Persistence and Availability of Web Services in Computational Biology

PubMed Central

Schultheiss, Sebastian J.; Münch, Marc-Christian; Andreeva, Gergana D.; Rätsch, Gunnar

2011-01-01

We have conducted a study on the long-term availability of bioinformatics Web services: an observation of 927 Web services published in the annual Nucleic Acids Research Web Server Issues between 2003 and 2009. We found that 72% of Web sites are still available at the published addresses, only 9% of services are completely unavailable. Older addresses often redirect to new pages. We checked the functionality of all available services: for 33%, we could not test functionality because there was no example data or a related problem; 13% were truly no longer working as expected; we could positively confirm functionality only for 45% of all services. Additionally, we conducted a survey among 872 Web Server Issue corresponding authors; 274 replied. 78% of all respondents indicate their services have been developed solely by students and researchers without a permanent position. Consequently, these services are in danger of falling into disrepair after the original developers move to another institution, and indeed, for 24% of services, there is no plan for maintenance, according to the respondents. We introduce a Web service quality scoring system that correlates with the number of citations: services with a high score are cited 1.8 times more often than low-scoring services. We have identified key characteristics that are predictive of a service's survival, providing reviewers, editors, and Web service developers with the means to assess or improve Web services. A Web service conforming to these criteria receives more citations and provides more reliable service for its users. The most effective way of ensuring continued access to a service is a persistent Web address, offered either by the publishing journal, or created on the authors' own initiative, for example at http://bioweb.me. The community would benefit the most from a policy requiring any source code needed to reproduce results to be deposited in a public repository. PMID:21966383

Colour Coding of Maps for Colour Deficient Observers.

PubMed

Røise, Anne Kari; Kvitle, Anne Kristin; Green, Phil

2016-01-01

We evaluate the colour coding of a web map traffic information service based on profiles simulating colour vision deficiencies. Based on these simulations and principles for universal design, we propose adjustments of the existing colours creating more readable maps for the colour vision deficient observers.

Using JavaScript and the FDSN web service to create an interactive earthquake information system

NASA Astrophysics Data System (ADS)

Fischer, Kasper D.

2015-04-01

The FDSN web service provides a web interface to access earthquake meta-data (e. g. event or station information) and waveform date over the internet. Requests are send to a server as URLs and the output is either XML or miniSEED. This makes it hard to read by humans but easy to process with different software. Different data centers are already supporting the FDSN web service, e. g. USGS, IRIS, ORFEUS. The FDSN web service is also part of the Seiscomp3 (http://www.seiscomp3.org) software. The Seismological Observatory of the Ruhr-University switched to Seiscomp3 as the standard software for the analysis of mining induced earthquakes at the beginning of 2014. This made it necessary to create a new web-based earthquake information service for the publication of results to the general public. This has be done by processing the output of a FDSN web service query by javascript running in a standard browser. The result is an interactive map presenting the observed events and further information of events and stations on a single web page as a table and on a map. In addition the user can download event information, waveform data and station data in different formats like miniSEED, quakeML or FDSNxml. The developed code and all used libraries are open source and freely available.

Data Quality Screening Service

NASA Technical Reports Server (NTRS)

Strub, Richard; Lynnes, Christopher; Hearty, Thomas; Won, Young-In; Fox, Peter; Zednik, Stephan

2013-01-01

A report describes the Data Quality Screening Service (DQSS), which is designed to help automate the filtering of remote sensing data on behalf of science users. Whereas this process often involves much research through quality documents followed by laborious coding, the DQSS is a Web Service that provides data users with data pre-filtered to their particular criteria, while at the same time guiding the user with filtering recommendations of the cognizant data experts. The DQSS design is based on a formal semantic Web ontology that describes data fields and the quality fields for applying quality control within a data product. The accompanying code base handles several remote sensing datasets and quality control schemes for data products stored in Hierarchical Data Format (HDF), a common format for NASA remote sensing data. Together, the ontology and code support a variety of quality control schemes through the implementation of the Boolean expression with simple, reusable conditional expressions as operands. Additional datasets are added to the DQSS simply by registering instances in the ontology if they follow a quality scheme that is already modeled in the ontology. New quality schemes are added by extending the ontology and adding code for each new scheme.

Sharing environmental models: An Approach using GitHub repositories and Web Processing Services

NASA Astrophysics Data System (ADS)

Stasch, Christoph; Nuest, Daniel; Pross, Benjamin

2016-04-01

The GLUES (Global Assessment of Land Use Dynamics, Greenhouse Gas Emissions and Ecosystem Services) project established a spatial data infrastructure for scientific geospatial data and metadata (http://geoportal-glues.ufz.de), where different regional collaborative projects researching the impacts of climate and socio-economic changes on sustainable land management can share their underlying base scenarios and datasets. One goal of the project is to ease the sharing of computational models between institutions and to make them easily executable in Web-based infrastructures. In this work, we present such an approach for sharing computational models relying on GitHub repositories (http://github.com) and Web Processing Services. At first, model providers upload their model implementations to GitHub repositories in order to share them with others. The GitHub platform allows users to submit changes to the model code. The changes can be discussed and reviewed before merging them. However, while GitHub allows sharing and collaborating of model source code, it does not actually allow running these models, which requires efforts to transfer the implementation to a model execution framework. We thus have extended an existing implementation of the OGC Web Processing Service standard (http://www.opengeospatial.org/standards/wps), the 52°North Web Processing Service (http://52north.org/wps) platform to retrieve all model implementations from a git (http://git-scm.com) repository and add them to the collection of published geoprocesses. The current implementation is restricted to models implemented as R scripts using WPS4R annotations (Hinz et al.) and to Java algorithms using the 52°North WPS Java API. The models hence become executable through a standardized Web API by multiple clients such as desktop or browser GIS and modelling frameworks. If the model code is changed on the GitHub platform, the changes are retrieved by the service and the processes will be updated accordingly. The admin tool of the 52°North WPS was extended to support automated retrieval and deployment of computational models from GitHub repositories. Once the R code is available in the GitHub repo, the contained process can be easily deployed and executed by simply defining the GitHub repository URL in the WPS admin tool. We illustrate the usage of the approach by sharing and running a model for land use system archetypes developed by the Helmholtz Centre for Environmental Research (UFZ, see Vaclavik et al.). The original R code was extended and published in the 52°North WPS using both, public and non-public datasets (Nüst et al., see also https://github.com/52North/glues-wps). Hosting the analysis in a Git repository now allows WPS administrators, client developers, and modelers to easily work together on new versions or completely new web processes using the powerful GitHub collaboration platform. References: Hinz, M. et. al. (2013): Spatial Statistics on the Geospatial Web. In: The 16th AGILE International Conference on Geographic Information Science, Short Papers. http://www.agile-online.org/Conference_Paper/CDs/agile_2013/Short_Papers/SP_S3.1_Hinz.pdf Nüst, D. et. al.: (2015): Open and reproducible global land use classification. In: EGU General Assembly Conference Abstracts . Vol. 17. European Geophysical Union, 2015, p. 9125, http://meetingorganizer.copernicus. org/EGU2015/EGU2015- 9125.pdf Vaclavik, T., et. al. (2013): Mapping global land system archetypes. Global Environmental Change 23(6): 1637-1647. Online available: October 9, 2013, DOI: 10.1016/j.gloenvcha.2013.09.004

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...

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.

Implementation of Web 2.0 services in academic, medical and research libraries: a scoping review.

PubMed

Gardois, Paolo; Colombi, Nicoletta; Grillo, Gaetano; Villanacci, Maria C

2012-06-01

Academic, medical and research libraries frequently implement Web 2.0 services for users. Several reports notwithstanding, characteristics and effectiveness of services are unclear. To find out: the Web 2.0 services implemented by medical, academic and research libraries; study designs, measures and types of data used in included articles to evaluate effectiveness; whether the identified body of literature is amenable to a systematic review of results. Scoping review mapping the literature on the topic. Searches were performed in 19 databases. research articles in English, Italian, German, French and Spanish (publication date ≥ 2006) about Web 2.0 services for final users implemented by academic, medical and research libraries. Reviewers' agreement was measured by Cohen's kappa. From a data set of 6461 articles, 255 (4%) were coded and analysed. Conferencing/chat/instant messaging, blogging, podcasts, social networking, wikis and aggregators were frequently examined. Services were mainly targeted at general academic users of English-speaking countries. Data prohibit a reliable estimate of the relative frequency of implemented Web 2.0 services. Case studies were the prevalent design. Most articles evaluated different outcomes using diverse assessment methodologies. A systematic review is recommended to assess the effectiveness of such services. © 2012 The authors. Health Information and Libraries Journal © 2012 Health Libraries Group.

Accessing the SEED genome databases via Web services API: tools for programmers.

PubMed

Disz, Terry; Akhter, Sajia; Cuevas, Daniel; Olson, Robert; Overbeek, Ross; Vonstein, Veronika; Stevens, Rick; Edwards, Robert A

2010-06-14

The SEED integrates many publicly available genome sequences into a single resource. The database contains accurate and up-to-date annotations based on the subsystems concept that leverages clustering between genomes and other clues to accurately and efficiently annotate microbial genomes. The backend is used as the foundation for many genome annotation tools, such as the Rapid Annotation using Subsystems Technology (RAST) server for whole genome annotation, the metagenomics RAST server for random community genome annotations, and the annotation clearinghouse for exchanging annotations from different resources. In addition to a web user interface, the SEED also provides Web services based API for programmatic access to the data in the SEED, allowing the development of third-party tools and mash-ups. The currently exposed Web services encompass over forty different methods for accessing data related to microbial genome annotations. The Web services provide comprehensive access to the database back end, allowing any programmer access to the most consistent and accurate genome annotations available. The Web services are deployed using a platform independent service-oriented approach that allows the user to choose the most suitable programming platform for their application. Example code demonstrate that Web services can be used to access the SEED using common bioinformatics programming languages such as Perl, Python, and Java. We present a novel approach to access the SEED database. Using Web services, a robust API for access to genomics data is provided, without requiring large volume downloads all at once. The API ensures timely access to the most current datasets available, including the new genomes as soon as they come online.

Phylowood: interactive web-based animations of biogeographic and phylogeographic histories.

PubMed

Landis, Michael J; Bedford, Trevor

2014-01-01

Phylowood is a web service that uses JavaScript to generate in-browser animations of biogeographic and phylogeographic histories from annotated phylogenetic input. The animations are interactive, allowing the user to adjust spatial and temporal resolution, and highlight phylogenetic lineages of interest. All documentation and source code for Phylowood is freely available at https://github.com/mlandis/phylowood, and a live web application is available at https://mlandis.github.io/phylowood.

Model-Driven Engineering: Automatic Code Generation and Beyond

DTIC Science & Technology

2015-03-01

and Weblogic as well as cloud environments such as Mi- crosoft Azure and Amazon Web Services®. Finally, while the generated code has dependencies on...code generation in the context of the full system lifecycle from development to sustainment. Acquisition programs in govern- ment or large commercial...Acquirers are concerned with the full system lifecycle, and they need confidence that the development methods will enable the system to meet the functional

Conducting Retrospective Ontological Clinical Trials in ICD-9-CM in the Age of ICD-10-CM.

PubMed

Venepalli, Neeta K; Shergill, Ardaman; Dorestani, Parvaneh; Boyd, Andrew D

2014-01-01

To quantify the impact of International Classification of Disease 10th Revision Clinical Modification (ICD-10-CM) transition in cancer clinical trials by comparing coding accuracy and data discontinuity in backward ICD-10-CM to ICD-9-CM mapping via two tools, and to develop a standard ICD-9-CM and ICD-10-CM bridging methodology for retrospective analyses. While the transition to ICD-10-CM has been delayed until October 2015, its impact on cancer-related studies utilizing ICD-9-CM diagnoses has been inadequately explored. Three high impact journals with broad national and international readerships were reviewed for cancer-related studies utilizing ICD-9-CM diagnoses codes in study design, methods, or results. Forward ICD-9-CM to ICD-10-CM mapping was performing using a translational methodology with the Motif web portal ICD-9-CM conversion tool. Backward mapping from ICD-10-CM to ICD-9-CM was performed using both Centers for Medicare and Medicaid Services (CMS) general equivalence mappings (GEMs) files and the Motif web portal tool. Generated ICD-9-CM codes were compared with the original ICD-9-CM codes to assess data accuracy and discontinuity. While both methods yielded additional ICD-9-CM codes, the CMS GEMs method provided incomplete coverage with 16 of the original ICD-9-CM codes missing, whereas the Motif web portal method provided complete coverage. Of these 16 codes, 12 ICD-9-CM codes were present in 2010 Illinois Medicaid data, and accounted for 0.52% of patient encounters and 0.35% of total Medicaid reimbursements. Extraneous ICD-9-CM codes from both methods (Centers for Medicare and Medicaid Services general equivalent mapping [CMS GEMs, n = 161; Motif web portal, n = 246]) in excess of original ICD-9-CM codes accounted for 2.1% and 2.3% of total patient encounters and 3.4% and 4.1% of total Medicaid reimbursements from the 2010 Illinois Medicare database. Longitudinal data analyses post-ICD-10-CM transition will require backward ICD-10-CM to ICD-9-CM coding, and data comparison for accuracy. Researchers must be aware that all methods for backward coding are not comparable in yielding original ICD-9-CM codes. The mandated delay is an opportunity for organizations to better understand areas of financial risk with regards to data management via backward coding. Our methodology is relevant for all healthcare-related coding data, and can be replicated by organizations as a strategy to mitigate financial risk.

mORCA: sailing bioinformatics world with mobile devices.

