include new models has largely been automated the addition of new models is straightforward and people are invited to submit their models to be included in the database.

Threats and risks to information security: a practical analysis of free access wireless networks

NASA Astrophysics Data System (ADS)

Quirumbay, Daniel I.; Coronel, Iván. A.; Bayas, Marcia M.; Rovira, Ronald H.; Gromaszek, Konrad; Tleshova, Akmaral; Kozbekova, Ainur

2017-08-01

Nowadays, there is an ever-growing need to investigate, consult and communicate through the internet. This need leads to the intensification of free access to the web in strategic and functional points for the benefit of the community. However, this open access is also related to the increase of information insecurity. The existing works on computer security primarily focus on the development of techniques to reduce cyber-attacks. However, these approaches do not address the sector of inexperienced users who have difficulty understanding browser settings. Two methods can solve this problem: first the development of friendly browsers with intuitive setups for new users and on the other hand, by implementing awareness programs on essential security without deepening on technical information. This article addresses an analysis of the vulnerabilities of wireless equipment that provides internet service in the open access zones and the potential risks that could be found when using these means.

18 CFR 358.3 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-04-01

....1 of this chapter), affiliate shall have the meaning set forth in § 366.1 of this chapter, or any...) Internet Web site refers to the Internet location where an interstate natural gas pipeline or a public... functions. (e) Open Access Same Time Information System or OASIS refers to the Internet location where a...

WINDS: A Web-Based Intelligent Interactive Course on Data-Structures

ERIC Educational Resources Information Center

Sirohi, Vijayalaxmi

2007-01-01

The Internet has opened new ways of learning and has brought several advantages to computer-aided education. Global access, self-paced learning, asynchronous teaching, interactivity, and multimedia usage are some of these. Along with the advantages comes the challenge of designing the software using the available facilities. Integrating online…

Scan This Book!

ERIC Educational Resources Information Center

Albanese, Andrew Richard

2007-01-01

In this article, the author presents an interview with Brewster Kahle, leader of the Open Content Alliance (OCA). OCA book scan program is an alternative to Google's library project that aims to make books accessible online. In this interview, Kahle discusses his views on the challenges of getting books on the Web, on Google's library…

Geoscience Information Network (USGIN) Solutions for Interoperable Open Data Access Requirements

NASA Astrophysics Data System (ADS)

Allison, M. L.; Richard, S. M.; Patten, K.

2014-12-01

The geosciences are leading development of free, interoperable open access to data. US Geoscience Information Network (USGIN) is a freely available data integration framework, jointly developed by the USGS and the Association of American State Geologists (AASG), in compliance with international standards and protocols to provide easy discovery, access, and interoperability for geoscience data. USGIN standards include the geologic exchange language 'GeoSciML' (v 3.2 which enables instant interoperability of geologic formation data) which is also the base standard used by the 117-nation OneGeology consortium. The USGIN deployment of NGDS serves as a continent-scale operational demonstration of the expanded OneGeology vision to provide access to all geoscience data worldwide. USGIN is developed to accommodate a variety of applications; for example, the International Renewable Energy Agency streams data live to the Global Atlas of Renewable Energy. Alternatively, users without robust data sharing systems can download and implement a free software packet, "GINstack" to easily deploy web services for exposing data online for discovery and access. The White House Open Data Access Initiative requires all federally funded research projects and federal agencies to make their data publicly accessible in an open source, interoperable format, with metadata. USGIN currently incorporates all aspects of the Initiative as it emphasizes interoperability. The system is successfully deployed as the National Geothermal Data System (NGDS), officially launched at the White House Energy Datapalooza in May, 2014. The USGIN Foundation has been established to ensure this technology continues to be accessible and available.

ClusterControl: a web interface for distributing and monitoring bioinformatics applications on a Linux cluster.

PubMed

Stocker, Gernot; Rieder, Dietmar; Trajanoski, Zlatko

2004-03-22

ClusterControl is a web interface to simplify distributing and monitoring bioinformatics applications on Linux cluster systems. We have developed a modular concept that enables integration of command line oriented program into the application framework of ClusterControl. The systems facilitate integration of different applications accessed through one interface and executed on a distributed cluster system. The package is based on freely available technologies like Apache as web server, PHP as server-side scripting language and OpenPBS as queuing system and is available free of charge for academic and non-profit institutions. http://genome.tugraz.at/Software/ClusterControl

The Evolution of Digital Chemistry at Southampton.

PubMed

Bird, Colin; Coles, Simon J; Frey, Jeremy G

2015-09-01

In this paper we take a historical view of e-Science and e-Research developments within the Chemical Sciences at the University of Southampton, showing the development of several stages of the evolving data ecosystem as Chemistry moves into the digital age of the 21(st) Century. We cover our research on aspects of the representation of chemical information in the context of the world wide web (WWW) and its semantic enhancement (the Semantic Web) and illustrate this with the example of the representation of quantities and units within the Semantic Web. We explore the changing nature of laboratories as computing power becomes increasing powerful and pervasive and specifically look at the function and role of electronic or digital notebooks. Having focussed on the creation of chemical data and information in context, we finish the paper by following the use and reuse of this data as facilitated by the features provided by digital repositories and their importance in facilitating the exchange of chemical information touching on the issues of open and or intelligent access to the data. © 2015 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Open access to the scientific journal literature: situation 2009.

PubMed

Björk, Bo-Christer; Welling, Patrik; Laakso, Mikael; Majlender, Peter; Hedlund, Turid; Gudnason, Gudni

2010-06-23

The Internet has recently made possible the free global availability of scientific journal articles. Open Access (OA) can occur either via OA scientific journals, or via authors posting manuscripts of articles published in subscription journals in open web repositories. So far there have been few systematic studies showing how big the extent of OA is, in particular studies covering all fields of science. The proportion of peer reviewed scholarly journal articles, which are available openly in full text on the web, was studied using a random sample of 1837 titles and a web search engine. Of articles published in 2008, 8.5% were freely available at the publishers' sites. For an additional 11.9% free manuscript versions could be found using search engines, making the overall OA percentage 20.4%. Chemistry (13%) had the lowest overall share of OA, Earth Sciences (33%) the highest. In medicine, biochemistry and chemistry publishing in OA journals was more common. In all other fields author-posted manuscript copies dominated the picture. The results show that OA already has a significant positive impact on the availability of the scientific journal literature and that there are big differences between scientific disciplines in the uptake. Due to the lack of awareness of OA-publishing among scientists in most fields outside physics, the results should be of general interest to all scholars. The results should also interest academic publishers, who need to take into account OA in their business strategies and copyright policies, as well as research funders, who like the NIH are starting to require OA availability of results from research projects they fund. The method and search tools developed also offer a good basis for more in-depth studies as well as longitudinal studies.

Open Access to the Scientific Journal Literature: Situation 2009

PubMed Central

Björk, Bo-Christer; Welling, Patrik; Laakso, Mikael; Majlender, Peter; Hedlund, Turid; Guðnason, Guðni

2010-01-01

Background The Internet has recently made possible the free global availability of scientific journal articles. Open Access (OA) can occur either via OA scientific journals, or via authors posting manuscripts of articles published in subscription journals in open web repositories. So far there have been few systematic studies showing how big the extent of OA is, in particular studies covering all fields of science. Methodology/Principal Findings The proportion of peer reviewed scholarly journal articles, which are available openly in full text on the web, was studied using a random sample of 1837 titles and a web search engine. Of articles published in 2008, 8,5% were freely available at the publishers' sites. For an additional 11,9% free manuscript versions could be found using search engines, making the overall OA percentage 20,4%. Chemistry (13%) had the lowest overall share of OA, Earth Sciences (33%) the highest. In medicine, biochemistry and chemistry publishing in OA journals was more common. In all other fields author-posted manuscript copies dominated the picture. Conclusions/Significance The results show that OA already has a significant positive impact on the availability of the scientific journal literature and that there are big differences between scientific disciplines in the uptake. Due to the lack of awareness of OA-publishing among scientists in most fields outside physics, the results should be of general interest to all scholars. The results should also interest academic publishers, who need to take into account OA in their business strategies and copyright policies, as well as research funders, who like the NIH are starting to require OA availability of results from research projects they fund. The method and search tools developed also offer a good basis for more in-depth studies as well as longitudinal studies. PMID:20585653

Web-client based distributed generalization and geoprocessing

USGS Publications Warehouse

Wolf, E.B.; Howe, K.

2009-01-01

Generalization and geoprocessing operations on geospatial information were once the domain of complex software running on high-performance workstations. Currently, these computationally intensive processes are the domain of desktop applications. Recent efforts have been made to move geoprocessing operations server-side in a distributed, web accessible environment. This paper initiates research into portable client-side generalization and geoprocessing operations as part of a larger effort in user-centered design for the US Geological Survey's The National Map. An implementation of the Ramer-Douglas-Peucker (RDP) line simplification algorithm was created in the open source OpenLayers geoweb client. This algorithm implementation was benchmarked using differing data structures and browser platforms. The implementation and results of the benchmarks are discussed in the general context of client-side geoprocessing. (Abstract).

Thin client (web browser)-based collaboration for medical imaging and web-enabled data.

PubMed

Le, Tuong Huu; Malhi, Nadeem

2002-01-01

Utilizing thin client software and open source server technology, a collaborative architecture was implemented allowing for sharing of Digital Imaging and Communications in Medicine (DICOM) and non-DICOM images with real-time markup. Using the Web browser as a thin client integrated with standards-based components, such as DHTML (dynamic hypertext markup language), JavaScript, and Java, collaboration was achieved through a Web server/proxy server combination utilizing Java Servlets and Java Server Pages. A typical collaborative session involved the driver, who directed the navigation of the other collaborators, the passengers, and provided collaborative markups of medical and nonmedical images. The majority of processing was performed on the server side, allowing for the client to remain thin and more accessible.

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

PubMed Central

Rose, Peter W.; Prlić, Andreas; Bi, Chunxiao; Bluhm, Wolfgang F.; Christie, Cole H.; Dutta, Shuchismita; Green, Rachel Kramer; Goodsell, David S.; Westbrook, John D.; Woo, Jesse; Young, Jasmine; Zardecki, Christine; Berman, Helen M.; Bourne, Philip E.; Burley, Stephen K.

2015-01-01

The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine. PMID:25428375

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.

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.

In an Age of Open Access to Research Policies: Physician and Public Health NGO Staff Research Use and Policy Awareness

PubMed Central

Maggio, Lauren A.; Steinberg, Ryan M.; Willinsky, John

2015-01-01

Introduction Through funding agency and publisher policies, an increasing proportion of the health sciences literature is being made open access. Such an increase in access raises questions about the awareness and potential utilization of this literature by those working in health fields. Methods A sample of physicians (N=336) and public health non-governmental organization (NGO) staff (N=92) were provided with relatively complete access to the research literature indexed in PubMed, as well as access to the point-of-care service UpToDate, for up to one year, with their usage monitored through the tracking of web-log data. The physicians also participated in a one-month trial of relatively complete or limited access. Results The study found that participants' research interests were not satisfied by article abstracts alone nor, in the case of the physicians, by a clinical summary service such as UpToDate. On average, a third of the physicians viewed research a little more frequently than once a week, while two-thirds of the public health NGO staff viewed more than three articles a week. Those articles were published since the 2008 adoption of the NIH Public Access Policy, as well as prior to 2008 and during the maximum 12-month embargo period. A portion of the articles in each period was already open access, but complete access encouraged a viewing of more research articles. Conclusion Those working in health fields will utilize more research in the course of their work as a result of (a) increasing open access to research, (b) improving awareness of and preparation for this access, and (c) adjusting public and open access policies to maximize the extent of potential access, through reduction in embargo periods and access to pre-policy literature. PMID:26200794

Human rights abuses, transparency, impunity and the Web.

PubMed

Miles, Steven H

2007-01-01

This paper reviews how human rights advocates during the "war-on-terror" have found new ways to use the World Wide Web (Web) to combat human rights abuses. These include posting of human rights reports; creating large, open-access and updated archives of government documents and other data, tracking CIA rendition flights and maintaining blogs, e-zines, list-serves and news services that rapidly distribute information between journalists, scholars and human rights advocates. The Web is a powerful communication tool for human rights advocates. It is international, instantaneous, and accessible for uploading, archiving, locating and downloading information. For its human rights potential to be fully realized, international law must be strengthened to promote the declassification of government documents, as is done by various freedom of information acts. It is too early to assess the final impact of the Web on human rights abuses in the "war-on-terror". Wide dissemination of government documents and human rights advocates' reports has put the United States government on the defensive and some of its policies have changed in response to public pressure. Even so, the essential elements of secret prisons, detention without charges or trials, and illegal rendition remain intact.

Can Internet Access Growth Help Reduce the Global Burden Of Noncommunicable Diseases?

PubMed Central

Kohler, Stefan

2013-01-01

Noncommunicable diseases, such as cardiovascular diseases, cancer, chronic respiratory diseases, and diabetes, are currently the leading causes of death in several regions of the world. The continuing fast increase in the global burden of noncommunicable diseases is accompanied by a speedy worldwide internet access growth. The worldwide number of internet users has doubled over the past five years. As the internet can make the access to information on a healthy lifestyle and disease prevention activities easier, internet access growth may help to promote good health. Against this background, I discuss the roles the internet and access to information can play in health promotion. I also present an open access web portal on local prevention and health promotion activities. It was initiated by two German states to link health information from disparate sources and to organize this information in a user-friendly way. The web portal focuses on reducing preventable lifestyle-related risk factors associated with noncommunicable diseases, including physical inactivity, unhealthy diet, tobacco use, and the harmful use of alcohol. This local initiative has the potential for scaling up and can serve as a blueprint for other areas that have or will acquire internet access. PMID:23923103

National Geothermal Data System (USA): an Exemplar of Open Access to Data

NASA Astrophysics Data System (ADS)

Allison, M. Lee; Richard, Stephen; Blackman, Harold; Anderson, Arlene; Patten, Kim

2014-05-01

The National Geothermal Data System's (NGDS - www.geothermaldata.org) formal launch in April, 2014 will provide open access to millions of data records, sharing -relevant geoscience and longer term to land use data to propel geothermal development and production. NGDS serves information from all of the U.S. Department of Energy's sponsored development and research projects and geologic data from all 50 states, using free and open source software. This interactive online system is opening new exploration opportunities and potentially shortening project development by making data easily discoverable, accessible, and interoperable. We continue to populate our prototype functional data system with multiple data nodes and nationwide data online and available to the public. Data from state geological surveys and partners includes more than 6 million records online, including 1.72 million well headers (oil and gas, water, geothermal), 670,000 well logs, and 497,000 borehole temperatures and is growing rapidly. There are over 312 interoperable Web services and another 106 WMS (Web Map Services) registered in the system as of January, 2014. Companion projects run by Southern Methodist University and U.S. Geological Survey (USGS) are adding millions of additional data records. The DOE Geothermal Data Repository, currently hosted on OpenEI, is a system node and clearinghouse for data from hundreds of U.S. DOE-funded geothermal projects. 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). NGDS complies with the White House Executive Order of May 2013, requiring all federal agencies to make their data holdings publicly accessible online in open source, interoperable formats with common core and extensible metadata. The National Geothermal Data System is being designed, built, deployed, and populated primarily with support from the US Department of Energy, Geothermal Technologies Office. To keep this system operational after the original implementation will require four core elements: continued serving of data and applications by providers; maintenance of system operations; a governance structure; and an effective business model. Each of these presents a number of challenges currently under consideration.

Open access to high-level data and analysis tools in the CMS experiment at the LHC

DOE PAGES

Calderon, A.; Colling, D.; Huffman, A.; ...

2015-12-23

The CMS experiment, in recognition of its commitment to data preservation and open access as well as to education and outreach, has made its first public release of high-level data under the CC0 waiver: up to half of the proton-proton collision data (by volume) at 7 TeV from 2010 in CMS Analysis Object Data format. CMS has prepared, in collaboration with CERN and the other LHC experiments, an open-data web portal based on Invenio. The portal provides access to CMS public data as well as to analysis tools and documentation for the public. The tools include an event display andmore » histogram application that run in the browser. In addition a virtual machine containing a CMS software environment along with XRootD access to the data is available. Within the virtual machine the public can analyse CMS data, example code is provided. As a result, we describe the accompanying tools and documentation and discuss the first experiences of data use.« less

Environmental Models as a Service: Enabling Interoperability ...

EPA Pesticide Factsheets

Achieving interoperability in environmental modeling has evolved as software technology has progressed. The recent rise of cloud computing and proliferation of web services initiated a new stage for creating interoperable systems. Scientific programmers increasingly take advantage of streamlined deployment processes and affordable cloud access to move algorithms and data to the web for discoverability and consumption. In these deployments, environmental models can become available to end users through RESTful web services and consistent application program interfaces (APIs) that consume, manipulate, and store modeling data. RESTful modeling APIs also promote discoverability and guide usability through self-documentation. Embracing the RESTful paradigm allows models to be accessible via a web standard, and the resulting endpoints are platform- and implementation-agnostic while simultaneously presenting significant computational capabilities for spatial and temporal scaling. RESTful APIs present data in a simple verb-noun web request interface: the verb dictates how a resource is consumed using HTTP methods (e.g., GET, POST, and PUT) and the noun represents the URL reference of the resource on which the verb will act. The RESTful API can self-document in both the HTTP response and an interactive web page using the Open API standard. This lets models function as an interoperable service that promotes sharing, documentation, and discoverability. Here, we discuss the

AMBIT RESTful web services: an implementation of the OpenTox application programming interface.

PubMed

Jeliazkova, Nina; Jeliazkov, Vedrin

2011-05-16

The AMBIT web services package is one of the several existing independent implementations of the OpenTox Application Programming Interface and is built according to the principles of the Representational State Transfer (REST) architecture. The Open Source Predictive Toxicology Framework, developed by the partners in the EC FP7 OpenTox project, aims at providing a unified access to toxicity data and predictive models, as well as validation procedures. This is achieved by i) an information model, based on a common OWL-DL ontology ii) links to related ontologies; iii) data and algorithms, available through a standardized REST web services interface, where every compound, data set or predictive method has a unique web address, used to retrieve its Resource Description Framework (RDF) representation, or initiate the associated calculations.The AMBIT web services package has been developed as an extension of AMBIT modules, adding the ability to create (Quantitative) Structure-Activity Relationship (QSAR) models and providing an OpenTox API compliant interface. The representation of data and processing resources in W3C Resource Description Framework facilitates integrating the resources as Linked Data. By uploading datasets with chemical structures and arbitrary set of properties, they become automatically available online in several formats. The services provide unified interfaces to several descriptor calculation, machine learning and similarity searching algorithms, as well as to applicability domain and toxicity prediction models. All Toxtree modules for predicting the toxicological hazard of chemical compounds are also integrated within this package. The complexity and diversity of the processing is reduced to the simple paradigm "read data from a web address, perform processing, write to a web address". The online service allows to easily run predictions, without installing any software, as well to share online datasets and models. The downloadable web application allows researchers to setup an arbitrary number of service instances for specific purposes and at suitable locations. These services could be used as a distributed framework for processing of resource-intensive tasks and data sharing or in a fully independent way, according to the specific needs. The advantage of exposing the functionality via the OpenTox API is seamless interoperability, not only within a single web application, but also in a network of distributed services. Last, but not least, the services provide a basis for building web mashups, end user applications with friendly GUIs, as well as embedding the functionalities in existing workflow systems.

AMBIT RESTful web services: an implementation of the OpenTox application programming interface

PubMed Central

2011-01-01

The AMBIT web services package is one of the several existing independent implementations of the OpenTox Application Programming Interface and is built according to the principles of the Representational State Transfer (REST) architecture. The Open Source Predictive Toxicology Framework, developed by the partners in the EC FP7 OpenTox project, aims at providing a unified access to toxicity data and predictive models, as well as validation procedures. This is achieved by i) an information model, based on a common OWL-DL ontology ii) links to related ontologies; iii) data and algorithms, available through a standardized REST web services interface, where every compound, data set or predictive method has a unique web address, used to retrieve its Resource Description Framework (RDF) representation, or initiate the associated calculations. The AMBIT web services package has been developed as an extension of AMBIT modules, adding the ability to create (Quantitative) Structure-Activity Relationship (QSAR) models and providing an OpenTox API compliant interface. The representation of data and processing resources in W3C Resource Description Framework facilitates integrating the resources as Linked Data. By uploading datasets with chemical structures and arbitrary set of properties, they become automatically available online in several formats. The services provide unified interfaces to several descriptor calculation, machine learning and similarity searching algorithms, as well as to applicability domain and toxicity prediction models. All Toxtree modules for predicting the toxicological hazard of chemical compounds are also integrated within this package. The complexity and diversity of the processing is reduced to the simple paradigm "read data from a web address, perform processing, write to a web address". The online service allows to easily run predictions, without installing any software, as well to share online datasets and models. The downloadable web application allows researchers to setup an arbitrary number of service instances for specific purposes and at suitable locations. These services could be used as a distributed framework for processing of resource-intensive tasks and data sharing or in a fully independent way, according to the specific needs. The advantage of exposing the functionality via the OpenTox API is seamless interoperability, not only within a single web application, but also in a network of distributed services. Last, but not least, the services provide a basis for building web mashups, end user applications with friendly GUIs, as well as embedding the functionalities in existing workflow systems. PMID:21575202

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!

Using a web-based application to define the accuracy of diagnostic tests when the gold standard is imperfect.

PubMed

Lim, Cherry; Wannapinij, Prapass; White, Lisa; Day, Nicholas P J; Cooper, Ben S; Peacock, Sharon J; Limmathurotsakul, Direk

2013-01-01

Estimates of the sensitivity and specificity for new diagnostic tests based on evaluation against a known gold standard are imprecise when the accuracy of the gold standard is imperfect. Bayesian latent class models (LCMs) can be helpful under these circumstances, but the necessary analysis requires expertise in computational programming. Here, we describe open-access web-based applications that allow non-experts to apply Bayesian LCMs to their own data sets via a user-friendly interface. Applications for Bayesian LCMs were constructed on a web server using R and WinBUGS programs. The models provided (http://mice.tropmedres.ac) include two Bayesian LCMs: the two-tests in two-population model (Hui and Walter model) and the three-tests in one-population model (Walter and Irwig model). Both models are available with simplified and advanced interfaces. In the former, all settings for Bayesian statistics are fixed as defaults. Users input their data set into a table provided on the webpage. Disease prevalence and accuracy of diagnostic tests are then estimated using the Bayesian LCM, and provided on the web page within a few minutes. With the advanced interfaces, experienced researchers can modify all settings in the models as needed. These settings include correlation among diagnostic test results and prior distributions for all unknown parameters. The web pages provide worked examples with both models using the original data sets presented by Hui and Walter in 1980, and by Walter and Irwig in 1988. We also illustrate the utility of the advanced interface using the Walter and Irwig model on a data set from a recent melioidosis study. The results obtained from the web-based applications were comparable to those published previously. The newly developed web-based applications are open-access and provide an important new resource for researchers worldwide to evaluate new diagnostic tests.

Qualitative study of physicians' varied uses of biomedical research in the USA

PubMed Central

Maggio, Lauren A; Moorhead, Laura L; Willinsky, John M

2016-01-01

Objective To investigate the nature of physicians' use of research evidence in experimental conditions of open access to inform training and policy. Design This qualitative study was a component of a larger mixed-methods initiative that provided 336 physicians with relatively complete access to research literature via PubMed and UpToDate, for 1 year via an online portal, with their usage recorded in web logs. Using a semistructured interview protocol, a subset of 38 physician participants were interviewed about their use of research articles in general and were probed about their reasons for accessing specific articles as identified through their web logs. Transcripts were analysed using a general inductive approach. Setting Physician participants were recruited from and registered in the USA. Participants 38 physicians from 16 US states, engaged in 22 medical specialties, possessing more than 1 year of experience postresidency training participated. Results 26 participants attested to the value of consulting research literature within the context of the study by making reference to their roles as clinicians, educators, researchers, learners, administrators and advocates. The physicians reported previously encountering what they experienced as a prohibitive paywall barrier to the research literature and other frustrations with the nature of information systems, such as the need for passwords. Conclusions The findings, against the backdrop of growing open access to biomedical research, indicate that a minority of physicians, at least initially, is likely to seek out and use research and do so in a variety of common roles. Physicians' use of research in these roles has not traditionally been part of their training or part of the considerations for open access policies. The findings have implications for educational and policy initiatives directed towards increasing the effectiveness of this access to and use of research in improving the quality of healthcare. PMID:27872121

Brokered virtual hubs for facilitating access and use of geospatial Open Data

NASA Astrophysics Data System (ADS)

Mazzetti, Paolo; Latre, Miguel; Kamali, Nargess; Brumana, Raffaella; Braumann, Stefan; Nativi, Stefano

2016-04-01

Open Data is a major trend in current information technology scenario and it is often publicised as one of the pillars of the information society in the near future. In particular, geospatial Open Data have a huge potential also for Earth Sciences, through the enablement of innovative applications and services integrating heterogeneous information. However, open does not mean usable. As it was recognized at the very beginning of the Web revolution, many different degrees of openness exist: from simple sharing in a proprietary format to advanced sharing in standard formats and including semantic information. Therefore, to fully unleash the potential of geospatial Open Data, advanced infrastructures are needed to increase the data openness degree, enhancing their usability. In October 2014, the ENERGIC OD (European NEtwork for Redistributing Geospatial Information to user Communities - Open Data) project, funded by the European Union under the Competitiveness and Innovation framework Programme (CIP), has started. In response to the EU call, the general objective of the project is to "facilitate the use of open (freely available) geographic data from different sources for the creation of innovative applications and services through the creation of Virtual Hubs". The ENERGIC OD Virtual Hubs aim to facilitate the use of geospatial Open Data by lowering and possibly removing the main barriers which hampers geo-information (GI) usage by end-users and application developers. Data and services heterogeneity is recognized as one of the major barriers to Open Data (re-)use. It imposes end-users and developers to spend a lot of effort in accessing different infrastructures and harmonizing datasets. Such heterogeneity cannot be completely removed through the adoption of standard specifications for service interfaces, metadata and data models, since different infrastructures adopt different standards to answer to specific challenges and to address specific use-cases. Thus, beyond a certain extent, heterogeneity is irreducible especially in interdisciplinary contexts. ENERGIC OD Virtual Hubs address heterogeneity adopting a mediation and brokering approach: specific components (brokers) are dedicated to harmonize service interfaces, metadata and data models, enabling seamless discovery and access to heterogeneous infrastructures and datasets. As an innovation project, ENERGIC OD integrates several existing technologies to implement Virtual Hubs as single points of access to geospatial datasets provided by new or existing platforms and infrastructures, including INSPIRE-compliant systems and Copernicus services. A first version of the ENERGIC OD brokers has been implemented based on the GI-Suite Brokering Framework developed by CNR-IIA, and complemented with other tools under integration and development. It already enables mediated discovery and harmonized access to different geospatial Open Data sources. It is accessible by users as Software-as-a-Service through a browser. Moreover, open APIs and a Javascript library are available for application developers. Six ENERGIC OD Virtual Hubs have been currently deployed: one at regional level (Berlin metropolitan area) and five at national-level (in France, Germany, Italy, Poland and Spain). Each Virtual Hub manager decided the deployment strategy (local infrastructure or commercial Infrastructure-as-a-Service cloud), and the list of connected Open Data sources. The ENERGIC OD Virtual Hubs are under test and validation through the development of ten different mobile and Web applications.

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

Collecting behavioural data using the world wide web: considerations for researchers

PubMed Central

Rhodes, S; Bowie, D; Hergenrather, K

2003-01-01

Objective: To identify and describe advantages, challenges, and ethical considerations of web based behavioural data collection. Methods: This discussion is based on the authors' experiences in survey development and study design, respondent recruitment, and internet research, and on the experiences of others as found in the literature. Results: The advantages of using the world wide web to collect behavioural data include rapid access to numerous potential respondents and previously hidden populations, respondent openness and full participation, opportunities for student research, and reduced research costs. Challenges identified include issues related to sampling and sample representativeness, competition for the attention of respondents, and potential limitations resulting from the much cited "digital divide", literacy, and disability. Ethical considerations include anonymity and privacy, providing and substantiating informed consent, and potential risks of malfeasance. Conclusions: Computer mediated communications, including electronic mail, the world wide web, and interactive programs will play an ever increasing part in the future of behavioural science research. Justifiable concerns regarding the use of the world wide web in research exist, but as access to, and use of, the internet becomes more widely and representatively distributed globally, the world wide web will become more applicable. In fact, the world wide web may be the only research tool able to reach some previously hidden population subgroups. Furthermore, many of the criticisms of online data collection are common to other survey research methodologies. PMID:12490652

Collecting behavioural data using the world wide web: considerations for researchers.

PubMed

Rhodes, S D; Bowie, D A; Hergenrather, K C

2003-01-01

To identify and describe advantages, challenges, and ethical considerations of web based behavioural data collection. This discussion is based on the authors' experiences in survey development and study design, respondent recruitment, and internet research, and on the experiences of others as found in the literature. The advantages of using the world wide web to collect behavioural data include rapid access to numerous potential respondents and previously hidden populations, respondent openness and full participation, opportunities for student research, and reduced research costs. Challenges identified include issues related to sampling and sample representativeness, competition for the attention of respondents, and potential limitations resulting from the much cited "digital divide", literacy, and disability. Ethical considerations include anonymity and privacy, providing and substantiating informed consent, and potential risks of malfeasance. Computer mediated communications, including electronic mail, the world wide web, and interactive programs will play an ever increasing part in the future of behavioural science research. Justifiable concerns regarding the use of the world wide web in research exist, but as access to, and use of, the internet becomes more widely and representatively distributed globally, the world wide web will become more applicable. In fact, the world wide web may be the only research tool able to reach some previously hidden population subgroups. Furthermore, many of the criticisms of online data collection are common to other survey research methodologies.

First Prototype of a Web Map Interface for ESA's Planetary Science Archive (PSA)

NASA Astrophysics Data System (ADS)

Manaud, N.; Gonzalez, J.

2014-04-01

We present a first prototype of a Web Map Interface that will serve as a proof of concept and design for ESA's future fully web-based Planetary Science Archive (PSA) User Interface. The PSA is ESA's planetary science archiving authority and central repository for all scientific and engineering data returned by ESA's Solar System missions [1]. All data are compliant with NASA's Planetary Data System (PDS) Standards and are accessible through several interfaces [2]: in addition to serving all public data via FTP and the Planetary Data Access Protocol (PDAP), a Java-based User Interface provides advanced search, preview, download, notification and delivery-basket functionality. It allows the user to query and visualise instrument observations footprints using a map-based interface (currently only available for Mars Express HRSC and OMEGA instruments). During the last decade, the planetary mapping science community has increasingly been adopting Geographic Information System (GIS) tools and standards, originally developed for and used in Earth science. There is an ongoing effort to produce and share cartographic products through Open Geospatial Consortium (OGC) Web Services, or as standalone data sets, so that they can be readily used in existing GIS applications [3,4,5]. Previous studies conducted at ESAC [6,7] have helped identify the needs of Planetary GIS users, and define key areas of improvement for the future Web PSA User Interface. Its web map interface shall will provide access to the full geospatial content of the PSA, including (1) observation geometry footprints of all remote sensing instruments, and (2) all georeferenced cartographic products, such as HRSC map-projected data or OMEGA global maps from Mars Express. It shall aim to provide a rich user experience for search and visualisation of this content using modern and interactive web mapping technology. A comprehensive set of built-in context maps from external sources, such as MOLA topography, TES infrared maps or planetary surface nomenclature, provided in both simple cylindrical and polar stereographic projections, shall enhance this user experience. In addition, users should be able to import and export data in commonly used open- GIS formats. It is also intended to serve all PSA geospatial data through OGC-compliant Web Services so that they can be captured, visualised and analysed directly from GIS software, along with data from other sources. The following figure illustrates how the PSA web map interface and services shall fit in a typical Planetary GIS user working environment.

HELI-DEM portal for geo-processing services

NASA Astrophysics Data System (ADS)

Cannata, Massimiliano; Antonovic, Milan; Molinari, Monia

2014-05-01

HELI-DEM (Helvetia-Italy Digital Elevation Model) is a project developed in the framework of Italy/Switzerland Operational Programme for Trans-frontier Cooperation 2007-2013 whose major aim is to create a unified digital terrain model that includes the alpine and sub-alpine areas between Italy and Switzerland. The partners of the project are: Lombardy Region, Piedmont Region, Polytechnic of Milan, Polytechnic of Turin and Fondazione Politecnico from Italy; Institute of Earth Sciences (SUPSI) from Switzerland. The digital terrain model has been produced by integrating and validating the different elevation data available for the areas of interest, characterized by different reference frame, resolutions and accuracies: DHM at 25 m resolution from Swisstopo, DTM at 20 m resolution from Lombardy Region, DTM at 5 m resolution from Piedmont Region and DTM LiDAR PST-A at about 1 m resolution, that covers the main river bed areas and is produced by the Italian Ministry of the Environment. Further results of the project are: the generation of a unique Italian Swiss geoid with an accuracy of few centimeters (Gilardoni et al. 2012); the establishment of a GNSS permanent network, prototype of a transnational positioning service; the development of a geo-portal, entirely based on open source technologies and open standards, which provides the cross-border DTM and offers some capabilities of analysis and processing through the Internet. With this talk, the authors want to present the main steps of the project with a focus on the HELI-DEM geo-portal development carried out by the Institute of Earth Sciences, which is the access point to the DTM outputted from the project. The portal, accessible at http://geoservice.ist.supsi.ch/helidem, is a demonstration of open source technologies combined for providing access to geospatial functionalities to wide non GIS expert public. In fact, the system is entirely developed using only Open Standards and Free and Open Source Software (FOSS) both on the server side (services) and on the client side (interface). In addition to self developed code the system relies mainly on teh software GRASS 7 [1], ZOO-project [2], Geoserver [3] and OpenLayers [4] and the standards WMS [5], WCS [6] and WPS [7]. At the time of writing, the portal offers features like profiling, contour extraction, watershed delineation and analysis, derivatives calculation, data extraction, coordinate conversion but it is evolving and it is planned to extend to a series of environmental modeling that the IST developed in the past like dam break simulation, landslide run-out estimation and floods due to landslide impact in artificial basins. [1] Neteler M., Mitasova H., Open Source GIS: A GRASS GIS Approach. 3rd Ed. 406 pp, Springer, New York, 2008. [2] Fenoy G., Bozon N., Raghavan V., ZOO Project: The Open Wps Platform. Proceeding of 1st International Workshop on Pervasive Web Mapping, Geoprocessing and Services (WebMGS). Como, http://www.isprs.org/proceedings/XXXVIII/4-W13/ID_32.pdf, 26-27 agosto 2010. [3] Giannecchini S., Aime A., GeoServer, il server open source per la gestione interoperabile dei dati geospaziali. Atti 15a Conferenza Nazionale ASITA. Reggia di Colorno, 15-18 novembre 2011. [4] Perez A.S., OpenLayers Cookbook. Packt Publishing, 2012. ISBN 1849517843. [5] OGC, OpenGIS Web Map Server Implementation Specification, http://www.opengeospatial.org/standards/wms, 2006. [6] OGC, OGC WCS 2.0 Interface Standard - Core, http://portal.opengeospatial.org/files/?artifact_id=41437, 2010b. [7] OGC, OpenGIS Web Processing Service, http://portal.opengeospatial.org/files/?artifact_id=24151, 2007.