PubMed

Díaz-Del-Pino, Sergio; Falgueras, Juan; Perez-Wohlfeil, Esteban; Trelles, Oswaldo

2018-03-01

Nearly 10 years have passed since the first mobile apps appeared. Given the fact that bioinformatics is a web-based world and that mobile devices are endowed with web-browsers, it seemed natural that bioinformatics would transit from personal computers to mobile devices but nothing could be further from the truth. The transition demands new paradigms, designs and novel implementations. Throughout an in-depth analysis of requirements of existing bioinformatics applications we designed and deployed an easy-to-use web-based lightweight mobile client. Such client is able to browse, select, compose automatically interface parameters, invoke services and monitor the execution of Web Services using the service's metadata stored in catalogs or repositories. mORCA is available at http://bitlab-es.com/morca/app as a web-app. It is also available in the App store by Apple and Play Store by Google. The software will be available for at least 2 years. ortrelles@uma.es. Source code, final web-app, training material and documentation is available at http://bitlab-es.com/morca. © The Author(s) 2017. Published by Oxford University Press.

Performance modeling codes for the QuakeSim problem solving environment

NASA Technical Reports Server (NTRS)

Parker, J. W.; Donnellan, A.; Lyzenga, G.; Rundle, J.; Tullis, T.

2003-01-01

The QuakeSim Problem Solving Environment uses a web-services approach to unify and deploy diverse remote data sources and processing services within a browser environment. Here we focus on the high-performance crustal modeling applications that will be included in this set of remote but interoperable applications.

OOSTethys - Open Source Software for the Global Earth Observing Systems of Systems

NASA Astrophysics Data System (ADS)

Bridger, E.; Bermudez, L. E.; Maskey, M.; Rueda, C.; Babin, B. L.; Blair, R.

2009-12-01

An open source software project is much more than just picking the right license, hosting modular code and providing effective documentation. Success in advancing in an open collaborative way requires that the process match the expected code functionality to the developer's personal expertise and organizational needs as well as having an enthusiastic and responsive core lead group. We will present the lessons learned fromOOSTethys , which is a community of software developers and marine scientists who develop open source tools, in multiple languages, to integrate ocean observing systems into an Integrated Ocean Observing System (IOOS). OOSTethys' goal is to dramatically reduce the time it takes to install, adopt and update standards-compliant web services. OOSTethys has developed servers, clients and a registry. Open source PERL, PYTHON, JAVA and ASP tool kits and reference implementations are helping the marine community publish near real-time observation data in interoperable standard formats. In some cases publishing an OpenGeospatial Consortium (OGC), Sensor Observation Service (SOS) from NetCDF files or a database or even CSV text files could take only minutes depending on the skills of the developer. OOSTethys is also developing an OGC standard registry, Catalog Service for Web (CSW). This open source CSW registry was implemented to easily register and discover SOSs using ISO 19139 service metadata. A web interface layer over the CSW registry simplifies the registration process by harvesting metadata describing the observations and sensors from the “GetCapabilities” response of SOS. OPENIOOS is the web client, developed in PERL to visualize the sensors in the SOS services. While the number of OOSTethys software developers is small, currently about 10 around the world, the number of OOSTethys toolkit implementers is larger and growing and the ease of use has played a large role in spreading the use of interoperable standards compliant web services widely in the marine community.

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

NASA Astrophysics Data System (ADS)

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

2014-01-01

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

Opal web services for biomedical applications.

PubMed

Ren, Jingyuan; Williams, Nadya; Clementi, Luca; Krishnan, Sriram; Li, Wilfred W

2010-07-01

Biomedical applications have become increasingly complex, and they often require large-scale high-performance computing resources with a large number of processors and memory. The complexity of application deployment and the advances in cluster, grid and cloud computing require new modes of support for biomedical research. Scientific Software as a Service (sSaaS) enables scalable and transparent access to biomedical applications through simple standards-based Web interfaces. Towards this end, we built a production web server (http://ws.nbcr.net) in August 2007 to support the bioinformatics application called MEME. The server has grown since to include docking analysis with AutoDock and AutoDock Vina, electrostatic calculations using PDB2PQR and APBS, and off-target analysis using SMAP. All the applications on the servers are powered by Opal, a toolkit that allows users to wrap scientific applications easily as web services without any modification to the scientific codes, by writing simple XML configuration files. Opal allows both web forms-based access and programmatic access of all our applications. The Opal toolkit currently supports SOAP-based Web service access to a number of popular applications from the National Biomedical Computation Resource (NBCR) and affiliated collaborative and service projects. In addition, Opal's programmatic access capability allows our applications to be accessed through many workflow tools, including Vision, Kepler, Nimrod/K and VisTrails. From mid-August 2007 to the end of 2009, we have successfully executed 239,814 jobs. The number of successfully executed jobs more than doubled from 205 to 411 per day between 2008 and 2009. The Opal-enabled service model is useful for a wide range of applications. It provides for interoperation with other applications with Web Service interfaces, and allows application developers to focus on the scientific tool and workflow development. Web server availability: http://ws.nbcr.net.

Templet Web: the use of volunteer computing approach in PaaS-style cloud

NASA Astrophysics Data System (ADS)

Vostokin, Sergei; Artamonov, Yuriy; Tsarev, Daniil

2018-03-01

This article presents the Templet Web cloud service. The service is designed for high-performance scientific computing automation. The use of high-performance technology is specifically required by new fields of computational science such as data mining, artificial intelligence, machine learning, and others. Cloud technologies provide a significant cost reduction for high-performance scientific applications. The main objectives to achieve this cost reduction in the Templet Web service design are: (a) the implementation of "on-demand" access; (b) source code deployment management; (c) high-performance computing programs development automation. The distinctive feature of the service is the approach mainly used in the field of volunteer computing, when a person who has access to a computer system delegates his access rights to the requesting user. We developed an access procedure, algorithms, and software for utilization of free computational resources of the academic cluster system in line with the methods of volunteer computing. The Templet Web service has been in operation for five years. It has been successfully used for conducting laboratory workshops and solving research problems, some of which are considered in this article. The article also provides an overview of research directions related to service development.

Embedding QR codes in tumor board presentations, enhancing educational content for oncology information management.

PubMed

Siderits, Richard; Yates, Stacy; Rodriguez, Arelis; Lee, Tina; Rimmer, Cheryl; Roche, Mark

2011-01-01

Quick Response (QR) Codes are standard in supply management and seen with increasing frequency in advertisements. They are now present regularly in healthcare informatics and education. These 2-dimensional square bar codes, originally designed by the Toyota car company, are free of license and have a published international standard. The codes can be generated by free online software and the resulting images incorporated into presentations. The images can be scanned by "smart" phones and tablets using either the iOS or Android platforms, which link the device with the information represented by the QR code (uniform resource locator or URL, online video, text, v-calendar entries, short message service [SMS] and formatted text). Once linked to the device, the information can be viewed at any time after the original presentation, saved in the device or to a Web-based "cloud" repository, printed, or shared with others via email or Bluetooth file transfer. This paper describes how we use QR codes in our tumor board presentations, discusses the benefits, the different QR codes from Web links and how QR codes facilitate the distribution of educational content.

Gobe: an interactive, web-based tool for comparative genomic visualization.

PubMed

Pedersen, Brent S; Tang, Haibao; Freeling, Michael

2011-04-01

Gobe is a web-based tool for viewing comparative genomic data. It supports viewing multiple genomic regions simultaneously. Its simple text format and flash-based rendering make it an interactive, exploratory research tool. Gobe can be used without installation through our web service, or downloaded and customized with stylesheets and javascript callback functions. Gobe is a flash application that runs in all modern web-browsers. The full source-code, including that for the online web application is available under the MIT license at: http://github.com/brentp/gobe. Sample applications are hosted at http://try-gobe.appspot.com/ and http://synteny.cnr.berkeley.edu/gobe-app/.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Data as a Service: A Seismic Web Service Pipeline

NASA Astrophysics Data System (ADS)

Martinez, E.

2016-12-01

Publishing data as a service pipeline provides an improved, dynamic approach over static data archives. A service pipeline is a collection of micro web services that each perform a specific task and expose the results of that task. Structured request/response formats allow micro web services to be chained together into a service pipeline to provide more complex results. The U.S. Geological Survey adopted service pipelines to publish seismic hazard and design data supporting both specific and generalized audiences. The seismic web service pipeline starts at source data and exposes probability and deterministic hazard curves, response spectra, risk-targeted ground motions, and seismic design provision metadata. This pipeline supports public/private organizations and individual engineers/researchers. Publishing data as a service pipeline provides a variety of benefits. Exposing the component services enables advanced users to inspect or use the data at each processing step. Exposing a composite service enables new users quick access to published data with a very low barrier to entry. Advanced users may re-use micro web services by chaining them in new ways or injecting new micros services into the pipeline. This allows the user to test hypothesis and compare their results to published results. Exposing data at each step in the pipeline enables users to review and validate the data and process more quickly and accurately. Making the source code open source, per USGS policy, further enables this transparency. Each micro service may be scaled independent of any other micro service. This ensures data remains available and timely in a cost-effective manner regardless of load. Additionally, if a new or more efficient approach to processing the data is discovered, this new approach may replace the old approach at any time, keeping the pipeline running while not affecting other micro services.

FROG: Time Series Analysis for the Web Service Era

NASA Astrophysics Data System (ADS)

Allan, A.

2005-12-01

The FROG application is part of the next generation Starlink{http://www.starlink.ac.uk} software work (Draper et al. 2005) and released under the GNU Public License{http://www.gnu.org/copyleft/gpl.html} (GPL). Written in Java, it has been designed for the Web and Grid Service era as an extensible, pluggable, tool for time series analysis and display. With an integrated SOAP server the packages functionality is exposed to the user for use in their own code, and to be used remotely over the Grid, as part of the Virtual Observatory (VO).

Detecting Heap-Spraying Code Injection Attacks in Malicious Web Pages Using Runtime Execution

NASA Astrophysics Data System (ADS)

Choi, Younghan; Kim, Hyoungchun; Lee, Donghoon

The growing use of web services is increasing web browser attacks exponentially. Most attacks use a technique called heap spraying because of its high success rate. Heap spraying executes a malicious code without indicating the exact address of the code by copying it into many heap objects. For this reason, the attack has a high potential to succeed if only the vulnerability is exploited. Thus, attackers have recently begun using this technique because it is easy to use JavaScript to allocate the heap memory area. This paper proposes a novel technique that detects heap spraying attacks by executing a heap object in a real environment, irrespective of the version and patch status of the web browser. This runtime execution is used to detect various forms of heap spraying attacks, such as encoding and polymorphism. Heap objects are executed after being filtered on the basis of patterns of heap spraying attacks in order to reduce the overhead of the runtime execution. Patterns of heap spraying attacks are based on analysis of how an web browser accesses benign web sites. The heap objects are executed forcibly by changing the instruction register into the address of them after being loaded into memory. Thus, we can execute the malicious code without having to consider the version and patch status of the browser. An object is considered to contain a malicious code if the execution reaches a call instruction and then the instruction accesses the API of system libraries, such as kernel32.dll and ws_32.dll. To change registers and monitor execution flow, we used a debugger engine. A prototype, named HERAD(HEap spRAying Detector), is implemented and evaluated. In experiments, HERAD detects various forms of exploit code that an emulation cannot detect, and some heap spraying attacks that NOZZLE cannot detect. Although it has an execution overhead, HERAD produces a low number of false alarms. The processing time of several minutes is negligible because our research focuses on detecting heap spraying. This research can be applied to existing systems that collect malicious codes, such as Honeypot.

Mobile cloud-computing-based healthcare service by noncontact ECG monitoring.

PubMed

Fong, Ee-May; Chung, Wan-Young

2013-12-02

Noncontact electrocardiogram (ECG) measurement technique has gained popularity these days owing to its noninvasive features and convenience in daily life use. This paper presents mobile cloud computing for a healthcare system where a noncontact ECG measurement method is employed to capture biomedical signals from users. Healthcare service is provided to continuously collect biomedical signals from multiple locations. To observe and analyze the ECG signals in real time, a mobile device is used as a mobile monitoring terminal. In addition, a personalized healthcare assistant is installed on the mobile device; several healthcare features such as health status summaries, medication QR code scanning, and reminders are integrated into the mobile application. Health data are being synchronized into the healthcare cloud computing service (Web server system and Web server dataset) to ensure a seamless healthcare monitoring system and anytime and anywhere coverage of network connection is available. Together with a Web page application, medical data are easily accessed by medical professionals or family members. Web page performance evaluation was conducted to ensure minimal Web server latency. The system demonstrates better availability of off-site and up-to-the-minute patient data, which can help detect health problems early and keep elderly patients out of the emergency room, thus providing a better and more comprehensive healthcare cloud computing service.