Commercial Social Media and the Erosion of the Commons: Implications for Academic Libraries

ERIC Educational Resources Information Center

Lilburn, Jeff

2012-01-01

Recent scholarship challenges the celebratory discourse surrounding Web 2.0. This paper engages with this scholarship to examine critically the implications of academic libraries' presence within commercially owned social media spaces. It considers the apparent contradiction between work to promote the principles of open access and the idea of the…

EnviroAtlas: A New Geospatial Tool to Foster Ecosystem Services Science and Resource Management

EPA Science Inventory

In this article we present EnviroAtlas, a web-based, open access tool that seeks to meet a range of needs by bringing together environmental, economic and demographic data in an ecosystem services framework. Within EnviroAtlas, there are three primary types of geospatial data: r...

Learning about Language and Learners from Computer Programs

ERIC Educational Resources Information Center

Cobb, Tom

2010-01-01

Making Nation's text analysis software accessible via the World Wide Web has opened up an exploration of how his learning principles can best be realized in practice. This paper discusses 3 representative episodes in the ongoing exploration. The first concerns an examination of the assumptions behind modeling what texts look like to learners with…

A Method of Cross-Level Frequent Pattern Mining for Web-Based Instruction

ERIC Educational Resources Information Center

Huang, Yueh-Min; Chen, Juei-Nan; Cheng, Shu-Chen

2007-01-01

Due to the rise of e-Learning, more and more useful learning materials are open to public access. Therefore, an appropriate learning suggestion mechanism is an important tool to enable learners to work more efficiently. A smoother learning process increases the learning effect, avoiding unnecessarily difficult concepts and disorientation during…

Usability Evaluation of a Research Repository and Collaboration Web Site

ERIC Educational Resources Information Center

Zhang, Tao; Maron, Deborah J.; Charles, Christopher C.

2013-01-01

This article reports results from an empirical usability evaluation of Human-Animal Bond Research Initiative Central as part of the effort to develop an open access research repository and collaboration platform for human-animal bond researchers. By repurposing and altering key features of the original HUBzero system, Human-Animal Bond Research…

Net Neutrality: What Librarians Should Know

ERIC Educational Resources Information Center

Anderson, Byron

2007-01-01

The openness of the Internet has greatly facilitated scholarly communication and led to creative developments in many fields. The Internet has been called the most democratic of media. In many countries, one does not need permission to post a new Web page. Public domain information flows freely and is widely accessible on an impartial basis to…

What Trends Do Turkish Biology Education Studies Indicate?

ERIC Educational Resources Information Center

Topsakal, Unsal Umdu; Calik, Muammer; Cavus, Ragip

2012-01-01

The aim of this study is to determine what trends Turkish biology education studies indicate. To achieve this aim, the researchers examined online databases of the Higher Education Council and open access archives of graduate theses in web sites of Turkish universities. Finally, totally 138 graduate theses were elicited to analyze in regard to…

The Canon, the Web, and the Long Tail

ERIC Educational Resources Information Center

Sanderhoff, Merete

2017-01-01

This article argues that releasing images of artworks into the public domain creates a new possibility for the public to challenge the canon or create their own, based on access to previously inaccessible images. Through the dissemination of openly licensed artworks across the Internet, museums can support the public in expanding their engagement…

A Scalable Infrastructure for Lidar Topography Data Distribution, Processing, and Discovery

NASA Astrophysics Data System (ADS)

Crosby, C. J.; Nandigam, V.; Krishnan, S.; Phan, M.; Cowart, C. A.; Arrowsmith, R.; Baru, C.

2010-12-01

High-resolution topography data acquired with lidar (light detection and ranging) technology have emerged as a fundamental tool in the Earth sciences, and are also being widely utilized for ecological, planning, engineering, and environmental applications. Collected from airborne, terrestrial, and space-based platforms, these data are revolutionary because they permit analysis of geologic and biologic processes at resolutions essential for their appropriate representation. Public domain lidar data collection by federal, state, and local agencies are a valuable resource to the scientific community, however the data pose significant distribution challenges because of the volume and complexity of data that must be stored, managed, and processed. Lidar data acquisition may generate terabytes of data in the form of point clouds, digital elevation models (DEMs), and derivative products. This massive volume of data is often challenging to host for resource-limited agencies. Furthermore, these data can be technically challenging for users who lack appropriate software, computing resources, and expertise. The National Science Foundation-funded OpenTopography Facility (www.opentopography.org) has developed a cyberinfrastructure-based solution to enable online access to Earth science-oriented high-resolution lidar topography data, online processing tools, and derivative products. OpenTopography provides access to terabytes of point cloud data, standard DEMs, and Google Earth image data, all co-located with computational resources for on-demand data processing. The OpenTopography portal is built upon a cyberinfrastructure platform that utilizes a Services Oriented Architecture (SOA) to provide a modular system that is highly scalable and flexible enough to support the growing needs of the Earth science lidar community. OpenTopography strives to host and provide access to datasets as soon as they become available, and also to expose greater application level functionalities to our end-users (such as generation of custom DEMs via various gridding algorithms, and hydrological modeling algorithms). In the future, the SOA will enable direct authenticated access to back-end functionality through simple Web service Application Programming Interfaces (APIs), so that users may access our data and compute resources via clients other than Web browsers. In addition to an overview of the OpenTopography SOA, this presentation will discuss our recently developed lidar data ingestion and management system for point cloud data delivered in the binary LAS standard. This system compliments our existing partitioned database approach for data delivered in ASCII format, and permits rapid ingestion of data. The system has significantly reduced data ingestion times and has implications for data distribution in emergency response situations. We will also address on ongoing work to develop a community lidar metadata catalog based on the OGC Catalogue Service for Web (CSW) standard, which will help to centralize discovery of public domain lidar data.

OC ToGo: bed site image integration into OpenClinica with mobile devices

NASA Astrophysics Data System (ADS)

Haak, Daniel; Gehlen, Johan; Jonas, Stephan; Deserno, Thomas M.

2014-03-01

Imaging and image-based measurements nowadays play an essential role in controlled clinical trials, but electronic data capture (EDC) systems insufficiently support integration of captured images by mobile devices (e.g. smartphones and tablets). The web application OpenClinica has established as one of the world's leading EDC systems and is used to collect, manage and store data of clinical trials in electronic case report forms (eCRFs). In this paper, we present a mobile application for instantaneous integration of images into OpenClinica directly during examination on patient's bed site. The communication between the Android application and OpenClinica is based on the simple object access protocol (SOAP) and representational state transfer (REST) web services for metadata, and secure file transfer protocol (SFTP) for image transfer, respectively. OpenClinica's web services are used to query context information (e.g. existing studies, events and subjects) and to import data into the eCRF, as well as export of eCRF metadata and structural information. A stable image transfer is ensured and progress information (e.g. remaining time) visualized to the user. The workflow is demonstrated for a European multi-center registry, where patients with calciphylaxis disease are included. Our approach improves the EDC workflow, saves time, and reduces costs. Furthermore, data privacy is enhanced, since storage of private health data on the imaging devices becomes obsolete.

Web-based faculty development: e-learning for clinical teachers in the London Deanery.

PubMed

McKimm, Judy; Swanwick, Tim

2010-03-01

the London Deanery has provided a web-based resource for supporting the educational development needs of clinical teachers since 2002. This forms part of a range of resources supporting the professional development of clinical teachers and postgraduate supervisors. Following a review in 2007, the deanery commissioned a series of new e-learning modules designed as an introduction to clinical teaching. the deanery's faculty development initiatives are one response to requirements of the Postgraduate Medical Education and Training Board (PMETB), other policy drivers, workforce demands and service changes. Increasingly, doctors are required to provide an educational portfolio of evidence, and satisfy the teaching and training component of Good Medical Practice in revalidation or recertification. 'E-learning for clinical teachers' comprises 16 short, open-access, free-standing modules. The modules are built around a unifying structure, and cover core topics in clinical teaching: feedback; supervision; workplace-based learning; assessment; diversity and equal opportunities; career development; appraisal; lecturing; small group teaching; interprofessional education; and setting learning objectives. The modules can be used as a complementary resource to award-bearing programmes. On completion of a module, a certificate can be printed out for the teacher's portfolio. reflective practice and engagement with an individual's teaching practice is encouraged through self-assessment and a reflective log. The open-access, web-based format enables engagement with the material to suit a doctor's working and learning patterns, and is a valuable adjunct to other forms of learning. The site has been accessed by over 64000 health professionals (including students, trainees, qualified professionals, supervisors and staff developers) from 155 countries. Blackwell Publishing Ltd 2010.

An accessible, scalable ecosystem for enabling and sharing diverse mass spectrometry imaging analyses

DOE PAGES

Fischer, Curt R.; Ruebel, Oliver; Bowen, Benjamin P.

2015-09-11

Mass spectrometry imaging (MSI) is used in an increasing number of biological applications. Typical MSI datasets contain unique, high-resolution mass spectra from tens of thousands of spatial locations, resulting in raw data sizes of tens of gigabytes per sample. In this paper, we review technical progress that is enabling new biological applications and that is driving an increase in the complexity and size of MSI data. Handling such data often requires specialized computational infrastructure, software, and expertise. OpenMSI, our recently described platform, makes it easy to explore and share MSI datasets via the web – even when larger than 50more » GB. Here we describe the integration of OpenMSI with IPython notebooks for transparent, sharable, and replicable MSI research. An advantage of this approach is that users do not have to share raw data along with analyses; instead, data is retrieved via OpenMSI's web API. The IPython notebook interface provides a low-barrier entry point for data manipulation that is accessible for scientists without extensive computational training. Via these notebooks, analyses can be easily shared without requiring any data movement. We provide example notebooks for several common MSI analysis types including data normalization, plotting, clustering, and classification, and image registration.« less

An accessible, scalable ecosystem for enabling and sharing diverse mass spectrometry imaging analyses.

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

Fischer, CR; Ruebel, O; Bowen, BP

Mass spectrometry imaging (MSI) is used in an increasing number of biological applications. Typical MSI datasets contain unique, high-resolution mass spectra from tens of thousands of spatial locations, resulting in raw data sizes of tens of gigabytes per sample. In this paper, we review technical progress that is enabling new biological applications and that is driving an increase in the complexity and size of MSI data. Handling such data often requires specialized computational infrastructure, software, and expertise. OpenMSI, our recently described platform, makes it easy to explore and share MSI datasets via the web - even when larger than 50 GB.more » Here we describe the integration of OpenMSI with IPython notebooks for transparent, sharable, and replicable MSI research. An advantage of this approach is that users do not have to share raw data along with analyses; instead, data is retrieved via OpenMSI's web API. The IPython notebook interface provides a low-barrier entry point for data manipulation that is accessible for scientists without extensive computational training. Via these notebooks, analyses can be easily shared without requiring any data movement. We provide example notebooks for several common MSI analysis types including data normalization, plotting, clustering, and classification, and image registration.« less

An accessible, scalable ecosystem for enabling and sharing diverse mass spectrometry imaging analyses

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

Fischer, Curt R.; Ruebel, Oliver; Bowen, Benjamin P.

Mass spectrometry imaging (MSI) is used in an increasing number of biological applications. Typical MSI datasets contain unique, high-resolution mass spectra from tens of thousands of spatial locations, resulting in raw data sizes of tens of gigabytes per sample. In this paper, we review technical progress that is enabling new biological applications and that is driving an increase in the complexity and size of MSI data. Handling such data often requires specialized computational infrastructure, software, and expertise. OpenMSI, our recently described platform, makes it easy to explore and share MSI datasets via the web – even when larger than 50more » GB. Here we describe the integration of OpenMSI with IPython notebooks for transparent, sharable, and replicable MSI research. An advantage of this approach is that users do not have to share raw data along with analyses; instead, data is retrieved via OpenMSI's web API. The IPython notebook interface provides a low-barrier entry point for data manipulation that is accessible for scientists without extensive computational training. Via these notebooks, analyses can be easily shared without requiring any data movement. We provide example notebooks for several common MSI analysis types including data normalization, plotting, clustering, and classification, and image registration.« less

RelFinder: Revealing Relationships in RDF Knowledge Bases

NASA Astrophysics Data System (ADS)

Heim, Philipp; Hellmann, Sebastian; Lehmann, Jens; Lohmann, Steffen; Stegemann, Timo

The Semantic Web has recently seen a rise of large knowledge bases (such as DBpedia) that are freely accessible via SPARQL endpoints. The structured representation of the contained information opens up new possibilities in the way it can be accessed and queried. In this paper, we present an approach that extracts a graph covering relationships between two objects of interest. We show an interactive visualization of this graph that supports the systematic analysis of the found relationships by providing highlighting, previewing, and filtering features.

Web-based access, aggregation, and visualization of future climate projections with emphasis on agricultural assessments

NASA Astrophysics Data System (ADS)

Villoria, Nelson B.; Elliott, Joshua; Müller, Christoph; Shin, Jaewoo; Zhao, Lan; Song, Carol

2018-01-01

Access to climate and spatial datasets by non-specialists is restricted by technical barriers involving hardware, software and data formats. We discuss an open-source online tool that facilitates downloading the climate data from the global circulation models used by the Inter-Sectoral Impacts Model Intercomparison Project. The tool also offers temporal and spatial aggregation capabilities for incorporating future climate scenarios in applications where spatial aggregation is important. We hope that streamlined access to these data facilitates analysis of climate related issues while considering the uncertainties derived from future climate projections and temporal aggregation choices.

GENESIS SciFlo: Choreographing Interoperable Web Services on the Grid using a Semantically-Enabled Dataflow Execution Environment

NASA Astrophysics Data System (ADS)

Wilson, B. D.; Manipon, G.; Xing, Z.

2007-12-01

The General Earth Science Investigation Suite (GENESIS) project is a NASA-sponsored partnership between the Jet Propulsion Laboratory, academia, and NASA data centers to develop a new suite of Web Services tools to facilitate multi-sensor investigations in Earth System Science. The goal of GENESIS is to enable large-scale, multi-instrument atmospheric science using combined datasets from the AIRS, MODIS, MISR, and GPS sensors. Investigations include cross-comparison of spaceborne climate sensors, cloud spectral analysis, study of upper troposphere-stratosphere water transport, study of the aerosol indirect cloud effect, and global climate model validation. The challenges are to bring together very large datasets, reformat and understand the individual instrument retrievals, co-register or re-grid the retrieved physical parameters, perform computationally-intensive data fusion and data mining operations, and accumulate complex statistics over months to years of data. To meet these challenges, we have developed a Grid computing and dataflow framework, named SciFlo, in which we are deploying a set of versatile and reusable operators for data access, subsetting, registration, mining, fusion, compression, and advanced statistical analysis. SciFlo leverages remote Web Services, called via Simple Object Access Protocol (SOAP) or REST (one-line) URLs, and the Grid Computing standards (WS-* & Globus Alliance toolkits), and enables scientists to do multi- instrument Earth Science by assembling reusable Web Services and native executables into a distributed computing flow (tree of operators). The SciFlo client & server engines optimize the execution of such distributed data flows and allow the user to transparently find and use datasets and operators without worrying about the actual location of the Grid resources. In particular, SciFlo exploits the wealth of datasets accessible by OpenGIS Consortium (OGC) Web Mapping Servers & Web Coverage Servers (WMS/WCS), and by Open Data Access Protocol (OpenDAP) servers. SciFlo also publishes its own SOAP services for space/time query and subsetting of Earth Science datasets, and automated access to large datasets via lists of (FTP, HTTP, or DAP) URLs which point to on-line HDF or netCDF files. Typical distributed workflows obtain datasets by calling standard WMS/WCS servers or discovering and fetching data granules from ftp sites; invoke remote analysis operators available as SOAP services (interface described by a WSDL document); and merge results into binary containers (netCDF or HDF files) for further analysis using local executable operators. Naming conventions (HDFEOS and CF-1.0 for netCDF) are exploited to automatically understand and read on-line datasets. More interoperable conventions, and broader adoption of existing converntions, are vital if we are to "scale up" automated choreography of Web Services beyond toy applications. Recently, the ESIP Federation sponsored a collaborative activity in which several ESIP members developed some collaborative science scenarios for atmospheric and aerosol science, and then choreographed services from multiple groups into demonstration workflows using the SciFlo engine and a Business Process Execution Language (BPEL) workflow engine. We will discuss the lessons learned from this activity, the need for standardized interfaces (like WMS/WCS), the difficulty in agreeing on even simple XML formats and interfaces, the benefits of doing collaborative science analysis at the "touch of a button" once services are connected, and further collaborations that are being pursued.

Web-based encyclopedia on physical effects

NASA Astrophysics Data System (ADS)

Papliatseyeu, Andrey; Repich, Maryna; Ilyushonak, Boris; Hurbo, Aliaksandr; Makarava, Katerina; Lutkovski, Vladimir M.

2004-07-01

Web-based learning applications open new horizons for educators. In this work we present the computer encyclopedia designed to overcome drawbacks of traditional paper information sources such as awkward search, low update rate, limited copies count and high cost. Moreover, we intended to improve access and search functions in comparison with some Internet sources in order to make it more convenient. The system is developed using modern Java technologies (Jave Servlets, Java Server Pages) and contains systemized information about most important and explored physical effects. It also may be used in other fields of science. The system is accessible via Intranet/Internet networks by means of any up-to-date Internet browser. It may be used for general learning purposes and as a study guide or tutorial for performing laboratory works.

Finding research information on the web: how to make the most of Google and other free search tools.

PubMed

Blakeman, Karen

2013-01-01

The Internet and the World Wide Web has had a major impact on the accessibility of research information. The move towards open access and development of institutional repositories has resulted in increasing amounts of information being made available free of charge. Many of these resources are not included in conventional subscription databases and Google is not always the best way to ensure that one is picking up all relevant material on a topic. This article will look at how Google's search engine works, how to use Google more effectively for identifying research information, alternatives to Google and will review some of the specialist tools that have evolved to cope with the diverse forms of information that now exist in electronic form.

A SOA-based approach to geographical data sharing

NASA Astrophysics Data System (ADS)

Li, Zonghua; Peng, Mingjun; Fan, Wei

2009-10-01

In the last few years, large volumes of spatial data have been available in different government departments in China, but these data are mainly used within these departments. With the e-government project initiated, spatial data sharing become more and more necessary. Currently, the Web has been used not only for document searching but also for the provision and use of services, known as Web services, which are published in a directory and may be automatically discovered by software agents. Particularly in the spatial domain, the possibility of accessing these large spatial datasets via Web services has motivated research into the new field of Spatial Data Infrastructure (SDI) implemented using service-oriented architecture. In this paper a Service-Oriented Architecture (SOA) based Geographical Information Systems (GIS) is proposed, and a prototype system is deployed based on Open Geospatial Consortium (OGC) standard in Wuhan, China, thus that all the departments authorized can access the spatial data within the government intranet, and also these spatial data can be easily integrated into kinds of applications.

WormQTL—public archive and analysis web portal for natural variation data in Caenorhabditis spp

PubMed Central

Snoek, L. Basten; Van der Velde, K. Joeri; Arends, Danny; Li, Yang; Beyer, Antje; Elvin, Mark; Fisher, Jasmin; Hajnal, Alex; Hengartner, Michael O.; Poulin, Gino B.; Rodriguez, Miriam; Schmid, Tobias; Schrimpf, Sabine; Xue, Feng; Jansen, Ritsert C.; Kammenga, Jan E.; Swertz, Morris A.

2013-01-01

Here, we present WormQTL (http://www.wormqtl.org), an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp. Over the past decade, Caenorhabditis elegans has become instrumental for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a valuable amount of phenotypic, high-throughput molecular and genotypic data across different developmental worm stages and environments in hundreds of C. elegans strains. WormQTL provides a workbench of analysis tools for genotype–phenotype linkage and association mapping based on but not limited to R/qtl (http://www.rqtl.org). All data can be uploaded and downloaded using simple delimited text or Excel formats and are accessible via a public web user interface for biologists and R statistic and web service interfaces for bioinformaticians, based on open source MOLGENIS and xQTL workbench software. WormQTL welcomes data submissions from other worm researchers. PMID:23180786

WormQTL--public archive and analysis web portal for natural variation data in Caenorhabditis spp.

PubMed

Snoek, L Basten; Van der Velde, K Joeri; Arends, Danny; Li, Yang; Beyer, Antje; Elvin, Mark; Fisher, Jasmin; Hajnal, Alex; Hengartner, Michael O; Poulin, Gino B; Rodriguez, Miriam; Schmid, Tobias; Schrimpf, Sabine; Xue, Feng; Jansen, Ritsert C; Kammenga, Jan E; Swertz, Morris A

2013-01-01

Here, we present WormQTL (http://www.wormqtl.org), an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp. Over the past decade, Caenorhabditis elegans has become instrumental for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a valuable amount of phenotypic, high-throughput molecular and genotypic data across different developmental worm stages and environments in hundreds of C. elegans strains. WormQTL provides a workbench of analysis tools for genotype-phenotype linkage and association mapping based on but not limited to R/qtl (http://www.rqtl.org). All data can be uploaded and downloaded using simple delimited text or Excel formats and are accessible via a public web user interface for biologists and R statistic and web service interfaces for bioinformaticians, based on open source MOLGENIS and xQTL workbench software. WormQTL welcomes data submissions from other worm researchers.

An open data mining framework for the analysis of medical images: application on obstructive nephropathy microscopy images.

PubMed

Doukas, Charalampos; Goudas, Theodosis; Fischer, Simon; Mierswa, Ingo; Chatziioannou, Aristotle; Maglogiannis, Ilias

2010-01-01

This paper presents an open image-mining framework that provides access to tools and methods for the characterization of medical images. Several image processing and feature extraction operators have been implemented and exposed through Web Services. Rapid-Miner, an open source data mining system has been utilized for applying classification operators and creating the essential processing workflows. The proposed framework has been applied for the detection of salient objects in Obstructive Nephropathy microscopy images. Initial classification results are quite promising demonstrating the feasibility of automated characterization of kidney biopsy images.

Open Marketplace for Simulation Software on the Basis of a Web Platform

NASA Astrophysics Data System (ADS)

Kryukov, A. P.; Demichev, A. P.

2016-02-01

The focus in development of a new generation of middleware shifts from the global grid systems to building convenient and efficient web platforms for remote access to individual computing resources. Further line of their development, suggested in this work, is related not only with the quantitative increase in their number and with the expansion of scientific, engineering, and manufacturing areas in which they are used, but also with improved technology for remote deployment of application software on the resources interacting with the web platforms. Currently, the services for providers of application software in the context of scientific-oriented web platforms is not developed enough. The proposed in this work new web platforms of application software market should have all the features of the existing web platforms for submissions of jobs to remote resources plus the provision of specific web services for interaction on market principles between the providers and consumers of application packages. The suggested approach will be approved on the example of simulation applications in the field of nonlinear optics.

VISIBIOweb: visualization and layout services for BioPAX pathway models

PubMed Central

Dilek, Alptug; Belviranli, Mehmet E.; Dogrusoz, Ugur

2010-01-01

With recent advancements in techniques for cellular data acquisition, information on cellular processes has been increasing at a dramatic rate. Visualization is critical to analyzing and interpreting complex information; representing cellular processes or pathways is no exception. VISIBIOweb is a free, open-source, web-based pathway visualization and layout service for pathway models in BioPAX format. With VISIBIOweb, one can obtain well-laid-out views of pathway models using the standard notation of the Systems Biology Graphical Notation (SBGN), and can embed such views within one's web pages as desired. Pathway views may be navigated using zoom and scroll tools; pathway object properties, including any external database references available in the data, may be inspected interactively. The automatic layout component of VISIBIOweb may also be accessed programmatically from other tools using Hypertext Transfer Protocol (HTTP). The web site is free and open to all users and there is no login requirement. It is available at: http://visibioweb.patika.org. PMID:20460470

Web Content Accessibility of Consumer Health Information Web Sites for People with Disabilities: A Cross Sectional Evaluation

PubMed Central

Parmanto, Bambang

2004-01-01

Background The World Wide Web (WWW) has become an increasingly essential resource for health information consumers. The ability to obtain accurate medical information online quickly, conveniently and privately provides health consumers with the opportunity to make informed decisions and participate actively in their personal care. Little is known, however, about whether the content of this online health information is equally accessible to people with disabilities who must rely on special devices or technologies to process online information due to their visual, hearing, mobility, or cognitive limitations. Objective To construct a framework for an automated Web accessibility evaluation; to evaluate the state of accessibility of consumer health information Web sites; and to investigate the possible relationships between accessibility and other features of the Web sites, including function, popularity and importance. Methods We carried out a cross-sectional study of the state of accessibility of health information Web sites to people with disabilities. We selected 108 consumer health information Web sites from the directory service of a Web search engine. A measurement framework was constructed to automatically measure the level of Web Accessibility Barriers (WAB) of Web sites following Web accessibility specifications. We investigated whether there was a difference between WAB scores across various functional categories of the Web sites, and also evaluated the correlation between the WAB and Alexa traffic rank and Google Page Rank of the Web sites. Results We found that none of the Web sites we looked at are completely accessible to people with disabilities, i.e., there were no sites that had no violation of Web accessibility rules. However, governmental and educational health information Web sites do exhibit better Web accessibility than the other categories of Web sites (P < 0.001). We also found that the correlation between the WAB score and the popularity of a Web site is statistically significant (r = 0.28, P < 0.05), although there is no correlation between the WAB score and the importance of the Web sites (r = 0.15, P = 0.111). Conclusions Evaluation of health information Web sites shows that no Web site scrupulously abides by Web accessibility specifications, even for entities mandated under relevant laws and regulations. Government and education Web sites show better performance than Web sites among other categories. Accessibility of a Web site may have a positive impact on its popularity in general. However, the Web accessibility of a Web site may not have a significant relationship with its importance on the Web. PMID:15249268

Collaborative Science Using Web Services and the SciFlo Grid Dataflow Engine

NASA Astrophysics Data System (ADS)

Wilson, B. D.; Manipon, G.; Xing, Z.; Yunck, T.

2006-12-01

The General Earth Science Investigation Suite (GENESIS) project is a NASA-sponsored partnership between the Jet Propulsion Laboratory, academia, and NASA data centers to develop a new suite of Web Services tools to facilitate multi-sensor investigations in Earth System Science. The goal of GENESIS is to enable large-scale, multi-instrument atmospheric science using combined datasets from the AIRS, MODIS, MISR, and GPS sensors. Investigations include cross-comparison of spaceborne climate sensors, cloud spectral analysis, study of upper troposphere-stratosphere water transport, study of the aerosol indirect cloud effect, and global climate model validation. The challenges are to bring together very large datasets, reformat and understand the individual instrument retrievals, co-register or re-grid the retrieved physical parameters, perform computationally-intensive data fusion and data mining operations, and accumulate complex statistics over months to years of data. To meet these challenges, we have developed a Grid computing and dataflow framework, named SciFlo, in which we are deploying a set of versatile and reusable operators for data access, subsetting, registration, mining, fusion, compression, and advanced statistical analysis. SciFlo leverages remote Web Services, called via Simple Object Access Protocol (SOAP) or REST (one-line) URLs, and the Grid Computing standards (WS-* &Globus Alliance toolkits), and enables scientists to do multi-instrument Earth Science by assembling reusable Web Services and native executables into a distributed computing flow (tree of operators). The SciFlo client &server engines optimize the execution of such distributed data flows and allow the user to transparently find and use datasets and operators without worrying about the actual location of the Grid resources. In particular, SciFlo exploits the wealth of datasets accessible by OpenGIS Consortium (OGC) Web Mapping Servers & Web Coverage Servers (WMS/WCS), and by Open Data Access Protocol (OpenDAP) servers. The scientist injects a distributed computation into the Grid by simply filling out an HTML form or directly authoring the underlying XML dataflow document, and results are returned directly to the scientist's desktop. Once an analysis has been specified for a chunk or day of data, it can be easily repeated with different control parameters or over months of data. Recently, the Earth Science Information Partners (ESIP) Federation sponsored a collaborative activity in which several ESIP members advertised their respective WMS/WCS and SOAP services, developed some collaborative science scenarios for atmospheric and aerosol science, and then choreographed services from multiple groups into demonstration workflows using the SciFlo engine and a Business Process Execution Language (BPEL) workflow engine. For several scenarios, the same collaborative workflow was executed in three ways: using hand-coded scripts, by executing a SciFlo document, and by executing a BPEL workflow document. We will discuss the lessons learned from this activity, the need for standardized interfaces (like WMS/WCS), the difficulty in agreeing on even simple XML formats and interfaces, and further collaborations that are being pursued.

Software Application Profile: Opal and Mica: open-source software solutions for epidemiological data management, harmonization and dissemination

PubMed Central

Doiron, Dany; Marcon, Yannick; Fortier, Isabel; Burton, Paul; Ferretti, Vincent

2017-01-01

Abstract Motivation Improving the dissemination of information on existing epidemiological studies and facilitating the interoperability of study databases are essential to maximizing the use of resources and accelerating improvements in health. To address this, Maelstrom Research proposes Opal and Mica, two inter-operable open-source software packages providing out-of-the-box solutions for epidemiological data management, harmonization and dissemination. Implementation Opal and Mica are two standalone but inter-operable web applications written in Java, JavaScript and PHP. They provide web services and modern user interfaces to access them. General features Opal allows users to import, manage, annotate and harmonize study data. Mica is used to build searchable web portals disseminating study and variable metadata. When used conjointly, Mica users can securely query and retrieve summary statistics on geographically dispersed Opal servers in real-time. Integration with the DataSHIELD approach allows conducting more complex federated analyses involving statistical models. Availability Opal and Mica are open-source and freely available at [www.obiba.org] under a General Public License (GPL) version 3, and the metadata models and taxonomies that accompany them are available under a Creative Commons licence. PMID:29025122

Mapping and Modeling Web Portal to Advance Global Monitoring and Climate Research

NASA Astrophysics Data System (ADS)

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

2011-12-01

Today, the principal investigators of NASA Earth Science missions develop their own software to manipulate, visualize, and analyze the data collected from Earth, space, and airborne observation instruments. There is very little, if any, collaboration among these principal investigators due to the lack of collaborative tools, which would allow these scientists to share data and results. At NASA's Jet Propulsion Laboratory (JPL), under the Lunar Mapping and Modeling Project (LMMP), we have built a web portal that exposes a set of common services to users to allow search, visualization, subset, and download lunar science data. Users also have access to a set of tools that visualize, analyze and annotate the data. These services are developed according to industry standards for data access and manipulation, such REST and Open Geospatial Consortium (OGC) web services. As a result, users can access the datasets through custom written applications or off-the-shelf applications such as Google Earth. Even though it's currently used to store and process lunar data, this web portal infrastructure has been designed to support other solar system bodies such as asteroids and planets, including Earth. The infrastructure uses a combination of custom, commercial, and open-source software as well as off-the-shelf hardware and pay-by-use cloud computing services. The use of standardized web service interfaces facilitates platform and application-independent access to the services and data. For instance, we have software clients for the LMMP portal that provide a rich browsing and analysis experience from a variety of platforms including iOS and Android mobile platforms and large screen multi-touch displays with 3-D terrain viewing functions. The service-oriented architecture and design principles utilized in the implementation of the portal lends itself to be reusable and scalable and could naturally be extended to include a collaborative environment that enables scientists and principal investigators to share their research and analysis seamlessly. In addition, this extension will allow users to easily share their tools and data, and to enrich their mapping and analysis experiences. In this talk, we will describe the advanced data management and portal technologies used to power this collaborative environment. We will further illustrate how this environment can enable, enhance and advance global monitoring and climate research.

Usage and Effectiveness of a Fully Automated, Open-Access, Spanish Web-Based Smoking Cessation Program: Randomized Controlled Trial

PubMed Central

2014-01-01

Background The Internet is an optimal setting to provide massive access to tobacco treatments. To evaluate open-access Web-based smoking cessation programs in a real-world setting, adherence and retention data should be taken into account as much as abstinence rate. Objective The objective was to analyze the usage and effectiveness of a fully automated, open-access, Web-based smoking cessation program by comparing interactive versus noninteractive versions. Methods Participants were randomly assigned either to the interactive or noninteractive version of the program, both with identical content divided into 4 interdependent modules. At baseline, we collected demographic, psychological, and smoking characteristics of the smokers self-enrolled in the Web-based program of Universidad Nacional de Educación a Distancia (National Distance Education University; UNED) in Madrid, Spain. The following questionnaires were administered: the anxiety and depression subscales from the Symptom Checklist-90-Revised, the 4-item Perceived Stress Scale, and the Heaviness of Smoking Index. At 3 months, we analyzed dropout rates, module completion, user satisfaction, follow-up response rate, and self-assessed smoking abstinence. Results A total of 23,213 smokers were registered, 50.06% (11,620/23,213) women and 49.94% (11,593/23,213) men, with a mean age of 39.5 years (SD 10.3). Of these, 46.10% (10,701/23,213) were married and 34.43% (7992/23,213) were single, 46.03% (10,686/23,213) had university education, and 78.73% (18,275/23,213) were employed. Participants smoked an average of 19.4 cigarettes per day (SD 10.3). Of the 11,861 smokers randomly assigned to the interactive version, 2720 (22.93%) completed the first module, 1052 (8.87%) the second, 624 (5.26%) the third, and 355 (2.99%) the fourth. Completion data was not available for the noninteractive version (no way to record it automatically). The 3-month follow-up questionnaire was completed by 1085 of 23,213 enrolled smokers (4.67%). Among them, 406 (37.42%) self-reported not smoking. No difference between groups was found. Assuming missing respondents continued to smoke, the abstinence rate was 1.74% (406/23,213), in which 22,678 were missing respondents. Among follow-up respondents, completing the 4 modules of the intervention increased the chances of smoking cessation (OR 1.95, 95% CI 1.27-2.97, P<.001), as did smoking 30 minutes (OR 1.58, 95% CI 1.04-2.39, P=.003) or 1 hour after waking (OR 1.93, 95% CI 1.27-2.93, P<.001) compared to smoking within the first 5 minutes after waking. Conclusions The findings suggest that the UNED Web-based smoking cessation program was very accessible, but a high level of attrition was confirmed. This could be related to the ease of enrollment, its free character, and the absence of direct contact with professionals. It is concluded that, in practice, the greater the accessibility to the program, the lower the adherence and retention. Professional support from health services and the payment of a reimbursable fee could prevent high rates of attrition. PMID:24760951

Incentives to Encourage Scientific Web Contribution (Invited)

NASA Astrophysics Data System (ADS)

Antunes, A. K.

2010-12-01

We suggest improvements to citation standards and creation of remuneration opportunities to encourage career scientist contributions to Web2.0 and social media science channels. At present, agencies want to accomplish better outreach and engagement with no funding, while scientists sacrifice their personal time to contribute to web and social media sites. Securing active participation by scientists requires career recognition of the value scientists provide to web knowledge bases and to the general public. One primary mechanism to encourage participation is citation standards, which let a contributor improve their reputation in a quantifiable way. But such standards must be recognized by their scientific and workplace communities. Using case studies such as the acceptance of web in the workplace and the growth of open access journals, we examine what agencies and individual can do as well as the time scales needed to secure increased active contribution by scientists. We also discuss ways to jumpstart this process.

FragFit: a web-application for interactive modeling of protein segments into cryo-EM density maps.

PubMed

Tiemann, Johanna K S; Rose, Alexander S; Ismer, Jochen; Darvish, Mitra D; Hilal, Tarek; Spahn, Christian M T; Hildebrand, Peter W

2018-05-21

Cryo-electron microscopy (cryo-EM) is a standard method to determine the three-dimensional structures of molecular complexes. However, easy to use tools for modeling of protein segments into cryo-EM maps are sparse. Here, we present the FragFit web-application, a web server for interactive modeling of segments of up to 35 amino acids length into cryo-EM density maps. The fragments are provided by a regularly updated database containing at the moment about 1 billion entries extracted from PDB structures and can be readily integrated into a protein structure. Fragments are selected based on geometric criteria, sequence similarity and fit into a given cryo-EM density map. Web-based molecular visualization with the NGL Viewer allows interactive selection of fragments. The FragFit web-application, accessible at http://proteinformatics.de/FragFit, is free and open to all users, without any login requirements.

New Generation Sensor Web Enablement

PubMed Central

Bröring, Arne; Echterhoff, Johannes; Jirka, Simon; Simonis, Ingo; Everding, Thomas; Stasch, Christoph; Liang, Steve; Lemmens, Rob

2011-01-01

Many sensor networks have been deployed to monitor Earth’s environment, and more will follow in the future. Environmental sensors have improved continuously by becoming smaller, cheaper, and more intelligent. Due to the large number of sensor manufacturers and differing accompanying protocols, integrating diverse sensors into observation systems is not straightforward. A coherent infrastructure is needed to treat sensors in an interoperable, platform-independent and uniform way. The concept of the Sensor Web reflects such a kind of infrastructure for sharing, finding, and accessing sensors and their data across different applications. It hides the heterogeneous sensor hardware and communication protocols from the applications built on top of it. The Sensor Web Enablement initiative of the Open Geospatial Consortium standardizes web service interfaces and data encodings which can be used as building blocks for a Sensor Web. This article illustrates and analyzes the recent developments of the new generation of the Sensor Web Enablement specification framework. Further, we relate the Sensor Web to other emerging concepts such as the Web of Things and point out challenges and resulting future work topics for research on Sensor Web Enablement. PMID:22163760

Open Data and Open Science for better Research in the Geo and Space Domain

NASA Astrophysics Data System (ADS)

Ritschel, B.; Seelus, C.; Neher, G.; Iyemori, T.; Koyama, Y.; Yatagai, A. I.; Murayama, Y.; King, T. A.; Hughes, S.; Fung, S. F.; Galkin, I. A.; Hapgood, M. A.; Belehaki, A.

2015-12-01

Main open data principles had been worked out in the run-up and finally adopted in the Open Data Charta at the G8 summit in Lough Erne, Northern Ireland in June 2013. Important principles are also valid for science data, such as Open Data by Default, Quality and Quantity, Useable by All, Releasing Data for Improved Governance, Releasing Data for Innovation. There is also an explicit relationship to such areas of high values as earth observation, education and geospatial data. The European union implementation plan of the Open Data Charta identifies among other things objectives such as making data available in an open format, enabling semantic interoperability, ensuring quality, documentation and where appropriate reconciliation across different data sources, implementing software solutionsallowing easy management, publication or visualization of datasets and simplifying clearance of intellectual property rights.Open Science is not just a list of already for a longer time known principles but stands for a lot of initiatives and projects around a better handling of scientific data and openly shared scientific knowledge. It is also about transparency in methodology and collection of data, availability and reuse of scientific data, public accessibility to scientific communication and using of social media to facility scientific collaboration. Some projects are concentrating on open sharing of free and open source software and even further hardware in kind of processing capabilities. In addition question about the mashup of data and publication and an open peer review process are addressed.Following the principles of open data and open science the newest results of the collaboration efforts in mashing up the data servers related to the Japanese IUGONET, the European Union ESPAS and the GFZ ISDC semantic Web projects will be presented here. The semantic Web based approach for the mashup is focusing on the design and implementation of a common but still distributed data catalog based on semantical interoperability including the transparent access to data in relational data bases. References: https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/207772/Open_Data_Charter.pdfhttp://www.openscience.org/blog/wp-content/uploads/2013/06/OpenSciencePoster.pdf

OpenVigil FDA - Inspection of U.S. American Adverse Drug Events Pharmacovigilance Data and Novel Clinical Applications.

PubMed

Böhm, Ruwen; von Hehn, Leocadie; Herdegen, Thomas; Klein, Hans-Joachim; Bruhn, Oliver; Petri, Holger; Höcker, Jan

2016-01-01

Pharmacovigilance contributes to health care. However, direct access to the underlying data for academic institutions and individual physicians or pharmacists is intricate, and easily employable analysis modes for everyday clinical situations are missing. This underlines the need for a tool to bring pharmacovigilance to the clinics. To address these issues, we have developed OpenVigil FDA, a novel web-based pharmacovigilance analysis tool which uses the openFDA online interface of the Food and Drug Administration (FDA) to access U.S. American and international pharmacovigilance data from the Adverse Event Reporting System (AERS). OpenVigil FDA provides disproportionality analyses to (i) identify the drug most likely evoking a new adverse event, (ii) compare two drugs concerning their safety profile, (iii) check arbitrary combinations of two drugs for unknown drug-drug interactions and (iv) enhance the relevance of results by identifying confounding factors and eliminating them using background correction. We present examples for these applications and discuss the promises and limits of pharmacovigilance, openFDA and OpenVigil FDA. OpenVigil FDA is the first public available tool to apply pharmacovigilance findings directly to real-life clinical problems. OpenVigil FDA does not require special licenses or statistical programs.

Opportunities for strategic use of e-learning in scaling up disaster management capacity in Eastern Africa: a descriptive analysis.

PubMed

William, Mayega Roy; Elzie, D; Sebuwufu, D; Kiguli, J; Bazeyo, W

2013-06-01

The growing need for disaster management skills at all levels in Eastern Africa requires innovative approaches to training planners at all levels. While information technology tools provide a viable option, few studies have assessed the capacity for training institutions to use technology for cascading disaster management skills. The design was an explorative survey. A pre-training survey was conducted among 16 faculty members (9 academic staff and 7 information technology (IT) staff) from 7 schools of public health in Eastern Africa. Key informant interviews with 4 students and 4 staff members were conducted at the school of public health in Makerere. IT staff also conducted observations on trends of use of information technology infrastructure. Current levels of use of ICT among teaching and IT staff is variable. On-site use of the internet is high, but off-site access is low. Personal computers, e-mail, discussion forums and other web-based learning management platforms and open education resources (OERs) have been variably used by faculty and students to facilitate learning. On the other hand, videos, web-conferencing, social media, web-based document management tools, and mobile telephone applications were much less frequently used. A disaster management short course produced by the Health Emergencies Management Project (HEMP) has been adapted to a web-based open education resource and an interactive CD-ROM. Challenges included low levels of awareness and skills in technology options among students and faculty and access to reliable internet. Despite the existing challenges, technology tools are a viable platform for cascading disaster management skills in Eastern Africa.

[How to get free articles on biomedicine from web sites abroad].

PubMed

Lu, Huaiming

2010-12-01

Since "Budapest Open Access Initiative" signed in 2002, there have been more and more open-access journals coming out on Internet, thus brining the best condition to the researchers. It has made better the phenomenon of not having enough foreign language periodicals in our country. The present author has selected part of free biomedicine periodical websites: High Wire Press; PubMed Central; BioMed Central; BioLine International; Free Medical Journals Site; Scientific Electronic Library; Hindawi; Academic Journals Inc; Biomedical Journals from India. And then, analysis and demonstration are made with respect to the search channels of 3 main free electronic periodical websites. It is the intent of this paper to make things convenient for researchers to get information from the websites quickly.

Looking into Pandora's Box: The Content of Sci-Hub and its Usage.

PubMed

Greshake, Bastian

2017-01-01

Despite the growth of Open Access, potentially illegally circumventing paywalls to access scholarly publications is becoming a more mainstream phenomenon. The web service Sci-Hub is amongst the biggest facilitators of this, offering free access to around 62 million publications. So far it is not well studied how and why its users are accessing publications through Sci-Hub. By utilizing the recently released corpus of Sci-Hub and comparing it to the data of  ~28 million downloads done through the service, this study tries to address some of these questions. The comparative analysis shows that both the usage and complete corpus is largely made up of recently published articles, with users disproportionately favoring newer articles and 35% of downloaded articles being published after 2013. These results hint that embargo periods before publications become Open Access are frequently circumnavigated using Guerilla Open Access approaches like Sci-Hub. On a journal level, the downloads show a bias towards some scholarly disciplines, especially Chemistry, suggesting increased barriers to access for these. Comparing the use and corpus on a publisher level, it becomes clear that only 11% of publishers are highly requested in comparison to the baseline frequency, while 45% of all publishers are significantly less accessed than expected. Despite this, the oligopoly of publishers is even more remarkable on the level of content consumption, with 80% of all downloads being published through only 9 publishers. All of this suggests that Sci-Hub is used by different populations and for a number of different reasons, and that there is still a lack of access to the published scientific record. A further analysis of these openly available data resources will undoubtedly be valuable for the investigation of academic publishing.

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

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.

Interoperative fundus image and report sharing in compliance with integrating the healthcare enterprise conformance and web access to digital imaging and communication in medicine persistent object protocol.

PubMed

Wu, Hui-Qun; Lv, Zheng-Min; Geng, Xing-Yun; Jiang, Kui; Tang, Le-Min; Zhou, Guo-Min; Dong, Jian-Cheng

2013-01-01

To address issues in interoperability between different fundus image systems, we proposed a web eye-picture archiving and communication system (PACS) framework in conformance with digital imaging and communication in medicine (DICOM) and health level 7 (HL7) protocol to realize fundus images and reports sharing and communication through internet. Firstly, a telemedicine-based eye care work flow was established based on integrating the healthcare enterprise (IHE) Eye Care technical framework. Then, a browser/server architecture eye-PACS system was established in conformance with the web access to DICOM persistent object (WADO) protocol, which contains three tiers. In any client system installed with web browser, clinicians could log in the eye-PACS to observe fundus images and reports. Multipurpose internet mail extensions (MIME) type of a structured report is saved as pdf/html with reference link to relevant fundus image using the WADO syntax could provide enough information for clinicians. Some functions provided by open-source Oviyam could be used to query, zoom, move, measure, view DICOM fundus images. Such web eye-PACS in compliance to WADO protocol could be used to store and communicate fundus images and reports, therefore is of great significance for teleophthalmology.

A new reference implementation of the PSICQUIC web service.

PubMed

del-Toro, Noemi; Dumousseau, Marine; Orchard, Sandra; Jimenez, Rafael C; Galeota, Eugenia; Launay, Guillaume; Goll, Johannes; Breuer, Karin; Ono, Keiichiro; Salwinski, Lukasz; Hermjakob, Henning

2013-07-01

The Proteomics Standard Initiative Common QUery InterfaCe (PSICQUIC) specification was created by the Human Proteome Organization Proteomics Standards Initiative (HUPO-PSI) to enable computational access to molecular-interaction data resources by means of a standard Web Service and query language. Currently providing >150 million binary interaction evidences from 28 servers globally, the PSICQUIC interface allows the concurrent search of multiple molecular-interaction information resources using a single query. Here, we present an extension of the PSICQUIC specification (version 1.3), which has been released to be compliant with the enhanced standards in molecular interactions. The new release also includes a new reference implementation of the PSICQUIC server available to the data providers. It offers augmented web service capabilities and improves the user experience. PSICQUIC has been running for almost 5 years, with a user base growing from only 4 data providers to 28 (April 2013) allowing access to 151 310 109 binary interactions. The power of this web service is shown in PSICQUIC View web application, an example of how to simultaneously query, browse and download results from the different PSICQUIC servers. This application is free and open to all users with no login requirement (http://www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml).

Development of an IHE MRRT-compliant open-source web-based reporting platform.

PubMed

Pinto Dos Santos, Daniel; Klos, G; Kloeckner, R; Oberle, R; Dueber, C; Mildenberger, P

2017-01-01

To develop a platform that uses structured reporting templates according to the IHE Management of Radiology Report Templates (MRRT) profile, and to implement this platform into clinical routine. The reporting platform uses standard web technologies (HTML / JavaScript and PHP / MySQL) only. Several freely available external libraries were used to simplify the programming. The platform runs on a standard web server, connects with the radiology information system (RIS) and PACS, and is easily accessible via a standard web browser. A prototype platform that allows structured reporting to be easily incorporated into the clinical routine was developed and successfully tested. To date, 797 reports were generated using IHE MRRT-compliant templates (many of them downloaded from the RSNA's radreport.org website). Reports are stored in a MySQL database and are easily accessible for further analyses. Development of an IHE MRRT-compliant platform for structured reporting is feasible using only standard web technologies. All source code will be made available upon request under a free license, and the participation of other institutions in further development is welcome. • A platform for structured reporting using IHE MRRT-compliant templates is presented. • Incorporating structured reporting into clinical routine is feasible. • Full source code will be provided upon request under a free license.

Systematic plan of building Web geographic information system based on ActiveX control

NASA Astrophysics Data System (ADS)

Zhang, Xia; Li, Deren; Zhu, Xinyan; Chen, Nengcheng

2003-03-01

A systematic plan of building Web Geographic Information System (WebGIS) using ActiveX technology is proposed in this paper. In the proposed plan, ActiveX control technology is adopted in building client-side application, and two different schemas are introduced to implement communication between controls in users¡ browser and middle application server. One is based on Distribute Component Object Model (DCOM), the other is based on socket. In the former schema, middle service application is developed as a DCOM object that communicates with ActiveX control through Object Remote Procedure Call (ORPC) and accesses data in GIS Data Server through Open Database Connectivity (ODBC). In the latter, middle service application is developed using Java language. It communicates with ActiveX control through socket based on TCP/IP and accesses data in GIS Data Server through Java Database Connectivity (JDBC). The first one is usually developed using C/C++, and it is difficult to develop and deploy. The second one is relatively easy to develop, but its performance of data transfer relies on Web bandwidth. A sample application is developed using the latter schema. It is proved that the performance of the sample application is better than that of some other WebGIS applications in some degree.

45 CFR 159.120 - Data submission for the individual and small group markets.

Code of Federal Regulations, 2011 CFR

2011-10-01

... submit pricing and benefit data for portal plans associated with products that are newly open or newly... 45 Public Welfare 1 2011-10-01 2011-10-01 false Data submission for the individual and small group... RELATING TO HEALTH CARE ACCESS HEALTH CARE REFORM INSURANCE WEB PORTAL § 159.120 Data submission for the...

45 CFR 159.120 - Data submission for the individual and small group markets.

Code of Federal Regulations, 2010 CFR

2010-10-01

... submit pricing and benefit data for portal plans associated with products that are newly open or newly... 45 Public Welfare 1 2010-10-01 2010-10-01 false Data submission for the individual and small group... RELATING TO HEALTH CARE ACCESS HEALTH CARE REFORM INSURANCE WEB PORTAL § 159.120 Data submission for the...

Internet-Based Public Health E-Learning Student Perceptions: An Evaluation from the People's Open Access Education Initiative (Peoples-uni)

ERIC Educational Resources Information Center

Awofeso, Niyi; Philip, Keir; Heller, Richard F.

2012-01-01

Current public health training infrastructure and facilitators in most developing nations are insufficient relative to public health service delivery needs. We examined five areas of student perceptions of a web-based public health learning initiative, the Peoples-uni, which focused on: reasons for enrolling, learning expectations; technical…

77 FR 61041 - Self-Regulatory Organizations; NASDAQ OMX BX, Inc.; Notice of Filing and Immediate Effectiveness...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-05

.... Purpose The Exchange is proposing to adopt the new QView service. QView is a web-based, front-end... dashboard interface. The dashboard also allows a QView subscriber to track his/her executions and open...-based tool that, among other things, allows users access to all of the BX order and execution...

About | Galaxy of Images

Science.gov Websites

-resolution images directly from the web site for personal, research or study purposes for free. This includes , promotional material, etc. The usage fee is not a copyright fee. You are free to obtain a copy of these images and how our images may be used. Smithsonian Libraries provides free and open access to its digital

Investigating the Effect of Users' Tagging Motivation on the Digital Educational Resources Metadata Descriptions

ERIC Educational Resources Information Center

Zervas, Panagiotis; Sampson, Demetrios G.; Aristeidou, Maria

2012-01-01

Over the past years, several Open Educational Resources (OERs) initiatives have been emerged worldwide aiming to create, share and reuse digital educational resources among educational communities. As a result, organizing, offering and accessing these resources over the web have been key issues for both the research and the educational community.…

BookMeUp: Creating a Book Suggestion App

ERIC Educational Resources Information Center

Clark, Jason

2012-01-01

The rise of apps and mobile devices has opened the door to small, dedicated software programs that are focused on singular tasks. From the author's perspective as head of digital access and web service manager at Montana State University, these apps offered an opportunity to build a focused digital service aimed at allowing someone to enter a…

Supporting the Process of Developing and Managing LOM Application Profiles: The ASK-LOM-AP Tool

ERIC Educational Resources Information Center

Sampson, D. G.; Zervas, P.; Chloros, G.

2012-01-01

A number of international initiatives, such as the Open Educational Resources initiative, have recognized the potential value of sharing and reusing digital resources among educational communities. As a result, organizing, offering, and accessing these resources over the web have been key issues for both the research and the educational community.…

Providing Access to a Diverse Set of Global Reanalysis Dataset Collections

NASA Astrophysics Data System (ADS)

Schuster, D.; Worley, S. J.

2015-12-01

The National Center for Atmospheric Research (NCAR) Research Data Archive (RDA, http://rda.ucar.edu) provides open access to a variety of global reanalysis dataset collections to support atmospheric and related sciences research worldwide. These include products from the European Centre for Medium-Range Weather Forecasts (ECMWF), Japan Meteorological Agency (JMA), National Centers for Environmental Prediction (NCEP), National Oceanic and Atmospheric Administration (NOAA), and NCAR.All RDA hosted reanalysis collections are freely accessible to registered users through a variety of methods. Standard access methods include traditional browser and scripted HTTP file download. Enhanced downloads are available through the Globus GridFTP "fire and forget" data transfer service, which provides an efficient, reliable, and preferred alternative to traditional HTTP-based methods. For those that favor interoperable access using compatible tools, the Unidata THREDDS Data server provides remote access to complete reanalysis collections by virtual dataset aggregation "files". Finally, users can request data subsets and format conversions to be prepared for them through web interface form requests or web service API batch requests. This approach uses NCAR HPC and central file systems to effectively prepare products from the high-resolution and very large reanalyses archives. The presentation will include a detailed inventory of all RDA reanalysis dataset collection holdings, and highlight access capabilities to these collections through use case examples.

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;

Web-based services for drug design and discovery.

PubMed

Frey, Jeremy G; Bird, Colin L

2011-09-01

Reviews of the development of drug discovery through the 20(th) century recognised the importance of chemistry and increasingly bioinformatics, but had relatively little to say about the importance of computing and networked computing in particular. However, the design and discovery of new drugs is arguably the most significant single application of bioinformatics and cheminformatics to have benefitted from the increases in the range and power of the computational techniques since the emergence of the World Wide Web, commonly now referred to as simply 'the Web'. Web services have enabled researchers to access shared resources and to deploy standardized calculations in their search for new drugs. This article first considers the fundamental principles of Web services and workflows, and then explores the facilities and resources that have evolved to meet the specific needs of chem- and bio-informatics. This strategy leads to a more detailed examination of the basic components that characterise molecules and the essential predictive techniques, followed by a discussion of the emerging networked services that transcend the basic provisions, and the growing trend towards embracing modern techniques, in particular the Semantic Web. In the opinion of the authors, the issues that require community action are: increasing the amount of chemical data available for open access; validating the data as provided; and developing more efficient links between the worlds of cheminformatics and bioinformatics. The goal is to create ever better drug design services.

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

GeoChronos: An On-line Collaborative Platform for Earth Observation Scientists

NASA Astrophysics Data System (ADS)

Gamon, J. A.; Kiddle, C.; Curry, R.; Markatchev, N.; Zonta-Pastorello, G., Jr.; Rivard, B.; Sanchez-Azofeifa, G. A.; Simmonds, R.; Tan, T.

2009-12-01

Recent advances in cyberinfrastructure are offering new solutions to the growing challenges of managing and sharing large data volumes. Web 2.0 and social networking technologies, provide the means for scientists to collaborate and share information more effectively. Cloud computing technologies can provide scientists with transparent and on-demand access to applications served over the Internet in a dynamic and scalable manner. Semantic Web technologies allow for data to be linked together in a manner understandable by machines, enabling greater automation. Combining all of these technologies together can enable the creation of very powerful platforms. GeoChronos (http://geochronos.org/), part of a CANARIE Network Enabled Platforms project, is an online collaborative platform that incorporates these technologies to enable members of the earth observation science community to share data and scientific applications and to collaborate more effectively. The GeoChronos portal is built on an open source social networking platform called Elgg. Elgg provides a full set of social networking functionalities similar to Facebook including blogs, tags, media/document sharing, wikis, friends/contacts, groups, discussions, message boards, calendars, status, activity feeds and more. An underlying cloud computing infrastructure enables scientists to access dynamically provisioned applications via the portal for visualizing and analyzing data. Users are able to access and run the applications from any computer that has a Web browser and Internet connectivity and do not need to manage and maintain the applications themselves. Semantic Web Technologies, such as the Resource Description Framework (RDF) are being employed for relating and linking together spectral, satellite, meteorological and other data. Social networking functionality plays an integral part in facilitating the sharing of data and applications. Examples of recent GeoChronos users during the early testing phase have included the IAI International Wireless Sensor Networking Summer School at the University of Alberta, and the IAI Tropi-Dry community. Current GeoChronos activities include the development of a web-based spectral library and related analytical and visualization tools, in collaboration with members of the SpecNet community. The GeoChronos portal will be open to all members of the earth observation science community when the project nears completion at the end of 2010.

Evaluation of Web Accessibility of Consumer Health Information Websites

PubMed Central

Zeng, Xiaoming; Parmanto, Bambang

2003-01-01

The objectives of the study are to construct a comprehensive framework for web accessibility evaluation, to evaluate the current status of web accessibility of consumer health information websites and to investigate the relationship between web accessibility and property of the websites. We selected 108 consumer health information websites from the directory service of a Web search engine. We used Web accessibility specifications to construct a framework for the measurement of Web Accessibility Barriers (WAB) of website. We found that none of the websites is completely accessible to people with disabilities, but governmental and educational health information websites exhibit better performance on web accessibility than other categories of websites. We also found that the correlation between the WAB score and the popularity of a website is statistically significant. PMID:14728272

Evaluation of web accessibility of consumer health information websites.

PubMed

Zeng, Xiaoming; Parmanto, Bambang

2003-01-01

The objectives of the study are to construct a comprehensive framework for web accessibility evaluation, to evaluate the current status of web accessibility of consumer health information websites and to investigate the relationship between web accessibility and property of the websites. We selected 108 consumer health information websites from the directory service of a Web search engine. We used Web accessibility specifications to construct a framework for the measurement of Web Accessibility Barriers (WAB) of website. We found that none of the websites is completely accessible to people with disabilities, but governmental and educational health information websites exhibit better performance on web accessibility than other categories of websites. We also found that the correlation between the WAB score and the popularity of a website is statistically significant.

Vascular Access Tracking System: a Web-Based Clinical Tracking Tool for Identifying Catheter Related Blood Stream Infections in Interventional Radiology Placed Central Venous Catheters.

PubMed

Morrison, James; Kaufman, John

2016-12-01

Vascular access is invaluable in the treatment of hospitalized patients. Central venous catheters provide a durable and long-term solution while saving patients from repeated needle sticks for peripheral IVs and blood draws. The initial catheter placement procedure and long-term catheter usage place patients at risk for infection. The goal of this project was to develop a system to track and evaluate central line-associated blood stream infections related to interventional radiology placement of central venous catheters. A customized web-based clinical database was developed via open-source tools to provide a dashboard for data mining and analysis of the catheter placement and infection information. Preliminary results were gathered over a 4-month period confirming the utility of the system. The tools and methodology employed to develop the vascular access tracking system could be easily tailored to other clinical scenarios to assist in quality control and improvement programs.

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.

PubMed

Rose, Peter W; Prlić, Andreas; Bi, Chunxiao; Bluhm, Wolfgang F; Christie, Cole H; Dutta, Shuchismita; Green, Rachel Kramer; Goodsell, David S; Westbrook, John D; Woo, Jesse; Young, Jasmine; Zardecki, Christine; Berman, Helen M; Bourne, Philip E; Burley, Stephen K

2015-01-01

The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

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/

WebArray: an online platform for microarray data analysis

PubMed Central

Xia, Xiaoqin; McClelland, Michael; Wang, Yipeng

2005-01-01

Background Many cutting-edge microarray analysis tools and algorithms, including commonly used limma and affy packages in Bioconductor, need sophisticated knowledge of mathematics, statistics and computer skills for implementation. Commercially available software can provide a user-friendly interface at considerable cost. To facilitate the use of these tools for microarray data analysis on an open platform we developed an online microarray data analysis platform, WebArray, for bench biologists to utilize these tools to explore data from single/dual color microarray experiments. Results The currently implemented functions were based on limma and affy package from Bioconductor, the spacings LOESS histogram (SPLOSH) method, PCA-assisted normalization method and genome mapping method. WebArray incorporates these packages and provides a user-friendly interface for accessing a wide range of key functions of limma and others, such as spot quality weight, background correction, graphical plotting, normalization, linear modeling, empirical bayes statistical analysis, false discovery rate (FDR) estimation, chromosomal mapping for genome comparison. Conclusion WebArray offers a convenient platform for bench biologists to access several cutting-edge microarray data analysis tools. The website is freely available at . It runs on a Linux server with Apache and MySQL. PMID:16371165

Formats and Network Protocols for Browser Access to 2D Raster Data

NASA Astrophysics Data System (ADS)

Plesea, L.

2015-12-01

Tiled web maps in browsers are a major success story, forming the foundation of many current web applications. Enabling tiled data access is the next logical step, and is likely to meet with similar success. Many ad-hoc approaches have already started to appear, and something similar is explored within the Open Geospatial Consortium. One of the main obstacles in making browser data access a reality is the lack of a well-known data format. This obstacle also represents an opportunity to analyze the requirements and possible candidates, applying lessons learned from web tiled image services and protocols. Similar to the image counterpart, a web tile raster data format needs to have good intrinsic compression and be able to handle high byte count data types including floating point. An overview of a possible solution to the format problem, a 2D data raster compression algorithm called Limited Error Raster Compression (LERC) will be presented. In addition to the format, best practices for high request rate HTTP services also need to be followed. In particular, content delivery network (CDN) caching suitability needs to be part of any design, not an after-thought. Last but not least, HTML 5 browsers will certainly be part of any solution since they provide improved access to binary data, as well as more powerful ways to view and interact with the data in the browser. In a simple but relevant application, digital elevation model (DEM) raster data is served as LERC compressed data tiles which are used to generate terrain by a HTML5 scene viewer.

Resolving the problem of multiple accessions of the same transcript deposited across various public databases.

PubMed

Weirick, Tyler; John, David; Uchida, Shizuka

2017-03-01

Maintaining the consistency of genomic annotations is an increasingly complex task because of the iterative and dynamic nature of assembly and annotation, growing numbers of biological databases and insufficient integration of annotations across databases. As information exchange among databases is poor, a 'novel' sequence from one reference annotation could be annotated in another. Furthermore, relationships to nearby or overlapping annotated transcripts are even more complicated when using different genome assemblies. To better understand these problems, we surveyed current and previous versions of genomic assemblies and annotations across a number of public databases containing long noncoding RNA. We identified numerous discrepancies of transcripts regarding their genomic locations, transcript lengths and identifiers. Further investigation showed that the positional differences between reference annotations of essentially the same transcript could lead to differences in its measured expression at the RNA level. To aid in resolving these problems, we present the algorithm 'Universal Genomic Accession Hash (UGAHash)' and created an open source web tool to encourage the usage of the UGAHash algorithm. The UGAHash web tool (http://ugahash.uni-frankfurt.de) can be accessed freely without registration. The web tool allows researchers to generate Universal Genomic Accessions for genomic features or to explore annotations deposited in the public databases of the past and present versions. We anticipate that the UGAHash web tool will be a valuable tool to check for the existence of transcripts before judging the newly discovered transcripts as novel. © The Author 2016. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

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.

Availability of the OGC geoprocessing standard: March 2011 reality check

NASA Astrophysics Data System (ADS)

Lopez-Pellicer, Francisco J.; Rentería-Agualimpia, Walter; Béjar, Rubén; Muro-Medrano, Pedro R.; Zarazaga-Soria, F. Javier

2012-10-01

This paper presents an investigation about the servers available in March 2011 conforming to the Web Processing Service interface specification published by the geospatial standards organization Open Geospatial Consortium (OGC) in 2007. This interface specification gives support to standard Web-based geoprocessing. The data used in this research were collected using a focused crawler configured for finding OGC Web services. The research goals are (i) to provide a reality check of the availability of Web Processing Service servers, (ii) to provide quantitative data about the use of different features defined in the standard that are relevant for a scalable Geoprocessing Web (e.g. long-running processes, Web-accessible data outputs), and (iii) to test if the advances in the use of search engines and focused crawlers for finding Web services can be applied for finding geoscience processing systems. Research results show the feasibility of the discovery approach and provide data about the implementation of the Web Processing Service specification. These results also show extensive use of features related to scalability, except for those related to technical and semantic interoperability.

Automated Rocket Propulsion Test Management

NASA Technical Reports Server (NTRS)

Walters, Ian; Nelson, Cheryl; Jones, Helene

2007-01-01

The Rocket Propulsion Test-Automated Management System provides a central location for managing activities associated with Rocket Propulsion Test Management Board, National Rocket Propulsion Test Alliance, and the Senior Steering Group business management activities. A set of authorized users, both on-site and off-site with regard to Stennis Space Center (SSC), can access the system through a Web interface. Web-based forms are used for user input with generation and electronic distribution of reports easily accessible. Major functions managed by this software include meeting agenda management, meeting minutes, action requests, action items, directives, and recommendations. Additional functions include electronic review, approval, and signatures. A repository/library of documents is available for users, and all items are tracked in the system by unique identification numbers and status (open, closed, percent complete, etc.). The system also provides queries and version control for input of all items.

Corrections to: Use of the BOADICEA Web Application in clinical practice: appraisals by clinicians from various countries.

PubMed

Brédart, Anne; Kop, Jean-Luc; Antoniou, Antonis C; Cunningham, Alex P; De Pauw, Antoine; Tischkowitz, Marc; Ehrencrona, Hans; Dolbeault, Sylvie; Robieux, Léonore; Rhiem, Kerstin; Easton, Douglas F; Devilee, Peter; Stoppa-Lyonnet, Dominique; Schmutlzer, Rita

2018-07-01

The article "Use of the BOADICEA Web Application in clinical practice: appraisals by clinicians from various countries" written by Anne Brédart · Jean‑Luc Kop · Antonis C. Antoniou · Alex P. Cunningham · Antoine De Pauw ·Marc Tischkowitz · Hans Ehrencrona · Sylvie Dolbeault · Léonore Robieux · Kerstin Rhiem ·Douglas F. Easton · Peter Devilee · Dominique Stoppa‑Lyonnet· Rita Schmutlzer, was originally published electronically on the publisher's internet portal (currently SpringerLink) on 16th June 2017 without open access.

The transcription factor encyclopedia.

PubMed

Yusuf, Dimas; Butland, Stefanie L; Swanson, Magdalena I; Bolotin, Eugene; Ticoll, Amy; Cheung, Warren A; Zhang, Xiao Yu Cindy; Dickman, Christopher T D; Fulton, Debra L; Lim, Jonathan S; Schnabl, Jake M; Ramos, Oscar H P; Vasseur-Cognet, Mireille; de Leeuw, Charles N; Simpson, Elizabeth M; Ryffel, Gerhart U; Lam, Eric W-F; Kist, Ralf; Wilson, Miranda S C; Marco-Ferreres, Raquel; Brosens, Jan J; Beccari, Leonardo L; Bovolenta, Paola; Benayoun, Bérénice A; Monteiro, Lara J; Schwenen, Helma D C; Grontved, Lars; Wederell, Elizabeth; Mandrup, Susanne; Veitia, Reiner A; Chakravarthy, Harini; Hoodless, Pamela A; Mancarelli, M Michela; Torbett, Bruce E; Banham, Alison H; Reddy, Sekhar P; Cullum, Rebecca L; Liedtke, Michaela; Tschan, Mario P; Vaz, Michelle; Rizzino, Angie; Zannini, Mariastella; Frietze, Seth; Farnham, Peggy J; Eijkelenboom, Astrid; Brown, Philip J; Laperrière, David; Leprince, Dominique; de Cristofaro, Tiziana; Prince, Kelly L; Putker, Marrit; del Peso, Luis; Camenisch, Gieri; Wenger, Roland H; Mikula, Michal; Rozendaal, Marieke; Mader, Sylvie; Ostrowski, Jerzy; Rhodes, Simon J; Van Rechem, Capucine; Boulay, Gaylor; Olechnowicz, Sam W Z; Breslin, Mary B; Lan, Michael S; Nanan, Kyster K; Wegner, Michael; Hou, Juan; Mullen, Rachel D; Colvin, Stephanie C; Noy, Peter John; Webb, Carol F; Witek, Matthew E; Ferrell, Scott; Daniel, Juliet M; Park, Jason; Waldman, Scott A; Peet, Daniel J; Taggart, Michael; Jayaraman, Padma-Sheela; Karrich, Julien J; Blom, Bianca; Vesuna, Farhad; O'Geen, Henriette; Sun, Yunfu; Gronostajski, Richard M; Woodcroft, Mark W; Hough, Margaret R; Chen, Edwin; Europe-Finner, G Nicholas; Karolczak-Bayatti, Magdalena; Bailey, Jarrod; Hankinson, Oliver; Raman, Venu; LeBrun, David P; Biswal, Shyam; Harvey, Christopher J; DeBruyne, Jason P; Hogenesch, John B; Hevner, Robert F; Héligon, Christophe; Luo, Xin M; Blank, Marissa Cathleen; Millen, Kathleen Joyce; Sharlin, David S; Forrest, Douglas; Dahlman-Wright, Karin; Zhao, Chunyan; Mishima, Yuriko; Sinha, Satrajit; Chakrabarti, Rumela; Portales-Casamar, Elodie; Sladek, Frances M; Bradley, Philip H; Wasserman, Wyeth W

2012-01-01

Here we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded on the principles of open access and collaboration. Our consortium of over 100 researchers has collectively contributed over 130 mini review articles on pertinent human, mouse and rat TFs. Notable features of the TFe website include a high-quality PDF generator and web API for programmatic data retrieval. TFe aims to rapidly educate scientists about the TFs they encounter through the delivery of succinct summaries written and vetted by experts in the field. TFe is available at http://www.cisreg.ca/tfe.