Mobile Cloud-Computing-Based Healthcare Service by Noncontact ECG Monitoring

PubMed Central

Fong, Ee-May; Chung, Wan-Young

2013-01-01

Noncontact electrocardiogram (ECG) measurement technique has gained popularity these days owing to its noninvasive features and convenience in daily life use. This paper presents mobile cloud computing for a healthcare system where a noncontact ECG measurement method is employed to capture biomedical signals from users. Healthcare service is provided to continuously collect biomedical signals from multiple locations. To observe and analyze the ECG signals in real time, a mobile device is used as a mobile monitoring terminal. In addition, a personalized healthcare assistant is installed on the mobile device; several healthcare features such as health status summaries, medication QR code scanning, and reminders are integrated into the mobile application. Health data are being synchronized into the healthcare cloud computing service (Web server system and Web server dataset) to ensure a seamless healthcare monitoring system and anytime and anywhere coverage of network connection is available. Together with a Web page application, medical data are easily accessed by medical professionals or family members. Web page performance evaluation was conducted to ensure minimal Web server latency. The system demonstrates better availability of off-site and up-to-the-minute patient data, which can help detect health problems early and keep elderly patients out of the emergency room, thus providing a better and more comprehensive healthcare cloud computing service. PMID:24316562

Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services.

PubMed

Damkliang, Kasikrit; Tandayya, Pichaya; Sangket, Unitsa; Pasomsub, Ekawat

2016-11-28

At the present, coding sequence (CDS) has been discovered and larger CDS is being revealed frequently. Approaches and related tools have also been developed and upgraded concurrently, especially for phylogenetic tree analysis. This paper proposes an integrated automatic Taverna workflow for the phylogenetic tree inferring analysis using public access web services at European Bioinformatics Institute (EMBL-EBI) and Swiss Institute of Bioinformatics (SIB), and our own deployed local web services. The workflow input is a set of CDS in the Fasta format. The workflow supports 1,000 to 20,000 numbers in bootstrapping replication. The workflow performs the tree inferring such as Parsimony (PARS), Distance Matrix - Neighbor Joining (DIST-NJ), and Maximum Likelihood (ML) algorithms of EMBOSS PHYLIPNEW package based on our proposed Multiple Sequence Alignment (MSA) similarity score. The local web services are implemented and deployed into two types using the Soaplab2 and Apache Axis2 deployment. There are SOAP and Java Web Service (JWS) providing WSDL endpoints to Taverna Workbench, a workflow manager. The workflow has been validated, the performance has been measured, and its results have been verified. Our workflow's execution time is less than ten minutes for inferring a tree with 10,000 replicates of the bootstrapping numbers. This paper proposes a new integrated automatic workflow which will be beneficial to the bioinformaticians with an intermediate level of knowledge and experiences. All local services have been deployed at our portal http://bioservices.sci.psu.ac.th.

Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services.

PubMed

Damkliang, Kasikrit; Tandayya, Pichaya; Sangket, Unitsa; Pasomsub, Ekawat

2016-03-01

At the present, coding sequence (CDS) has been discovered and larger CDS is being revealed frequently. Approaches and related tools have also been developed and upgraded concurrently, especially for phylogenetic tree analysis. This paper proposes an integrated automatic Taverna workflow for the phylogenetic tree inferring analysis using public access web services at European Bioinformatics Institute (EMBL-EBI) and Swiss Institute of Bioinformatics (SIB), and our own deployed local web services. The workflow input is a set of CDS in the Fasta format. The workflow supports 1,000 to 20,000 numbers in bootstrapping replication. The workflow performs the tree inferring such as Parsimony (PARS), Distance Matrix - Neighbor Joining (DIST-NJ), and Maximum Likelihood (ML) algorithms of EMBOSS PHYLIPNEW package based on our proposed Multiple Sequence Alignment (MSA) similarity score. The local web services are implemented and deployed into two types using the Soaplab2 and Apache Axis2 deployment. There are SOAP and Java Web Service (JWS) providing WSDL endpoints to Taverna Workbench, a workflow manager. The workflow has been validated, the performance has been measured, and its results have been verified. Our workflow's execution time is less than ten minutes for inferring a tree with 10,000 replicates of the bootstrapping numbers. This paper proposes a new integrated automatic workflow which will be beneficial to the bioinformaticians with an intermediate level of knowledge and experiences. The all local services have been deployed at our portal http://bioservices.sci.psu.ac.th.

What to do with a Dead Research Code

NASA Astrophysics Data System (ADS)

Nemiroff, Robert J.

2016-01-01

The project has ended -- should all of the computer codes that enabled the project be deleted? No. Like research papers, research codes typically carry valuable information past project end dates. Several possible end states to the life of research codes are reviewed. Historically, codes are typically left dormant on an increasingly obscure local disk directory until forgotten. These codes will likely become any or all of: lost, impossible to compile and run, difficult to decipher, and likely deleted when the code's proprietor moves on or dies. It is argued here, though, that it would be better for both code authors and astronomy generally if project codes were archived after use in some way. Archiving is advantageous for code authors because archived codes might increase the author's ADS citable publications, while astronomy as a science gains transparency and reproducibility. Paper-specific codes should be included in the publication of the journal papers they support, just like figures and tables. General codes that support multiple papers, possibly written by multiple authors, including their supporting websites, should be registered with a code registry such as the Astrophysics Source Code Library (ASCL). Codes developed on GitHub can be archived with a third party service such as, currently, BackHub. An important code version might be uploaded to a web archiving service like, currently, Zenodo or Figshare, so that this version receives a Digital Object Identifier (DOI), enabling it to found at a stable address into the future. Similar archiving services that are not DOI-dependent include perma.cc and the Internet Archive Wayback Machine at archive.org. Perhaps most simply, copies of important codes with lasting value might be kept on a cloud service like, for example, Google Drive, while activating Google's Inactive Account Manager.

Performance evaluation of MPEG internet video coding

NASA Astrophysics Data System (ADS)

Luo, Jiajia; Wang, Ronggang; Fan, Kui; Wang, Zhenyu; Li, Ge; Wang, Wenmin

2016-09-01

Internet Video Coding (IVC) has been developed in MPEG by combining well-known existing technology elements and new coding tools with royalty-free declarations. In June 2015, IVC project was approved as ISO/IEC 14496-33 (MPEG- 4 Internet Video Coding). It is believed that this standard can be highly beneficial for video services in the Internet domain. This paper evaluates the objective and subjective performances of IVC by comparing it against Web Video Coding (WVC), Video Coding for Browsers (VCB) and AVC High Profile. Experimental results show that IVC's compression performance is approximately equal to that of the AVC High Profile for typical operational settings, both for streaming and low-delay applications, and is better than WVC and VCB.

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

David Lawrence

Calibrations and conditions databases can be accessed from within the JANA Event Processing framework through the API defined in its JCalibration base class. The API is designed to support everything from databases, to web services to flat files for the backend. A Web Service backend using the gSOAP toolkit has been implemented which is particularly interesting since it addresses many modern cybersecurity issues including support for SSL. The API allows constants to be retrieved through a single line of C++ code with most of the context, including the transport mechanism, being implied by the run currently being analyzed and themore » environment relieving developers from implementing such details.« less

The JANA calibrations and conditions database API

NASA Astrophysics Data System (ADS)

Lawrence, David

2010-04-01

Calibrations and conditions databases can be accessed from within the JANA Event Processing framework through the API defined in its JCalibration base class. The API is designed to support everything from databases, to web services to flat files for the backend. A Web Service backend using the gSOAP toolkit has been implemented which is particularly interesting since it addresses many modern cybersecurity issues including support for SSL. The API allows constants to be retrieved through a single line of C++ code with most of the context, including the transport mechanism, being implied by the run currently being analyzed and the environment relieving developers from implementing such details.

14 CFR 234.11 - Disclosure to consumers.

Code of Federal Regulations, 2011 CFR

2011-01-01

.... (b) For each domestic flight for which schedule information is available on its Web site, including domestic code-share flights, a reporting carrier shall display the following information regarding the...) ECONOMIC REGULATIONS AIRLINE SERVICE QUALITY PERFORMANCE REPORTS § 234.11 Disclosure to consumers. (a...

14 CFR 234.11 - Disclosure to consumers.

Code of Federal Regulations, 2012 CFR

2012-01-01

.... (b) For each domestic flight for which schedule information is available on its Web site, including domestic code-share flights, a reporting carrier shall display the following information regarding the...) ECONOMIC REGULATIONS AIRLINE SERVICE QUALITY PERFORMANCE REPORTS § 234.11 Disclosure to consumers. (a...

14 CFR 234.11 - Disclosure to consumers.

Code of Federal Regulations, 2013 CFR

2013-01-01

.... (b) For each domestic flight for which schedule information is available on its Web site, including domestic code-share flights, a reporting carrier shall display the following information regarding the...) ECONOMIC REGULATIONS AIRLINE SERVICE QUALITY PERFORMANCE REPORTS § 234.11 Disclosure to consumers. (a...

14 CFR 234.11 - Disclosure to consumers.

Code of Federal Regulations, 2014 CFR

2014-01-01

.... (b) For each domestic flight for which schedule information is available on its Web site, including domestic code-share flights, a reporting carrier shall display the following information regarding the...) ECONOMIC REGULATIONS AIRLINE SERVICE QUALITY PERFORMANCE REPORTS § 234.11 Disclosure to consumers. (a...

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.

Software architecture and design of the web services facilitating climate model diagnostic analysis

NASA Astrophysics Data System (ADS)

Pan, L.; Lee, S.; Zhang, J.; Tang, B.; Zhai, C.; Jiang, J. H.; Wang, W.; Bao, Q.; Qi, M.; Kubar, T. L.; Teixeira, J.

2015-12-01

Climate model diagnostic analysis is a computationally- and data-intensive task because it involves multiple numerical model outputs and satellite observation data that can both be high resolution. We have built an online tool that facilitates this process. The tool is called Climate Model Diagnostic Analyzer (CMDA). It employs the web service technology and provides a web-based user interface. The benefits of these choices include: (1) No installation of any software other than a browser, hence it is platform compatable; (2) Co-location of computation and big data on the server side, and small results and plots to be downloaded on the client side, hence high data efficiency; (3) multi-threaded implementation to achieve parallel performance on multi-core servers; and (4) cloud deployment so each user has a dedicated virtual machine. In this presentation, we will focus on the computer science aspects of this tool, namely the architectural design, the infrastructure of the web services, the implementation of the web-based user interface, the mechanism of provenance collection, the approach to virtualization, and the Amazon Cloud deployment. As an example, We will describe our methodology to transform an existing science application code into a web service using a Python wrapper interface and Python web service frameworks (i.e., Flask, Gunicorn, and Tornado). Another example is the use of Docker, a light-weight virtualization container, to distribute and deploy CMDA onto an Amazon EC2 instance. Our tool of CMDA has been successfully used in the 2014 Summer School hosted by the JPL Center for Climate Science. Students had positive feedbacks in general and we will report their comments. An enhanced version of CMDA with several new features, some requested by the 2014 students, will be used in the 2015 Summer School soon.

Web-based network analysis and visualization using CellMaps

PubMed Central

Salavert, Francisco; García-Alonso, Luz; Sánchez, Rubén; Alonso, Roberto; Bleda, Marta; Medina, Ignacio; Dopazo, Joaquín

2016-01-01

Summary: CellMaps is an HTML5 open-source web tool that allows displaying, editing, exploring and analyzing biological networks as well as integrating metadata into them. Computations and analyses are remotely executed in high-end servers, and all the functionalities are available through RESTful web services. CellMaps can easily be integrated in any web page by using an available JavaScript API. Availability and Implementation: The application is available at: http://cellmaps.babelomics.org/ and the code can be found in: https://github.com/opencb/cell-maps. The client is implemented in JavaScript and the server in C and Java. Contact: jdopazo@cipf.es Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27296979

Web-based network analysis and visualization using CellMaps.

PubMed

Salavert, Francisco; García-Alonso, Luz; Sánchez, Rubén; Alonso, Roberto; Bleda, Marta; Medina, Ignacio; Dopazo, Joaquín

2016-10-01

: CellMaps is an HTML5 open-source web tool that allows displaying, editing, exploring and analyzing biological networks as well as integrating metadata into them. Computations and analyses are remotely executed in high-end servers, and all the functionalities are available through RESTful web services. CellMaps can easily be integrated in any web page by using an available JavaScript API. The application is available at: http://cellmaps.babelomics.org/ and the code can be found in: https://github.com/opencb/cell-maps The client is implemented in JavaScript and the server in C and Java. jdopazo@cipf.es Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

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

Wagner, Robert; Rivers, Wilmer

any single computer program for seismic data analysis will not have all the capabilities needed to study reference events, since hese detailed studies will be highly specialized. It may be necessary to develop and test new algorithms, and then these special ;odes must be integrated with existing software to use their conventional data-processing routines. We have investigated two neans of establishing communications between the legacy and new codes: CORBA and XML/SOAP Web services. We have nvestigated making new Java code communicate with a legacy C-language program, geotool, running under Linux. Both methods vere successful, but both were difficult to implement.more » C programs on UNIX/Linux are poorly supported for Web services, compared vith the Java and .NET languages and platforms. Easier-to-use middleware will be required for scientists to construct distributed applications as easily as stand-alone ones. Considerable difficulty was encountered in modifying geotool, and this problem shows he need to use component-based user interfaces instead of large C-language codes where changes to one part of the program nay introduce side effects into other parts. We have nevertheless made bug fixes and enhancements to that legacy program, but t remains difficult to expand it through communications with external software.« less

Transimulation - protein biosynthesis web service.