HTML5 PivotViewer: high-throughput visualization and querying of image data on the web.

PubMed

Taylor, Stephen; Noble, Roger

2014-09-15

Visualization and analysis of large numbers of biological images has generated a bottle neck in research. We present HTML5 PivotViewer, a novel, open source, platform-independent viewer making use of the latest web technologies that allows seamless access to images and associated metadata for each image. This provides a powerful method to allow end users to mine their data. Documentation, examples and links to the software are available from http://www.cbrg.ox.ac.uk/data/pivotviewer/. The software is licensed under GPLv2. © The Author 2014. Published by Oxford University Press.

Free-access open-source e-learning in comprehensive neurosurgery skills training.

PubMed

Jotwani, Payal; Srivastav, Vinkle; Tripathi, Manjul; Deo, Rama Chandra; Baby, Britty; Damodaran, Natesan; Singh, Ramandeep; Suri, Ashish; Bettag, Martin; Roy, Tara Sankar; Busert, Christoph; Mehlitz, Marcus; Lalwani, Sanjeev; Garg, Kanwaljeet; Paul, Kolin; Prasad, Sanjiva; Banerjee, Subhashis; Kalra, Prem; Kumar, Subodh; Sharma, Bhavani Shankar; Mahapatra, Ashok Kumar

2014-01-01

Since the end of last century, technology has taken a front seat in dispersion of medical education. Advancements of technology in neurosurgery and traditional training methods are now being challenged by legal and ethical concerns of patient safety, resident work-hour restriction and cost of operating-room time. To supplement the existing neurosurgery education pattern, various e-learning platforms are introduced as structured, interactive learning system. This study focuses on the concept, formulation, development and impact of web based learning platforms dedicated to neurosurgery discipline to disseminate education, supplement surgical knowledge and improve skills of neurosurgeons. 'Neurosurgery Education and Training School (NETS), e-learning platform' has integration of web-based technologies like 'Content Management System' for organizing the education material and 'Learning Management System' for updating neurosurgeons. NETS discussion forum networks neurosurgeons, neuroscientists and neuro-technologists across the globe facilitating collaborative translational research. Multi-authored neurosurgical e-learning material supplements the deficiencies of regular time-bound education. Interactive open-source, global, free-access e-learning platform of NETS has around 1) 425 visitors/month from 73 countries; ratio of new visitors to returning visitors 42.3; 57.7 (2); 64,380 views from 190 subscribers for surgical videos, 3-D animation, graphics based training modules (3); average 402 views per post. The e-Learning platforms provide updated educational content that make them "quick, surf, find and extract" resources. e-Learning tools like web-based education, social interactive platform and question-answer forum will save unnecessary expenditure of time and travel of neurosurgeons seeking knowledge. The need for free access platforms is more pronounced for the neurosurgeons and patients in developing nations.

MetaNET--a web-accessible interactive platform for biological metabolic network analysis.

PubMed

Narang, Pankaj; Khan, Shawez; Hemrom, Anmol Jaywant; Lynn, Andrew Michael

2014-01-01

Metabolic reactions have been extensively studied and compiled over the last century. These have provided a theoretical base to implement models, simulations of which are used to identify drug targets and optimize metabolic throughput at a systemic level. While tools for the perturbation of metabolic networks are available, their applications are limited and restricted as they require varied dependencies and often a commercial platform for full functionality. We have developed MetaNET, an open source user-friendly platform-independent and web-accessible resource consisting of several pre-defined workflows for metabolic network analysis. MetaNET is a web-accessible platform that incorporates a range of functions which can be combined to produce different simulations related to metabolic networks. These include (i) optimization of an objective function for wild type strain, gene/catalyst/reaction knock-out/knock-down analysis using flux balance analysis. (ii) flux variability analysis (iii) chemical species participation (iv) cycles and extreme paths identification and (v) choke point reaction analysis to facilitate identification of potential drug targets. The platform is built using custom scripts along with the open-source Galaxy workflow and Systems Biology Research Tool as components. Pre-defined workflows are available for common processes, and an exhaustive list of over 50 functions are provided for user defined workflows. MetaNET, available at http://metanet.osdd.net , provides a user-friendly rich interface allowing the analysis of genome-scale metabolic networks under various genetic and environmental conditions. The framework permits the storage of previous results, the ability to repeat analysis and share results with other users over the internet as well as run different tools simultaneously using pre-defined workflows, and user-created custom workflows.

Implementing Recommendations From Web Accessibility Guidelines: Would They Also Provide Benefits to Nondisabled Users.

PubMed

Schmutz, Sven; Sonderegger, Andreas; Sauer, Juergen

2016-06-01

We examined the consequences of implementing Web accessibility guidelines for nondisabled users. Although there are Web accessibility guidelines for people with disabilities available, they are rarely used in practice, partly due to the fact that practitioners believe that such guidelines provide no benefits, or even have negative consequences, for nondisabled people, who represent the main user group of Web sites. Despite these concerns, there is a lack of empirical research on the effects of current Web accessibility guidelines on nondisabled users. Sixty-one nondisabled participants used one of three Web sites differing in levels of accessibility (high, low, and very low). Accessibility levels were determined by following established Web accessibility guidelines (WCAG 2.0). A broad methodological approach was used, including performance measures (e.g., task completion time) and user ratings (e.g., perceived usability). A high level of Web accessibility led to better performance (i.e., task completion time and task completion rate) than low or very low accessibility. Likewise, high Web accessibility improved user ratings (i.e., perceived usability, aesthetics, workload, and trustworthiness) compared to low or very low Web accessibility. There was no difference between the very low and low Web accessibility conditions for any of the outcome measures. Contrary to some concerns in the literature and among practitioners, high conformance with Web accessibility guidelines may provide benefits to users without disabilities. The findings may encourage more practitioners to implement WCAG 2.0 for the benefit of users with disabilities and nondisabled users. © 2016, Human Factors and Ergonomics Society.

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.

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.

PAVICS: A Platform for the Analysis and Visualization of Climate Science

NASA Astrophysics Data System (ADS)

Gauvin St-Denis, B.; Landry, T.; Huard, D. B.; Byrns, D.; Chaumont, D.; Foucher, S.

2016-12-01

Climate service providers are boundary organizations working at the interface of climate science research and users of climate information. Users include academics in other disciplines looking for credible, customized future climate scenarios, government planners, resource managers, asset owners, as well as service utilities. These users are looking for relevant information regarding the impacts of climate change as well as informing decisions regarding adaptation options. As climate change concerns become mainstream, the pressure on climate service providers to deliver tailored, high quality information in a timely manner increases rapidly. To meet this growing demand, Ouranos, a climate service center located in Montreal, is collaborating with the Centre de recherche informatique de Montreal (CRIM) to develop a climate data analysis web-based platform interacting with RESTful services covering data access and retrieval, geospatial analysis, bias correction, distributed climate indicator computing and results visualization. The project, financed by CANARIE, relies on the experience of the UV-CDAT and ESGF-CWT teams, as well as on the Birdhouse framework developed by the German Climate Research Center (DKRZ) and French IPSL. Climate data is accessed through OPEnDAP, while computations are carried through WPS. Regions such as watersheds or user-defined polygons, used as spatial selections for computations, are managed by GeoServer, also providing WMS, WFS and WPS capabilities. The services are hosted on independent servers communicating by high throughput network. Deployment, maintenance and collaboration with other development teams are eased by the use of Docker and OpenStack VMs. Web-based tools are developed with modern web frameworks such as React-Redux, OpenLayers 3, Cesium and Plotly. Although the main objective of the project is to build a functioning, usable data analysis pipeline within two years, time is also devoted to explore emerging technologies and assess their potential. For instance, sandbox environments will store climate data in HDFS, process it with Apache Spark and allow interaction through Jupyter Notebooks. Data streaming of observational data with OpenGL and Cesium is also considered.

MUSTANG: A Community-Facing Web Service to Improve Seismic Data Quality Awareness Through Metrics

NASA Astrophysics Data System (ADS)

Templeton, M. E.; Ahern, T. K.; Casey, R. E.; Sharer, G.; Weertman, B.; Ashmore, S.

2014-12-01

IRIS DMC is engaged in a new effort to provide broad and deep visibility into the quality of data and metadata found in its terabyte-scale geophysical data archive. Taking advantage of large and fast disk capacity, modern advances in open database technologies, and nimble provisioning of virtual machine resources, we are creating an openly accessible treasure trove of data measurements for scientists and the general public to utilize in providing new insights into the quality of this data. We have branded this statistical gathering system MUSTANG, and have constructed it as a component of the web services suite that IRIS DMC offers. MUSTANG measures over forty data metrics addressing issues with archive status, data statistics and continuity, signal anomalies, noise analysis, metadata checks, and station state of health. These metrics could potentially be used both by network operators to diagnose station problems and by data users to sort suitable data from unreliable or unusable data. Our poster details what MUSTANG is, how users can access it, what measurements they can find, and how MUSTANG fits into the IRIS DMC's data access ecosystem. Progress in data processing, approaches to data visualization, and case studies of MUSTANG's use for quality assurance will be presented. We want to illustrate what is possible with data quality assurance, the need for data quality assurance, and how the seismic community will benefit from this freely available analytics service.

The U.S. Geological Survey Monthly Water Balance Model Futures Portal

USGS Publications Warehouse

Bock, Andrew R.; Hay, Lauren E.; Markstrom, Steven L.; Emmerich, Christopher; Talbert, Marian

2017-05-03

The U.S. Geological Survey Monthly Water Balance Model Futures Portal (https://my.usgs.gov/mows/) is a user-friendly interface that summarizes monthly historical and simulated future conditions for seven hydrologic and meteorological variables (actual evapotranspiration, potential evapotranspiration, precipitation, runoff, snow water equivalent, atmospheric temperature, and streamflow) at locations across the conterminous United States (CONUS).The estimates of these hydrologic and meteorological variables were derived using a Monthly Water Balance Model (MWBM), a modular system that simulates monthly estimates of components of the hydrologic cycle using monthly precipitation and atmospheric temperature inputs. Precipitation and atmospheric temperature from 222 climate datasets spanning historical conditions (1952 through 2005) and simulated future conditions (2020 through 2099) were summarized for hydrographic features and used to drive the MWBM for the CONUS. The MWBM input and output variables were organized into an open-access database. An Open Geospatial Consortium, Inc., Web Feature Service allows the querying and identification of hydrographic features across the CONUS. To connect the Web Feature Service to the open-access database, a user interface—the Monthly Water Balance Model Futures Portal—was developed to allow the dynamic generation of summary files and plots  based on plot type, geographic location, specific climate datasets, period of record, MWBM variable, and other options. Both the plots and the data files are made available to the user for download 

A DS106 Thing Happened on the Way to the 3M Tech Forum

ERIC Educational Resources Information Center

Lockridge, Rochelle; Levine, Alan; Funes, Mariana

2014-01-01

This case study illustrates how DS106, a computer science course in Digital Storytelling from the University of Mary Washington (UMW) and accessible as an open course on the web, is being explored in a corporate environment at 3M, an American multinational corporation based in St. Paul, Minnesota, to build community, collaboration, and more…

Development of an Innovative Interactive Virtual Classroom System for K-12 Education Using Google App Engine

ERIC Educational Resources Information Center

Mumba, Frackson; Zhu, Mengxia

2013-01-01

This paper presents a Simulation-based interactive Virtual ClassRoom web system (SVCR: www.vclasie.com) powered by the state-of-the-art cloud computing technology from Google SVCR integrates popular free open-source math, science and engineering simulations and provides functions such as secure user access control and management of courses,…

75 FR 82365 - Determinations Concerning Need for Error Correction, Partial Approval and Partial Disapproval...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-30

...) for Texas. This action is based on EPA's determination that Texas's PSD program is flawed because the...://www.regulations.gov Web site is an ``anonymous access'' system, which means EPA will not know your... open from 8:30 a.m. to 4:30 p.m., Monday through Friday, excluding legal holidays. The telephone number...

An Easy-to-Build Remote Laboratory with Data Transfer Using the Internet School Experimental System

ERIC Educational Resources Information Center

Schauer, Frantisek; Lustig, Frantisek; Dvorak, Jiri; Ozvoldova, Miroslava

2008-01-01

The present state of information communication technology makes it possible to devise and run computer-based e-laboratories accessible to any user with a connection to the Internet, equipped with very simple technical means and making full use of web services. Thus, the way is open for a new strategy of physics education with strongly global…

Improving Web Accessibility in a University Setting

ERIC Educational Resources Information Center

Olive, Geoffrey C.

2010-01-01

Improving Web accessibility for disabled users visiting a university's Web site is explored following the World Wide Web Consortium (W3C) guidelines and Section 508 of the Rehabilitation Act rules for Web page designers to ensure accessibility. The literature supports the view that accessibility is sorely lacking, not only in the USA, but also…

Electronic Ramp to Success: Designing Campus Web Pages for Users with Disabilities.

ERIC Educational Resources Information Center

Coombs, Norman

2002-01-01

Discusses key issues in addressing the challenge of Web accessibility for people with disabilities, including tools for Web authoring, repairing, and accessibility validation, and relevant legal issues. Presents standards for Web accessibility, including the Section 508 Standards from the Federal Access Board, and the World Wide Web Consortium's…

A framework for integration of scientific applications into the OpenTopography workflow

NASA Astrophysics Data System (ADS)

Nandigam, V.; Crosby, C.; Baru, C.

2012-12-01

The NSF-funded OpenTopography facility provides online access to Earth science-oriented high-resolution LIDAR topography data, online processing tools, and derivative products. The underlying cyberinfrastructure employs a multi-tier service oriented architecture that is comprised of an infrastructure tier, a processing services tier, and an application tier. The infrastructure tier consists of storage, compute resources as well as supporting databases. The services tier consists of the set of processing routines each deployed as a Web service. The applications tier provides client interfaces to the system. (e.g. Portal). We propose a "pluggable" infrastructure design that will allow new scientific algorithms and processing routines developed and maintained by the community to be integrated into the OpenTopography system so that the wider earth science community can benefit from its availability. All core components in OpenTopography are available as Web services using a customized open-source Opal toolkit. The Opal toolkit provides mechanisms to manage and track job submissions, with the help of a back-end database. It allows monitoring of job and system status by providing charting tools. All core components in OpenTopography have been developed, maintained and wrapped as Web services using Opal by OpenTopography developers. However, as the scientific community develops new processing and analysis approaches this integration approach is not scalable efficiently. Most of the new scientific applications will have their own active development teams performing regular updates, maintenance and other improvements. It would be optimal to have the application co-located where its developers can continue to actively work on it while still making it accessible within the OpenTopography workflow for processing capabilities. We will utilize a software framework for remote integration of these scientific applications into the OpenTopography system. This will be accomplished by virtually extending the OpenTopography service over the various infrastructures running these scientific applications and processing routines. This involves packaging and distributing a customized instance of the Opal toolkit that will wrap the software application as an OPAL-based web service and integrate it into the OpenTopography framework. We plan to make this as automated as possible. A structured specification of service inputs and outputs along with metadata annotations encoded in XML can be utilized to automate the generation of user interfaces, with appropriate tools tips and user help features, and generation of other internal software. The OpenTopography Opal toolkit will also include the customizations that will enable security authentication, authorization and the ability to write application usage and job statistics back to the OpenTopography databases. This usage information could then be reported to the original service providers and used for auditing and performance improvements. This pluggable framework will enable the application developers to continue to work on enhancing their application while making the latest iteration available in a timely manner to the earth sciences community. This will also help us establish an overall framework that other scientific application providers will also be able to use going forward.

Current state of web accessibility of Malaysian ministries websites

NASA Astrophysics Data System (ADS)

Ahmi, Aidi; Mohamad, Rosli

2016-08-01

Despite the fact that Malaysian public institutions have progressed considerably on website and portal usage, web accessibility has been reported as one of the issues deserves special attention. Consistent with the government moves to promote an effective use of web and portal, it is essential for the government institutions to ensure compliance with established standards and guidelines on web accessibility. This paper evaluates accessibility of 25 Malaysian ministries websites using automated tools i.e. WAVE and Achecker. Both tools are designed to objectively evaluate web accessibility in conformance with Web Content Accessibility Guidelines 2.0 (WCAG 2.0) and United States Rehabilitation Act 1973 (Section 508). The findings reported somewhat low compliance to web accessibility standard amongst the ministries. Further enhancement is needed in the aspect of input elements such as label and checkbox to be associated with text as well as image-related elements. This findings could be used as a mechanism for webmasters to locate and rectify errors pertaining to the web accessibility and to ensure equal access of the web information and services to all citizen.

Leveraging Open Standards and Technologies to Enhance Community Access to Earth Science Lidar Data

NASA Astrophysics Data System (ADS)

Crosby, C. J.; Nandigam, V.; Krishnan, S.; Cowart, C.; Baru, C.; Arrowsmith, R.

2011-12-01

Lidar (Light Detection and Ranging) data, collected from space, airborne and terrestrial platforms, have emerged as an invaluable tool for a variety of Earth science applications ranging from ice sheet monitoring to modeling of earth surface processes. However, lidar present a unique suite of challenges from the perspective of building cyberinfrastructure systems that enable the scientific community to access these valuable research datasets. Lidar data are typically characterized by millions to billions of individual measurements of x,y,z position plus attributes; these "raw" data are also often accompanied by derived raster products and are frequently terabytes in size. As a relatively new and rapidly evolving data collection technology, relevant open data standards and software projects are immature compared to those for other remote sensing platforms. The NSF-funded OpenTopography Facility project has developed an online lidar data access and processing system that co-locates data with on-demand processing tools to enable users to access both raw point cloud data as well as custom derived products and visualizations. OpenTopography is built on a Service Oriented Architecture (SOA) in which applications and data resources are deployed as standards compliant (XML and SOAP) Web services with the open source Opal Toolkit. To develop the underlying applications for data access, filtering and conversion, and various processing tasks, OpenTopography has heavily leveraged existing open source software efforts for both lidar and raster data. Operating on the de facto LAS binary point cloud format (maintained by ASPRS), open source libLAS and LASlib libraries provide OpenTopography data ingestion, query and translation capabilities. Similarly, raster data manipulation is performed through a suite of services built on the Geospatial Data Abstraction Library (GDAL). OpenTopography has also developed our own algorithm for high-performance gridding of lidar point cloud data, Points2Grid, and have released the code as an open source project. An emerging conversation that the lidar community and OpenTopography are actively engaged in is the need for open, community supported standards and metadata for both full waveform and terrestrial (waveform and discrete return) lidar data. Further, given the immature nature of many lidar data archives and limited online access to public domain data, there is an opportunity to develop interoperable data catalogs based on an open standard such as the OGC CSW specification to facilitate discovery and access to Earth science oriented lidar data.

BrainBrowser: distributed, web-based neurological data visualization.

PubMed

Sherif, Tarek; Kassis, Nicolas; Rousseau, Marc-Étienne; Adalat, Reza; Evans, Alan C

2014-01-01

Recent years have seen massive, distributed datasets become the norm in neuroimaging research, and the methodologies used to analyze them have, in response, become more collaborative and exploratory. Tools and infrastructure are continuously being developed and deployed to facilitate research in this context: grid computation platforms to process the data, distributed data stores to house and share them, high-speed networks to move them around and collaborative, often web-based, platforms to provide access to and sometimes manage the entire system. BrainBrowser is a lightweight, high-performance JavaScript visualization library built to provide easy-to-use, powerful, on-demand visualization of remote datasets in this new research environment. BrainBrowser leverages modern web technologies, such as WebGL, HTML5 and Web Workers, to visualize 3D surface and volumetric neuroimaging data in any modern web browser without requiring any browser plugins. It is thus trivial to integrate BrainBrowser into any web-based platform. BrainBrowser is simple enough to produce a basic web-based visualization in a few lines of code, while at the same time being robust enough to create full-featured visualization applications. BrainBrowser can dynamically load the data required for a given visualization, so no network bandwidth needs to be waisted on data that will not be used. BrainBrowser's integration into the standardized web platform also allows users to consider using 3D data visualization in novel ways, such as for data distribution, data sharing and dynamic online publications. BrainBrowser is already being used in two major online platforms, CBRAIN and LORIS, and has been used to make the 1TB MACACC dataset openly accessible.

BrainBrowser: distributed, web-based neurological data visualization

PubMed Central

Sherif, Tarek; Kassis, Nicolas; Rousseau, Marc-Étienne; Adalat, Reza; Evans, Alan C.

2015-01-01

Recent years have seen massive, distributed datasets become the norm in neuroimaging research, and the methodologies used to analyze them have, in response, become more collaborative and exploratory. Tools and infrastructure are continuously being developed and deployed to facilitate research in this context: grid computation platforms to process the data, distributed data stores to house and share them, high-speed networks to move them around and collaborative, often web-based, platforms to provide access to and sometimes manage the entire system. BrainBrowser is a lightweight, high-performance JavaScript visualization library built to provide easy-to-use, powerful, on-demand visualization of remote datasets in this new research environment. BrainBrowser leverages modern web technologies, such as WebGL, HTML5 and Web Workers, to visualize 3D surface and volumetric neuroimaging data in any modern web browser without requiring any browser plugins. It is thus trivial to integrate BrainBrowser into any web-based platform. BrainBrowser is simple enough to produce a basic web-based visualization in a few lines of code, while at the same time being robust enough to create full-featured visualization applications. BrainBrowser can dynamically load the data required for a given visualization, so no network bandwidth needs to be waisted on data that will not be used. BrainBrowser's integration into the standardized web platform also allows users to consider using 3D data visualization in novel ways, such as for data distribution, data sharing and dynamic online publications. BrainBrowser is already being used in two major online platforms, CBRAIN and LORIS, and has been used to make the 1TB MACACC dataset openly accessible. PMID:25628562

Installation of the National Transport Code Collaboration Data Server at the ITPA International Multi-tokamak Confinement Profile Database

NASA Astrophysics Data System (ADS)

Roach, Colin; Carlsson, Johan; Cary, John R.; Alexander, David A.

2002-11-01

The National Transport Code Collaboration (NTCC) has developed an array of software, including a data client/server. The data server, which is written in C++, serves local data (in the ITER Profile Database format) as well as remote data (by accessing one or several MDS+ servers). The client, a web-invocable Java applet, provides a uniform, intuitive, user-friendly, graphical interface to the data server. The uniformity of the interface relieves the user from the trouble of mastering the differences between different data formats and lets him/her focus on the essentials: plotting and viewing the data. The user runs the client by visiting a web page using any Java capable Web browser. The client is automatically downloaded and run by the browser. A reference to the data server is then retrieved via the standard Web protocol (HTTP). The communication between the client and the server is then handled by the mature, industry-standard CORBA middleware. CORBA has bindings for all common languages and many high-quality implementations are available (both Open Source and commercial). The NTCC data server has been installed at the ITPA International Multi-tokamak Confinement Profile Database, which is hosted by the UKAEA at Culham Science Centre. The installation of the data server is protected by an Internet firewall. To make it accessible to clients outside the firewall some modifications of the server were required. The working version of the ITPA confinement profile database is not open to the public. Authentification of legitimate users is done utilizing built-in Java security features to demand a password to download the client. We present an overview of the NTCC data client/server and some details of how the CORBA firewall-traversal issues were resolved and how the user authentification is implemented.

Accessibility and usability OCW data: The UTPL OCW.

PubMed

Rodríguez, Germania; Perez, Jennifer; Cueva, Samanta; Torres, Rommel

2017-08-01

This data article provides a data description on article entitled "A framework for improving web accessibility and usability of Open Course Ware sites" [3] This Data in Brief presents the data obtained from the accessibility and usability evaluation of the UTPL OCW. The data obtained from the framework evaluation consists of the manual evaluation of the standards criteria and the automatic evaluation of the tools Google PageSpeed and Google Analytics. In addition, this article presents the synthetized tables from standards that are used by the framework to evaluate the accessibility and usability of OCW, and the questionnaires required to extract the data. As a result, the article also provides the data required to reproduce the evaluation of other OCW.

Standards-based sensor interoperability and networking SensorWeb: an overview

NASA Astrophysics Data System (ADS)

Bolling, Sam

2012-06-01

The War fighter lacks a unified Intelligence, Surveillance, and Reconnaissance (ISR) environment to conduct mission planning, command and control (C2), tasking, collection, exploitation, processing, and data discovery of disparate sensor data across the ISR Enterprise. Legacy sensors and applications are not standardized or integrated for assured, universal access. Existing tasking and collection capabilities are not unified across the enterprise, inhibiting robust C2 of ISR including near-real time, cross-cueing operations. To address these critical needs, the National Measurement and Signature Intelligence (MASINT) Office (NMO), and partnering Combatant Commands and Intelligence Agencies are developing SensorWeb, an architecture that harmonizes heterogeneous sensor data to a common standard for users to discover, access, observe, subscribe to and task sensors. The SensorWeb initiative long term goal is to establish an open commercial standards-based, service-oriented framework to facilitate plug and play sensors. The current development effort will produce non-proprietary deliverables, intended as a Government off the Shelf (GOTS) solution to address the U.S. and Coalition nations' inability to quickly and reliably detect, identify, map, track, and fully understand security threats and operational activities.

Web-based visualization of very large scientific astronomy imagery

NASA Astrophysics Data System (ADS)

Bertin, E.; Pillay, R.; Marmo, C.

2015-04-01

Visualizing and navigating through large astronomy images from a remote location with current astronomy display tools can be a frustrating experience in terms of speed and ergonomics, especially on mobile devices. In this paper, we present a high performance, versatile and robust client-server system for remote visualization and analysis of extremely large scientific images. Applications of this work include survey image quality control, interactive data query and exploration, citizen science, as well as public outreach. The proposed software is entirely open source and is designed to be generic and applicable to a variety of datasets. It provides access to floating point data at terabyte scales, with the ability to precisely adjust image settings in real-time. The proposed clients are light-weight, platform-independent web applications built on standard HTML5 web technologies and compatible with both touch and mouse-based devices. We put the system to the test and assess the performance of the system and show that a single server can comfortably handle more than a hundred simultaneous users accessing full precision 32 bit astronomy data.

Best Practices for Making Scientific Data Discoverable and Accessible through Integrated, Standards-Based Data Portals

NASA Astrophysics Data System (ADS)

Lucido, J. M.

2013-12-01

Scientists in the fields of hydrology, geophysics, and climatology are increasingly using the vast quantity of publicly-available data to address broadly-scoped scientific questions. For example, researchers studying contamination of nearshore waters could use a combination of radar indicated precipitation, modeled water currents, and various sources of in-situ monitoring data to predict water quality near a beach. In discovering, gathering, visualizing and analyzing potentially useful data sets, data portals have become invaluable tools. The most effective data portals often aggregate distributed data sets seamlessly and allow multiple avenues for accessing the underlying data, facilitated by the use of open standards. Additionally, adequate metadata are necessary for attribution, documentation of provenance and relating data sets to one another. Metadata also enable thematic, geospatial and temporal indexing of data sets and entities. Furthermore, effective portals make use of common vocabularies for scientific methods, units of measure, geologic features, chemical, and biological constituents as they allow investigators to correctly interpret and utilize data from external sources. One application that employs these principles is the National Ground Water Monitoring Network (NGWMN) Data Portal (http://cida.usgs.gov/ngwmn), which makes groundwater data from distributed data providers available through a single, publicly accessible web application by mediating and aggregating native data exposed via web services on-the-fly into Open Geospatial Consortium (OGC) compliant service output. That output may be accessed either through the map-based user interface or through the aforementioned OGC web services. Furthermore, the Geo Data Portal (http://cida.usgs.gov/climate/gdp/), which is a system that provides users with data access, subsetting and geospatial processing of large and complex climate and land use data, exemplifies the application of International Standards Organization (ISO) metadata records to enhance data discovery for both human and machine interpretation. Lastly, the Water Quality Portal (http://www.waterqualitydata.us/) achieves interoperable dissemination of water quality data by referencing a vocabulary service for mapping constituents and methods between the USGS and USEPA. The NGWMN Data Portal, Geo Data Portal and Water Quality Portal are three examples of best practices when implementing data portals that provide distributed scientific data in an integrated, standards-based approach.

Software Application Profile: Opal and Mica: open-source software solutions for epidemiological data management, harmonization and dissemination.

PubMed

Doiron, Dany; Marcon, Yannick; Fortier, Isabel; Burton, Paul; Ferretti, Vincent

2017-10-01

Improving the dissemination of information on existing epidemiological studies and facilitating the interoperability of study databases are essential to maximizing the use of resources and accelerating improvements in health. To address this, Maelstrom Research proposes Opal and Mica, two inter-operable open-source software packages providing out-of-the-box solutions for epidemiological data management, harmonization and dissemination. Opal and Mica are two standalone but inter-operable web applications written in Java, JavaScript and PHP. They provide web services and modern user interfaces to access them. Opal allows users to import, manage, annotate and harmonize study data. Mica is used to build searchable web portals disseminating study and variable metadata. When used conjointly, Mica users can securely query and retrieve summary statistics on geographically dispersed Opal servers in real-time. Integration with the DataSHIELD approach allows conducting more complex federated analyses involving statistical models. Opal and Mica are open-source and freely available at [www.obiba.org] under a General Public License (GPL) version 3, and the metadata models and taxonomies that accompany them are available under a Creative Commons licence. © The Author 2017; all rights reserved. Published by Oxford University Press on behalf of the International Epidemiological Association

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.

WMT: The CSDMS Web Modeling Tool

NASA Astrophysics Data System (ADS)

Piper, M.; Hutton, E. W. H.; Overeem, I.; Syvitski, J. P.

2015-12-01

The Community Surface Dynamics Modeling System (CSDMS) has a mission to enable model use and development for research in earth surface processes. CSDMS strives to expand the use of quantitative modeling techniques, promotes best practices in coding, and advocates for the use of open-source software. To streamline and standardize access to models, CSDMS has developed the Web Modeling Tool (WMT), a RESTful web application with a client-side graphical interface and a server-side database and API that allows users to build coupled surface dynamics models in a web browser on a personal computer or a mobile device, and run them in a high-performance computing (HPC) environment. With WMT, users can: Design a model from a set of components Edit component parameters Save models to a web-accessible server Share saved models with the community Submit runs to an HPC system Download simulation results The WMT client is an Ajax application written in Java with GWT, which allows developers to employ object-oriented design principles and development tools such as Ant, Eclipse and JUnit. For deployment on the web, the GWT compiler translates Java code to optimized and obfuscated JavaScript. The WMT client is supported on Firefox, Chrome, Safari, and Internet Explorer. The WMT server, written in Python and SQLite, is a layered system, with each layer exposing a web service API: wmt-db: database of component, model, and simulation metadata and output wmt-api: configure and connect components wmt-exe: launch simulations on remote execution servers The database server provides, as JSON-encoded messages, the metadata for users to couple model components, including descriptions of component exchange items, uses and provides ports, and input parameters. Execution servers are network-accessible computational resources, ranging from HPC systems to desktop computers, containing the CSDMS software stack for running a simulation. Once a simulation completes, its output, in NetCDF, is packaged and uploaded to a data server where it is stored and from which a user can download it as a single compressed archive file.

HDF-EOS Web Server

NASA Technical Reports Server (NTRS)

Ullman, Richard; Bane, Bob; Yang, Jingli

2008-01-01

A shell script has been written as a means of automatically making HDF-EOS-formatted data sets available via the World Wide Web. ("HDF-EOS" and variants thereof are defined in the first of the two immediately preceding articles.) The shell script chains together some software tools developed by the Data Usability Group at Goddard Space Flight Center to perform the following actions: Extract metadata in Object Definition Language (ODL) from an HDF-EOS file, Convert the metadata from ODL to Extensible Markup Language (XML), Reformat the XML metadata into human-readable Hypertext Markup Language (HTML), Publish the HTML metadata and the original HDF-EOS file to a Web server and an Open-source Project for a Network Data Access Protocol (OPeN-DAP) server computer, and Reformat the XML metadata and submit the resulting file to the EOS Clearinghouse, which is a Web-based metadata clearinghouse that facilitates searching for, and exchange of, Earth-Science data.

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.

In-field Access to Geoscientific Metadata through GPS-enabled Mobile Phones

NASA Astrophysics Data System (ADS)

Hobona, Gobe; Jackson, Mike; Jordan, Colm; Butchart, Ben

2010-05-01

Fieldwork is an integral part of much geosciences research. But whilst geoscientists have physical or online access to data collections whilst in the laboratory or at base stations, equivalent in-field access is not standard or straightforward. The increasing availability of mobile internet and GPS-supported mobile phones, however, now provides the basis for addressing this issue. The SPACER project was commissioned by the Rapid Innovation initiative of the UK Joint Information Systems Committee (JISC) to explore the potential for GPS-enabled mobile phones to access geoscientific metadata collections. Metadata collections within the geosciences and the wider geospatial domain can be disseminated through web services based on the Catalogue Service for Web(CSW) standard of the Open Geospatial Consortium (OGC) - a global grouping of over 380 private, public and academic organisations aiming to improve interoperability between geospatial technologies. CSW offers an XML-over-HTTP interface for querying and retrieval of geospatial metadata. By default, the metadata returned by CSW is based on the ISO19115 standard and encoded in XML conformant to ISO19139. The SPACER project has created a prototype application that enables mobile phones to send queries to CSW containing user-defined keywords and coordinates acquired from GPS devices built-into the phones. The prototype has been developed using the free and open source Google Android platform. The mobile application offers views for listing titles, presenting multiple metadata elements and a Google Map with an overlay of bounding coordinates of datasets. The presentation will describe the architecture and approach applied in the development of the prototype.

Interoperability in planetary research for geospatial data analysis

NASA Astrophysics Data System (ADS)

Hare, Trent M.; Rossi, Angelo P.; Frigeri, Alessandro; Marmo, Chiara

2018-01-01

For more than a decade there has been a push in the planetary science community to support interoperable methods for accessing and working with geospatial data. Common geospatial data products for planetary research include image mosaics, digital elevation or terrain models, geologic maps, geographic location databases (e.g., craters, volcanoes) or any data that can be tied to the surface of a planetary body (including moons, comets or asteroids). Several U.S. and international cartographic research institutions have converged on mapping standards that embrace standardized geospatial image formats, geologic mapping conventions, U.S. Federal Geographic Data Committee (FGDC) cartographic and metadata standards, and notably on-line mapping services as defined by the Open Geospatial Consortium (OGC). The latter includes defined standards such as the OGC Web Mapping Services (simple image maps), Web Map Tile Services (cached image tiles), Web Feature Services (feature streaming), Web Coverage Services (rich scientific data streaming), and Catalog Services for the Web (data searching and discoverability). While these standards were developed for application to Earth-based data, they can be just as valuable for planetary domain. Another initiative, called VESPA (Virtual European Solar and Planetary Access), will marry several of the above geoscience standards and astronomy-based standards as defined by International Virtual Observatory Alliance (IVOA). This work outlines the current state of interoperability initiatives in use or in the process of being researched within the planetary geospatial community.

Using Cloud Computing infrastructure with CloudBioLinux, CloudMan and Galaxy

PubMed Central

Afgan, Enis; Chapman, Brad; Jadan, Margita; Franke, Vedran; Taylor, James

2012-01-01

Cloud computing has revolutionized availability and access to computing and storage resources; making it possible to provision a large computational infrastructure with only a few clicks in a web browser. However, those resources are typically provided in the form of low-level infrastructure components that need to be procured and configured before use. In this protocol, we demonstrate how to utilize cloud computing resources to perform open-ended bioinformatics analyses, with fully automated management of the underlying cloud infrastructure. By combining three projects, CloudBioLinux, CloudMan, and Galaxy into a cohesive unit, we have enabled researchers to gain access to more than 100 preconfigured bioinformatics tools and gigabytes of reference genomes on top of the flexible cloud computing infrastructure. The protocol demonstrates how to setup the available infrastructure and how to use the tools via a graphical desktop interface, a parallel command line interface, and the web-based Galaxy interface. PMID:22700313

Using cloud computing infrastructure with CloudBioLinux, CloudMan, and Galaxy.

PubMed

Afgan, Enis; Chapman, Brad; Jadan, Margita; Franke, Vedran; Taylor, James

2012-06-01

Cloud computing has revolutionized availability and access to computing and storage resources, making it possible to provision a large computational infrastructure with only a few clicks in a Web browser. However, those resources are typically provided in the form of low-level infrastructure components that need to be procured and configured before use. In this unit, we demonstrate how to utilize cloud computing resources to perform open-ended bioinformatic analyses, with fully automated management of the underlying cloud infrastructure. By combining three projects, CloudBioLinux, CloudMan, and Galaxy, into a cohesive unit, we have enabled researchers to gain access to more than 100 preconfigured bioinformatics tools and gigabytes of reference genomes on top of the flexible cloud computing infrastructure. The protocol demonstrates how to set up the available infrastructure and how to use the tools via a graphical desktop interface, a parallel command-line interface, and the Web-based Galaxy interface.

How Accessible Are Public Libraries' Web Sites? A Study of Georgia Public Libraries

ERIC Educational Resources Information Center

Ingle, Emma; Green, Ravonne A.; Huprich, Julia

2009-01-01

One issue that public librarians must consider when planning Web site design is accessibility for patrons with disabilities. This article reports a study of Web site accessibility of public libraries in Georgia. The focus of the report is whether public libraries use accessible guidelines and standards in making their Web sites accessible. An…

EarthServer: Use of Rasdaman as a data store for use in visualisation of complex EO data

NASA Astrophysics Data System (ADS)

Clements, Oliver; Walker, Peter; Grant, Mike

2013-04-01

The European Commission FP7 project EarthServer is establishing open access and ad-hoc analytics on extreme-size Earth Science data, based on and extending cutting-edge Array Database technology. EarthServer is built around the Rasdaman Raster Data Manager which extends standard relational database systems with the ability to store and retrieve multi-dimensional raster data of unlimited size through an SQL style query language. Rasdaman facilitates visualisation of data by providing several Open Geospatial Consortium (OGC) standard interfaces through its web services wrapper, Petascope. These include the well established standards, Web Coverage Service (WCS) and Web Map Service (WMS) as well as the emerging standard, Web Coverage Processing Service (WCPS). The WCPS standard allows the running of ad-hoc queries on the data stored within Rasdaman, creating an infrastructure where users are not restricted by bandwidth when manipulating or querying huge datasets. Here we will show that the use of EarthServer technologies and infrastructure allows access and visualisation of massive scale data through a web client with only marginal bandwidth use as opposed to the current mechanism of copying huge amounts of data to create visualisations locally. For example if a user wanted to generate a plot of global average chlorophyll for a complete decade time series they would only have to download the result instead of Terabytes of data. Firstly we will present a brief overview of the capabilities of Rasdaman and the WCPS query language to introduce the ways in which it is used in a visualisation tool chain. We will show that there are several ways in which WCPS can be utilised to create both standard and novel web based visualisations. An example of a standard visualisation is the production of traditional 2d plots, allowing users the ability to plot data products easily. However, the query language allows the creation of novel/custom products, which can then immediately be plotted with the same system. For more complex multi-spectral data, WCPS allows the user to explore novel combinations of bands in standard band-ratio algorithms through a web browser with dynamic updating of the resultant image. To visualise very large datasets Rasdaman has the capability to dynamically scale a dataset or query result so that it can be appraised quickly for use in later unscaled queries. All of these techniques are accessible through a web based GIS interface increasing the number of potential users of the system. Lastly we will show the advances in dynamic web based 3D visualisations being explored within the EarthServer project. By utilising the emerging declarative 3D web standard X3DOM as a tool to visualise the results of WCPS queries we introduce several possible benefits, including quick appraisal of data for outliers or anomalous data points and visualisation of the uncertainty of data alongside the actual data values.

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).

A RESTful API for accessing microbial community data for MG-RAST.

PubMed

Wilke, Andreas; Bischof, Jared; Harrison, Travis; Brettin, Tom; D'Souza, Mark; Gerlach, Wolfgang; Matthews, Hunter; Paczian, Tobias; Wilkening, Jared; Glass, Elizabeth M; Desai, Narayan; Meyer, Folker

2015-01-01

Metagenomic sequencing has produced significant amounts of data in recent years. For example, as of summer 2013, MG-RAST has been used to annotate over 110,000 data sets totaling over 43 Terabases. With metagenomic sequencing finding even wider adoption in the scientific community, the existing web-based analysis tools and infrastructure in MG-RAST provide limited capability for data retrieval and analysis, such as comparative analysis between multiple data sets. Moreover, although the system provides many analysis tools, it is not comprehensive. By opening MG-RAST up via a web services API (application programmers interface) we have greatly expanded access to MG-RAST data, as well as provided a mechanism for the use of third-party analysis tools with MG-RAST data. This RESTful API makes all data and data objects created by the MG-RAST pipeline accessible as JSON objects. As part of the DOE Systems Biology Knowledgebase project (KBase, http://kbase.us) we have implemented a web services API for MG-RAST. This API complements the existing MG-RAST web interface and constitutes the basis of KBase's microbial community capabilities. In addition, the API exposes a comprehensive collection of data to programmers. This API, which uses a RESTful (Representational State Transfer) implementation, is compatible with most programming environments and should be easy to use for end users and third parties. It provides comprehensive access to sequence data, quality control results, annotations, and many other data types. Where feasible, we have used standards to expose data and metadata. Code examples are provided in a number of languages both to show the versatility of the API and to provide a starting point for users. We present an API that exposes the data in MG-RAST for consumption by our users, greatly enhancing the utility of the MG-RAST service.

A web GIS based integrated flood assessment modeling tool for coastal urban watersheds

NASA Astrophysics Data System (ADS)

Kulkarni, A. T.; Mohanty, J.; Eldho, T. I.; Rao, E. P.; Mohan, B. K.

2014-03-01

Urban flooding has become an increasingly important issue in many parts of the world. In this study, an integrated flood assessment model (IFAM) is presented for the coastal urban flood simulation. A web based GIS framework has been adopted to organize the spatial datasets for the study area considered and to run the model within this framework. The integrated flood model consists of a mass balance based 1-D overland flow model, 1-D finite element based channel flow model based on diffusion wave approximation and a quasi 2-D raster flood inundation model based on the continuity equation. The model code is written in MATLAB and the application is integrated within a web GIS server product viz: Web Gram Server™ (WGS), developed at IIT Bombay, using Java, JSP and JQuery technologies. Its user interface is developed using open layers and the attribute data are stored in MySQL open source DBMS. The model is integrated within WGS and is called via Java script. The application has been demonstrated for two coastal urban watersheds of Navi Mumbai, India. Simulated flood extents for extreme rainfall event of 26 July, 2005 in the two urban watersheds of Navi Mumbai city are presented and discussed. The study demonstrates the effectiveness of the flood simulation tool in a web GIS environment to facilitate data access and visualization of GIS datasets and simulation results.

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

Science as a Web of Trails: Redesigning Science Education with the Tools of the Present to Meet the Needs of the Future

NASA Astrophysics Data System (ADS)

Karno, Donna; Glassman, Michael

2013-12-01

Science education has experienced significant changes since the mid-20th century, most recently with the creation of STEM curricula (DeBoer 1991; Yager 2000). The emergence of the World Wide Web as a tool in research and discovery offers Pre-K-12 science education an opportunity to share information and perspectives which engage students with the scientific community (Zoller 2011). Students are able to access open, transparent sites creating common resources pools and autonomous working groups which can be used for shared problem solving. Science teachers should carefully build web 2.0 technology into their practice based on a changing pedagogy. Instead of focusing on teaching rule-based concepts and processes in which the teacher's role is that of expert, education should be focusing on possibilities of the web both in scientific research and understanding. In addition, web-focused education can also help remake scientific product as a public good in the lives of both science researchers and science consumers.

Non-visual Web Browsing: Beyond Web Accessibility

PubMed Central

Ramakrishnan, I.V.; Ashok, Vikas

2017-01-01

People with vision impairments typically use screen readers to browse the Web. To facilitate non-visual browsing, web sites must be made accessible to screen readers, i.e., all the visible elements in the web site must be readable by the screen reader. But even if web sites are accessible, screen-reader users may not find them easy to use and/or easy to navigate. For example, they may not be able to locate the desired information without having to listen to a lot of irrelevant contents. These issues go beyond web accessibility and directly impact web usability. Several techniques have been reported in the accessibility literature for making the Web usable for screen reading. This paper is a review of these techniques. Interestingly, the review reveals that understanding the semantics of the web content is the overarching theme that drives these techniques for improving web usability. PMID:29202137

Non-visual Web Browsing: Beyond Web Accessibility.

PubMed

Ramakrishnan, I V; Ashok, Vikas; Billah, Syed Masum

2017-07-01

People with vision impairments typically use screen readers to browse the Web. To facilitate non-visual browsing, web sites must be made accessible to screen readers, i.e., all the visible elements in the web site must be readable by the screen reader. But even if web sites are accessible, screen-reader users may not find them easy to use and/or easy to navigate. For example, they may not be able to locate the desired information without having to listen to a lot of irrelevant contents. These issues go beyond web accessibility and directly impact web usability. Several techniques have been reported in the accessibility literature for making the Web usable for screen reading. This paper is a review of these techniques. Interestingly, the review reveals that understanding the semantics of the web content is the overarching theme that drives these techniques for improving web usability.

Cyberinfrastructure for Open Science at the Montreal Neurological Institute

PubMed Central

Das, Samir; Glatard, Tristan; Rogers, Christine; Saigle, John; Paiva, Santiago; MacIntyre, Leigh; Safi-Harab, Mouna; Rousseau, Marc-Etienne; Stirling, Jordan; Khalili-Mahani, Najmeh; MacFarlane, David; Kostopoulos, Penelope; Rioux, Pierre; Madjar, Cecile; Lecours-Boucher, Xavier; Vanamala, Sandeep; Adalat, Reza; Mohaddes, Zia; Fonov, Vladimir S.; Milot, Sylvain; Leppert, Ilana; Degroot, Clotilde; Durcan, Thomas M.; Campbell, Tara; Moreau, Jeremy; Dagher, Alain; Collins, D. Louis; Karamchandani, Jason; Bar-Or, Amit; Fon, Edward A.; Hoge, Rick; Baillet, Sylvain; Rouleau, Guy; Evans, Alan C.

2017-01-01

Data sharing is becoming more of a requirement as technologies mature and as global research and communications diversify. As a result, researchers are looking for practical solutions, not only to enhance scientific collaborations, but also to acquire larger amounts of data, and to access specialized datasets. In many cases, the realities of data acquisition present a significant burden, therefore gaining access to public datasets allows for more robust analyses and broadly enriched data exploration. To answer this demand, the Montreal Neurological Institute has announced its commitment to Open Science, harnessing the power of making both clinical and research data available to the world (Owens, 2016a,b). As such, the LORIS and CBRAIN (Das et al., 2016) platforms have been tasked with the technical challenges specific to the institutional-level implementation of open data sharing, including: Comprehensive linking of multimodal data (phenotypic, clinical, neuroimaging, biobanking, and genomics, etc.)Secure database encryption, specifically designed for institutional and multi-project data sharing, ensuring subject confidentiality (using multi-tiered identifiers).Querying capabilities with multiple levels of single study and institutional permissions, allowing public data sharing for all consented and de-identified subject data.Configurable pipelines and flags to facilitate acquisition and analysis, as well as access to High Performance Computing clusters for rapid data processing and sharing of software tools.Robust Workflows and Quality Control mechanisms ensuring transparency and consistency in best practices.Long term storage (and web access) of data, reducing loss of institutional data assets.Enhanced web-based visualization of imaging, genomic, and phenotypic data, allowing for real-time viewing and manipulation of data from anywhere in the world.Numerous modules for data filtering, summary statistics, and personalized and configurable dashboards. Implementing the vision of Open Science at the Montreal Neurological Institute will be a concerted undertaking that seeks to facilitate data sharing for the global research community. Our goal is to utilize the years of experience in multi-site collaborative research infrastructure to implement the technical requirements to achieve this level of public data sharing in a practical yet robust manner, in support of accelerating scientific discovery. PMID:28111547

National Geothermal Data System: an Exemplar of Open Access to Data

NASA Astrophysics Data System (ADS)

Allison, M. L.; Richard, S. M.; Blackman, H.; Anderson, A.

2013-12-01

The National Geothermal Data System's (NGDS - www.geothermaldata.org) formal launch in 2014 will provide open access to millions of datasets, sharing technical geothermal-relevant data across the geosciences to propel geothermal development and production. With information from all of the Department of Energy's sponsored development and research projects and geologic data from all 50 states, this free, interactive tool is opening new exploration opportunities and shortening project development by making data easily discoverable and accessible. We continue to populate our prototype functional data system with multiple data nodes and nationwide data online and available to the public. Data from state geological surveys and partners includes more than 5 million records online, including 1.48 million well headers (oil and gas, water, geothermal), 732,000 well logs, and 314,000 borehole temperatures and is growing rapidly. There are over 250 Web services and another 138 WMS (Web Map Services) registered in the system as of August, 2013. Companion projects run by Boise State University, Southern Methodist University, and USGS are adding millions of additional data records. The National Renewable Energy Laboratory is managing the Geothermal Data Repository which will serve as a system node and clearinghouse for data from hundreds of DOE-funded geothermal projects. NGDS is built on the US Geoscience Information Network data integration framework, which is a joint undertaking of the USGS and the Association of American State Geologists (AASG). NGDS is fully compliant with the White House Executive Order of May 2013, requiring all federal agencies to make their data holdings publicly accessible online in open source, interoperable formats with common core and extensible metadata. The National Geothermal Data System is being designed, built, deployed, and populated primarily with grants from the US Department of Energy, Geothermal Technologies Office. To keep this operational system sustainable after the original implementation will require four core elements: continued serving of data and applications by providers; maintenance of system operations; a governance structure; and an effective business model. Each of these presents a number of challenges currently under consideration.

Cyberinfrastructure for Open Science at the Montreal Neurological Institute.

PubMed

Das, Samir; Glatard, Tristan; Rogers, Christine; Saigle, John; Paiva, Santiago; MacIntyre, Leigh; Safi-Harab, Mouna; Rousseau, Marc-Etienne; Stirling, Jordan; Khalili-Mahani, Najmeh; MacFarlane, David; Kostopoulos, Penelope; Rioux, Pierre; Madjar, Cecile; Lecours-Boucher, Xavier; Vanamala, Sandeep; Adalat, Reza; Mohaddes, Zia; Fonov, Vladimir S; Milot, Sylvain; Leppert, Ilana; Degroot, Clotilde; Durcan, Thomas M; Campbell, Tara; Moreau, Jeremy; Dagher, Alain; Collins, D Louis; Karamchandani, Jason; Bar-Or, Amit; Fon, Edward A; Hoge, Rick; Baillet, Sylvain; Rouleau, Guy; Evans, Alan C

2016-01-01

Data sharing is becoming more of a requirement as technologies mature and as global research and communications diversify. As a result, researchers are looking for practical solutions, not only to enhance scientific collaborations, but also to acquire larger amounts of data, and to access specialized datasets. In many cases, the realities of data acquisition present a significant burden, therefore gaining access to public datasets allows for more robust analyses and broadly enriched data exploration. To answer this demand, the Montreal Neurological Institute has announced its commitment to Open Science, harnessing the power of making both clinical and research data available to the world (Owens, 2016a,b). As such, the LORIS and CBRAIN (Das et al., 2016) platforms have been tasked with the technical challenges specific to the institutional-level implementation of open data sharing, including: Comprehensive linking of multimodal data (phenotypic, clinical, neuroimaging, biobanking, and genomics, etc.)Secure database encryption, specifically designed for institutional and multi-project data sharing, ensuring subject confidentiality (using multi-tiered identifiers).Querying capabilities with multiple levels of single study and institutional permissions, allowing public data sharing for all consented and de-identified subject data.Configurable pipelines and flags to facilitate acquisition and analysis, as well as access to High Performance Computing clusters for rapid data processing and sharing of software tools.Robust Workflows and Quality Control mechanisms ensuring transparency and consistency in best practices.Long term storage (and web access) of data, reducing loss of institutional data assets.Enhanced web-based visualization of imaging, genomic, and phenotypic data, allowing for real-time viewing and manipulation of data from anywhere in the world.Numerous modules for data filtering, summary statistics, and personalized and configurable dashboards. Implementing the vision of Open Science at the Montreal Neurological Institute will be a concerted undertaking that seeks to facilitate data sharing for the global research community. Our goal is to utilize the years of experience in multi-site collaborative research infrastructure to implement the technical requirements to achieve this level of public data sharing in a practical yet robust manner, in support of accelerating scientific discovery.

Access of primary and secondary literature by health personnel in an academic health center: implications for open access*

PubMed Central

Steinberg, Ryan M.; Moorhead, Laura; O'Brien, Bridget; Willinsky, John

2013-01-01

Purpose: The research sought to ascertain the types and quantity of research evidence accessed by health personnel through PubMed and UpToDate in a university medical center over the course of a year in order to better estimate the impact that increasing levels of open access to biomedical research can be expected to have on clinical practice in the years ahead. Methods: Web log data were gathered from the 5,042 health personnel working in the Stanford University Hospitals (SUH) during 2011. Data were analyzed for access to the primary literature (abstracts and full-text) through PubMed and UpToDate and to the secondary literature, represented by UpToDate (research summaries), to establish the frequency and nature of literature consulted. Results: In 2011, SUH health personnel accessed 81,851 primary literature articles and visited UpToDate 110,336 times. Almost a third of the articles (24,529) accessed were reviews. Twenty percent (16,187) of the articles viewed were published in 2011. Conclusion: When it is available, health personnel in a clinical care setting frequently access the primary literature. While further studies are needed, this preliminary finding speaks to the value of the National Institutes of Health public access policy and the need for medical librarians and educators to prepare health personnel for increasing public access to medical research. PMID:23930091

Web Accessibility and Guidelines

NASA Astrophysics Data System (ADS)

Harper, Simon; Yesilada, Yeliz

Access to, and movement around, complex online environments, of which the World Wide Web (Web) is the most popular example, has long been considered an important and major issue in the Web design and usability field. The commonly used slang phrase ‘surfing the Web’ implies rapid and free access, pointing to its importance among designers and users alike. It has also been long established that this potentially complex and difficult access is further complicated, and becomes neither rapid nor free, if the user is disabled. There are millions of people who have disabilities that affect their use of the Web. Web accessibility aims to help these people to perceive, understand, navigate, and interact with, as well as contribute to, the Web, and thereby the society in general. This accessibility is, in part, facilitated by the Web Content Accessibility Guidelines (WCAG) currently moving from version one to two. These guidelines are intended to encourage designers to make sure their sites conform to specifications, and in that conformance enable the assistive technologies of disabled users to better interact with the page content. In this way, it was hoped that accessibility could be supported. While this is in part true, guidelines do not solve all problems and the new WCAG version two guidelines are surrounded by controversy and intrigue. This chapter aims to establish the published literature related to Web accessibility and Web accessibility guidelines, and discuss limitations of the current guidelines and future directions.

Web-conference supervision for advanced psychotherapy training: a practical guide.

PubMed

Abbass, Allan; Arthey, Stephen; Elliott, Jason; Fedak, Tim; Nowoweiski, Dion; Markovski, Jasmina; Nowoweiski, Sarah

2011-06-01

The advent of readily accessible, inexpensive Web-conferencing applications has opened the door for distance psychotherapy supervision, using video recordings of treated clients. Although relatively new, this method of supervision is advantageous given the ease of use and low cost of various Internet applications. This method allows periodic supervision from point to point around the world, with no travel costs and no long gaps between direct training contacts. Web-conferencing permits face-to-face training so that the learner and supervisor can read each other's emotional responses while reviewing case material. It allows group learning from direct supervision to complement local peer-to-peer learning methods. In this article, we describe the relevant literature on this type of learning method, the practical points in its utilization, its limitations, and its benefits.

High Availability Applications for NOMADS at the NOAA Web Operations Center Aimed at Providing Reliable Real Time Access to Operational Model Data

NASA Astrophysics Data System (ADS)

Alpert, J. C.; Rutledge, G.; Wang, J.; Freeman, P.; Kang, C. Y.

2009-05-01

The NOAA Operational Modeling Archive Distribution System (NOMADS) is now delivering high availability services as part of NOAA's official real time data dissemination at its Web Operations Center (WOC). The WOC is a web service used by all organizational units in NOAA and acts as a data repository where public information can be posted to a secure and scalable content server. A goal is to foster collaborations among the research and education communities, value added retailers, and public access for science and development efforts aimed at advancing modeling and GEO-related tasks. The services used to access the operational model data output are the Open-source Project for a Network Data Access Protocol (OPeNDAP), implemented with the Grid Analysis and Display System (GrADS) Data Server (GDS), and applications for slicing, dicing and area sub-setting the large matrix of real time model data holdings. This approach insures an efficient use of computer resources because users transmit/receive only the data necessary for their tasks including metadata. Data sets served in this way with a high availability server offer vast possibilities for the creation of new products for value added retailers and the scientific community. New applications to access data and observations for verification of gridded model output, and progress toward integration with access to conventional and non-conventional observations will be discussed. We will demonstrate how users can use NOMADS services to repackage area subsets either using repackaging of GRIB2 files, or values selected by ensemble component, (forecast) time, vertical levels, global horizontal location, and by variable, virtually a 6- Dimensional analysis services across the internet.

A suite of R packages for web-enabled modeling and analysis of surface waters

NASA Astrophysics Data System (ADS)

Read, J. S.; Winslow, L. A.; Nüst, D.; De Cicco, L.; Walker, J. I.

2014-12-01

Researchers often create redundant methods for downloading, manipulating, and analyzing data from online resources. Moreover, the reproducibility of science can be hampered by complicated and voluminous data, lack of time for documentation and long-term maintenance of software, and fear of exposing programming skills. The combination of these factors can encourage unshared one-off programmatic solutions instead of openly provided reusable methods. Federal and academic researchers in the water resources and informatics domains have collaborated to address these issues. The result of this collaboration is a suite of modular R packages that can be used independently or as elements in reproducible analytical workflows. These documented and freely available R packages were designed to fill basic needs for the effective use of water data: the retrieval of time-series and spatial data from web resources (dataRetrieval, geoknife), performing quality assurance and quality control checks of these data with robust statistical methods (sensorQC), the creation of useful data derivatives (including physically- and biologically-relevant indices; GDopp, LakeMetabolizer), and the execution and evaluation of models (glmtools, rLakeAnalyzer). Here, we share details and recommendations for the collaborative coding process, and highlight the benefits of an open-source tool development pattern with a popular programming language in the water resources discipline (such as R). We provide examples of reproducible science driven by large volumes of web-available data using these tools, explore benefits of accessing packages as standardized web processing services (WPS) and present a working platform that allows domain experts to publish scientific algorithms in a service-oriented architecture (WPS4R). We assert that in the era of open data, tools that leverage these data should also be freely shared, transparent, and developed in an open innovation environment.

MetaLIMS, a simple open-source laboratory information management system for small metagenomic labs

PubMed Central

Gaultier, Nicolas Paul Eugène; Miller, Dana; Purbojati, Rikky Wenang; Lauro, Federico M.

2017-01-01

Abstract Background: As the cost of sequencing continues to fall, smaller groups increasingly initiate and manage larger sequencing projects and take on the complexity of data storage for high volumes of samples. This has created a need for low-cost laboratory information management systems (LIMS) that contain flexible fields to accommodate the unique nature of individual labs. Many labs do not have a dedicated information technology position, so LIMS must also be easy to setup and maintain with minimal technical proficiency. Findings: MetaLIMS is a free and open-source web-based application available via GitHub. The focus of MetaLIMS is to store sample metadata prior to sequencing and analysis pipelines. Initially designed for environmental metagenomics labs, in addition to storing generic sample collection information and DNA/RNA processing information, the user can also add fields specific to the user's lab. MetaLIMS can also produce a basic sequencing submission form compatible with the proprietary Clarity LIMS system used by some sequencing facilities. To help ease the technical burden associated with web deployment, MetaLIMS options the use of commercial web hosting combined with MetaLIMS bash scripts for ease of setup. Conclusions: MetaLIMS overcomes key challenges common in LIMS by giving labs access to a low-cost and open-source tool that also has the flexibility to meet individual lab needs and an option for easy deployment. By making the web application open source and hosting it on GitHub, we hope to encourage the community to build upon MetaLIMS, making it more robust and tailored to the needs of more researchers. PMID:28430964

MetaLIMS, a simple open-source laboratory information management system for small metagenomic labs.

PubMed

Heinle, Cassie Elizabeth; Gaultier, Nicolas Paul Eugène; Miller, Dana; Purbojati, Rikky Wenang; Lauro, Federico M

2017-06-01

As the cost of sequencing continues to fall, smaller groups increasingly initiate and manage larger sequencing projects and take on the complexity of data storage for high volumes of samples. This has created a need for low-cost laboratory information management systems (LIMS) that contain flexible fields to accommodate the unique nature of individual labs. Many labs do not have a dedicated information technology position, so LIMS must also be easy to setup and maintain with minimal technical proficiency. MetaLIMS is a free and open-source web-based application available via GitHub. The focus of MetaLIMS is to store sample metadata prior to sequencing and analysis pipelines. Initially designed for environmental metagenomics labs, in addition to storing generic sample collection information and DNA/RNA processing information, the user can also add fields specific to the user's lab. MetaLIMS can also produce a basic sequencing submission form compatible with the proprietary Clarity LIMS system used by some sequencing facilities. To help ease the technical burden associated with web deployment, MetaLIMS options the use of commercial web hosting combined with MetaLIMS bash scripts for ease of setup. MetaLIMS overcomes key challenges common in LIMS by giving labs access to a low-cost and open-source tool that also has the flexibility to meet individual lab needs and an option for easy deployment. By making the web application open source and hosting it on GitHub, we hope to encourage the community to build upon MetaLIMS, making it more robust and tailored to the needs of more researchers. © The Authors 2017. Published by Oxford University Press.

Web-Based Activity Within a Sexual Health Economy: Observational Study.

PubMed

Turner, Katy Me; Zienkiewicz, Adam K; Syred, Jonathan; Looker, Katharine J; de Sa, Joia; Brady, Michael; Free, Caroline; Holdsworth, Gillian; Baraitser, Paula

2018-03-07

Regular testing for sexually transmitted infections (STIs) is important to maintain sexual health. Self-sampling kits ordered online and delivered in the post may increase access, convenience, and cost-effectiveness. Sexual health economies may target limited resources more effectively by signposting users toward Web-based or face-to-face services according to clinical need. The aim of this paper was to investigate the impact of two interventions on testing activity across a whole sexual health economy: (1) the introduction of open access Web-based STI testing services and (2) a clinic policy of triage and signpost online where users without symptoms who attended clinics for STI testing were supported to access the Web-based service instead. Data on attendances at all specialist public sexual health providers in an inner-London area were collated into a single database. Each record included information on user demographics, service type accessed, and clinical activity provided, including test results. Clinical activity was categorized as a simple STI test (could be done in a clinic or online), a complex visit (requiring face-to-face consultation), or other. Introduction of Web-based services increased total testing activity across the whole sexual health economy by 18.47% (from 36,373 to 43,091 in the same 6-month period-2014-2015 and 2015-2016), suggesting unmet need for testing in the area. Triage and signposting shifted activity out of the clinic onto the Web-based service, with simple STI testing in the clinic decreasing from 16.90% (920/5443) to 12.25% (511/4172) of total activity, P<.001, and complex activity in the clinic increasing from 69.15% (3764/5443) to 74.86% (3123/4172) of total activity, P<.001. This intervention created a new population of online users with different demographic and clinical profiles from those who use Web-based services spontaneously. Some triage and signposted users (29.62%, 375/1266) did not complete the Web-based testing process, suggesting the potential for missed diagnoses. This evaluation shows that users can effectively be transitioned from face-to-face to Web-based services and that this introduces a new population to Web-based service use and changes the focus of clinic-based activity. Further development is underway to optimize the triage and signposting process to support test completion. ©Katy ME Turner, Adam K Zienkiewicz, Jonathan Syred, Katharine J Looker, Joia de Sa, Michael Brady, Caroline Free, Gillian Holdsworth, Paula Baraitser. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 07.03.2018.

Web Accessibility in Europe and the United States: What We Are Doing to Increase Inclusion

ERIC Educational Resources Information Center

Wheaton, Joseph; Bertini, Patrizia

2007-01-01

Accessibility is hardly a new problem and certainly did not originate with the Web. Lack of access to buildings long preceded the call for accessible Web content. Although it is unlikely that rehabilitation educators look at Web page accessibility with indifference, many may also find it difficult to implement. The authors posit three reasons why…

International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data.

PubMed

Zhang, Junjun; Baran, Joachim; Cros, A; Guberman, Jonathan M; Haider, Syed; Hsu, Jack; Liang, Yong; Rivkin, Elena; Wang, Jianxin; Whitty, Brett; Wong-Erasmus, Marie; Yao, Long; Kasprzyk, Arek

2011-01-01

The International Cancer Genome Consortium (ICGC) is a collaborative effort to characterize genomic abnormalities in 50 different cancer types. To make this data available, the ICGC has created the ICGC Data Portal. Powered by the BioMart software, the Data Portal allows each ICGC member institution to manage and maintain its own databases locally, while seamlessly presenting all the data in a single access point for users. The Data Portal currently contains data from 24 cancer projects, including ICGC, The Cancer Genome Atlas (TCGA), Johns Hopkins University, and the Tumor Sequencing Project. It consists of 3478 genomes and 13 cancer types and subtypes. Available open access data types include simple somatic mutations, copy number alterations, structural rearrangements, gene expression, microRNAs, DNA methylation and exon junctions. Additionally, simple germline variations are available as controlled access data. The Data Portal uses a web-based graphical user interface (GUI) to offer researchers multiple ways to quickly and easily search and analyze the available data. The web interface can assist in constructing complicated queries across multiple data sets. Several application programming interfaces are also available for programmatic access. Here we describe the organization, functionality, and capabilities of the ICGC Data Portal.

Astronomical activities with disabled people

NASA Astrophysics Data System (ADS)

Ortiz-Gil, Amelia; Blay, Pere; Gallego Calvente, A. Teresa; Gómez, Miquel; Guirado, José Carlos; Lanzara, Mariana; Martínez Núñez, Silvia

2011-06-01

As we celebrate the International Year of Astronomy, we have been working on four different projects with the goal of making astronomy more accessible to people with special needs. These projects are 1) an astronomy book and web site for blind people, 2) an open source software for people with motor disabilities, 3) a planetarium program for the visually impaired and 4) educational material for intellectually disabled people.

Developing a WWW Resource Centre for Acquiring and Accessing Open Learning Materials on Research Methods (ReMOTE).

ERIC Educational Resources Information Center

Newton, Robert; Marcella, Rita; Middleton, Iain; McConnell, Michael

This paper reports on ReMOTE (Research Methods Online Teaching Environment), a Robert Gordon University (Scotland) project focusing on the development of a World Wide Web (WWW) site devoted to the teaching of research methods. The aim of ReMOTE is to provide an infrastructure that allows direct links to specialist sources in order to enable the…

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.

SFO-Project: The New Generation of Sharable, Editable and Open-Access CFD Tutorials

NASA Astrophysics Data System (ADS)

Javaherchi, Teymour; Javaherchi, Ardeshir; Aliseda, Alberto

2016-11-01

One of the most common approaches to develop a Computational Fluid Dynamic (CFD) simulation for a new case study of interest is to search for the most similar, previously developed and validated CFD simulation among other works. A simple search would result into a pool of written/visual tutorials. However, users should spend significant amount of time and effort to find the most correct, compatible and valid tutorial in this pool and further modify it toward their simulation of interest. SFO is an open-source project with the core idea of saving the above-mentioned time and effort. This is done via documenting/sharing scientific and methodological approaches to develop CFD simulations for a wide spectrum of fundamental and industrial case studies in three different CFD solvers; STAR-CCM +, FLUENT and Open FOAM (SFO). All of the steps and required files of these tutorials are accessible and editable under the common roof of Github (a web-based Git repository hosting service). In this presentation we will present the current library of 20 + developed CFD tutorials, discuss the idea and benefit of using them, their educational values and explain how the next generation of open-access and live resource of CFD tutorials can be built further hand-in-hand within our community.

An integrated and accessible sample data library for Mars sample return science

NASA Astrophysics Data System (ADS)

Tuite, M. L., Jr.; Williford, K. H.