PubMed

Siwiak, Marlena; Zielenkiewicz, Piotr

2013-01-01

Although translation is the key step during gene expression, it remains poorly characterized at the level of individual genes. For this reason, we developed Transimulation - a web service measuring translational activity of genes in three model organisms: Escherichia coli, Saccharomyces cerevisiae and Homo sapiens. The calculations are based on our previous computational model of translation and experimental data sets. Transimulation quantifies mean translation initiation and elongation time (expressed in SI units), and the number of proteins produced per transcript. It also approximates the number of ribosomes that typically occupy a transcript during translation, and simulates their propagation. The simulation of ribosomes' movement is interactive and allows modifying the coding sequence on the fly. It also enables uploading any coding sequence and simulating its translation in one of three model organisms. In such a case, ribosomes propagate according to mean codon elongation times of the host organism, which may prove useful for heterologous expression. Transimulation was used to examine evolutionary conservation of translational parameters of orthologous genes. Transimulation may be accessed at http://nexus.ibb.waw.pl/Transimulation (requires Java version 1.7 or higher). Its manual and source code, distributed under the GPL-2.0 license, is freely available at the website.

BioXSD: the common data-exchange format for everyday bioinformatics web services.

PubMed

Kalas, Matús; Puntervoll, Pål; Joseph, Alexandre; Bartaseviciūte, Edita; Töpfer, Armin; Venkataraman, Prabakar; Pettifer, Steve; Bryne, Jan Christian; Ison, Jon; Blanchet, Christophe; Rapacki, Kristoffer; Jonassen, Inge

2010-09-15

The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of the resources offer programmatic web-service interface. However, efficient use of the resources is hampered by the lack of widely used, standard data-exchange formats for the basic, everyday bioinformatics data types. BioXSD has been developed as a candidate for standard, canonical exchange format for basic bioinformatics data. BioXSD is represented by a dedicated XML Schema and defines syntax for biological sequences, sequence annotations, alignments and references to resources. We have adapted a set of web services to use BioXSD as the input and output format, and implemented a test-case workflow. This demonstrates that the approach is feasible and provides smooth interoperability. Semantics for BioXSD is provided by annotation with the EDAM ontology. We discuss in a separate section how BioXSD relates to other initiatives and approaches, including existing standards and the Semantic Web. The BioXSD 1.0 XML Schema is freely available at http://www.bioxsd.org/BioXSD-1.0.xsd under the Creative Commons BY-ND 3.0 license. The http://bioxsd.org web page offers documentation, examples of data in BioXSD format, example workflows with source codes in common programming languages, an updated list of compatible web services and tools and a repository of feature requests from the community.

Transcriptator: An Automated Computational Pipeline to Annotate Assembled Reads and Identify Non Coding RNA.

PubMed

Tripathi, Kumar Parijat; Evangelista, Daniela; Zuccaro, Antonio; Guarracino, Mario Rosario

2015-01-01

RNA-seq is a new tool to measure RNA transcript counts, using high-throughput sequencing at an extraordinary accuracy. It provides quantitative means to explore the transcriptome of an organism of interest. However, interpreting this extremely large data into biological knowledge is a problem, and biologist-friendly tools are lacking. In our lab, we developed Transcriptator, a web application based on a computational Python pipeline with a user-friendly Java interface. This pipeline uses the web services available for BLAST (Basis Local Search Alignment Tool), QuickGO and DAVID (Database for Annotation, Visualization and Integrated Discovery) tools. It offers a report on statistical analysis of functional and Gene Ontology (GO) annotation's enrichment. It helps users to identify enriched biological themes, particularly GO terms, pathways, domains, gene/proteins features and protein-protein interactions related informations. It clusters the transcripts based on functional annotations and generates a tabular report for functional and gene ontology annotations for each submitted transcript to the web server. The implementation of QuickGo web-services in our pipeline enable the users to carry out GO-Slim analysis, whereas the integration of PORTRAIT (Prediction of transcriptomic non coding RNA (ncRNA) by ab initio methods) helps to identify the non coding RNAs and their regulatory role in transcriptome. In summary, Transcriptator is a useful software for both NGS and array data. It helps the users to characterize the de-novo assembled reads, obtained from NGS experiments for non-referenced organisms, while it also performs the functional enrichment analysis of differentially expressed transcripts/genes for both RNA-seq and micro-array experiments. It generates easy to read tables and interactive charts for better understanding of the data. The pipeline is modular in nature, and provides an opportunity to add new plugins in the future. Web application is freely available at: http://www-labgtp.na.icar.cnr.it/Transcriptator.

Oceans 2.0: a Data Management Infrastructure as a Platform

NASA Astrophysics Data System (ADS)

Pirenne, B.; Guillemot, E.

2012-04-01

Oceans 2.0: a Data Management Infrastructure as a Platform Benoît Pirenne, Associate Director, IT, NEPTUNE Canada Eric Guillemot, Manager, Software Development, NEPTUNE Canada The Data Management and Archiving System (DMAS) serving the needs of a number of undersea observing networks such as VENUS and NEPTUNE Canada was conceived from the beginning as a Service-Oriented Infrastructure. Its core functional elements (data acquisition, transport, archiving, retrieval and processing) can interact with the outside world using Web Services. Those Web Services can be exploited by a variety of higher level applications. Over the years, DMAS has developed Oceans 2.0: an environment where these techniques are implemented. The environment thereby becomes a platform in that it allows for easy addition of new and advanced features that build upon the tools at the core of the system. The applications that have been developed include: data search and retrieval, including options such as data product generation, data decimation or averaging, etc. dynamic infrastructure description (search all observatory metadata) and visualization data visualization, including dynamic scalar data plots, integrated fast video segment search and viewing Building upon these basic applications are new concepts, coming from the Web 2.0 world that DMAS has added: They allow people equipped only with a web browser to collaborate and contribute their findings or work results to the wider community. Examples include: addition of metadata tags to any part of the infrastructure or to any data item (annotations) ability to edit and execute, share and distribute Matlab code on-line, from a simple web browser, with specific calls within the code to access data ability to interactively and graphically build pipeline processing jobs that can be executed on the cloud web-based, interactive instrument control tools that allow users to truly share the use of the instruments and communicate with each other and last but not least: a public tool in the form of a game, that crowd-sources the inventory of the underwater video archive content, thereby adding tremendous amounts of metadata Beyond those tools that represent the functionality presently available to users, a number of the Web Services dedicated to data access are being exposed for anyone to use. This allows not only for ad hoc data access by individuals who need non-interactive access, but will foster the development of new applications in a variety of areas.

The diagnosis related groups enhanced electronic medical record.

PubMed

Müller, Marcel Lucas; Bürkle, Thomas; Irps, Sebastian; Roeder, Norbert; Prokosch, Hans-Ulrich

2003-07-01

The introduction of Diagnosis Related Groups as a basis for hospital payment in Germany announced essential changes in the hospital reimbursement practice. A hospital's economical survival will depend vitally on the accuracy and completeness of the documentation of DRG relevant data like diagnosis and procedure codes. In order to enhance physicians' coding compliance, an easy-to-use interface integrating coding tasks seamlessly into clinical routine had to be developed. A generic approach should access coding and clinical guidelines from different information sources. Within the Electronic Medical Record (EMR) a user interface ('DRG Control Center') for all DRG relevant clinical and administrative data has been built. A comprehensive DRG-related web site gives online access to DRG grouping software and an electronic coding expert. Both components are linked together using an application supporting bi-directional communication. Other web based services like a guideline search engine can be integrated as well. With the proposed method, the clinician gains quick access to context sensitive clinical guidelines for appropriate treatment of his/her patient and administrative guidelines for the adequate coding of the diagnoses and procedures. This paper describes the design and current implementation and discusses our experiences.

Meta4: a web application for sharing and annotating metagenomic gene predictions using web services.

PubMed

Richardson, Emily J; Escalettes, Franck; Fotheringham, Ian; Wallace, Robert J; Watson, Mick

2013-01-01

Whole-genome shotgun metagenomics experiments produce DNA sequence data from entire ecosystems, and provide a huge amount of novel information. Gene discovery projects require up-to-date information about sequence homology and domain structure for millions of predicted proteins to be presented in a simple, easy-to-use system. There is a lack of simple, open, flexible tools that allow the rapid sharing of metagenomics datasets with collaborators in a format they can easily interrogate. We present Meta4, a flexible and extensible web application that can be used to share and annotate metagenomic gene predictions. Proteins and predicted domains are stored in a simple relational database, with a dynamic front-end which displays the results in an internet browser. Web services are used to provide up-to-date information about the proteins from homology searches against public databases. Information about Meta4 can be found on the project website, code is available on Github, a cloud image is available, and an example implementation can be seen at.

Local File Disclosure Vulnerability: A Case Study of Public-Sector Web Applications

NASA Astrophysics Data System (ADS)

Ahmed, M. Imran; Maruf Hassan, Md; Bhuyian, Touhid

2018-01-01

Almost all public-sector organisations in Bangladesh now offer online services through web applications, along with the existing channels, in their endeavour to realise the dream of a ‘Digital Bangladesh’. Nations across the world have joined the online environment thanks to training and awareness initiatives by their government. File sharing and downloading activities using web applications have now become very common, not only ensuring the easy distribution of different types of files and documents but also enormously reducing the time and effort of users. Although the online services that are being used frequently have made users’ life easier, it has increased the risk of exploitation of local file disclosure (LFD) vulnerability in the web applications of different public-sector organisations due to unsecure design and careless coding. This paper analyses the root cause of LFD vulnerability, its exploitation techniques, and its impact on 129 public-sector websites in Bangladesh by examining the use of manual black box testing approach.

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

PubMed

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

2011-01-01

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

Improving Inpatient Surveys: Web-Based Computer Adaptive Testing Accessed via Mobile Phone QR Codes

PubMed Central

2016-01-01

Background The National Health Service (NHS) 70-item inpatient questionnaire surveys inpatients on their perceptions of their hospitalization experience. However, it imposes more burden on the patient than other similar surveys. The literature shows that computerized adaptive testing (CAT) based on item response theory can help shorten the item length of a questionnaire without compromising its precision. Objective Our aim was to investigate whether CAT can be (1) efficient with item reduction and (2) used with quick response (QR) codes scanned by mobile phones. Methods After downloading the 2008 inpatient survey data from the Picker Institute Europe website and analyzing the difficulties of this 70-item questionnaire, we used an author-made Excel program using the Rasch partial credit model to simulate 1000 patients’ true scores followed by a standard normal distribution. The CAT was compared to two other scenarios of answering all items (AAI) and the randomized selection method (RSM), as we investigated item length (efficiency) and measurement accuracy. The author-made Web-based CAT program for gathering patient feedback was effectively accessed from mobile phones by scanning the QR code. Results We found that the CAT can be more efficient for patients answering questions (ie, fewer items to respond to) than either AAI or RSM without compromising its measurement accuracy. A Web-based CAT inpatient survey accessed by scanning a QR code on a mobile phone was viable for gathering inpatient satisfaction responses. Conclusions With advances in technology, patients can now be offered alternatives for providing feedback about hospitalization satisfaction. This Web-based CAT is a possible option in health care settings for reducing the number of survey items, as well as offering an innovative QR code access. PMID:26935793

Improving Inpatient Surveys: Web-Based Computer Adaptive Testing Accessed via Mobile Phone QR Codes.

PubMed

Chien, Tsair-Wei; Lin, Weir-Sen

2016-03-02

The National Health Service (NHS) 70-item inpatient questionnaire surveys inpatients on their perceptions of their hospitalization experience. However, it imposes more burden on the patient than other similar surveys. The literature shows that computerized adaptive testing (CAT) based on item response theory can help shorten the item length of a questionnaire without compromising its precision. Our aim was to investigate whether CAT can be (1) efficient with item reduction and (2) used with quick response (QR) codes scanned by mobile phones. After downloading the 2008 inpatient survey data from the Picker Institute Europe website and analyzing the difficulties of this 70-item questionnaire, we used an author-made Excel program using the Rasch partial credit model to simulate 1000 patients' true scores followed by a standard normal distribution. The CAT was compared to two other scenarios of answering all items (AAI) and the randomized selection method (RSM), as we investigated item length (efficiency) and measurement accuracy. The author-made Web-based CAT program for gathering patient feedback was effectively accessed from mobile phones by scanning the QR code. We found that the CAT can be more efficient for patients answering questions (ie, fewer items to respond to) than either AAI or RSM without compromising its measurement accuracy. A Web-based CAT inpatient survey accessed by scanning a QR code on a mobile phone was viable for gathering inpatient satisfaction responses. With advances in technology, patients can now be offered alternatives for providing feedback about hospitalization satisfaction. This Web-based CAT is a possible option in health care settings for reducing the number of survey items, as well as offering an innovative QR code access.

Molmil: a molecular viewer for the PDB and beyond.

PubMed

Bekker, Gert-Jan; Nakamura, Haruki; Kinjo, Akira R

2016-01-01

We have developed a new platform-independent web-based molecular viewer using JavaScript and WebGL. The molecular viewer, Molmil, has been integrated into several services offered by Protein Data Bank Japan and can be easily extended with new functionality by third party developers. Furthermore, the viewer can be used to load files in various formats from the user's local hard drive without uploading the data to a server. Molmil is available for all platforms supporting WebGL (e.g. Windows, Linux, iOS, Android) from http://gjbekker.github.io/molmil/. The source code is available at http://github.com/gjbekker/molmil under the LGPLv3 licence.

SemanticSCo: A platform to support the semantic composition of services for gene expression analysis.

PubMed

Guardia, Gabriela D A; Ferreira Pires, Luís; da Silva, Eduardo G; de Farias, Cléver R G

2017-02-01

Gene expression studies often require the combined use of a number of analysis tools. However, manual integration of analysis tools can be cumbersome and error prone. To support a higher level of automation in the integration process, efforts have been made in the biomedical domain towards the development of semantic web services and supporting composition environments. Yet, most environments consider only the execution of simple service behaviours and requires users to focus on technical details of the composition process. We propose a novel approach to the semantic composition of gene expression analysis services that addresses the shortcomings of the existing solutions. Our approach includes an architecture designed to support the service composition process for gene expression analysis, and a flexible strategy for the (semi) automatic composition of semantic web services. Finally, we implement a supporting platform called SemanticSCo to realize the proposed composition approach and demonstrate its functionality by successfully reproducing a microarray study documented in the literature. The SemanticSCo platform provides support for the composition of RESTful web services semantically annotated using SAWSDL. Our platform also supports the definition of constraints/conditions regarding the order in which service operations should be invoked, thus enabling the definition of complex service behaviours. Our proposed solution for semantic web service composition takes into account the requirements of different stakeholders and addresses all phases of the service composition process. It also provides support for the definition of analysis workflows at a high-level of abstraction, thus enabling users to focus on biological research issues rather than on the technical details of the composition process. The SemanticSCo source code is available at https://github.com/usplssb/SemanticSCo. Copyright © 2017 Elsevier Inc. All rights reserved.

Sudan: Humanitarian Crisis, Peace Talks, Terrorism, and U.S. Policy

DTIC Science & Technology

2002-03-19

Congressional Research Service ˜ The Library of Congress CRS Issue Brief for Congress Received through the CRS Web Order Code IB98043 Sudan...as articulated by President Clinton in a 1996 letter to President Isaias of Eritrea supports regional efforts and seeks to isolate the NIF regime for

Sudan: Humanitarian Crisis, Peace Talks, Terrorism, and U.S. Policy

DTIC Science & Technology

2002-05-08

Congressional Research Service ˜ The Library of Congress Issue Brief for Congress Received through the CRS Web Order Code IB98043 Sudan...U.S. policy toward Sudan as articulated by President Clinton in a 1996 letter to President Isaias of Eritrea supports regional efforts and seeks to

Web processing service for climate impact and extreme weather event analyses. Flyingpigeon (Version 1.0)

NASA Astrophysics Data System (ADS)

Hempelmann, Nils; Ehbrecht, Carsten; Alvarez-Castro, Carmen; Brockmann, Patrick; Falk, Wolfgang; Hoffmann, Jörg; Kindermann, Stephan; Koziol, Ben; Nangini, Cathy; Radanovics, Sabine; Vautard, Robert; Yiou, Pascal

2018-01-01

Analyses of extreme weather events and their impacts often requires big data processing of ensembles of climate model simulations. Researchers generally proceed by downloading the data from the providers and processing the data files ;at home; with their own analysis processes. However, the growing amount of available climate model and observation data makes this procedure quite awkward. In addition, data processing knowledge is kept local, instead of being consolidated into a common resource of reusable code. These drawbacks can be mitigated by using a web processing service (WPS). A WPS hosts services such as data analysis processes that are accessible over the web, and can be installed close to the data archives. We developed a WPS named 'flyingpigeon' that communicates over an HTTP network protocol based on standards defined by the Open Geospatial Consortium (OGC), to be used by climatologists and impact modelers as a tool for analyzing large datasets remotely. Here, we present the current processes we developed in flyingpigeon relating to commonly-used processes (preprocessing steps, spatial subsets at continent, country or region level, and climate indices) as well as methods for specific climate data analysis (weather regimes, analogues of circulation, segetal flora distribution, and species distribution models). We also developed a novel, browser-based interactive data visualization for circulation analogues, illustrating the flexibility of WPS in designing custom outputs. Bringing the software to the data instead of transferring the data to the code is becoming increasingly necessary, especially with the upcoming massive climate datasets.

BioXSD: the common data-exchange format for everyday bioinformatics web services

PubMed Central

Kalaš, Matúš; Puntervoll, Pæl; Joseph, Alexandre; Bartaševičiūtė, Edita; Töpfer, Armin; Venkataraman, Prabakar; Pettifer, Steve; Bryne, Jan Christian; Ison, Jon; Blanchet, Christophe; Rapacki, Kristoffer; Jonassen, Inge

2010-01-01

Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of the resources offer programmatic web-service interface. However, efficient use of the resources is hampered by the lack of widely used, standard data-exchange formats for the basic, everyday bioinformatics data types. Results: BioXSD has been developed as a candidate for standard, canonical exchange format for basic bioinformatics data. BioXSD is represented by a dedicated XML Schema and defines syntax for biological sequences, sequence annotations, alignments and references to resources. We have adapted a set of web services to use BioXSD as the input and output format, and implemented a test-case workflow. This demonstrates that the approach is feasible and provides smooth interoperability. Semantics for BioXSD is provided by annotation with the EDAM ontology. We discuss in a separate section how BioXSD relates to other initiatives and approaches, including existing standards and the Semantic Web. Availability: The BioXSD 1.0 XML Schema is freely available at http://www.bioxsd.org/BioXSD-1.0.xsd under the Creative Commons BY-ND 3.0 license. The http://bioxsd.org web page offers documentation, examples of data in BioXSD format, example workflows with source codes in common programming languages, an updated list of compatible web services and tools and a repository of feature requests from the community. Contact: matus.kalas@bccs.uib.no; developers@bioxsd.org; support@bioxsd.org PMID:20823319

The architecture of a virtual grid GIS server

NASA Astrophysics Data System (ADS)

Wu, Pengfei; Fang, Yu; Chen, Bin; Wu, Xi; Tian, Xiaoting

2008-10-01

The grid computing technology provides the service oriented architecture for distributed applications. The virtual Grid GIS server is the distributed and interoperable enterprise application GIS architecture running in the grid environment, which integrates heterogeneous GIS platforms. All sorts of legacy GIS platforms join the grid as members of GIS virtual organization. Based on Microkernel we design the ESB and portal GIS service layer, which compose Microkernel GIS. Through web portals, portal GIS services and mediation of service bus, following the principle of SoC, we separate business logic from implementing logic. Microkernel GIS greatly reduces the coupling degree between applications and GIS platforms. The enterprise applications are independent of certain GIS platforms, and making the application developers to pay attention to the business logic. Via configuration and orchestration of a set of fine-grained services, the system creates GIS Business, which acts as a whole WebGIS request when activated. In this way, the system satisfies a business workflow directly and simply, with little or no new code.

Providing web-based mental health services to at-risk women

PubMed Central

2011-01-01

Background We examined the feasibility of providing web-based mental health services, including synchronous internet video conferencing of an evidence-based support/education group, to at-risk women, specifically poor lone mothers. The objectives of this study were to: (i) adapt a face-to-face support/education group intervention to a web-based format for lone mothers, and (ii) evaluate lone mothers' response to web-based services, including an online video conferencing group intervention program. Methods Participating mothers were recruited through advertisements. To adapt the face-to-face intervention to a web-based format, we evaluated participant motivation through focus group/key informant interviews (n = 7), adapted the intervention training manual for a web-based environment and provided a computer training manual. To evaluate response to web-based services, we provided the intervention to two groups of lone mothers (n = 15). Pre-post quantitative evaluation of mood, self-esteem, social support and parenting was done. Post intervention follow up interviews explored responses to the group and to using technology to access a health service. Participants received $20 per occasion of data collection. Interviews were taped, transcribed and content analysis was used to code and interpret the data. Adherence to the intervention protocol was evaluated. Results Mothers participating in this project experienced multiple difficulties, including financial and mood problems. We adapted the intervention training manual for use in a web-based group environment and ensured adherence to the intervention protocol based on viewing videoconferencing group sessions and discussion with the leaders. Participant responses to the group intervention included decreased isolation, and increased knowledge and confidence in themselves and their parenting; the responses closely matched those of mothers who obtained same service in face-to-face groups. Pre-and post-group quantitative evaluations did not show significant improvements on measures, although the study was not powered to detect these. Conclusions We demonstrated that an evidence-based group intervention program for lone mothers developed and evaluated in face-to-face context transferred well to an online video conferencing format both in terms of group process and outcomes. PMID:21854563

Providing web-based mental health services to at-risk women.

PubMed

Lipman, Ellen L; Kenny, Meghan; Marziali, Elsa

2011-08-19

We examined the feasibility of providing web-based mental health services, including synchronous internet video conferencing of an evidence-based support/education group, to at-risk women, specifically poor lone mothers. The objectives of this study were to: (i) adapt a face-to-face support/education group intervention to a web-based format for lone mothers, and (ii) evaluate lone mothers' response to web-based services, including an online video conferencing group intervention program. Participating mothers were recruited through advertisements. To adapt the face-to-face intervention to a web-based format, we evaluated participant motivation through focus group/key informant interviews (n = 7), adapted the intervention training manual for a web-based environment and provided a computer training manual. To evaluate response to web-based services, we provided the intervention to two groups of lone mothers (n = 15). Pre-post quantitative evaluation of mood, self-esteem, social support and parenting was done. Post intervention follow up interviews explored responses to the group and to using technology to access a health service. Participants received $20 per occasion of data collection. Interviews were taped, transcribed and content analysis was used to code and interpret the data. Adherence to the intervention protocol was evaluated. Mothers participating in this project experienced multiple difficulties, including financial and mood problems. We adapted the intervention training manual for use in a web-based group environment and ensured adherence to the intervention protocol based on viewing videoconferencing group sessions and discussion with the leaders. Participant responses to the group intervention included decreased isolation, and increased knowledge and confidence in themselves and their parenting; the responses closely matched those of mothers who obtained same service in face-to-face groups. Pre-and post-group quantitative evaluations did not show significant improvements on measures, although the study was not powered to detect these. We demonstrated that an evidence-based group intervention program for lone mothers developed and evaluated in face-to-face context transferred well to an online video conferencing format both in terms of group process and outcomes.

MetaRanker 2.0: a web server for prioritization of genetic variation data

PubMed Central

Pers, Tune H.; Dworzyński, Piotr; Thomas, Cecilia Engel; Lage, Kasper; Brunak, Søren

2013-01-01

MetaRanker 2.0 is a web server for prioritization of common and rare frequency genetic variation data. Based on heterogeneous data sets including genetic association data, protein–protein interactions, large-scale text-mining data, copy number variation data and gene expression experiments, MetaRanker 2.0 prioritizes the protein-coding part of the human genome to shortlist candidate genes for targeted follow-up studies. MetaRanker 2.0 is made freely available at www.cbs.dtu.dk/services/MetaRanker-2.0. PMID:23703204

MetaRanker 2.0: a web server for prioritization of genetic variation data.

PubMed

Pers, Tune H; Dworzyński, Piotr; Thomas, Cecilia Engel; Lage, Kasper; Brunak, Søren

2013-07-01

MetaRanker 2.0 is a web server for prioritization of common and rare frequency genetic variation data. Based on heterogeneous data sets including genetic association data, protein-protein interactions, large-scale text-mining data, copy number variation data and gene expression experiments, MetaRanker 2.0 prioritizes the protein-coding part of the human genome to shortlist candidate genes for targeted follow-up studies. MetaRanker 2.0 is made freely available at www.cbs.dtu.dk/services/MetaRanker-2.0.

Saada: A Generator of Astronomical Database

NASA Astrophysics Data System (ADS)

Michel, L.

2011-11-01

Saada transforms a set of heterogeneous FITS files or VOtables of various categories (images, tables, spectra, etc.) in a powerful database deployed on the Web. Databases are located on your host and stay independent of any external server. This job doesn’t require writing code. Saada can mix data of various categories in multiple collections. Data collections can be linked each to others making relevant browsing paths and allowing data-mining oriented queries. Saada supports 4 VO services (Spectra, images, sources and TAP) . Data collections can be published immediately after the deployment of the Web interface.

78 FR 60876 - Advisory Committee to the Director (ACD), Centers for Disease Control and Prevention (CDC)

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-02

... DEPARTMENT OF HEALTH AND HUMAN SERVICES Centers for Disease Control and Prevention Advisory... by teleconference. Please dial (877) 930-8819 and enter code 1579739. Web links: Windows Connection-2: http://wm.onlinevideoservice.com/CDC2 Flash Connection-4 (For Safari and Google Chrome Users): http...

78 FR 60876 - Advisory Committee to the Director (ACD), Centers for Disease Control and Prevention (CDC)

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-02

... DEPARTMENT OF HEALTH AND HUMAN SERVICES Centers for Disease Control and Prevention Advisory... by teleconference. Please dial (877) 930-8819 and enter code 1579739. Web Links Windows Connection-2: http://wm.onlinevideoservice.com/CDC2 . Flash Connection-4 (For Safari and Google Chrome Users): http...

75 FR 70557 - Endocrine Disruptor Screening Program; Draft Policies and Procedures for Screening Safe Drinking...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-17

... intends to post the status of the test orders, including recipients' responses, on the EPA Web site so... screening program using appropriate validated test systems and other scientifically relevant information to... chemicals. Scientific research and development services (NAICS code 5417), e.g., persons who conduct testing...