2015-12-01

Over the course of the next decade or more, many thousands of geological samples will be collected and analyzed in a variety of ways by researchers at the Jet Propulsion Laboratory (California Institute of Technology) in order to facilitate discovery and contextualize observations made of Mars rocks both in situ and here on Earth if samples are eventually returned. Integration of data from multiple analyses of samples including petrography, thin section and SEM imaging, isotope and organic geochemistry, XRF, XRD, and Raman spectrometry is a challenge and a potential obstacle to discoveries that require supporting lines of evidence. We report the development of a web-accessible repository, the Sample Data Library (SDL) for the sample-based data that are generated by the laboratories and instruments that comprise JPL's Center for Analysis of Returned Samples (CARS) in order to facilitate collaborative interpretation of potential biosignatures in Mars-analog geological samples. The SDL is constructed using low-cost, open-standards-based Amazon Web Services (AWS), including web-accessible storage, relational data base services, and a virtual web server. The data structure is sample-centered with a shared registry for assigning unique identifiers to all samples including International Geo-Sample Numbers. Both raw and derived data produced by instruments and post-processing workflows are automatically uploaded to online storage and linked via the unique identifiers. Through the web interface, users are able to find all the analyses associated with a single sample or search across features shared by multiple samples, sample localities, and analysis types. Planned features include more sophisticated search and analytical interfaces as well as data discoverability through NSF's EarthCube program.

The Transcription Factor Encyclopedia

PubMed Central

2012-01-01

Here we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded on the principles of open access and collaboration. Our consortium of over 100 researchers has collectively contributed over 130 mini review articles on pertinent human, mouse and rat TFs. Notable features of the TFe website include a high-quality PDF generator and web API for programmatic data retrieval. TFe aims to rapidly educate scientists about the TFs they encounter through the delivery of succinct summaries written and vetted by experts in the field. TFe is available at http://www.cisreg.ca/tfe. PMID:22458515

75 FR 6063 - Availability of NRC Open Government Web Site

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-05

... NUCLEAR REGULATORY COMMISSION [NRC-2010-0003] Availability of NRC Open Government Web Site AGENCY: Nuclear Regulatory Commission. ACTION: Notice of Availability of Open Government Web site for Online... Register notice, informs the public that the Nuclear Regulatory Commission's (NRC) Open Government Web site...

Unbundled infrastructure firms: Competition and continuing regulation

NASA Astrophysics Data System (ADS)

Hogendorn, Christiaan Paul

Unbundled infrastructure firms provide conduits for electricity transmission, residential communications, etc. but are vertically disintegrated from "content" functions such as electricity generation or world-wide-web pages. These conduits are being deregulated, and this dissertation examines whether the deregulated conduits will behave in an efficient and competitive manner. The dissertation presents three essays, each of which develops a theoretical model of the behavior of conduit firms in a market environment. The first essay considers the prospects for competition between multiple conduits in the emerging market for broadband (high-speed) residential Internet access. It finds that such competition is likely to emerge as demand for these services increase. The second essay shows how a monopoly electricity or natural gas transmission conduit can facilitate collusion between suppliers of the good. It shows that this is an inefficient effect of standard price-cap regulation. The third essay considers the supply chain of residential Internet access and evaluates proposed "open access" regulation that would allow more than one firm to serve customers over the same physical infrastructure. It shows that the amount of content available to consumers does not necessarily increase under open access.

Accessibility and content of individualized adult reconstructive hip and knee/musculoskeletal oncology fellowship web sites.

PubMed

Young, Bradley L; Cantrell, Colin K; Patt, Joshua C; Ponce, Brent A

2018-06-01

Accessible, adequate online information is important to fellowship applicants. Program web sites can affect which programs applicants apply to, subsequently altering interview costs incurred by both parties and ultimately impacting rank lists. Web site analyses have been performed for all orthopaedic subspecialties other than those involved in the combined adult reconstruction and musculoskeletal (MSK) oncology fellowship match. A complete list of active programs was obtained from the official adult reconstruction and MSK oncology society web sites. Web site accessibility was assessed using a structured Google search. Accessible web sites were evaluated based on 21 previously reported content criteria. Seventy-four adult reconstruction programs and 11 MSK oncology programs were listed on the official society web sites. Web sites were identified and accessible for 58 (78%) adult reconstruction and 9 (82%) MSK oncology fellowship programs. No web site contained all content criteria and more than half of both adult reconstruction and MSK oncology web sites failed to include 12 of the 21 criteria. Several programs participating in the combined Adult Reconstructive Hip and Knee/Musculoskeletal Oncology Fellowship Match did not have accessible web sites. Of the web sites that were accessible, none contained comprehensive information and the majority lacked information that has been previously identified as being important to perspective applicants.

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.

The application of a Web-geographic information system for improving urban water cycle modelling.

PubMed

Mair, M; Mikovits, C; Sengthaler, M; Schöpf, M; Kinzel, H; Urich, C; Kleidorfer, M; Sitzenfrei, R; Rauch, W

2014-01-01

Research in urban water management has experienced a transition from traditional model applications to modelling water cycles as an integrated part of urban areas. This includes the interlinking of models of many research areas (e.g. urban development, socio-economy, urban water management). The integration and simulation is realized in newly developed frameworks (e.g. DynaMind and OpenMI) and often assumes a high knowledge in programming. This work presents a Web based urban water management modelling platform which simplifies the setup and usage of complex integrated models. The platform is demonstrated with a small application example on a case study within the Alpine region. The used model is a DynaMind model benchmarking the impact of newly connected catchments on the flooding behaviour of an existing combined sewer system. As a result the workflow of the user within a Web browser is demonstrated and benchmark results are shown. The presented platform hides implementation specific aspects behind Web services based technologies such that the user can focus on his main aim, which is urban water management modelling and benchmarking. Moreover, this platform offers a centralized data management, automatic software updates and access to high performance computers accessible with desktop computers and mobile devices.

Implications of Direct Patient Online Access to Radiology Reports Through Patient Web Portals.

PubMed

Lee, Christoph I; Langlotz, Curtis P; Elmore, Joann G

2016-12-01

In an era of increasing health information transparency and informed decision making, more patients are being provided with direct online access to their medical records, including radiology reports, via web-based portals. Although radiologists' narrative reports have previously been the purview of referring physicians, patients are now reading these on their own. Many potential benefits may result from patients reviewing their radiology reports, including improvements in patients' own understanding of their health, promotion of shared decision making and patient-physician communication, and, ultimately, improvements in patient outcomes. However, there may also be negative consequences, including confusion and anxiety among patients and longer patient-physician interactions. The rapid adoption of this new technology has led to major questions regarding ethics and professionalism for radiologists, including the following: Who is the intended audience of radiology reports? How should content be presented or worded? How will open access influence radiologists' relationships with patients and referring physicians? What legal ramifications may arise from increased patient access? The authors describe the current practices and research findings associated with patient online access to medical records, including radiology reports, and discuss several implications of this growing trend for the radiology profession. Copyright © 2016 American College of Radiology. Published by Elsevier Inc. All rights reserved.

Borderless Geospatial Web (bolegweb)

NASA Astrophysics Data System (ADS)

Cetl, V.; Kliment, T.; Kliment, M.

2016-06-01

The effective access and use of geospatial information (GI) resources acquires a critical value of importance in modern knowledge based society. Standard web services defined by Open Geospatial Consortium (OGC) are frequently used within the implementations of spatial data infrastructures (SDIs) to facilitate discovery and use of geospatial data. This data is stored in databases located in a layer, called the invisible web, thus are ignored by search engines. SDI uses a catalogue (discovery) service for the web as a gateway to the GI world through the metadata defined by ISO standards, which are structurally diverse to OGC metadata. Therefore, a crosswalk needs to be implemented to bridge the OGC resources discovered on mainstream web with those documented by metadata in an SDI to enrich its information extent. A public global wide and user friendly portal of OGC resources available on the web ensures and enhances the use of GI within a multidisciplinary context and bridges the geospatial web from the end-user perspective, thus opens its borders to everybody. Project "Crosswalking the layers of geospatial information resources to enable a borderless geospatial web" with the acronym BOLEGWEB is ongoing as a postdoctoral research project at the Faculty of Geodesy, University of Zagreb in Croatia (http://bolegweb.geof.unizg.hr/). The research leading to the results of the project has received funding from the European Union Seventh Framework Programme (FP7 2007-2013) under Marie Curie FP7-PEOPLE-2011-COFUND. The project started in the November 2014 and is planned to be finished by the end of 2016. This paper provides an overview of the project, research questions and methodology, so far achieved results and future steps.

How to Write Easy-to-Read Health Materials: MedlinePlus

MedlinePlus

... practices. An accessible Web site helps people with reading and learning disabilities. For more information on Web accessibility, see the WebAIM (Web Accessibility in Mind) site from the Center for Persons with Disabilities ...

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

The Virtual Geophysics Laboratory (VGL): Scientific Workflows Operating Across Organizations and Across Infrastructures

NASA Astrophysics Data System (ADS)

Cox, S. J.; Wyborn, L. A.; Fraser, R.; Rankine, T.; Woodcock, R.; Vote, J.; Evans, B.

2012-12-01

The Virtual Geophysics Laboratory (VGL) is web portal that provides geoscientists with an integrated online environment that: seamlessly accesses geophysical and geoscience data services from the AuScope national geoscience information infrastructure; loosely couples these data to a variety of gesocience software tools; and provides large scale processing facilities via cloud computing. VGL is a collaboration between CSIRO, Geoscience Australia, National Computational Infrastructure, Monash University, Australian National University and the University of Queensland. The VGL provides a distributed system whereby a user can enter an online virtual laboratory to seamlessly connect to OGC web services for geoscience data. The data is supplied in open standards formats using international standards like GeoSciML. A VGL user uses a web mapping interface to discover and filter the data sources using spatial and attribute filters to define a subset. Once the data is selected the user is not required to download the data. VGL collates the service query information for later in the processing workflow where it will be staged directly to the computing facilities. The combination of deferring data download and access to Cloud computing enables VGL users to access their data at higher resolutions and to undertake larger scale inversions, more complex models and simulations than their own local computing facilities might allow. Inside the Virtual Geophysics Laboratory, the user has access to a library of existing models, complete with exemplar workflows for specific scientific problems based on those models. For example, the user can load a geological model published by Geoscience Australia, apply a basic deformation workflow provided by a CSIRO scientist, and have it run in a scientific code from Monash. Finally the user can publish these results to share with a colleague or cite in a paper. This opens new opportunities for access and collaboration as all the resources (models, code, data, processing) are shared in the one virtual laboratory. VGL provides end users with access to an intuitive, user-centered interface that leverages cloud storage and cloud and cluster processing from both the research communities and commercial suppliers (e.g. Amazon). As the underlying data and information services are agnostic of the scientific domain, they can support many other data types. This fundamental characteristic results in a highly reusable virtual laboratory infrastructure that could also be used for example natural hazards, satellite processing, soil geochemistry, climate modeling, agriculture crop modeling.

Open Source Hardware for DIY Environmental Sensing

NASA Astrophysics Data System (ADS)

Aufdenkampe, A. K.; Hicks, S. D.; Damiano, S. G.; Montgomery, D. S.

2014-12-01

The Arduino open source electronics platform has been very popular within the DIY (Do It Yourself) community for several years, and it is now providing environmental science researchers with an inexpensive alternative to commercial data logging and transmission hardware. Here we present the designs for our latest series of custom Arduino-based dataloggers, which include wireless communication options like self-meshing radio networks and cellular phone modules. The main Arduino board uses a custom interface board to connect to various research-grade sensors to take readings of turbidity, dissolved oxygen, water depth and conductivity, soil moisture, solar radiation, and other parameters. Sensors with SDI-12 communications can be directly interfaced to the logger using our open Arduino-SDI-12 software library (https://github.com/StroudCenter/Arduino-SDI-12). Different deployment options are shown, like rugged enclosures to house the loggers and rigs for mounting the sensors in both fresh water and marine environments. After the data has been collected and transmitted by the logger, the data is received by a mySQL-PHP stack running on a web server that can be accessed from anywhere in the world. Once there, the data can be visualized on web pages or served though REST requests and Water One Flow (WOF) services. Since one of the main benefits of using open source hardware is the easy collaboration between users, we are introducing a new web platform for discussion and sharing of ideas and plans for hardware and software designs used with DIY environmental sensors and data loggers.

Tool independence for the Web Accessibility Quantitative Metric.

PubMed

Vigo, Markel; Brajnik, Giorgio; Arrue, Myriam; Abascal, Julio

2009-07-01

The Web Accessibility Quantitative Metric (WAQM) aims at accurately measuring the accessibility of web pages. One of the main features of WAQM among others is that it is evaluation tool independent for ranking and accessibility monitoring scenarios. This article proposes a method to attain evaluation tool independence for all foreseeable scenarios. After demonstrating that homepages have a more similar error profile than any other web page in a given web site, 15 homepages were measured with 10,000 different values of WAQM parameters using EvalAccess and LIFT, two automatic evaluation tools for accessibility. A similar procedure was followed with random pages and with several test files obtaining several tuples that minimise the difference between both tools. One thousand four hundred forty-nine web pages from 15 web sites were measured with these tuples and those values that minimised the difference between the tools were selected. Once the WAQM was tuned, the accessibility of 15 web sites was measured with two metrics for web sites, concluding that even if similar values can be produced, obtaining the same scores is undesirable since evaluation tools behave in a different way.

Open hydrology courseware using the United States Geological Survey’s National Water Census Data Portal

USGS Publications Warehouse

Nelson, Jake; Ames, Daniel P.; Blodgett, David L.

2018-01-01

The U.S. Geological Survey (USGS) is the primary U.S. Government agency for water data collection and dissemination. In this role, the USGS has recently created and deployed a National Water Census Data Portal (NWC-DP) which provides access to streamflow, evapotransporation, precipitation, aquatic biology and other data at the national level. Recognizing the value of these data sets for hydrologic science education, this paper presents an effort to bridge the gap between pencil–and-paper-based hydrology curriculum and the USGS NWC-DP resource. Specifically, we have developed an R package, National Water Census Education (NWCEd), and five associated laboratory exercises that integrate R- and web-services-based access to the NWC-DP data sets. Using custom functions built into the NWCEd, students are able to access unprecedented amounts of hydrologic data from the NWC-DP, which can be applied to current hydrology curriculum and analyzed using NWCEd and a number of other open-source R tools.

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

PubMed Central

Mathelier, Anthony; Zhao, Xiaobei; Zhang, Allen W.; Parcy, François; Worsley-Hunt, Rebecca; Arenillas, David J.; Buchman, Sorana; Chen, Chih-yu; Chou, Alice; Ienasescu, Hans; Lim, Jonathan; Shyr, Casper; Tan, Ge; Zhou, Michelle; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth W.

2014-01-01

JASPAR (http://jaspar.genereg.net) is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription factors from multiple species. The fifth major release greatly expands the heart of JASPAR—the JASPAR CORE subcollection, which contains curated, non-redundant profiles—with 135 new curated profiles (74 in vertebrates, 8 in Drosophila melanogaster, 10 in Caenorhabditis elegans and 43 in Arabidopsis thaliana; a 30% increase in total) and 43 older updated profiles (36 in vertebrates, 3 in D. melanogaster and 4 in A. thaliana; a 9% update in total). The new and updated profiles are mainly derived from published chromatin immunoprecipitation-seq experimental datasets. In addition, the web interface has been enhanced with advanced capabilities in browsing, searching and subsetting. Finally, the new JASPAR release is accompanied by a new BioPython package, a new R tool package and a new R/Bioconductor data package to facilitate access for both manual and automated methods. PMID:24194598

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles.

PubMed

Mathelier, Anthony; Zhao, Xiaobei; Zhang, Allen W; Parcy, François; Worsley-Hunt, Rebecca; Arenillas, David J; Buchman, Sorana; Chen, Chih-yu; Chou, Alice; Ienasescu, Hans; Lim, Jonathan; Shyr, Casper; Tan, Ge; Zhou, Michelle; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth W

2014-01-01

JASPAR (http://jaspar.genereg.net) is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription factors from multiple species. The fifth major release greatly expands the heart of JASPAR-the JASPAR CORE subcollection, which contains curated, non-redundant profiles-with 135 new curated profiles (74 in vertebrates, 8 in Drosophila melanogaster, 10 in Caenorhabditis elegans and 43 in Arabidopsis thaliana; a 30% increase in total) and 43 older updated profiles (36 in vertebrates, 3 in D. melanogaster and 4 in A. thaliana; a 9% update in total). The new and updated profiles are mainly derived from published chromatin immunoprecipitation-seq experimental datasets. In addition, the web interface has been enhanced with advanced capabilities in browsing, searching and subsetting. Finally, the new JASPAR release is accompanied by a new BioPython package, a new R tool package and a new R/Bioconductor data package to facilitate access for both manual and automated methods.

An analysis of water data systems to inform the Open Water Data Initiative

USGS Publications Warehouse

Blodgett, David L.; Read, Emily K.; Lucido, Jessica M.; Slawecki, Tad; Young, Dwane

2016-01-01

Improving access to data and fostering open exchange of water information is foundational to solving water resources issues. In this vein, the Department of the Interior's Assistant Secretary for Water and Science put forward the charge to undertake an Open Water Data Initiative (OWDI) that would prioritize and accelerate work toward better water data infrastructure. The goal of the OWDI is to build out the Open Water Web (OWW). We therefore considered the OWW in terms of four conceptual functions: water data cataloging, water data as a service, enriching water data, and community for water data. To describe the current state of the OWW and identify areas needing improvement, we conducted an analysis of existing systems using a standard model for describing distributed systems and their business requirements. Our analysis considered three OWDI-focused use cases—flooding, drought, and contaminant transport—and then examined the landscape of other existing applications that support the Open Water Web. The analysis, which includes a discussion of observed successful practices of cataloging, serving, enriching, and building community around water resources data, demonstrates that we have made significant progress toward the needed infrastructure, although challenges remain. The further development of the OWW can be greatly informed by the interpretation and findings of our analysis.

Topographic mapping data semantics through data conversion and enhancement: Chapter 7

USGS Publications Warehouse

Varanka, Dalia; Carter, Jonathan; Usery, E. Lynn; Shoberg, Thomas; Edited by Ashish, Naveen; Sheth, Amit P.

2011-01-01

This paper presents research on the semantics of topographic data for triples and ontologies to blend the capabilities of the Semantic Web and The National Map of the U.S. Geological Survey. Automated conversion of relational topographic data of several geographic sample areas to the triple data model standard resulted in relatively poor semantic associations. Further research employed vocabularies of feature type and spatial relation terms. A user interface was designed to model the capture of non-standard terms relevant to public users and to map those terms to existing data models of The National Map through the use of ontology. Server access for the study area triple stores was made publicly available, illustrating how the development of linked data may transform institutional policies to open government data resources to the public. This paper presents these data conversion and research techniques that were tested as open linked data concepts leveraged through a user-centered interface and open USGS server access to the public.

Moving toward a universally accessible web: Web accessibility and education.

PubMed

Kurt, Serhat

2017-12-08

The World Wide Web is an extremely powerful source of information, inspiration, ideas, and opportunities. As such, it has become an integral part of daily life for a great majority of people. Yet, for a significant number of others, the internet offers only limited value due to the existence of barriers which make accessing the Web difficult, if not impossible. This article illustrates some of the reasons that achieving equality of access to the online world of education is so critical, explores the current status of Web accessibility, discusses evaluative tools and methods that can help identify accessibility issues in educational websites, and provides practical recommendations and guidelines for resolving some of the obstacles that currently hinder the achievability of the goal of universal Web access.

Enhancing Discovery, Search, and Access of NASA Hydrological Data by Leveraging GEOSS

NASA Technical Reports Server (NTRS)

Teng, William L.

2015-01-01

An ongoing NASA-funded project has removed a longstanding barrier to accessing NASA data (i.e., accessing archived time-step array data as point-time series) for selected variables of the North American and Global Land Data Assimilation Systems (NLDAS and GLDAS, respectively) and other EOSDIS (Earth Observing System Data Information System) data sets (e.g., precipitation, soil moisture). These time series (data rods) are pre-generated. Data rods Web services are accessible through the CUAHSI Hydrologic Information System (HIS) and the Goddard Earth Sciences Data and Information Services Center (GES DISC) but are not easily discoverable by users of other non-NASA data systems. The Global Earth Observation System of Systems (GEOSS) is a logical mechanism for providing access to the data rods. An ongoing GEOSS Water Services project aims to develop a distributed, global registry of water data, map, and modeling services cataloged using the standards and procedures of the Open Geospatial Consortium and the World Meteorological Organization. The ongoing data rods project has demonstrated the feasibility of leveraging the GEOSS infrastructure to help provide access to time series of model grid information or grids of information over a geographical domain for a particular time interval. A recently-begun, related NASA-funded ACCESS-GEOSS project expands on these prior efforts. Current work is focused on both improving the performance of the generation of on-the-fly (OTF) data rods and the Web interfaces from which users can easily discover, search, and access NASA data.

Open Access Internet Resources for Nano-Materials Physics Education

NASA Astrophysics Data System (ADS)

Moeck, Peter; Seipel, Bjoern; Upreti, Girish; Harvey, Morgan; Garrick, Will

2006-05-01

Because a great deal of nano-material science and engineering relies on crystalline materials, materials physicists have to provide their own specific contributions to the National Nanotechnology Initiative. Here we briefly review two freely accessible internet-based crystallographic databases, the Nano-Crystallography Database (http://nanocrystallography.research.pdx.edu) and the Crystallography Open Database (http://crystallography.net). Information on over 34,000 full structure determinations are stored in these two databases in the Crystallographic Information File format. The availability of such crystallographic data on the internet in a standardized format allows for all kinds of web-based crystallographic calculations and visualizations. Two examples of which that are dealt with in this paper are: interactive crystal structure visualizations in three dimensions and calculations of lattice-fringe fingerprints for the identification of unknown nanocrystals from their atomic-resolution transmission electron microscopy images.

A Prototype Web-based system for GOES-R Space Weather Data

NASA Astrophysics Data System (ADS)

Sundaravel, A.; Wilkinson, D. C.

2010-12-01

The Geostationary Operational Environmental Satellite-R Series (GOES-R) makes use of advanced instruments and technologies to monitor the Earth's surface and provide with accurate space weather data. The first GOES-R series satellite is scheduled to be launched in 2015. The data from the satellite will be widely used by scientists for space weather modeling and predictions. This project looks into the ways of how these datasets can be made available to the scientists on the Web and to assist them on their research. We are working on to develop a prototype web-based system that allows users to browse, search and download these data. The GOES-R datasets will be archived in NetCDF (Network Common Data Form) and CSV (Comma Separated Values) format. The NetCDF is a self-describing data format that contains both the metadata information and the data. The data is stored in an array-oriented fashion. The web-based system will offer services in two ways: via a web application (portal) and via web services. Using the web application, the users can download data in NetCDF or CSV format and can also plot a graph of the data. The web page displays the various categories of data and the time intervals for which the data is available. The web application (client) sends the user query to the server, which then connects to the data sources to retrieve the data and delivers it to the users. Data access will also be provided via SOAP (Simple Object Access Protocol) and REST (Representational State Transfer) web services. These provide functions which can be used by other applications to fetch data and use the data for further processing. To build the prototype system, we are making use of proxy data from existing GOES and POES space weather datasets. Java is the programming language used in developing tools that formats data to NetCDF and CSV. For the web technology we have chosen Grails to develop both the web application and the services. Grails is an open source web application framework based on the Groovy language. We are also making use of the THREDDS (Thematic Realtime Environmental Distributed Data Services) server to publish and access the NetCDF files. We have completed developing software tools to generate NetCDF and CSV data files and also tools to translate NetCDF to CSV. The current phase of the project involves in designing and developing the web interface.

Design and Deployment of a General Purpose, Open Source LoRa to Wi-Fi Hub and Data Logger

NASA Astrophysics Data System (ADS)

DeBell, T. C.; Udell, C.; Kwon, M.; Selker, J. S.; Lopez Alcala, J. M.

2017-12-01

Methods and technologies facilitating internet connectivity and near-real-time status updates for in site environmental sensor data are of increasing interest in Earth Science. However, Open Source, Do-It-Yourself technologies that enable plug and play functionality for web-connected sensors and devices remain largely inaccessible for typical researchers in our community. The Openly Published Environmental Sensing Lab at Oregon State University (OPEnS Lab) constructed an Open Source 900 MHz Long Range Radio (LoRa) receiver hub with SD card data logger, Ethernet and Wi-Fi shield, and 3D printed enclosure that dynamically uploads transmissions from multiple wirelessly-connected environmental sensing devices. Data transmissions may be received from devices up to 20km away. The hub time-stamps, saves to SD card, and uploads all transmissions to a Google Drive spreadsheet to be accessed in near-real-time by researchers and GeoVisualization applications (such as Arc GIS) for access, visualization, and analysis. This research expands the possibilities of scientific observation of our Earth, transforming the technology, methods, and culture by combining open-source development and cutting edge technology. This poster details our methods and evaluates the application of using 3D printing, Arduino Integrated Development Environment (IDE), Adafruit's Open-Hardware Feather development boards, and the WIZNET5500 Ethernet shield for designing this open-source, general purpose LoRa to Wi-Fi data logger.

Web-based asynchronous teleconsulting for consumers in Colombia: a case study.

PubMed

Valenzuela, José Ignacio; Arguello, Arturo; Cendales, Juan Gabriel; Rizo, Carlos A

2007-10-22

Fourteen years after the reform to Colombia's health system, the promises of universality, improved equity, efficiency, and better quality of care have not materialized. Remote areas remain underserved and access to care very limited. Recognizing teleconsultation as an effective way to improve access to health care and health information, a noncommercial open-access Web-based application for teleconsultation called Doctor Chat was developed. The objective was to report the experience of the Center for Virtual Education and Simulation eHealth (Centro de Educación Virtual y Simulación e-Salud) with open-access Web-based asynchronous teleconsultation for consumers in Colombia. A teleconsultation service in Spanish was developed and implemented in 2006. Teleconsultation requests were classified on three axes: (1) the purpose of the query, (2) the specialty, and (3) the geographic area of the query. Content analysis was performed on the free-text queries submitted to Doctor Chat, and descriptive statistics were gathered for each of the data categories (name, email, city, country, age, and gender). From September 2006 to March 2007, there were 270 asynchronous teleconsultations documented from 102 (37.8%) men and 168 (62.2%) women. On average, 1.4 requests were received per day. By age group, the largest number of requests (n = 80; 30%) were from users 24-29 years, followed by users (n = 66; 24%) 18-23 years. Requests were mainly from Colombia (n = 204; 75.6%) but also from Spain (n = 17; 6.3%), Mexico (n = 11; 4.1%), and other countries. In Colombia, 137 requests (67.2%) originated in Bogotá, the nation's capital, 25 (12.4%) from other main cities of the country, 40 (19.7%) from intermediate cities, and 2 (0.7%) from remote areas. The purpose of the majority of requests was for information about symptoms, health-related problems, or diseases (n = 149; 55.2%) and medications/treatments (n = 70; 25.9%). By specialty, information was most requested for gynecology and obstetrics (n = 71; 26%), dermatology (n = 28; 10%), urology (n = 22; 8%), and gastroenterology (n = 18; 7%), with anesthesiology, critical care, physical medicine and rehabilitation, and pathology being the least requested (n = 0; 0%). Overall, sexual and reproductive health (n = 93; 34%) issues constituted the main query subject. The average time to deliver a response was 120 hours in 2006 and 59 hours in 2007. Only 19 out of 270 users (7%) completed a survey with comments and perceptions about the system, of which 18 out of 19 (95%) corresponded to positive perceptions and 1 out of 19 (5%) expressed dissatisfaction with the service. The implementation of a Web-based teleconsulting service in Colombia appeared to be an innovative way to improve access to health care and information in the community and encouraged open and explicit discussion. Extending the service to underserved areas could improve access to health services and health information and could potentially improve economic indicators such as waiting times for consultations and the rate of pregnancy among teenagers; however, cultural, infrastructural, and Internet connectivity barriers are to be solved before successful implementation can derive population-wide positive impacts.

Web-Based Asynchronous Teleconsulting for Consumers in Colombia: A Case Study

PubMed Central

Valenzuela, José Ignacio; Arguello, Arturo; Cendales, Juan Gabriel

2007-01-01

Background Fourteen years after the reform to Colombia’s health system, the promises of universality, improved equity, efficiency, and better quality of care have not materialized. Remote areas remain underserved and access to care very limited. Recognizing teleconsultation as an effective way to improve access to health care and health information, a noncommercial open-access Web-based application for teleconsultation called Doctor Chat was developed. Objective The objective was to report the experience of the Center for Virtual Education and Simulation eHealth (Centro de Educación Virtual y Simulación e-Salud) with open-access Web-based asynchronous teleconsultation for consumers in Colombia. Methods A teleconsultation service in Spanish was developed and implemented in 2006. Teleconsultation requests were classified on three axes: (1) the purpose of the query, (2) the specialty, and (3) the geographic area of the query. Content analysis was performed on the free-text queries submitted to Doctor Chat, and descriptive statistics were gathered for each of the data categories (name, email, city, country, age, and gender). Results From September 2006 to March 2007, there were 270 asynchronous teleconsultations documented from 102 (37.8%) men and 168 (62.2%) women. On average, 1.4 requests were received per day. By age group, the largest number of requests (n = 80; 30%) were from users 24-29 years, followed by users (n = 66; 24%) 18-23 years. Requests were mainly from Colombia (n = 204; 75.6%) but also from Spain (n = 17; 6.3%), Mexico (n = 11; 4.1%), and other countries. In Colombia, 137 requests (67.2%) originated in Bogotá, the nation’s capital, 25 (12.4%) from other main cities of the country, 40 (19.7%) from intermediate cities, and 2 (0.7%) from remote areas. The purpose of the majority of requests was for information about symptoms, health-related problems, or diseases (n = 149; 55.2%) and medications/treatments (n = 70; 25.9%). By specialty, information was most requested for gynecology and obstetrics (n = 71; 26%), dermatology (n = 28; 10%), urology (n = 22; 8%), and gastroenterology (n = 18; 7%), with anesthesiology, critical care, physical medicine and rehabilitation, and pathology being the least requested (n = 0; 0%). Overall, sexual and reproductive health (n = 93; 34%) issues constituted the main query subject. The average time to deliver a response was 120 hours in 2006 and 59 hours in 2007. Only 19 out of 270 users (7%) completed a survey with comments and perceptions about the system, of which 18 out of 19 (95%) corresponded to positive perceptions and 1 out of 19 (5%) expressed dissatisfaction with the service. Conclusion The implementation of a Web-based teleconsulting service in Colombia appeared to be an innovative way to improve access to health care and information in the community and encouraged open and explicit discussion. Extending the service to underserved areas could improve access to health services and health information and could potentially improve economic indicators such as waiting times for consultations and the rate of pregnancy among teenagers; however, cultural, infrastructural, and Internet connectivity barriers are to be solved before successful implementation can derive population-wide positive impacts. PMID:17954469

The Namibia Early Flood Warning System, A CEOS Pilot Project

NASA Technical Reports Server (NTRS)

Mandl, Daniel; Frye, Stuart; Cappelaere, Pat; Sohlberg, Robert; Handy, Matthew; Grossman, Robert

2012-01-01

Over the past year few years, an international collaboration has developed a pilot project under the auspices of Committee on Earth Observation Satellite (CEOS) Disasters team. The overall team consists of civilian satellite agencies. For this pilot effort, the development team consists of NASA, Canadian Space Agency, Univ. of Maryland, Univ. of Colorado, Univ. of Oklahoma, Ukraine Space Research Institute and Joint Research Center(JRC) for European Commission. This development team collaborates with regional , national and international agencies to deliver end-to-end disaster coverage. In particular, the team in collaborating on this effort with the Namibia Department of Hydrology to begin in Namibia . However, the ultimate goal is to expand the functionality to provide early warning over the South Africa region. The initial collaboration was initiated by United Nations Office of Outer Space Affairs and CEOS Working Group for Information Systems and Services (WGISS). The initial driver was to demonstrate international interoperability using various space agency sensors and models along with regional in-situ ground sensors. In 2010, the team created a preliminary semi-manual system to demonstrate moving and combining key data streams and delivering the data to the Namibia Department of Hydrology during their flood season which typically is January through April. In this pilot, a variety of moderate resolution and high resolution satellite flood imagery was rapidly delivered and used in conjunction with flood predictive models in Namibia. This was collected in conjunction with ground measurements and was used to examine how to create a customized flood early warning system. During the first year, the team made use of SensorWeb technology to gather various sensor data which was used to monitor flood waves traveling down basins originating in Angola, but eventually flooding villages in Namibia. The team made use of standardized interfaces such as those articulated under the Open Cloud Consortium (OGC) Sensor Web Enablement (SWE) set of web services was good [1][2]. However, it was discovered that in order to make a system like this functional, there were many performance issues. Data sets were large and located in a variety of location behind firewalls and had to be accessed across open networks, so security was an issue. Furthermore, the network access acted as bottleneck to transfer map products to where they are needed. Finally, during disasters, many users and computer processes act in parallel and thus it was very easy to overload the single string of computers stitched together in a virtual system that was initially developed. To address some of these performance issues, the team partnered with the Open Cloud Consortium (OCC) who supplied a Computation Cloud located at the University of Illinois at Chicago and some manpower to administer this Cloud. The Flood SensorWeb [3] system was interfaced to the Cloud to provide a high performance user interface and product development engine. Figure 1 shows the functional diagram of the Flood SensorWeb. Figure 2 shows some of the functionality of the Computation Cloud that was integrated. A significant portion of the original system was ported to the Cloud and during the past year, technical issues were resolved which included web access to the Cloud, security over the open Internet, beginning experiments on how to handle surge capacity by using the virtual machines in the cloud in parallel, using tiling techniques to render large data sets as layers on map, interfaces to allow user to customize the data processing/product chain and other performance enhancing techniques. The conclusion reached from the effort and this presentation is that defining the interoperability standards in a small fraction of the work. For example, once open web service standards were defined, many users could not make use of the standards due to security restrictions. Furthermore, once an interoperable sysm is functional, then a surge of users can render a system unusable, especially in the disaster domain.

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.

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.

The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles.

PubMed

Piwowar, Heather; Priem, Jason; Larivière, Vincent; Alperin, Juan Pablo; Matthias, Lisa; Norlander, Bree; Farley, Ashley; West, Jevin; Haustein, Stefanie

2018-01-01

Despite growing interest in Open Access (OA) to scholarly literature, there is an unmet need for large-scale, up-to-date, and reproducible studies assessing the prevalence and characteristics of OA. We address this need using oaDOI, an open online service that determines OA status for 67 million articles. We use three samples, each of 100,000 articles, to investigate OA in three populations: (1) all journal articles assigned a Crossref DOI, (2) recent journal articles indexed in Web of Science, and (3) articles viewed by users of Unpaywall, an open-source browser extension that lets users find OA articles using oaDOI. We estimate that at least 28% of the scholarly literature is OA (19M in total) and that this proportion is growing, driven particularly by growth in Gold and Hybrid. The most recent year analyzed (2015) also has the highest percentage of OA (45%). Because of this growth, and the fact that readers disproportionately access newer articles, we find that Unpaywall users encounter OA quite frequently: 47% of articles they view are OA. Notably, the most common mechanism for OA is not Gold, Green, or Hybrid OA, but rather an under-discussed category we dub Bronze: articles made free-to-read on the publisher website, without an explicit Open license. We also examine the citation impact of OA articles, corroborating the so-called open-access citation advantage: accounting for age and discipline, OA articles receive 18% more citations than average, an effect driven primarily by Green and Hybrid OA. We encourage further research using the free oaDOI service, as a way to inform OA policy and practice.

The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles

PubMed Central

Larivière, Vincent; Alperin, Juan Pablo; Matthias, Lisa; Norlander, Bree; Farley, Ashley; West, Jevin; Haustein, Stefanie

2018-01-01

Despite growing interest in Open Access (OA) to scholarly literature, there is an unmet need for large-scale, up-to-date, and reproducible studies assessing the prevalence and characteristics of OA. We address this need using oaDOI, an open online service that determines OA status for 67 million articles. We use three samples, each of 100,000 articles, to investigate OA in three populations: (1) all journal articles assigned a Crossref DOI, (2) recent journal articles indexed in Web of Science, and (3) articles viewed by users of Unpaywall, an open-source browser extension that lets users find OA articles using oaDOI. We estimate that at least 28% of the scholarly literature is OA (19M in total) and that this proportion is growing, driven particularly by growth in Gold and Hybrid. The most recent year analyzed (2015) also has the highest percentage of OA (45%). Because of this growth, and the fact that readers disproportionately access newer articles, we find that Unpaywall users encounter OA quite frequently: 47% of articles they view are OA. Notably, the most common mechanism for OA is not Gold, Green, or Hybrid OA, but rather an under-discussed category we dub Bronze: articles made free-to-read on the publisher website, without an explicit Open license. We also examine the citation impact of OA articles, corroborating the so-called open-access citation advantage: accounting for age and discipline, OA articles receive 18% more citations than average, an effect driven primarily by Green and Hybrid OA. We encourage further research using the free oaDOI service, as a way to inform OA policy and practice. PMID:29456894

WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata

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

Putman, Tim E.; Lelong, Sebastien; Burgstaller-Muehlbacher, Sebastian

With the advancement of genome-sequencing technologies, new genomes are being sequenced daily. Although these sequences are deposited in publicly available data warehouses, their functional and genomic annotations (beyond genes which are predicted automatically) mostly reside in the text of primary publications. Professional curators are hard at work extracting those annotations from the literature for the most studied organisms and depositing them in structured databases. However, the resources don’t exist to fund the comprehensive curation of the thousands of newly sequenced organisms in this manner. Here, we describe WikiGenomes (wikigenomes.org), a web application that facilitates the consumption and curation of genomicmore » data by the entire scientific community. WikiGenomes is based on Wikidata, an openly editable knowledge graph with the goal of aggregating published knowledge into a free and open database. WikiGenomes empowers the individual genomic researcher to contribute their expertise to the curation effort and integrates the knowledge into Wikidata, enabling it to be accessed by anyone without restriction.« less

Web Map Apps using NASA's Earth Observing Fleet

NASA Astrophysics Data System (ADS)

Boller, R. A.; Baynes, K.; Pressley, N. N.; Thompson, C. K.; Cechini, M. F.; Schmaltz, J. E.; Alarcon, C.; De Cesare, C.; Gunnoe, T.; Wong, M. M.; King, B. A.; Roberts, J. T.; Rodriguez, J.; De Luca, A. P.; King, J.

2016-12-01

Through the miracle of open web mapping services for satellite imagery, a garden of new applications has sprouted to monitor the planet across a variety of domains. The Global Imagery Browse Services (GIBS) provide free and open access to full resolution imagery captured by NASA's Earth observing fleet. Spanning 15+ years and running through as recently as "a few hours ago", GIBS aims to provide a general-purpose window into NASA's vast archive of the planet. While the vast nature of this archive can be daunting, many domain-specific applications have been built to meet the needs of their respective communities. This presentation will demonstrate a diverse set of these new applications which can take planetarium visitors into (virtual) orbit, guide fire resource managers to hotspots, help anglers find their next catch, illustrate global air quality patterns to local regulators, and even spur a friendly competition to find clouds which are shaped the most like cats. We hope this garden will continue to grow and will illustrate upcoming upgrades to GIBS which may open new pathways for development.

WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata

DOE PAGES

Putman, Tim E.; Lelong, Sebastien; Burgstaller-Muehlbacher, Sebastian; ...

2017-03-06

With the advancement of genome-sequencing technologies, new genomes are being sequenced daily. Although these sequences are deposited in publicly available data warehouses, their functional and genomic annotations (beyond genes which are predicted automatically) mostly reside in the text of primary publications. Professional curators are hard at work extracting those annotations from the literature for the most studied organisms and depositing them in structured databases. However, the resources don’t exist to fund the comprehensive curation of the thousands of newly sequenced organisms in this manner. Here, we describe WikiGenomes (wikigenomes.org), a web application that facilitates the consumption and curation of genomicmore » data by the entire scientific community. WikiGenomes is based on Wikidata, an openly editable knowledge graph with the goal of aggregating published knowledge into a free and open database. WikiGenomes empowers the individual genomic researcher to contribute their expertise to the curation effort and integrates the knowledge into Wikidata, enabling it to be accessed by anyone without restriction.« less

Interoperability In The New Planetary Science Archive (PSA)

NASA Astrophysics Data System (ADS)

Rios, C.; Barbarisi, I.; Docasal, R.; Macfarlane, A. J.; Gonzalez, J.; Arviset, C.; Grotheer, E.; Besse, S.; Martinez, S.; Heather, D.; De Marchi, G.; Lim, T.; Fraga, D.; Barthelemy, M.

2015-12-01

As the world becomes increasingly interconnected, there is a greater need to provide interoperability with software and applications that are commonly being used globally. For this purpose, the development of the new Planetary Science Archive (PSA), by the European Space Astronomy Centre (ESAC) Science Data Centre (ESDC), is focused on building a modern science archive that takes into account internationally recognised standards in order to provide access to the archive through tools from third parties, for example by the NASA Planetary Data System (PDS), the VESPA project from the Virtual Observatory of Paris as well as other international institutions. The protocols and standards currently being supported by the new Planetary Science Archive at this time are the Planetary Data Access Protocol (PDAP), the EuroPlanet-Table Access Protocol (EPN-TAP) and Open Geospatial Consortium (OGC) standards. The architecture of the PSA consists of a Geoserver (an open-source map server), the goal of which is to support use cases such as the distribution of search results, sharing and processing data through a OGC Web Feature Service (WFS) and a Web Map Service (WMS). This server also allows the retrieval of requested information in several standard output formats like Keyhole Markup Language (KML), Geography Markup Language (GML), shapefile, JavaScript Object Notation (JSON) and Comma Separated Values (CSV), among others. The provision of these various output formats enables end-users to be able to transfer retrieved data into popular applications such as Google Mars and NASA World Wind.

Giovanni in the Cloud: Earth Science Data Exploration in Amazon Web Services

NASA Astrophysics Data System (ADS)

Hegde, M.; Petrenko, M.; Smit, C.; Zhang, H.; Pilone, P.; Zasorin, A. A.; Pham, L.

2017-12-01

Giovanni (https://giovanni.gsfc.nasa.gov/giovanni/) is a popular online data exploration tool at the NASA Goddard Earth Sciences Data Information Services Center (GES DISC), providing 22 analysis and visualization services for over 1600 Earth Science data variables. Owing to its popularity, Giovanni has experienced a consistent growth in overall demand, with periodic usage spikes attributed to trainings by education organizations, extensive data analysis in response to natural disasters, preparations for science meetings, etc. Furthermore, the new generation of spaceborne sensors and high resolution models have resulted in an exponential growth in data volume with data distributed across the traditional boundaries of datacenters. Seamless exploration of data (without users having to worry about data center boundaries) has been a key recommendation of the GES DISC User Working Group. These factors have required new strategies for delivering acceptable performance. The cloud-based Giovanni, built on Amazon Web Services (AWS), evaluates (1) AWS native solutions to provide a scalable, serverless architecture; (2) open standards for data storage in the Cloud; (3) a cost model for operations; and (4) end-user performance. Our preliminary findings indicate that the use of serverless architecture has a potential to significantly reduce development and operational cost of Giovanni. The combination of using AWS managed services, storage of data in open standards, and schema-on-read data access strategy simplifies data access and analytics, in addition to making data more accessible to the end users of Giovanni through popular programming languages.

Giovanni in the Cloud: Earth Science Data Exploration in Amazon Web Services

NASA Technical Reports Server (NTRS)

Petrenko, Maksym; Hegde, Mahabal; Smit, Christine; Zhang, Hailiang; Pilone, Paul; Zasorin, Andrey A.; Pham, Long

2017-01-01

Giovanni is an exploration tool at the NASA Goddard Earth Sciences Data Information Services Center (GES DISC), providing 22 analysis and visualization services for over 1600 Earth Science data variables. Owing to its popularity, Giovanni has experienced a consistent growth in overall demand, with periodic usage spikes attributed to trainings by education organizations, extensive data analysis in response to natural disasters, preparations for science meetings, etc. Furthermore, the new generation of spaceborne sensors and high resolution models have resulted in an exponential growth in data volume with data distributed across the traditional boundaries of data centers. Seamless exploration of data (without users having to worry about data center boundaries) has been a key recommendation of the GES DISC User Working Group. These factors have required new strategies for delivering acceptable performance. The cloud-based Giovanni, built on Amazon Web Services (AWS), evaluates (1) AWS native solutions to provide a scalable, serverless architecture; (2) open standards for data storage in the Cloud; (3) a cost model for operations; and (4) end-user performance. Our preliminary findings indicate that the use of serverless architecture has a potential to significantly reduce development and operational cost of Giovanni. The combination of using AWS managed services, storage of data in open standards, and schema-on-read data access strategy simplifies data access and analytics, in addition to making data more accessible to the end users of Giovanni through popular programming languages.

Architecture of the local spatial data infrastructure for regional climate change research

NASA Astrophysics Data System (ADS)

Titov, Alexander; Gordov, Evgeny

2013-04-01

Georeferenced datasets (meteorological databases, modeling and reanalysis results, etc.) are actively used in modeling and analysis of climate change for various spatial and temporal scales. Due to inherent heterogeneity of environmental datasets as well as their size which might constitute up to tens terabytes for a single dataset studies in the area of climate and environmental change require a special software support based on SDI approach. A dedicated architecture of the local spatial data infrastructure aiming at regional climate change analysis using modern web mapping technologies is presented. Geoportal is a key element of any SDI, allowing searching of geoinformation resources (datasets and services) using metadata catalogs, producing geospatial data selections by their parameters (data access functionality) as well as managing services and applications of cartographical visualization. It should be noted that due to objective reasons such as big dataset volume, complexity of data models used, syntactic and semantic differences of various datasets, the development of environmental geodata access, processing and visualization services turns out to be quite a complex task. Those circumstances were taken into account while developing architecture of the local spatial data infrastructure as a universal framework providing geodata services. So that, the architecture presented includes: 1. Effective in terms of search, access, retrieval and subsequent statistical processing, model of storing big sets of regional georeferenced data, allowing in particular to store frequently used values (like monthly and annual climate change indices, etc.), thus providing different temporal views of the datasets 2. General architecture of the corresponding software components handling geospatial datasets within the storage model 3. Metadata catalog describing in detail using ISO 19115 and CF-convention standards datasets used in climate researches as a basic element of the spatial data infrastructure as well as its publication according to OGC CSW (Catalog Service Web) specification 4. Computational and mapping web services to work with geospatial datasets based on OWS (OGC Web Services) standards: WMS, WFS, WPS 5. Geoportal as a key element of thematic regional spatial data infrastructure providing also software framework for dedicated web applications development To realize web mapping services Geoserver software is used since it provides natural WPS implementation as a separate software module. To provide geospatial metadata services GeoNetwork Opensource (http://geonetwork-opensource.org) product is planned to be used for it supports ISO 19115/ISO 19119/ISO 19139 metadata standards as well as ISO CSW 2.0 profile for both client and server. To implement thematic applications based on geospatial web services within the framework of local SDI geoportal the following open source software have been selected: 1. OpenLayers JavaScript library, providing basic web mapping functionality for the thin client such as web browser 2. GeoExt/ExtJS JavaScript libraries for building client-side web applications working with geodata services. The web interface developed will be similar to the interface of such popular desktop GIS applications, as uDIG, QuantumGIS etc. The work is partially supported by RF Ministry of Education and Science grant 8345, SB RAS Program VIII.80.2.1 and IP 131.

Use of a web 2.0 portal to improve education and communication in young patients with families: randomized controlled trial.

PubMed

Hanberger, Lena; Ludvigsson, Johnny; Nordfeldt, Sam

2013-08-23

Diabetes requires extensive self-care and comprehensive knowledge, making patient education central to diabetes self-management. Web 2.0 systems have great potential to enhance health information and open new ways for patients and practitioners to communicate. To develop a Web portal designed to facilitate self-management, including diabetes-related information and social networking functions, and to study its use and effects in pediatric patients with diabetes. A Web 2.0 portal was developed in collaboration with patients, parents, and practitioners. It offered communication with local practitioners, interaction with peers, and access to relevant information and services. Children and adolescents with diabetes in a geographic population of two pediatric clinics in Sweden were randomized to a group receiving passwords for access to the portal or a control group with no access (n=230) for 1 year. All subjects had access during a second study year. Users' activity was logged by site and page visits. Health-related quality of life (HRQOL), empowerment (DES), and quality of information (QPP) questionnaires were given at baseline and after 1 and 2 study years. Clinical data came from the Swedish pediatric diabetes quality registry SWEDIABKIDS. There was a continuous flow of site visits, decreasing in summer and Christmas periods. In 119/233 families (51%), someone visited the portal the first study year and 169/484 (35%) the second study year. The outcome variables did not differ between intervention and control group. No adverse treatment or self-care effects were identified. A higher proportion of mothers compared to fathers visited once or more the first year (P<.001) and the second year (P<.001). The patients who had someone in the family visiting the portal 5 times or more, had shorter diabetes duration (P=.006), were younger (P=.008), had lower HbA1c after 1 year of access (P=.010), and were more often girls (P<.001). Peer interaction seems to be a valued aspect. The Web 2.0 portal may be useful as a complement to traditional care for this target group. Widespread use of a portal would need integration in routine care and promotion by diabetes team members. International Standard Randomized Controlled Trial Number (ISRCTN):92107365; http://www.controlled-trials.com/ISRCTN92107365/ (Archived by WebCite at http://webcitation.org/6IkiIvtSb).

Earth science big data at users' fingertips: the EarthServer Science Gateway Mobile

NASA Astrophysics Data System (ADS)

Barbera, Roberto; Bruno, Riccardo; Calanducci, Antonio; Fargetta, Marco; Pappalardo, Marco; Rundo, Francesco

2014-05-01

The EarthServer project (www.earthserver.eu), funded by the European Commission under its Seventh Framework Program, aims at establishing open access and ad-hoc analytics on extreme-size Earth Science data, based on and extending leading-edge Array Database technology. The core idea is to use database query languages as client/server interface to achieve barrier-free "mix & match" access to multi-source, any-size, multi-dimensional space-time data -- in short: "Big Earth Data Analytics" - based on the open standards of the Open Geospatial Consortium Web Coverage Processing Service (OGC WCPS) and the W3C XQuery. EarthServer combines both, thereby achieving a tight data/metadata integration. Further, the rasdaman Array Database System (www.rasdaman.com) is extended with further space-time coverage data types. On server side, highly effective optimizations - such as parallel and distributed query processing - ensure scalability to Exabyte volumes. In this contribution we will report on the EarthServer Science Gateway Mobile, an app for both iOS and Android-based devices that allows users to seamlessly access some of the EarthServer applications using SAML-based federated authentication and fine-grained authorisation mechanisms.

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.

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.

SEnviro: a sensorized platform proposal using open hardware and open standards.

PubMed

Trilles, Sergio; Luján, Alejandro; Belmonte, Óscar; Montoliu, Raúl; Torres-Sospedra, Joaquín; Huerta, Joaquín

2015-03-06

The need for constant monitoring of environmental conditions has produced an increase in the development of wireless sensor networks (WSN). The drive towards smart cities has produced the need for smart sensors to be able to monitor what is happening in our cities. This, combined with the decrease in hardware component prices and the increase in the popularity of open hardware, has favored the deployment of sensor networks based on open hardware. The new trends in Internet Protocol (IP) communication between sensor nodes allow sensor access via the Internet, turning them into smart objects (Internet of Things and Web of Things). Currently, WSNs provide data in different formats. There is a lack of communication protocol standardization, which turns into interoperability issues when connecting different sensor networks or even when connecting different sensor nodes within the same network. This work presents a sensorized platform proposal that adheres to the principles of the Internet of Things and theWeb of Things. Wireless sensor nodes were built using open hardware solutions, and communications rely on the HTTP/IP Internet protocols. The Open Geospatial Consortium (OGC) SensorThings API candidate standard was used as a neutral format to avoid interoperability issues. An environmental WSN developed following the proposed architecture was built as a proof of concept. Details on how to build each node and a study regarding energy concerns are presented.

SEnviro: A Sensorized Platform Proposal Using Open Hardware and Open Standards

PubMed Central

Trilles, Sergio; Luján, Alejandro; Belmonte, Óscar; Montoliu, Raúl; Torres-Sospedra, Joaquín; Huerta, Joaquín

2015-01-01

The need for constant monitoring of environmental conditions has produced an increase in the development of wireless sensor networks (WSN). The drive towards smart cities has produced the need for smart sensors to be able to monitor what is happening in our cities. This, combined with the decrease in hardware component prices and the increase in the popularity of open hardware, has favored the deployment of sensor networks based on open hardware. The new trends in Internet Protocol (IP) communication between sensor nodes allow sensor access via the Internet, turning them into smart objects (Internet of Things and Web of Things). Currently, WSNs provide data in different formats. There is a lack of communication protocol standardization, which turns into interoperability issues when connecting different sensor networks or even when connecting different sensor nodes within the same network. This work presents a sensorized platform proposal that adheres to the principles of the Internet of Things and the Web of Things. Wireless sensor nodes were built using open hardware solutions, and communications rely on the HTTP/IP Internet protocols. The Open Geospatial Consortium (OGC) SensorThings API candidate standard was used as a neutral format to avoid interoperability issues. An environmental WSN developed following the proposed architecture was built as a proof of concept. Details on how to build each node and a study regarding energy concerns are presented. PMID:25756864

Opening Reproducible Research

NASA Astrophysics Data System (ADS)

Nüst, Daniel; Konkol, Markus; Pebesma, Edzer; Kray, Christian; Klötgen, Stephanie; Schutzeichel, Marc; Lorenz, Jörg; Przibytzin, Holger; Kussmann, Dirk

2016-04-01

Open access is not only a form of publishing such that research papers become available to the large public free of charge, it also refers to a trend in science that the act of doing research becomes more open and transparent. When science transforms to open access we not only mean access to papers, research data being collected, or data being generated, but also access to the data used and the procedures carried out in the research paper. Increasingly, scientific results are generated by numerical manipulation of data that were already collected, and may involve simulation experiments that are completely carried out computationally. Reproducibility of research findings, the ability to repeat experimental procedures and confirm previously found results, is at the heart of the scientific method (Pebesma, Nüst and Bivand, 2012). As opposed to the collection of experimental data in labs or nature, computational experiments lend themselves very well for reproduction. Some of the reasons why scientists do not publish data and computational procedures that allow reproduction will be hard to change, e.g. privacy concerns in the data, fear for embarrassment or of losing a competitive advantage. Others reasons however involve technical aspects, and include the lack of standard procedures to publish such information and the lack of benefits after publishing them. We aim to resolve these two technical aspects. We propose a system that supports the evolution of scientific publications from static papers into dynamic, executable research documents. The DFG-funded experimental project Opening Reproducible Research (ORR) aims for the main aspects of open access, by improving the exchange of, by facilitating productive access to, and by simplifying reuse of research results that are published over the Internet. Central to the project is a new form for creating and providing research results, the executable research compendium (ERC), which not only enables third parties to reproduce the original research and hence recreate the original research results (figures, tables), but also facilitates interaction with them as well as their recombination with new data or methods. Building on existing open standards and software, this project develops standards and tools for ERCs, and will demonstrate and evaluate these, focusing on the geosciences domains. The project goes beyond a technical solution for ERCs by evaluating the system from the perspectives of geoscience researchers as participants in a scientific publication process. It will focus on the statistical environment R, but also evaluate larger run time systems captured in virtual environments (Docker containers). ERCs are built upon and integrate well with both established day-to-day workflows of digital research and the scientific publication process. They make research accessible on different levels at any stage to anyone via open web platforms. Other scientists can transfer a compendium of software and tools to their own local environment and collaborate, while others make minimal changes and compare changed results in a web browser. Building on recent advances in mainstream IT, ORR envisions a new architecture for storing, executing and interacting with the original analysis environment alongside the corresponding research data and text. ORR bridges the gap between long-term archives, practical geoscience researchers, as well as publication media. Consequently, the project team seeks input and feedback from researchers working with geospatial data to ensure usable and useful open access publications as well as a publication process that minimizes effort while maximizing usability and re-usability. {References} Pebesma, E., D. Nüst, R. Bivand, 2012. The R software environment in reproducible geoscientific research. Eos, Transactions American Geophysical Union 93, vol 16, p. http://dx.doi.org/10.1029/2012EO160003{163-164}. Opening Reproducible Research project description and website: https://www.uni-muenster.de/forschungaz/project/9520?lang=en

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.

Web Accessibility and Accessibility Instruction

ERIC Educational Resources Information Center

Green, Ravonne A.; Huprich, Julia

2009-01-01

Section 508 of the Americans with Disabilities Act (ADA) mandates that programs and services be accessible to people with disabilities. While schools of library and information science (SLIS*) and university libraries should model accessible Web sites, this may not be the case. This article examines previous studies about the Web accessibility of…

General Practitioners' Attitudes Toward a Web-Based Mental Health Service for Adolescents: Implications for Service Design and Delivery.

PubMed

Subotic-Kerry, Mirjana; King, Catherine; O'Moore, Kathleen; Achilles, Melinda; O'Dea, Bridianne

2018-03-23

Anxiety disorders and depression are prevalent among youth. General practitioners (GPs) are often the first point of professional contact for treating health problems in young people. A Web-based mental health service delivered in partnership with schools may facilitate increased access to psychological care among adolescents. However, for such a model to be implemented successfully, GPs' views need to be measured. This study aimed to examine the needs and attitudes of GPs toward a Web-based mental health service for adolescents, and to identify the factors that may affect the provision of this type of service and likelihood of integration. Findings will inform the content and overall service design. GPs were interviewed individually about the proposed Web-based service. Qualitative analysis of transcripts was performed using thematic coding. A short follow-up questionnaire was delivered to assess background characteristics, level of acceptability, and likelihood of integration of the Web-based mental health service. A total of 13 GPs participated in the interview and 11 completed a follow-up online questionnaire. Findings suggest strong support for the proposed Web-based mental health service. A wide range of factors were found to influence the likelihood of GPs integrating a Web-based service into their clinical practice. Coordinated collaboration with parents, students, school counselors, and other mental health care professionals were considered important by nearly all GPs. Confidence in Web-based care, noncompliance of adolescents and GPs, accessibility, privacy, and confidentiality were identified as potential barriers to adopting the proposed Web-based service. GPs were open to a proposed Web-based service for the monitoring and management of anxiety and depression in adolescents, provided that a collaborative approach to care is used, the feedback regarding the client is clear, and privacy and security provisions are assured. ©Mirjana Subotic-Kerry, Catherine King, Kathleen O'Moore, Melinda Achilles, Bridianne O'Dea. Originally published in JMIR Human Factors (http://humanfactors.jmir.org), 23.03.2018.

78 FR 71676 - Submission for Review: 3206-0201, Federal Employees Health Benefits (FEHB) Open Season Express...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-29

... (FEHB) Open Season Express Interactive Voice Response (IVR) System and Open Season Web site AGENCY: U.S... Benefits (FEHB) Open Season Express Interactive Voice Response (IVR) System and the Open Season Web site... Season Express Interactive Voice Response (IVR) System, and the Open Season Web site, Open Season Online...

Emerging technologies and web accessibility: research challenges and opportunities focussing on vision issues.

PubMed

Harper, Simon; Yesilada, Yeliz

2012-01-01

This is a technological review paper focussed on identifying both the research challenges and opportunities for further investigation arising from emerging technologies, and it does not aim to propose any recommendation or standard. It is focussed on blind and partially sighted World Wide Web (Web) users along with others who use assistive technologies. The Web is a fast moving interdisciplinary domain in which new technologies, techniques and research is in perpetual development. It is often difficult to maintain a holistic view of new developments within the multiple domains which together make up the Web. This suggests that knowledge of the current developments and predictions of future developments are additionally important for the accessibility community. Web accessibility has previously been characterised by the correction of our past mistakes to make the current Web fulfil the original vision of access for all. New technologies were not designed with accessibility in mind and technologies that could be useful for addressing accessibility issues were not identified or adopted by the accessibility community. We wish to enable the research community to undertake preventative measures and proactively address challenges, while recognising opportunities, before they become unpreventable or require retrospective technological enhancement. This article then reviews emerging trends within the Web and Web Accessibility domains.

Onco-STS: a web-based laboratory information management system for sample and analysis tracking in oncogenomic experiments.

PubMed

Gavrielides, Mike; Furney, Simon J; Yates, Tim; Miller, Crispin J; Marais, Richard

2014-01-01

Whole genomes, whole exomes and transcriptomes of tumour samples are sequenced routinely to identify the drivers of cancer. The systematic sequencing and analysis of tumour samples, as well other oncogenomic experiments, necessitates the tracking of relevant sample information throughout the investigative process. These meta-data of the sequencing and analysis procedures include information about the samples and projects as well as the sequencing centres, platforms, data locations, results locations, alignments, analysis specifications and further information relevant to the experiments. The current work presents a sample tracking system for oncogenomic studies (Onco-STS) to store these data and make them easily accessible to the researchers who work with the samples. The system is a web application, which includes a database and a front-end web page that allows the remote access, submission and updating of the sample data in the database. The web application development programming framework Grails was used for the development and implementation of the system. The resulting Onco-STS solution is efficient, secure and easy to use and is intended to replace the manual data handling of text records. Onco-STS allows simultaneous remote access to the system making collaboration among researchers more effective. The system stores both information on the samples in oncogenomic studies and details of the analyses conducted on the resulting data. Onco-STS is based on open-source software, is easy to develop and can be modified according to a research group's needs. Hence it is suitable for laboratories that do not require a commercial system.

Design and Analysis of a Model Reconfigurable Cyber-Exercise Laboratory (RCEL) for Information Assurance Education

DTIC Science & Technology

2004-03-01

with MySQL . This choice was made because MySQL is open source. Any significant database engine such as Oracle or MS- SQL or even MS Access can be used...10 Figure 6. The DoD vs . Commercial Life Cycle...necessarily be interested in SCADA network security 13. MySQL (Database server) – This station represents a typical data server for a web page

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

Educational Resources for Global Health in Otolaryngology.

PubMed

Hancock, Melyssa; Hoa, Michael; Malekzadeh, Sonya

2018-06-01

Advances in modern communications and information technology have helped to improve access to, and quality of, health care and education. These enhancements include a variety of World Wide Web-based and mobile learning platforms, such as eLearning, mLearning, and open education resources. This article highlights the innovative approaches that have fostered improved collaboration and coordination of global health efforts in otolaryngology. Copyright © 2018 Elsevier Inc. All rights reserved.

NASA Update for Unidata Stratcomm

NASA Technical Reports Server (NTRS)

Lynnes, Chris

2017-01-01

The NASA representative to the Unidata Strategic Committee presented a semiannual update on NASAs work with and use of Unidata technologies. The talk updated Unidata on the program of cloud computing prototypes underway for the Earth Observing System Data and Information System (EOSDIS). Also discussed was a trade study on the use of the Open source Project for a Network Data Access Protocol (OPeNDAP) with Web Object Storage in the cloud.

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

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.

PubMed

Khan, Aziz; Fornes, Oriol; Stigliani, Arnaud; Gheorghe, Marius; Castro-Mondragon, Jaime A; van der Lee, Robin; Bessy, Adrien; Chèneby, Jeanne; Kulkarni, Shubhada R; Tan, Ge; Baranasic, Damir; Arenillas, David J; Sandelin, Albin; Vandepoele, Klaas; Lenhard, Boris; Ballester, Benoît; Wasserman, Wyeth W; Parcy, François; Mathelier, Anthony

2018-01-04

JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six taxonomic groups. In the 2018 release of JASPAR, the CORE collection has been expanded with 322 new PFMs (60 for vertebrates and 262 for plants) and 33 PFMs were updated (24 for vertebrates, 8 for plants and 1 for insects). These new profiles represent a 30% expansion compared to the 2016 release. In addition, we have introduced 316 TFFMs (95 for vertebrates, 218 for plants and 3 for insects). This release incorporates clusters of similar PFMs in each taxon and each TF class per taxon. The JASPAR 2018 CORE vertebrate collection of PFMs was used to predict TF-binding sites in the human genome. The predictions are made available to the scientific community through a UCSC Genome Browser track data hub. Finally, this update comes with a new web framework with an interactive and responsive user-interface, along with new features. All the underlying data can be retrieved programmatically using a RESTful API and through the JASPAR 2018 R/Bioconductor package. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

PubMed Central

Fornes, Oriol; Stigliani, Arnaud; Gheorghe, Marius; Castro-Mondragon, Jaime A; Bessy, Adrien; Chèneby, Jeanne; Kulkarni, Shubhada R; Tan, Ge; Baranasic, Damir; Arenillas, David J; Vandepoele, Klaas; Parcy, François

2018-01-01

Abstract JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six taxonomic groups. In the 2018 release of JASPAR, the CORE collection has been expanded with 322 new PFMs (60 for vertebrates and 262 for plants) and 33 PFMs were updated (24 for vertebrates, 8 for plants and 1 for insects). These new profiles represent a 30% expansion compared to the 2016 release. In addition, we have introduced 316 TFFMs (95 for vertebrates, 218 for plants and 3 for insects). This release incorporates clusters of similar PFMs in each taxon and each TF class per taxon. The JASPAR 2018 CORE vertebrate collection of PFMs was used to predict TF-binding sites in the human genome. The predictions are made available to the scientific community through a UCSC Genome Browser track data hub. Finally, this update comes with a new web framework with an interactive and responsive user-interface, along with new features. All the underlying data can be retrieved programmatically using a RESTful API and through the JASPAR 2018 R/Bioconductor package. PMID:29140473

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.

Reactome graph database: Efficient access to complex pathway data

PubMed Central

Korninger, Florian; Viteri, Guilherme; Marin-Garcia, Pablo; Ping, Peipei; Wu, Guanming; Stein, Lincoln; D’Eustachio, Peter

2018-01-01

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its query language, Cypher, provide efficient access to the complex Reactome data model, facilitating easy traversal and knowledge discovery. The adoption of this technology greatly improved query efficiency, reducing the average query time by 93%. The web service built on top of the graph database provides programmatic access to Reactome data by object oriented queries, but also supports more complex queries that take advantage of the new underlying graph-based data storage. By adopting graph database technology we are providing a high performance pathway data resource to the community. The Reactome graph database use case shows the power of NoSQL database engines for complex biological data types. PMID:29377902

Reactome graph database: Efficient access to complex pathway data.

PubMed

Fabregat, Antonio; Korninger, Florian; Viteri, Guilherme; Sidiropoulos, Konstantinos; Marin-Garcia, Pablo; Ping, Peipei; Wu, Guanming; Stein, Lincoln; D'Eustachio, Peter; Hermjakob, Henning

2018-01-01

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its query language, Cypher, provide efficient access to the complex Reactome data model, facilitating easy traversal and knowledge discovery. The adoption of this technology greatly improved query efficiency, reducing the average query time by 93%. The web service built on top of the graph database provides programmatic access to Reactome data by object oriented queries, but also supports more complex queries that take advantage of the new underlying graph-based data storage. By adopting graph database technology we are providing a high performance pathway data resource to the community. The Reactome graph database use case shows the power of NoSQL database engines for complex biological data types.

Advances in a distributed approach for ocean model data interoperability

USGS Publications Warehouse

Signell, Richard P.; Snowden, Derrick P.

2014-01-01

An infrastructure for earth science data is emerging across the globe based on common data models and web services. As we evolve from custom file formats and web sites to standards-based web services and tools, data is becoming easier to distribute, find and retrieve, leaving more time for science. We describe recent advances that make it easier for ocean model providers to share their data, and for users to search, access, analyze and visualize ocean data using MATLAB® and Python®. These include a technique for modelers to create aggregated, Climate and Forecast (CF) metadata convention datasets from collections of non-standard Network Common Data Form (NetCDF) output files, the capability to remotely access data from CF-1.6-compliant NetCDF files using the Open Geospatial Consortium (OGC) Sensor Observation Service (SOS), a metadata standard for unstructured grid model output (UGRID), and tools that utilize both CF and UGRID standards to allow interoperable data search, browse and access. We use examples from the U.S. Integrated Ocean Observing System (IOOS®) Coastal and Ocean Modeling Testbed, a project in which modelers using both structured and unstructured grid model output needed to share their results, to compare their results with other models, and to compare models with observed data. The same techniques used here for ocean modeling output can be applied to atmospheric and climate model output, remote sensing data, digital terrain and bathymetric data.

Secure Web-Site Access with Tickets and Message-Dependent Digests

USGS Publications Warehouse

Donato, David I.

2008-01-01

Although there are various methods for restricting access to documents stored on a World Wide Web (WWW) site (a Web site), none of the widely used methods is completely suitable for restricting access to Web applications hosted on an otherwise publicly accessible Web site. A new technique, however, provides a mix of features well suited for restricting Web-site or Web-application access to authorized users, including the following: secure user authentication, tamper-resistant sessions, simple access to user state variables by server-side applications, and clean session terminations. This technique, called message-dependent digests with tickets, or MDDT, maintains secure user sessions by passing single-use nonces (tickets) and message-dependent digests of user credentials back and forth between client and server. Appendix 2 provides a working implementation of MDDT with PHP server-side code and JavaScript client-side code.