VO-KOREL: A Fourier Disentangling Service of the Virtual Observatory

NASA Astrophysics Data System (ADS)

Škoda, Petr; Hadrava, Petr; Fuchs, Jan

2012-04-01

VO-KOREL is a web service exploiting the technology of the Virtual Observatory for providing astronomers with the intuitive graphical front-end and distributed computing back-end running the most recent version of the Fourier disentangling code KOREL. The system integrates the ideas of the e-shop basket, conserving the privacy of every user by transfer encryption and access authentication, with features of laboratory notebook, allowing the easy housekeeping of both input parameters and final results, as well as it explores a newly emerging technology of cloud computing. While the web-based front-end allows the user to submit data and parameter files, edit parameters, manage a job list, resubmit or cancel running jobs and mainly watching the text and graphical results of a disentangling process, the main part of the back-end is a simple job queue submission system executing in parallel multiple instances of the FORTRAN code KOREL. This may be easily extended for GRID-based deployment on massively parallel computing clusters. The short introduction into underlying technologies is given, briefly mentioning advantages as well as bottlenecks of the design used.

EarthServer2 : The Marine Data Service - Web based and Programmatic Access to Ocean Colour Open Data

NASA Astrophysics Data System (ADS)

Clements, Oliver; Walker, Peter

2017-04-01

The ESA Ocean Colour - Climate Change Initiative (ESA OC-CCI) has produced a long-term high quality global dataset with associated per-pixel uncertainty data. This dataset has now grown to several hundred terabytes (uncompressed) and is freely available to download. However, the sheer size of the dataset can act as a barrier to many users; large network bandwidth, local storage and processing requirements can prevent researchers without the backing of a large organisation from taking advantage of this raw data. The EC H2020 project, EarthServer2, aims to create a federated data service providing access to more than 1 petabyte of earth science data. Within this federation the Marine Data Service already provides an innovative on-line tool-kit for filtering, analysing and visualising OC-CCI data. Data are made available, filtered and processed at source through a standards-based interface, the Open Geospatial Consortium Web Coverage Service and Web Coverage Processing Service. This work was initiated in the EC FP7 EarthServer project where it was found that the unfamiliarity and complexity of these interfaces itself created a barrier to wider uptake. The continuation project, EarthServer2, addresses these issues by providing higher level tools for working with these data. We will present some examples of these tools. Many researchers wish to extract time series data from discrete points of interest. We will present a web based interface, based on NASA/ESA WebWorldWind, for selecting points of interest and plotting time series from a chosen dataset. In addition, a CSV file of locations and times, such as a ship's track, can be uploaded and these points extracted and returned in a CSV file allowing researchers to work with the extract locally, such as a spreadsheet. We will also present a set of Python and JavaScript APIs that have been created to complement and extend the web based GUI. These APIs allow the selection of single points and areas for extraction. The extracted data is returned as structured data (for instance a Python array) which can then be passed directly to local processing code. We will highlight how the libraries can be used by the community and integrated into existing systems, for instance by the use of Jupyter notebooks to share Python code examples which can then be used by other researchers as a basis for their own work.

User Interface Design in Medical Distributed Web Applications.

PubMed

Serban, Alexandru; Crisan-Vida, Mihaela; Mada, Leonard; Stoicu-Tivadar, Lacramioara

2016-01-01

User interfaces are important to facilitate easy learning and operating with an IT application especially in the medical world. An easy to use interface has to be simple and to customize the user needs and mode of operation. The technology in the background is an important tool to accomplish this. The present work aims to creating a web interface using specific technology (HTML table design combined with CSS3) to provide an optimized responsive interface for a complex web application. In the first phase, the current icMED web medical application layout is analyzed, and its structure is designed using specific tools, on source files. In the second phase, a new graphic adaptable interface to different mobile terminals is proposed, (using HTML table design (TD) and CSS3 method) that uses no source files, just lines of code for layout design, improving the interaction in terms of speed and simplicity. For a complex medical software application a new prototype layout was designed and developed using HTML tables. The method uses a CSS code with only CSS classes applied to one or multiple HTML table elements, instead of CSS styles that can be applied to just one DIV tag at once. The technique has the advantage of a simplified CSS code, and a better adaptability to different media resolutions compared to DIV-CSS style method. The presented work is a proof that adaptive web interfaces can be developed just using and combining different types of design methods and technologies, using HTML table design, resulting in a simpler to learn and use interface, suitable for healthcare services.

myChEMBL: a virtual machine implementation of open data and cheminformatics tools.

PubMed

Ochoa, Rodrigo; Davies, Mark; Papadatos, George; Atkinson, Francis; Overington, John P

2014-01-15

myChEMBL is a completely open platform, which combines public domain bioactivity data with open source database and cheminformatics technologies. myChEMBL consists of a Linux (Ubuntu) Virtual Machine featuring a PostgreSQL schema with the latest version of the ChEMBL database, as well as the latest RDKit cheminformatics libraries. In addition, a self-contained web interface is available, which can be modified and improved according to user specifications. The VM is available at: ftp://ftp.ebi.ac.uk/pub/databases/chembl/VM/myChEMBL/current. The web interface and web services code is available at: https://github.com/rochoa85/myChEMBL.

The CARMEN software as a service infrastructure.

PubMed

Weeks, Michael; Jessop, Mark; Fletcher, Martyn; Hodge, Victoria; Jackson, Tom; Austin, Jim

2013-01-28

The CARMEN platform allows neuroscientists to share data, metadata, services and workflows, and to execute these services and workflows remotely via a Web portal. This paper describes how we implemented a service-based infrastructure into the CARMEN Virtual Laboratory. A Software as a Service framework was developed to allow generic new and legacy code to be deployed as services on a heterogeneous execution framework. Users can submit analysis code typically written in Matlab, Python, C/C++ and R as non-interactive standalone command-line applications and wrap them as services in a form suitable for deployment on the platform. The CARMEN Service Builder tool enables neuroscientists to quickly wrap their analysis software for deployment to the CARMEN platform, as a service without knowledge of the service framework or the CARMEN system. A metadata schema describes each service in terms of both system and user requirements. The search functionality allows services to be quickly discovered from the many services available. Within the platform, services may be combined into more complicated analyses using the workflow tool. CARMEN and the service infrastructure are targeted towards the neuroscience community; however, it is a generic platform, and can be targeted towards any discipline.

Services for Emodnet-Chemistry Data Products

NASA Astrophysics Data System (ADS)

Santinelli, Giorgio; Hendriksen, Gerrit; Barth, Alexander

2016-04-01

In the framework of Emodnet Chemistry lot, data products from regional leaders were made available in order to transform information into a database. This has been done by using functions and scripts, reading so-called enriched ODV files and inserting data directly into a cloud relational geodatabase. The main table is the one of observations which contains the main data and meta-data associated with the enriched ODV files. A particular implementation in data loading is used in order to improve on-the-fly computational speed. Data from Baltic Sea, North Sea, Mediterrean, Black Sea and part of the Atlantic region has been entered into the geodatabase, and consequently being instantly available from the OceanBrowser Emodnet portal. Furthermore, Deltares has developed an application that provides additional visualisation services for the aggregated and validated data collections. The visualisations are produced by making use of part of the OpenEarthTool stack (http://www.openearth.eu), by the integration of Web Feature Services and by the implementation of Web Processing Services. The goal is the generation of server-side plots of timeseries, profiles, timeprofiles and maps of selected parameters from data sets of selected stations. Regional data collections are retrieved using Emodnet Chemistry cloud relational geo-database. The spatial resolution in time and the intensity of data availability for selected parameters is shown using Web Service requests via the OceanBrowser Emodnet Web portal. OceanBrowser also shows station reference codes, which are used to establish a link for additional metadata, further data shopping and download.

78 FR 5797 - Availability of e-Tag Information to Commission Staff; Notice Specifying webRegistry Code

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-28

... e-Tag Information to Commission Staff; Notice Specifying webRegistry Code In Order No. 771,\\1\\ the... stated that, ``following issuance of this Final Rule and the Commission's registration in the OATI web... in the Purchasing-Seller Entity section of OATI webRegistry. This code should be used to designate...

Ultrabroadband photonic internet: safety aspects

NASA Astrophysics Data System (ADS)

Kalicki, Arkadiusz; Romaniuk, Ryszard

2008-11-01

Web applications became most popular medium in the Internet. Popularity, easiness of web application frameworks together with careless development results in high number of vulnerabilities and attacks. There are several types of attacks possible because of improper input validation. SQL injection is ability to execute arbitrary SQL queries in a database through an existing application. Cross-site scripting is the vulnerability which allows malicious web users to inject code into the web pages viewed by other users. Cross-Site Request Forgery (CSRF) is an attack that tricks the victim into loading a page that contains malicious request. Web spam in blogs. There are several techniques to mitigate attacks. Most important are web application strong design, correct input validation, defined data types for each field and parameterized statements in SQL queries. Server hardening with firewall, modern security policies systems and safe web framework interpreter configuration are essential. It is advised to keep proper security level on client side, keep updated software and install personal web firewalls or IDS/IPS systems. Good habits are logging out from services just after finishing work and using even separate web browser for most important sites, like e-banking.

The NOAO NVO Portal

NASA Astrophysics Data System (ADS)

Miller, C. J.; Gasson, D.; Fuentes, E.

2007-10-01

The NOAO NVO Portal is a web application for one-stop discovery, analysis, and access to VO-compliant imaging data and services. The current release allows for GUI-based discovery of nearly a half million images from archives such as the NOAO Science Archive, the Hubble Space Telescope WFPC2 and ACS instruments, XMM-Newton, Chandra, and ESO's INT Wide-Field Survey, among others. The NOAO Portal allows users to view image metadata, footprint wire-frames, FITS image previews, and provides one-click access to science quality imaging data throughout the entire sky via the Firefox web browser (i.e., no applet or code to download). Users can stage images from multiple archives at the NOAO NVO Portal for quick and easy bulk downloads. The NOAO NVO Portal also provides simplified and direct access to VO analysis services, such as the WESIX catalog generation service. We highlight the features of the NOAO NVO Portal (http://nvo.noao.edu).

Space Weather Services and Products of RWC Russia in 2007

NASA Astrophysics Data System (ADS)

Burov, Viatcheslav; Avdyushin, Sergei; Denisova, Valentina

RWC Russia (Institute of Applied Geophysics) - forecasting center unites activity of the National Heliogeophysic Service of Russia and Regional Warning Center ISES. The Center has been operating since 1974. There are several services that carry out gathering, processing and spreading of the total information data flow, (including both Russian and foreign-exchange data), and forecasts. Forecasting activities results are issued in the form of special messages, the major part of which corresponds to standard codes. Our Web page: www.geospace.ru are represented the current data and the forecasts. At present both a weekly 7-day geomagnetic forecast and the actual disturbance activity information for the previous week are available on the Web page. And, the data of some ionosphere and magnetic stations are available on this page too. Various types of our forecast alert and routine observations are considered in the report

mORCA: ubiquitous access to life science web services.

PubMed

Diaz-Del-Pino, Sergio; Trelles, Oswaldo; Falgueras, Juan

2018-01-16

Technical advances in mobile devices such as smartphones and tablets have produced an extraordinary increase in their use around the world and have become part of our daily lives. The possibility of carrying these devices in a pocket, particularly mobile phones, has enabled ubiquitous access to Internet resources. Furthermore, in the life sciences world there has been a vast proliferation of data types and services that finish as Web Services. This suggests the need for research into mobile clients to deal with life sciences applications for effective usage and exploitation. Analysing the current features in existing bioinformatics applications managing Web Services, we have devised, implemented, and deployed an easy-to-use web-based lightweight mobile client. This client is able to browse, select, compose parameters, invoke, and monitor the execution of Web Services stored in catalogues or central repositories. The client is also able to deal with huge amounts of data between external storage mounts. In addition, we also present a validation use case, which illustrates the usage of the application while executing, monitoring, and exploring the results of a registered workflow. The software its available in the Apple Store and Android Market and the source code is publicly available in Github. Mobile devices are becoming increasingly important in the scientific world due to their strong potential impact on scientific applications. Bioinformatics should not fall behind this trend. We present an original software client that deals with the intrinsic limitations of such devices and propose different guidelines to provide location-independent access to computational resources in bioinformatics and biomedicine. Its modular design makes it easily expandable with the inclusion of new repositories, tools, types of visualization, etc.

\\Space: A new code to estimate \\temp, \\logg, and elemental abundances

NASA Astrophysics Data System (ADS)

Boeche, C.

2016-09-01

\\Space is a FORTRAN95 code that derives stellar parameters and elemental abundances from stellar spectra. To derive these parameters, \\Space does not measure equivalent widths of lines nor it uses templates of synthetic spectra, but it employs a new method based on a library of General Curve-Of-Growths. To date \\Space works on the wavelength range 5212-6860 Å and 8400-8921 Å, and at the spectral resolution R=2000-20000. Extensions of these limits are possible. \\Space is a highly automated code suitable for application to large spectroscopic surveys. A web front end to this service is publicly available at http://dc.g-vo.org/SP_ACE together with the library and the binary code.

ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser

PubMed Central

Almeida, Jonas S.; Iriabho, Egiebade E.; Gorrepati, Vijaya L.; Wilkinson, Sean R.; Grüneberg, Alexander; Robbins, David E.; Hackney, James R.