SalanderMaps: A rapid overview about felt earthquakes through data mining of web-accesses

NASA Astrophysics Data System (ADS)

Kradolfer, Urs

2013-04-01

While seismological observatories detect and locate earthquakes based on measurements of the ground motion, they neither know a priori whether an earthquake has been felt by the public nor is it known, where it has been felt. Such information is usually gathered by evaluating feedback reported by the public through on-line forms on the web. However, after a felt earthquake in Switzerland, many people visit the webpages of the Swiss Seismological Service (SED) at the ETH Zurich and each such visit leaves traces in the logfiles on our web-servers. Data mining techniques, applied to these logfiles and mining publicly available data bases on the internet open possibilities to obtain previously unknown information about our virtual visitors. In order to provide precise information to authorities and the media, it would be desirable to rapidly know from which locations these web-accesses origin. The method 'Salander' (Seismic Activitiy Linked to Area codes - Nimble Detection of Earthquake Rumbles) will be introduced and it will be explained, how the IP-addresses (each computer or router directly connected to the internet has a unique IP-address; an example would be 129.132.53.5) of a sufficient amount of our virtual visitors were linked to their geographical area. This allows us to unprecedentedly quickly know whether and where an earthquake was felt in Switzerland. It will also be explained, why the method Salander is superior to commercial so-called geolocation products. The corresponding products of the Salander method, animated SalanderMaps, which are routinely generated after each earthquake with a magnitude of M>2 in Switzerland (http://www.seismo.ethz.ch/prod/salandermaps/, available after March 2013), demonstrate how the wavefield of earthquakes propagates through Switzerland and where it was felt. Often, such information is available within less than 60 seconds after origin time, and we always get a clear picture within already five minutes after origin time. Furthermore, the method allows to detect earthquakes solely on the analysis of accesses to our web-servers. Analyzing more than 170 million web-accesses since 2003, all seismic events within or near Switzerland with magnitudes M>4 and most felt events with magnitudes between 3 and 4 were detected. The current system is very robust, as we only had one false alarm while re-processing the web-access logfiles of the past almost 10 years. We anticipate that this method will produce even faster results in the future as the number of both commercial and private internet users is - according to the statistics of our logfiles - still increasing.

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

Global OpenSearch

NASA Astrophysics Data System (ADS)

Newman, D. J.; Mitchell, A. E.

2015-12-01

At AGU 2014, NASA EOSDIS demonstrated a case-study of an OpenSearch framework for Earth science data discovery. That framework leverages the IDN and CWIC OpenSearch API implementations to provide seamless discovery of data through the 'two-step' discovery process as outlined by the Federation for Earth Sciences (ESIP) OpenSearch Best Practices. But how would an Earth Scientist leverage this framework and what are the benefits? Using a client that understands the OpenSearch specification and, for further clarity, the various best practices and extensions, a scientist can discovery a plethora of data not normally accessible either by traditional methods (NASA Earth Data Search, Reverb, etc) or direct methods (going to the source of the data) We will demonstrate, via the CWICSmart web client, how an earth scientist can access regional data on a regional phenomena in a uniform and aggregated manner. We will demonstrate how an earth scientist can 'globalize' their discovery. You want to find local data on 'sea surface temperature of the Indian Ocean'? We can help you with that. 'European meteorological data'? Yes. 'Brazilian rainforest satellite imagery'? That too. CWIC allows you to get earth science data in a uniform fashion from a large number of disparate, world-wide agencies. This is what we mean by Global OpenSearch.

BioServices: a common Python package to access biological Web Services programmatically.

PubMed

Cokelaer, Thomas; Pultz, Dennis; Harder, Lea M; Serra-Musach, Jordi; Saez-Rodriguez, Julio

2013-12-15

Web interfaces provide access to numerous biological databases. Many can be accessed to in a programmatic way thanks to Web Services. Building applications that combine several of them would benefit from a single framework. BioServices is a comprehensive Python framework that provides programmatic access to major bioinformatics Web Services (e.g. KEGG, UniProt, BioModels, ChEMBLdb). Wrapping additional Web Services based either on Representational State Transfer or Simple Object Access Protocol/Web Services Description Language technologies is eased by the usage of object-oriented programming. BioServices releases and documentation are available at http://pypi.python.org/pypi/bioservices under a GPL-v3 license.

Web-based interactive 2D/3D medical image processing and visualization software.

PubMed

Mahmoudi, Seyyed Ehsan; Akhondi-Asl, Alireza; Rahmani, Roohollah; Faghih-Roohi, Shahrooz; Taimouri, Vahid; Sabouri, Ahmad; Soltanian-Zadeh, Hamid

2010-05-01

There are many medical image processing software tools available for research and diagnosis purposes. However, most of these tools are available only as local applications. This limits the accessibility of the software to a specific machine, and thus the data and processing power of that application are not available to other workstations. Further, there are operating system and processing power limitations which prevent such applications from running on every type of workstation. By developing web-based tools, it is possible for users to access the medical image processing functionalities wherever the internet is available. In this paper, we introduce a pure web-based, interactive, extendable, 2D and 3D medical image processing and visualization application that requires no client installation. Our software uses a four-layered design consisting of an algorithm layer, web-user-interface layer, server communication layer, and wrapper layer. To compete with extendibility of the current local medical image processing software, each layer is highly independent of other layers. A wide range of medical image preprocessing, registration, and segmentation methods are implemented using open source libraries. Desktop-like user interaction is provided by using AJAX technology in the web-user-interface. For the visualization functionality of the software, the VRML standard is used to provide 3D features over the web. Integration of these technologies has allowed implementation of our purely web-based software with high functionality without requiring powerful computational resources in the client side. The user-interface is designed such that the users can select appropriate parameters for practical research and clinical studies. Copyright (c) 2009 Elsevier Ireland Ltd. All rights reserved.

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.

Deploying and sharing U-Compare workflows as web services.

PubMed

Kontonatsios, Georgios; Korkontzelos, Ioannis; Kolluru, Balakrishna; Thompson, Paul; Ananiadou, Sophia

2013-02-18

U-Compare is a text mining platform that allows the construction, evaluation and comparison of text mining workflows. U-Compare contains a large library of components that are tuned to the biomedical domain. Users can rapidly develop biomedical text mining workflows by mixing and matching U-Compare's components. Workflows developed using U-Compare can be exported and sent to other users who, in turn, can import and re-use them. However, the resulting workflows are standalone applications, i.e., software tools that run and are accessible only via a local machine, and that can only be run with the U-Compare platform. We address the above issues by extending U-Compare to convert standalone workflows into web services automatically, via a two-click process. The resulting web services can be registered on a central server and made publicly available. Alternatively, users can make web services available on their own servers, after installing the web application framework, which is part of the extension to U-Compare. We have performed a user-oriented evaluation of the proposed extension, by asking users who have tested the enhanced functionality of U-Compare to complete questionnaires that assess its functionality, reliability, usability, efficiency and maintainability. The results obtained reveal that the new functionality is well received by users. The web services produced by U-Compare are built on top of open standards, i.e., REST and SOAP protocols, and therefore, they are decoupled from the underlying platform. Exported workflows can be integrated with any application that supports these open standards. We demonstrate how the newly extended U-Compare enhances the cross-platform interoperability of workflows, by seamlessly importing a number of text mining workflow web services exported from U-Compare into Taverna, i.e., a generic scientific workflow construction platform.

Deploying and sharing U-Compare workflows as web services

PubMed Central

2013-01-01

Background U-Compare is a text mining platform that allows the construction, evaluation and comparison of text mining workflows. U-Compare contains a large library of components that are tuned to the biomedical domain. Users can rapidly develop biomedical text mining workflows by mixing and matching U-Compare’s components. Workflows developed using U-Compare can be exported and sent to other users who, in turn, can import and re-use them. However, the resulting workflows are standalone applications, i.e., software tools that run and are accessible only via a local machine, and that can only be run with the U-Compare platform. Results We address the above issues by extending U-Compare to convert standalone workflows into web services automatically, via a two-click process. The resulting web services can be registered on a central server and made publicly available. Alternatively, users can make web services available on their own servers, after installing the web application framework, which is part of the extension to U-Compare. We have performed a user-oriented evaluation of the proposed extension, by asking users who have tested the enhanced functionality of U-Compare to complete questionnaires that assess its functionality, reliability, usability, efficiency and maintainability. The results obtained reveal that the new functionality is well received by users. Conclusions The web services produced by U-Compare are built on top of open standards, i.e., REST and SOAP protocols, and therefore, they are decoupled from the underlying platform. Exported workflows can be integrated with any application that supports these open standards. We demonstrate how the newly extended U-Compare enhances the cross-platform interoperability of workflows, by seamlessly importing a number of text mining workflow web services exported from U-Compare into Taverna, i.e., a generic scientific workflow construction platform. PMID:23419017

The LandCarbon Web Application: Advanced Geospatial Data Delivery and Visualization Tools for Communication about Ecosystem Carbon Sequestration and Greenhouse Gas Fluxes

NASA Astrophysics Data System (ADS)

Thomas, N.; Galey, B.; Zhu, Z.; Sleeter, B. M.; Lehmer, E.

2015-12-01

The LandCarbon web application (http://landcarbon.org) is a collaboration between the U.S. Geological Survey and U.C. Berkeley's Geospatial Innovation Facility (GIF). The LandCarbon project is a national assessment focused on improved understanding of carbon sequestration and greenhouse gas fluxes in and out of ecosystems related to land use, using scientific capabilities from USGS and other organizations. The national assessment is conducted at a regional scale, covers all 50 states, and incorporates data from remote sensing, land change studies, aquatic and wetland data, hydrological and biogeochemical modeling, and wildfire mapping to estimate baseline and future potential carbon storage and greenhouse gas fluxes. The LandCarbon web application is a geospatial portal that allows for a sophisticated data delivery system as well as a suite of engaging tools that showcase the LandCarbon data using interactive web based maps and charts. The web application was designed to be flexible and accessible to meet the needs of a variety of users. Casual users can explore the input data and results of the assessment for a particular area of interest in an intuitive and interactive map, without the need for specialized software. Users can view and interact with maps, charts, and statistics that summarize the baseline and future potential carbon storage and fluxes for U.S. Level 2 Ecoregions for 3 IPCC emissions scenarios. The application allows users to access the primary data sources and assessment results for viewing and download, and also to learn more about the assessment's objectives, methods, and uncertainties through published reports and documentation. The LandCarbon web application is built on free and open source libraries including Django and D3. The GIF has developed the Django-Spillway package, which facilitates interactive visualization and serialization of complex geospatial raster data. The underlying LandCarbon data is available through an open application programming interface (API), which will allow other organizations to build their own custom applications and tools. New features such as finer scale aggregation and an online carbon calculator are being added to the LandCarbon web application to continue to make the site interactive, visually compelling, and useful for a wide range of users.

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.

Enhancing the Reuse of Digital Resources for Integrated Systems to Represent, Understand and Dynamize Complex Interactions in Architectural Cultural Heritage Environments

NASA Astrophysics Data System (ADS)

Delgado, F. J.; Martinez, R.; Finat, J.; Martinez, J.; Puche, J. C.; Finat, F. J.

2013-07-01

In this work we develop a multiply interconnected system which involves objects, agents and interactions between them from the use of ICT applied to open repositories, users communities and web services. Our approach is applied to Architectural Cultural Heritage Environments (ACHE). It includes components relative to digital accessibility (to augmented ACHE repositories), contents management (ontologies for the semantic web), semiautomatic recognition (to ease the reuse of materials) and serious videogames (for interaction in urban environments). Their combination provides a support for local real/remote virtual tourism (including some tools for low-level RT display of rendering in portable devices), mobile-based smart interactions (with a special regard to monitored environments) and CH related games (as extended web services). Main contributions to AR models on usual GIS applied to architectural environments, concern to an interactive support performed directly on digital files which allows to access to CH contents which are referred to GIS of urban districts (involving facades, historical or preindustrial buildings) and/or CH repositories in a ludic and transversal way to acquire cognitive, medial and social abilities in collaborative environments.

GeoNetwork powered GI-cat: a geoportal hybrid solution

NASA Astrophysics Data System (ADS)

Baldini, Alessio; Boldrini, Enrico; Santoro, Mattia; Mazzetti, Paolo

2010-05-01

To the aim of setting up a Spatial Data Infrastructures (SDI) the creation of a system for the metadata management and discovery plays a fundamental role. An effective solution is the use of a geoportal (e.g. FAO/ESA geoportal), that has the important benefit of being accessible from a web browser. With this work we present a solution based integrating two of the available frameworks: GeoNetwork and GI-cat. GeoNetwork is an opensource software designed to improve accessibility of a wide variety of data together with the associated ancillary information (metadata), at different scale and from multidisciplinary sources; data are organized and documented in a standard and consistent way. GeoNetwork implements both the Portal and Catalog components of a Spatial Data Infrastructure (SDI) defined in the OGC Reference Architecture. It provides tools for managing and publishing metadata on spatial data and related services. GeoNetwork allows harvesting of various types of web data sources e.g. OGC Web Services (e.g. CSW, WCS, WMS). GI-cat is a distributed catalog based on a service-oriented framework of modular components and can be customized and tailored to support different deployment scenarios. It can federate a multiplicity of catalogs services, as well as inventory and access services in order to discover and access heterogeneous ESS resources. The federated resources are exposed by GI-cat through several standard catalog interfaces (e.g. OGC CSW AP ISO, OpenSearch, etc.) and by the GI-cat extended interface. Specific components implement mediation services for interfacing heterogeneous service providers, each of which exposes a specific standard specification; such components are called Accessors. These mediating components solve providers data modelmultiplicity by mapping them onto the GI-cat internal data model which implements the ISO 19115 Core profile. Accessors also implement the query protocol mapping; first they translate the query requests expressed according to the interface protocols exposed by GI-cat into the multiple query dialects spoken by the resource service providers. Currently, a number of well-accepted catalog and inventory services are supported, including several OGC Web Services, THREDDS Data Server, SeaDataNet Common Data Index, GBIF and OpenSearch engines. A GeoNetwork powered GI-cat has been developed in order to exploit the best of the two frameworks. The new system uses a modified version of GeoNetwork web interface in order to add the capability of querying also the specified GI-cat catalog and not only the GeoNetwork internal database. The resulting system consists in a geoportal in which GI-cat plays the role of the search engine. This new system allows to distribute the query on the different types of data sources linked to a GI-cat. The metadata results of the query are then visualized by the Geonetwork web interface. This configuration was experimented in the framework of GIIDA, a project of the Italian National Research Council (CNR) focused on data accessibility and interoperability. A second advantage of this solution is achieved setting up a GeoNetwork catalog amongst the accessors of the GI-cat instance. Such a configuration will allow in turn GI-cat to run the query against the internal GeoNetwork database. This allows to have both the harvesting and the metadata editor functionalities provided by GeoNetwork and the distributed search functionality of GI-cat available in a consistent way through the same web interface.

Data-Driven Software Framework for Web-Based ISS Telescience

NASA Technical Reports Server (NTRS)

Tso, Kam S.

2005-01-01

Software that enables authorized users to monitor and control scientific payloads aboard the International Space Station (ISS) from diverse terrestrial locations equipped with Internet connections is undergoing development. This software reflects a data-driven approach to distributed operations. A Web-based software framework leverages prior developments in Java and Extensible Markup Language (XML) to create portable code and portable data, to which one can gain access via Web-browser software on almost any common computer. Open-source software is used extensively to minimize cost; the framework also accommodates enterprise-class server software to satisfy needs for high performance and security. To accommodate the diversity of ISS experiments and users, the framework emphasizes openness and extensibility. Users can take advantage of available viewer software to create their own client programs according to their particular preferences, and can upload these programs for custom processing of data, generation of views, and planning of experiments. The same software system, possibly augmented with a subset of data and additional software tools, could be used for public outreach by enabling public users to replay telescience experiments, conduct their experiments with simulated payloads, and create their own client programs and other custom software.

Modern Data Center Services Supporting Science

NASA Astrophysics Data System (ADS)

Varner, J. D.; Cartwright, J.; McLean, S. J.; Boucher, J.; Neufeld, D.; LaRocque, J.; Fischman, D.; McQuinn, E.; Fugett, C.

2011-12-01

The National Oceanic and Atmospheric Administration's National Geophysical Data Center (NGDC) World Data Center for Geophysics and Marine Geology provides scientific stewardship, products and services for geophysical data, including bathymetry, gravity, magnetics, seismic reflection, data derived from sediment and rock samples, as well as historical natural hazards data (tsunamis, earthquakes, and volcanoes). Although NGDC has long made many of its datasets available through map and other web services, it has now developed a second generation of services to improve the discovery and access to data. These new services use off-the-shelf commercial and open source software, and take advantage of modern JavaScript and web application frameworks. Services are accessible using both RESTful and SOAP queries as well as Open Geospatial Consortium (OGC) standard protocols such as WMS, WFS, WCS, and KML. These new map services (implemented using ESRI ArcGIS Server) are finer-grained than their predecessors, feature improved cartography, and offer dramatic speed improvements through the use of map caches. Using standards-based interfaces allows customers to incorporate the services without having to coordinate with the provider. Providing fine-grained services increases flexibility for customers building custom applications. The Integrated Ocean and Coastal Mapping program and Coastal and Marine Spatial Planning program are two examples of national initiatives that require common data inventories from multiple sources and benefit from these modern data services. NGDC is also consuming its own services, providing a set of new browser-based mapping applications which allow the user to quickly visualize and search for data. One example is a new interactive mapping application to search and display information about historical natural hazards. NGDC continues to increase the amount of its data holdings that are accessible and is augmenting the capabilities with modern web application frameworks such as Groovy and Grails. Data discovery is being improved and simplified by leveraging ISO metadata standards along with ESRI Geoportal Server.

HTML5 PivotViewer: high-throughput visualization and querying of image data on the web

PubMed Central

Taylor, Stephen; Noble, Roger

2014-01-01

Motivation: Visualization and analysis of large numbers of biological images has generated a bottle neck in research. We present HTML5 PivotViewer, a novel, open source, platform-independent viewer making use of the latest web technologies that allows seamless access to images and associated metadata for each image. This provides a powerful method to allow end users to mine their data. Availability and implementation: Documentation, examples and links to the software are available from http://www.cbrg.ox.ac.uk/data/pivotviewer/. The software is licensed under GPLv2. Contact:  stephen.taylor@imm.ox.ac.uk and roger@coritsu.com PMID:24849578

The Effects of Implementing Web Accessibility Standards on the Success of Secondary Adolescents

ERIC Educational Resources Information Center

Savi, Christine Opitz; Savenye, Wilhelmina; Rowland, Cynthia

2008-01-01

Web accessibility has become a paramount concern in providing equal access to audiences of all abilities. Unless web accessibility is supported and employed, the internet does not deliver worldwide access as it was intended. This study engaged 60 students in a secondary school setting in order to identify the navigational effectiveness and…

Monitoring and Evaluating Use of the World Wide Web in an Academic Library: An Exploratory Study.

ERIC Educational Resources Information Center

Abramson, Alicia D.

1998-01-01

Examines use of the World Wide Web on public-access computers at the American University Library (Washington, D.C.) to identify the most frequently accessed Web sites, the frequency with which library-owned Web resources were accessed, and Web-usage patterns in the library in relation to the time of day and day of the week. (Author/AEF)

Interoperability Using Lightweight Metadata Standards: Service & Data Casting, OpenSearch, OPM Provenance, and Shared SciFlo Workflows

NASA Astrophysics Data System (ADS)

Wilson, B. D.; Manipon, G.; Hua, H.; Fetzer, E.

2011-12-01

Under several NASA grants, we are generating multi-sensor merged atmospheric datasets to enable the detection of instrument biases and studies of climate trends over decades of data. For example, under a NASA MEASURES grant we are producing a water vapor climatology from the A-Train instruments, stratified by the Cloudsat cloud classification for each geophysical scene. The generation and proper use of such multi-sensor climate data records (CDR's) requires a high level of openness, transparency, and traceability. To make the datasets self-documenting and provide access to full metadata and traceability, we have implemented a set of capabilities and services using known, interoperable protocols. These protocols include OpenSearch, OPeNDAP, Open Provenance Model, service & data casting technologies using Atom feeds, and REST-callable analysis workflows implemented as SciFlo (XML) documents. We advocate that our approach can serve as a blueprint for how to openly "document and serve" complex, multi-sensor CDR's with full traceability. The capabilities and services provided include: - Discovery of the collections by keyword search, exposed using OpenSearch protocol; - Space/time query across the CDR's granules and all of the input datasets via OpenSearch; - User-level configuration of the production workflows so that scientists can select additional physical variables from the A-Train to add to the next iteration of the merged datasets; - Efficient data merging using on-the-fly OPeNDAP variable slicing & spatial subsetting of data out of input netCDF and HDF files (without moving the entire files); - Self-documenting CDR's published in a highly usable netCDF4 format with groups used to organize the variables, CF-style attributes for each variable, numeric array compression, & links to OPM provenance; - Recording of processing provenance and data lineage into a query-able provenance trail in Open Provenance Model (OPM) format, auto-captured by the workflow engine; - Open Publishing of all of the workflows used to generate products as machine-callable REST web services, using the capabilities of the SciFlo workflow engine; - Advertising of the metadata (e.g. physical variables provided, space/time bounding box, etc.) for our prepared datasets as "datacasts" using the Atom feed format; - Publishing of all datasets via our "DataDrop" service, which exploits the WebDAV protocol to enable scientists to access remote data directories as local files on their laptops; - Rich "web browse" of the CDR's with full metadata and the provenance trail one click away; - Advertising of all services as Google-discoverable "service casts" using the Atom format. The presentation will describe our use of the interoperable protocols and demonstrate the capabilities and service GUI's.

The Geogenomic Mutational Atlas of Pathogens (GoMAP) Web System

PubMed Central

Sargeant, David P.; Hedden, Michael W.; Deverasetty, Sandeep; Strong, Christy L.; Alaniz, Izua J.; Bartlett, Alexandria N.; Brandon, Nicholas R.; Brooks, Steven B.; Brown, Frederick A.; Bufi, Flaviona; Chakarova, Monika; David, Roxanne P.; Dobritch, Karlyn M.; Guerra, Horacio P.; Levit, Kelvy S.; Mathew, Kiran R.; Matti, Ray; Maza, Dorothea Q.; Mistry, Sabyasachy; Novakovic, Nemanja; Pomerantz, Austin; Rafalski, Timothy F.; Rathnayake, Viraj; Rezapour, Noura; Ross, Christian A.; Schooler, Steve G.; Songao, Sarah; Tuggle, Sean L.; Wing, Helen J.; Yousif, Sandy; Schiller, Martin R.

2014-01-01

We present a new approach for pathogen surveillance we call Geogenomics. Geogenomics examines the geographic distribution of the genomes of pathogens, with a particular emphasis on those mutations that give rise to drug resistance. We engineered a new web system called Geogenomic Mutational Atlas of Pathogens (GoMAP) that enables investigation of the global distribution of individual drug resistance mutations. As a test case we examined mutations associated with HIV resistance to FDA-approved antiretroviral drugs. GoMAP-HIV makes use of existing public drug resistance and HIV protein sequence data to examine the distribution of 872 drug resistance mutations in ∼502,000 sequences for many countries in the world. We also implemented a broadened classification scheme for HIV drug resistance mutations. Several patterns for geographic distributions of resistance mutations were identified by visual mining using this web tool. GoMAP-HIV is an open access web application available at http://www.bio-toolkit.com/GoMap/project/ PMID:24675726

The Geogenomic Mutational Atlas of Pathogens (GoMAP) web system.

PubMed

Sargeant, David P; Hedden, Michael W; Deverasetty, Sandeep; Strong, Christy L; Alaniz, Izua J; Bartlett, Alexandria N; Brandon, Nicholas R; Brooks, Steven B; Brown, Frederick A; Bufi, Flaviona; Chakarova, Monika; David, Roxanne P; Dobritch, Karlyn M; Guerra, Horacio P; Levit, Kelvy S; Mathew, Kiran R; Matti, Ray; Maza, Dorothea Q; Mistry, Sabyasachy; Novakovic, Nemanja; Pomerantz, Austin; Rafalski, Timothy F; Rathnayake, Viraj; Rezapour, Noura; Ross, Christian A; Schooler, Steve G; Songao, Sarah; Tuggle, Sean L; Wing, Helen J; Yousif, Sandy; Schiller, Martin R

2014-01-01

We present a new approach for pathogen surveillance we call Geogenomics. Geogenomics examines the geographic distribution of the genomes of pathogens, with a particular emphasis on those mutations that give rise to drug resistance. We engineered a new web system called Geogenomic Mutational Atlas of Pathogens (GoMAP) that enables investigation of the global distribution of individual drug resistance mutations. As a test case we examined mutations associated with HIV resistance to FDA-approved antiretroviral drugs. GoMAP-HIV makes use of existing public drug resistance and HIV protein sequence data to examine the distribution of 872 drug resistance mutations in ∼ 502,000 sequences for many countries in the world. We also implemented a broadened classification scheme for HIV drug resistance mutations. Several patterns for geographic distributions of resistance mutations were identified by visual mining using this web tool. GoMAP-HIV is an open access web application available at http://www.bio-toolkit.com/GoMap/project/

Mobile Web and Accessibility

NASA Astrophysics Data System (ADS)

Hori, Masahiro; Kato, Takashi

While focusing on the human-computer interaction side of the Web content delivery, this article discusses problems and prospects of the mobile Web and Web accessibility in terms of what lessons and experiences we have gained from Web accessibility and what they can say about the mobile Web. One aim is to draw particular attention to the importance of explicitly distinguishing between perceptual and cognitive aspects of the users’ interactions with the Web. Another is to emphasize the increased importance of scenario-based evaluation and remote testing for the mobile Web where the limited screen space and a variety of environmental factors of mobile use are critical design issues. A newly devised inspection type of evaluation method that focuses on the perceptual-cognitive distinction of accessibility and usability issues is presented as a viable means of scenario-based, remote testing for the Web.

Utilizing Free and Open Source Software to access, view and compare in situ observations, EO products and model output data

NASA Astrophysics Data System (ADS)

Vines, Aleksander; Hamre, Torill; Lygre, Kjetil

2014-05-01

The GreenSeas project (Development of global plankton data base and model system for eco-climate early warning) aims to advance the knowledge and predictive capacities of how marine ecosystems will respond to global change. A main task has been to set up a data delivery and monitoring core service following the open and free data access policy implemented in the Global Monitoring for the Environment and Security (GMES) programme. The aim is to ensure open and free access to historical plankton data, new data (EO products and in situ measurements), model data (including estimates of simulation error) and biological, environmental and climatic indicators to a range of stakeholders, such as scientists, policy makers and environmental managers. To this end, we have developed a geo-spatial database of both historical and new in situ physical, biological and chemical parameters for the Southern Ocean, Atlantic, Nordic Seas and the Arctic, and organized related satellite-derived quantities and model forecasts in a joint geo-spatial repository. For easy access to these data, we have implemented a web-based GIS (Geographical Information Systems) where observed, derived and forcasted parameters can be searched, displayed, compared and exported. Model forecasts can also be uploaded dynamically to the system, to allow modelers to quickly compare their results with available in situ and satellite observations. We have implemented the web-based GIS(Geographical Information Systems) system based on free and open source technologies: Thredds Data Server, ncWMS, GeoServer, OpenLayers, PostGIS, Liferay, Apache Tomcat, PRTree, NetCDF-Java, json-simple, Geotoolkit, Highcharts, GeoExt, MapFish, FileSaver, jQuery, jstree and qUnit. We also wanted to used open standards to communicate between the different services and we use WMS, WFS, netCDF, GML, OPeNDAP, JSON, and SLD. The main advantage we got from using FOSS was that we did not have to invent the wheel all over again, but could use already existing code and functionalities on our software for free: Of course most the software did not have to be open source for this, but in some cases we had to do minor modifications to make the different technologies work together. We could extract the parts of the code that we needed for a specific task. One example of this was to use part of the code from ncWMS and Thredds to help our main application to both read netCDF files and present them in the browser. This presentation will focus on both difficulties we had with and advantages we got from developing this tool with FOSS.

NASA's Earth Imagery Service as Open Source Software

NASA Astrophysics Data System (ADS)

De Cesare, C.; Alarcon, C.; Huang, T.; Roberts, J. T.; Rodriguez, J.; Cechini, M. F.; Boller, R. A.; Baynes, K.

2016-12-01

The NASA Global Imagery Browse Service (GIBS) is a software system that provides access to an archive of historical and near-real-time Earth imagery from NASA-supported satellite instruments. The imagery itself is open data, and is accessible via standards such as the Open Geospatial Consortium (OGC)'s Web Map Tile Service (WMTS) protocol. GIBS includes three core software projects: The Imagery Exchange (TIE), OnEarth, and the Meta Raster Format (MRF) project. These projects are developed using a variety of open source software, including: Apache HTTPD, GDAL, Mapserver, Grails, Zookeeper, Eclipse, Maven, git, and Apache Commons. TIE has recently been released for open source, and is now available on GitHub. OnEarth, MRF, and their sub-projects have been on GitHub since 2014, and the MRF project in particular receives many external contributions from the community. Our software has been successful beyond the scope of GIBS: the PO.DAAC State of the Ocean and COVERAGE visualization projects reuse components from OnEarth. The MRF source code has recently been incorporated into GDAL, which is a core library in many widely-used GIS software such as QGIS and GeoServer. This presentation will describe the challenges faced in incorporating open software and open data into GIBS, and also showcase GIBS as a platform on which scientists and the general public can build their own applications.

Web Accessibility Policies at Land-Grant Universities

ERIC Educational Resources Information Center

Bradbard, David A.; Peters, Cara; Caneva, Yoana

2010-01-01

The Web has become an integral part of postsecondary education within the United States. There are specific laws that legally mandate postsecondary institutions to have Web sites that are accessible for students with disabilities (e.g., the Americans with Disabilities Act (ADA)). Web accessibility policies are a way for universities to provide a…

School Web Sites: Are They Accessible to All?

ERIC Educational Resources Information Center

Wells, Julie A.; Barron, Ann E.

2006-01-01

In 2002, the National Center for Educational Statistics reported that 99% of public schools had Internet access and 86% of those schools had a web site or web page (Kleiner & Lewis, 2003). This study examined accessibility issues on elementary school homepages. Using a random sample of elementary school web sites, the researchers documented…

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.

NOAA's Big Data Partnership and Applications to Ocean Sciences

NASA Astrophysics Data System (ADS)

Kearns, E. J.

2016-02-01

New opportunities for the distribution of NOAA's oceanographic and other environmental data are being explored through NOAA's Big Data Partnership (BDP) with Amazon Web Services, Google Cloud Platform, IBM, Microsoft Corp. and the Open Cloud Consortium. This partnership was established in April 2015 through Cooperative Research and Development Agreements, and is seeking new, financially self-sustaining collaborations between the Partners and the federal government centered upon NOAA's data and their potential value in the information marketplace. We will discuss emerging opportunities for collaboration among businesses and NOAA, progress in making NOAA's ocean data more widely accessible through the Partnerships, and applications based upon this access to NOAA's data.

Utilizing online resources for taxonomy: a cybercatalog of Afrotropical apiocerid flies (Insecta: Diptera: Apioceridae).

PubMed

Dikow, Torsten; Agosti, Donat

2015-01-01

A cybercatalog to the Apioceridae (apiocerid flies) of the Afrotropical Region is provided. Each taxon entry includes links to open-access, online repositories such as ZooBank, BHL/BioStor/BLR, Plazi, GBIF, Morphbank, EoL, and a research web-site to access taxonomic information, digitized literature, morphological descriptions, specimen occurrence data, and images. Cybercatalogs as the one presented here will need to become the future of taxonomic catalogs taking advantage of the growing number of online repositories, linked data, and be easily updatable. Comments on the deposition of the holotype of Apiocera braunsi Melander, 1907 are made.

ReSEARCH: A Requirements Search Engine: Progress Report 2

DTIC Science & Technology

2008-09-01

and provides a convenient user interface for the search process. Ideally, the web application would be based on Tomcat, a free Java Servlet and JSP...Implementation issues Lucene Java is an Open Source project, available under the Apache License, which provides an accessible API for the development of...from the Apache Lucene website (Lucene- java Wiki , 2008). A search application developed with Lucene consists of the same two major com- ponents

Continued Funding for Prime Development

DTIC Science & Technology

2012-04-18

Portal The PrIMe Portal is based on the Drupal open-source software. During the past year we upgraded it to version 6. There are currently over 350...Primekinetics.org ( Drupal Data warehouse \\, WebDAV Access Layer - L qeirch Re~~ est Role validation/Authorization Authentication Module I ~ Module...PHP language with the help of CMF Drupal -6. The standard modules of the Drupal core set are developed by third parties and obtained from the

Explore, Visualize, and Analyze Functional Cancer Proteomic Data Using the Cancer Proteome Atlas. | Office of Cancer Genomics

Cancer.gov

Reverse-phase protein arrays (RPPA) represent a powerful functional proteomic approach to elucidate cancer-related molecular mechanisms and to develop novel cancer therapies. To facilitate community-based investigation of the large-scale protein expression data generated by this platform, we have developed a user-friendly, open-access bioinformatic resource, The Cancer Proteome Atlas (TCPA, http://tcpaportal.org), which contains two separate web applications.

LightWAVE: Waveform and Annotation Viewing and Editing in a Web Browser.

PubMed

Moody, George B

2013-09-01

This paper describes LightWAVE, recently-developed open-source software for viewing ECGs and other physiologic waveforms and associated annotations (event markers). It supports efficient interactive creation and modification of annotations, capabilities that are essential for building new collections of physiologic signals and time series for research. LightWAVE is constructed of components that interact in simple ways, making it straightforward to enhance or replace any of them. The back end (server) is a common gateway interface (CGI) application written in C for speed and efficiency. It retrieves data from its data repository (PhysioNet's open-access PhysioBank archives by default, or any set of files or web pages structured as in PhysioBank) and delivers them in response to requests generated by the front end. The front end (client) is a web application written in JavaScript. It runs within any modern web browser and does not require installation on the user's computer, tablet, or phone. Finally, LightWAVE's scribe is a tiny CGI application written in Perl, which records the user's edits in annotation files. LightWAVE's data repository, back end, and front end can be located on the same computer or on separate computers. The data repository may be split across multiple computers. For compatibility with the standard browser security model, the front end and the scribe must be loaded from the same domain.

NCBI GEO: mining millions of expression profiles--database and tools.

PubMed

Barrett, Tanya; Suzek, Tugba O; Troup, Dennis B; Wilhite, Stephen E; Ngau, Wing-Chi; Ledoux, Pierre; Rudnev, Dmitry; Lash, Alex E; Fujibuchi, Wataru; Edgar, Ron

2005-01-01

The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest fully public repository for high-throughput molecular abundance data, primarily gene expression data. The database has a flexible and open design that allows the submission, storage and retrieval of many data types. These data include microarray-based experiments measuring the abundance of mRNA, genomic DNA and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. GEO currently holds over 30,000 submissions representing approximately half a billion individual molecular abundance measurements, for over 100 organisms. Here, we describe recent database developments that facilitate effective mining and visualization of these data. Features are provided to examine data from both experiment- and gene-centric perspectives using user-friendly Web-based interfaces accessible to those without computational or microarray-related analytical expertise. The GEO database is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.

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.