2012-01-01

Background: Image bioinformatics infrastructure typically relies on a combination of server-side high-performance computing and client desktop applications tailored for graphic rendering. On the server side, matrix manipulation environments are often used as the back-end where deployment of specialized analytical workflows takes place. However, neither the server-side nor the client-side desktop solution, by themselves or combined, is conducive to the emergence of open, collaborative, computational ecosystems for image analysis that are both self-sustained and user driven. Materials and Methods: ImageJS was developed as a browser-based webApp, untethered from a server-side backend, by making use of recent advances in the modern web browser such as a very efficient compiler, high-end graphical rendering capabilities, and I/O tailored for code migration. Results: Multiple versioned code hosting services were used to develop distinct ImageJS modules to illustrate its amenability to collaborative deployment without compromise of reproducibility or provenance. The illustrative examples include modules for image segmentation, feature extraction, and filtering. The deployment of image analysis by code migration is in sharp contrast with the more conventional, heavier, and less safe reliance on data transfer. Accordingly, code and data are loaded into the browser by exactly the same script tag loading mechanism, which offers a number of interesting applications that would be hard to attain with more conventional platforms, such as NIH's popular ImageJ application. Conclusions: The modern web browser was found to be advantageous for image bioinformatics in both the research and clinical environments. This conclusion reflects advantages in deployment scalability and analysis reproducibility, as well as the critical ability to deliver advanced computational statistical procedures machines where access to sensitive data is controlled, that is, without local “download and installation”. PMID:22934238

ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser.

PubMed

Almeida, Jonas S; Iriabho, Egiebade E; Gorrepati, Vijaya L; Wilkinson, Sean R; Grüneberg, Alexander; Robbins, David E; Hackney, James R

2012-01-01

Image bioinformatics infrastructure typically relies on a combination of server-side high-performance computing and client desktop applications tailored for graphic rendering. On the server side, matrix manipulation environments are often used as the back-end where deployment of specialized analytical workflows takes place. However, neither the server-side nor the client-side desktop solution, by themselves or combined, is conducive to the emergence of open, collaborative, computational ecosystems for image analysis that are both self-sustained and user driven. ImageJS was developed as a browser-based webApp, untethered from a server-side backend, by making use of recent advances in the modern web browser such as a very efficient compiler, high-end graphical rendering capabilities, and I/O tailored for code migration. Multiple versioned code hosting services were used to develop distinct ImageJS modules to illustrate its amenability to collaborative deployment without compromise of reproducibility or provenance. The illustrative examples include modules for image segmentation, feature extraction, and filtering. The deployment of image analysis by code migration is in sharp contrast with the more conventional, heavier, and less safe reliance on data transfer. Accordingly, code and data are loaded into the browser by exactly the same script tag loading mechanism, which offers a number of interesting applications that would be hard to attain with more conventional platforms, such as NIH's popular ImageJ application. The modern web browser was found to be advantageous for image bioinformatics in both the research and clinical environments. This conclusion reflects advantages in deployment scalability and analysis reproducibility, as well as the critical ability to deliver advanced computational statistical procedures machines where access to sensitive data is controlled, that is, without local "download and installation".

Selling Internet Gambling: Advertising, New Media and the Content of Poker Promotion

ERIC Educational Resources Information Center

McMullan, John L.; Kervin, Melissa

2012-01-01

This study examines the web design and engineering, advertising and marketing, and pedagogical features present at a random sample of 71 international poker sites obtained from the Casino City directory in the summer of 2009. We coded for 22 variables related to access, appeal, player protection, customer services, on-site security, use of images,…

Open-Source Python Tools for Deploying Interactive GIS Dashboards for a Billion Datapoints on a Laptop

NASA Astrophysics Data System (ADS)

Steinberg, P. D.; Bednar, J. A.; Rudiger, P.; Stevens, J. L. R.; Ball, C. E.; Christensen, S. D.; Pothina, D.

2017-12-01

The rich variety of software libraries available in the Python scientific ecosystem provides a flexible and powerful alternative to traditional integrated GIS (geographic information system) programs. Each such library focuses on doing a certain set of general-purpose tasks well, and Python makes it relatively simple to glue the libraries together to solve a wide range of complex, open-ended problems in Earth science. However, choosing an appropriate set of libraries can be challenging, and it is difficult to predict how much "glue code" will be needed for any particular combination of libraries and tasks. Here we present a set of libraries that have been designed to work well together to build interactive analyses and visualizations of large geographic datasets, in standard web browsers. The resulting workflows run on ordinary laptops even for billions of data points, and easily scale up to larger compute clusters when available. The declarative top-level interface used in these libraries means that even complex, fully interactive applications can be built and deployed as web services using only a few dozen lines of code, making it simple to create and share custom interactive applications even for datasets too large for most traditional GIS systems. The libraries we will cover include GeoViews (HoloViews extended for geographic applications) for declaring visualizable/plottable objects, Bokeh for building visual web applications from GeoViews objects, Datashader for rendering arbitrarily large datasets faithfully as fixed-size images, Param for specifying user-modifiable parameters that model your domain, Xarray for computing with n-dimensional array data, Dask for flexibly dispatching computational tasks across processors, and Numba for compiling array-based Python code down to fast machine code. We will show how to use the resulting workflow with static datasets and with simulators such as GSSHA or AdH, allowing you to deploy flexible, high-performance web-based dashboards for your GIS data or simulations without needing major investments in code development or maintenance.

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.

Web GIS in practice VI: a demo playlist of geo-mashups for public health neogeographers

PubMed Central

Boulos, Maged N Kamel; Scotch, Matthew; Cheung, Kei-Hoi; Burden, David

2008-01-01

'Mashup' was originally used to describe the mixing together of musical tracks to create a new piece of music. The term now refers to Web sites or services that weave data from different sources into a new data source or service. Using a musical metaphor that builds on the origin of the word 'mashup', this paper presents a demonstration "playlist" of four geo-mashup vignettes that make use of a range of Web 2.0, Semantic Web, and 3-D Internet methods, with outputs/end-user interfaces spanning the flat Web (two-dimensional – 2-D maps), a three-dimensional – 3-D mirror world (Google Earth) and a 3-D virtual world (Second Life ®). The four geo-mashup "songs" in this "playlist" are: 'Web 2.0 and GIS (Geographic Information Systems) for infectious disease surveillance', 'Web 2.0 and GIS for molecular epidemiology', 'Semantic Web for GIS mashup', and 'From Yahoo! Pipes to 3-D, avatar-inhabited geo-mashups'. It is hoped that this showcase of examples and ideas, and the pointers we are providing to the many online tools that are freely available today for creating, sharing and reusing geo-mashups with minimal or no coding, will ultimately spark the imagination of many public health practitioners and stimulate them to start exploring the use of these methods and tools in their day-to-day practice. The paper also discusses how today's Web is rapidly evolving into a much more intensely immersive, mixed-reality and ubiquitous socio-experiential Metaverse that is heavily interconnected through various kinds of user-created mashups. PMID:18638385

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.

The EMBL-EBI bioinformatics web and programmatic tools framework.

PubMed

Li, Weizhong; Cowley, Andrew; Uludag, Mahmut; Gur, Tamer; McWilliam, Hamish; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Lopez, Rodrigo

2015-07-01

Since 2009 the EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications. These include sequence similarity search services (https://www.ebi.ac.uk/Tools/sss/) such as BLAST, FASTA and PSI-Search, multiple sequence alignment tools (https://www.ebi.ac.uk/Tools/msa/) such as Clustal Omega, MAFFT and T-Coffee, and other sequence analysis tools (https://www.ebi.ac.uk/Tools/pfa/) such as InterProScan. Through these services users can search mainstream sequence databases such as ENA, UniProt and Ensembl Genomes, utilising a uniform web interface or systematically through Web Services interfaces (https://www.ebi.ac.uk/Tools/webservices/) using common programming languages, and obtain enriched results with novel visualisations. Integration with EBI Search (https://www.ebi.ac.uk/ebisearch/) and the dbfetch retrieval service (https://www.ebi.ac.uk/Tools/dbfetch/) further expands the usefulness of the framework. New tools and updates such as NCBI BLAST+, InterProScan 5 and PfamScan, new categories such as RNA analysis tools (https://www.ebi.ac.uk/Tools/rna/), new databases such as ENA non-coding, WormBase ParaSite, Pfam and Rfam, and new workflow methods, together with the retirement of depreciated services, ensure that the framework remains relevant to today's biological community. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Ship to Shore Data Communication and Prioritization

DTIC Science & Technology

2011-12-01

First Out FTP File Transfer Protocol GCCS-M Global Command and Control System Maritime HAIPE High Assurance Internet Protocol Encryptor HTTP Hypertext...Transfer Protocol (world wide web protocol ) IBS Integrated Bar Code System IDEF0 Integration Definition IER Information Exchange Requirements...INTEL Intelligence IP Internet Protocol IPT Integrated Product Team ISEA In-Service Engineering Agent ISNS Integrated Shipboard Network System IT

Easy Web Interfaces to IDL Code for NSTX Data Analysis

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

W.M. Davis

Reusing code is a well-known Software Engineering practice to substantially increase the efficiency of code production, as well as to reduce errors and debugging time. A variety of "Web Tools" for the analysis and display of raw and analyzed physics data are in use on NSTX [1], and new ones can be produced quickly from existing IDL [2] code. A Web Tool with only a few inputs, and which calls an IDL routine written in the proper style, can be created in less than an hour; more typical Web Tools with dozens of inputs, and the need for some adaptationmore » of existing IDL code, can be working in a day or so. Efficiency is also increased for users of Web Tools because o f the familiar interface of the web browser, and not needing X-windows, accounts, passwords, etc. Web Tools were adapted for use by PPPL physicists accessing EAST data stored in MDSplus with only a few man-weeks of effort; adapting to additional sites should now be even easier. An overview of Web Tools in use on NSTX, and a list of the most useful features, is also presented.« less

Development of a web service for analysis in a distributed network.

PubMed

Jiang, Xiaoqian; Wu, Yuan; Marsolo, Keith; Ohno-Machado, Lucila

2014-01-01

We describe functional specifications and practicalities in the software development process for a web service that allows the construction of the multivariate logistic regression model, Grid Logistic Regression (GLORE), by aggregating partial estimates from distributed sites, with no exchange of patient-level data. We recently developed and published a web service for model construction and data analysis in a distributed environment. This recent paper provided an overview of the system that is useful for users, but included very few details that are relevant for biomedical informatics developers or network security personnel who may be interested in implementing this or similar systems. We focus here on how the system was conceived and implemented. We followed a two-stage development approach by first implementing the backbone system and incrementally improving the user experience through interactions with potential users during the development. Our system went through various stages such as concept proof, algorithm validation, user interface development, and system testing. We used the Zoho Project management system to track tasks and milestones. We leveraged Google Code and Apache Subversion to share code among team members, and developed an applet-servlet architecture to support the cross platform deployment. During the development process, we encountered challenges such as Information Technology (IT) infrastructure gaps and limited team experience in user-interface design. We figured out solutions as well as enabling factors to support the translation of an innovative privacy-preserving, distributed modeling technology into a working prototype. Using GLORE (a distributed model that we developed earlier) as a pilot example, we demonstrated the feasibility of building and integrating distributed modeling technology into a usable framework that can support privacy-preserving, distributed data analysis among researchers at geographically dispersed institutes.

Development of a Web Service for Analysis in a Distributed Network

PubMed Central

Jiang, Xiaoqian; Wu, Yuan; Marsolo, Keith; Ohno-Machado, Lucila

2014-01-01

Objective: We describe functional specifications and practicalities in the software development process for a web service that allows the construction of the multivariate logistic regression model, Grid Logistic Regression (GLORE), by aggregating partial estimates from distributed sites, with no exchange of patient-level data. Background: We recently developed and published a web service for model construction and data analysis in a distributed environment. This recent paper provided an overview of the system that is useful for users, but included very few details that are relevant for biomedical informatics developers or network security personnel who may be interested in implementing this or similar systems. We focus here on how the system was conceived and implemented. Methods: We followed a two-stage development approach by first implementing the backbone system and incrementally improving the user experience through interactions with potential users during the development. Our system went through various stages such as concept proof, algorithm validation, user interface development, and system testing. We used the Zoho Project management system to track tasks and milestones. We leveraged Google Code and Apache Subversion to share code among team members, and developed an applet-servlet architecture to support the cross platform deployment. Discussion: During the development process, we encountered challenges such as Information Technology (IT) infrastructure gaps and limited team experience in user-interface design. We figured out solutions as well as enabling factors to support the translation of an innovative privacy-preserving, distributed modeling technology into a working prototype. Conclusion: Using GLORE (a distributed model that we developed earlier) as a pilot example, we demonstrated the feasibility of building and integrating distributed modeling technology into a usable framework that can support privacy-preserving, distributed data analysis among researchers at geographically dispersed institutes. PMID:25848586

Climate Model Diagnostic Analyzer Web Service System

NASA Astrophysics Data System (ADS)

Lee, S.; Pan, L.; Zhai, C.; Tang, B.; Jiang, J. H.

2014-12-01

We have developed a cloud-enabled web-service system that empowers physics-based, multi-variable model performance evaluations and diagnoses through the comprehensive and synergistic use of multiple observational data, reanalysis data, and model outputs. We have developed a methodology to transform an existing science application code into a web service using a Python wrapper interface and Python web service frameworks. The web-service system, called Climate Model Diagnostic Analyzer (CMDA), currently supports (1) all the observational datasets from Obs4MIPs and a few ocean datasets from NOAA and Argo, which can serve as observation-based reference data for model evaluation, (2) many of CMIP5 model outputs covering a broad range of atmosphere, ocean, and land variables from the CMIP5 specific historical runs and AMIP runs, and (3) ECMWF reanalysis outputs for several environmental variables in order to supplement observational datasets. Analysis capabilities currently supported by CMDA are (1) the calculation of annual and seasonal means of physical variables, (2) the calculation of time evolution of the means in any specified geographical region, (3) the calculation of correlation between two variables, (4) the calculation of difference between two variables, and (5) the conditional sampling of one physical variable with respect to another variable. A web user interface is chosen for CMDA because it not only lowers the learning curve and removes the adoption barrier of the tool but also enables instantaneous use, avoiding the hassle of local software installation and environment incompatibility. CMDA will be used as an educational tool for the summer school organized by JPL's Center for Climate Science in 2014. In order to support 30+ simultaneous users during the school, we have deployed CMDA to the Amazon cloud environment. The cloud-enabled CMDA will provide each student with a virtual machine while the user interaction with the system will remain the same through web-browser interfaces. The summer school will serve as a valuable testbed for the tool development, preparing CMDA to serve its target community: Earth-science modeling and model-analysis community.

EPEPT: A web service for enhanced P-value estimation in permutation tests

PubMed Central

2011-01-01

Background In computational biology, permutation tests have become a widely used tool to assess the statistical significance of an event under investigation. However, the common way of computing the P-value, which expresses the statistical significance, requires a very large number of permutations when small (and thus interesting) P-values are to be accurately estimated. This is computationally expensive and often infeasible. Recently, we proposed an alternative estimator, which requires far fewer permutations compared to the standard empirical approach while still reliably estimating small P-values [1]. Results The proposed P-value estimator has been enriched with additional functionalities and is made available to the general community through a public website and web service, called EPEPT. This means that the EPEPT routines can be accessed not only via a website, but also programmatically using any programming language that can interact with the web. Examples of web service clients in multiple programming languages can be downloaded. Additionally, EPEPT accepts data of various common experiment types used in computational biology. For these experiment types EPEPT first computes the permutation values and then performs the P-value estimation. Finally, the source code of EPEPT can be downloaded. Conclusions Different types of users, such as biologists, bioinformaticians and software engineers, can use the method in an appropriate and simple way. Availability http://informatics.systemsbiology.net/EPEPT/ PMID:22024252

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.

Assessing uncertain human exposure to ambient air pollution using environmental models in the Web

NASA Astrophysics Data System (ADS)

Gerharz, L. E.; Pebesma, E.; Denby, B.

2012-04-01

Ambient air quality can have significant impact on human health by causing respiratory and cardio-vascular diseases. Thereby, the pollutant concentration a person is exposed to can differ considerably between individuals depending on their daily routine and movement patterns. Using a straight forward approach this exposure can be estimated by integration of individual space-time paths and spatio-temporally resolved ambient air quality data. To allow a realistic exposure assessment, it is furthermore important to consider uncertainties due to input and model errors. In this work, we present a generic, web-based approach for estimating individual exposure by integration of uncertain position and air quality information implemented as a web service. Following the Model Web initiative envisioning an infrastructure for deploying, executing and chaining environmental models as services, existing models and data sources for e.g. air quality, can be used to assess exposure. Therefore, the service needs to deal with different formats, resolutions and uncertainty representations provided by model or data services. Potential mismatch can be accounted for by transformation of uncertainties and (dis-)aggregation of data under consideration of changes in the uncertainties using components developed in the UncertWeb project. In UncertWeb, the Model Web vision is extended to an Uncertainty-enabled Model Web, where services can process and communicate uncertainties in the data and models. The propagation of uncertainty to the exposure results is quantified using Monte Carlo simulation by combining different realisations of positions and ambient concentrations. Two case studies were used to evaluate the developed exposure assessment service. In a first study, GPS tracks with a positional uncertainty of a few meters, collected in the urban area of Münster, Germany were used to assess exposure to PM10 (particulate matter smaller 10 µm). Air quality data was provided by an uncertainty-enabled air quality model system which provided realisations of concentrations per hour on a 250 m x 250 m resolved grid over Münster. The second case study uses modelled human trajectories in Rotterdam, The Netherlands. The trajectories were provided as realisations in 15 min resolution per 4 digit postal code from an activity model. Air quality estimates were provided for different pollutants as ensembles by a coupled meteorology and air quality model system on a 1 km x 1 km grid with hourly resolution. Both case studies show the successful application of the service to different resolutions and uncertainty representations.

SU-D-BRD-03: A Gateway for GPU Computing in Cancer Radiotherapy Research

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

Jia, X; Folkerts, M; Shi, F

Purpose: Graphics Processing Unit (GPU) has become increasingly important in radiotherapy. However, it is still difficult for general clinical researchers to access GPU codes developed by other researchers, and for developers to objectively benchmark their codes. Moreover, it is quite often to see repeated efforts spent on developing low-quality GPU codes. The goal of this project is to establish an infrastructure for testing GPU codes, cross comparing them, and facilitating code distributions in radiotherapy community. Methods: We developed a system called Gateway for GPU Computing in Cancer Radiotherapy Research (GCR2). A number of GPU codes developed by our group andmore » other developers can be accessed via a web interface. To use the services, researchers first upload their test data or use the standard data provided by our system. Then they can select the GPU device on which the code will be executed. Our system offers all mainstream GPU hardware for code benchmarking purpose. After the code running is complete, the system automatically summarizes and displays the computing results. We also released a SDK to allow the developers to build their own algorithm implementation and submit their binary codes to the system. The submitted code is then systematically benchmarked using a variety of GPU hardware and representative data provided by our system. The developers can also compare their codes with others and generate benchmarking reports. Results: It is found that the developed system is fully functioning. Through a user-friendly web interface, researchers are able to test various GPU codes. Developers also benefit from this platform by comprehensively benchmarking their codes on various GPU platforms and representative clinical data sets. Conclusion: We have developed an open platform allowing the clinical researchers and developers to access the GPUs and GPU codes. This development will facilitate the utilization of GPU in radiation therapy field.« less

Reactome Pengine: A web-logic API to the homo sapiens reactome.

PubMed

Neaves, Samuel R; Tsoka, Sophia; Millard, Louise A C

2018-03-30

Existing ways of accessing data from the Reactome database are limited. Either a researcher is restricted to particular queries defined by a web application programming interface (API), or they have to download the whole database. Reactome Pengine is a web service providing a logic programming based API to the human reactome. This gives researchers greater flexibility in data access than existing APIs, as users can send their own small programs (alongside queries) to Reactome Pengine. The server and an example notebook can be found at https://apps.nms.kcl.ac.uk/reactome-pengine. Source code is available at https://github.com/samwalrus/reactome-pengine and a Docker image is available at https://hub.docker.com/r/samneaves/rp4/ . samuel.neaves@kcl.ac.uk. Supplementary data are available at Bioinformatics online.

Metadata Sets for e-Government Resources: The Extended e-Government Metadata Schema (eGMS+)

NASA Astrophysics Data System (ADS)

Charalabidis, Yannis; Lampathaki, Fenareti; Askounis, Dimitris

In the dawn of the Semantic Web era, metadata appear as a key enabler that assists management of the e-Government resources related to the provision of personalized, efficient and proactive services oriented towards the real citizens’ needs. As different authorities typically use different terms to describe their resources and publish them in various e-Government Registries that may enhance the access to and delivery of governmental knowledge, but also need to communicate seamlessly at a national and pan-European level, the need for a unified e-Government metadata standard emerges. This paper presents the creation of an ontology-based extended metadata set for e-Government Resources that embraces services, documents, XML Schemas, code lists, public bodies and information systems. Such a metadata set formalizes the exchange of information between portals and registries and assists the service transformation and simplification efforts, while it can be further taken into consideration when applying Web 2.0 techniques in e-Government.

Optimizing Distribution of Pandemic Influenza Antiviral Drugs

PubMed Central

Huang, Hsin-Chan; Morton, David P.; Johnson, Gregory P.; Gutfraind, Alexander; Galvani, Alison P.; Clements, Bruce; Meyers, Lauren A.

2015-01-01

We provide a data-driven method for optimizing pharmacy-based distribution of antiviral drugs during an influenza pandemic in terms of overall access for a target population and apply it to the state of Texas, USA. We found that during the 2009 influenza pandemic, the Texas Department of State Health Services achieved an estimated statewide access of 88% (proportion of population willing to travel to the nearest dispensing point). However, access reached only 34.5% of US postal code (ZIP code) areas containing <1,000 underinsured persons. Optimized distribution networks increased expected access to 91% overall and 60% in hard-to-reach regions, and 2 or 3 major pharmacy chains achieved near maximal coverage in well-populated areas. Independent pharmacies were essential for reaching ZIP code areas containing <1,000 underinsured persons. This model was developed during a collaboration between academic researchers and public health officials and is available as a decision support tool for Texas Department of State Health Services at a Web-based interface. PMID:25625858

Tools for Interdisciplinary Data Assimilation and Sharing in Support of Hydrologic Science

NASA Astrophysics Data System (ADS)

Blodgett, D. L.; Walker, J.; Suftin, I.; Warren, M.; Kunicki, T.

2013-12-01

Information consumed and produced in hydrologic analyses is interdisciplinary and massive. These factors put a heavy information management burden on the hydrologic science community. The U.S. Geological Survey (USGS) Office of Water Information Center for Integrated Data Analytics (CIDA) seeks to assist hydrologic science investigators with all-components of their scientific data management life cycle. Ongoing data publication and software development projects will be presented demonstrating publically available data access services and manipulation tools being developed with support from two Department of the Interior initiatives. The USGS-led National Water Census seeks to provide both data and tools in support of nationally consistent water availability estimates. Newly available data include national coverages of radar-indicated precipitation, actual evapotranspiration, water use estimates aggregated by county, and South East region estimates of streamflow for 12-digit hydrologic unit code watersheds. Web services making these data available and applications to access them will be demonstrated. Web-available processing services able to provide numerous streamflow statistics for any USGS daily flow record or model result time series and other National Water Census processing tools will also be demonstrated. The National Climate Change and Wildlife Science Center is a USGS center leading DOI-funded academic global change adaptation research. It has a mission goal to ensure data used and produced by funded projects is available via web services and tools that streamline data management tasks in interdisciplinary science. For example, collections of downscaled climate projections, typically large collections of files that must be downloaded to be accessed, are being published using web services that allow access to the entire dataset via simple web-service requests and numerous processing tools. Recent progress on this front includes, data web services for Climate Model Intercomparison Phase 5 based downscaled climate projections, EPA's Integrated Climate and Land Use Scenarios projections of population and land cover metrics, and MODIS-derived land cover parameters from NASA's Land Processes Distributed Active Archive Center. These new services and ways to discover others will be presented through demonstration of a recently open-sourced project from a web-application or scripted workflow. Development and public deployment of server-based processing tools to subset and summarize these and other data is ongoing at the CIDA with partner groups such as 52 Degrees North and Unidata. The latest progress on subsetting, spatial summarization to areas of interest, and temporal summarization via common-statistical methods will be presented.

Development of Web Interfaces for Analysis Codes

NASA Astrophysics Data System (ADS)

Emoto, M.; Watanabe, T.; Funaba, H.; Murakami, S.; Nagayama, Y.; Kawahata, K.

Several codes have been developed to analyze plasma physics. However, most of them are developed to run on supercomputers. Therefore, users who typically use personal computers (PCs) find it difficult to use these codes. In order to facilitate the widespread use of these codes, a user-friendly interface is required. The authors propose Web interfaces for these codes. To demonstrate the usefulness of this approach, the authors developed Web interfaces for two analysis codes. One of them is for FIT developed by Murakami. This code is used to analyze the NBI heat deposition, etc. Because it requires electron density profiles, electron temperatures, and ion temperatures as polynomial expressions, those unfamiliar with the experiments find it difficult to use this code, especially visitors from other institutes. The second one is for visualizing the lines of force in the LHD (large helical device) developed by Watanabe. This code is used to analyze the interference caused by the lines of force resulting from the various structures installed in the vacuum vessel of the LHD. This code runs on PCs; however, it requires that the necessary parameters be edited manually. Using these Web interfaces, users can execute these codes interactively.

The new Gemini Observatory archive: a fast and low cost observatory data archive running in the cloud

NASA Astrophysics Data System (ADS)

Hirst, Paul; Cardenes, Ricardo

2016-08-01

We have developed and deployed a new data archive for the Gemini Observatory. Focused on simplicity and ease of use, the archive provides a number of powerful and novel features including automatic association of calibration data with the science data, and the ability to bookmark searches. A simple but powerful API allows programmatic search and download of data. The archive is hosted on Amazon Web Services, which provides us excellent internet connectivity and significant cost savings in both operations and development over more traditional deployment options. The code is written in python, utilizing a PostgreSQL database and Apache web server.

Enhanced functionalities for annotating and indexing clinical text with the NCBO Annotator.

PubMed

Tchechmedjiev, Andon; Abdaoui, Amine; Emonet, Vincent; Melzi, Soumia; Jonnagaddala, Jitendra; Jonquet, Clement

2018-06-01

Second use of clinical data commonly involves annotating biomedical text with terminologies and ontologies. The National Center for Biomedical Ontology Annotator is a frequently used annotation service, originally designed for biomedical data, but not very suitable for clinical text annotation. In order to add new functionalities to the NCBO Annotator without hosting or modifying the original Web service, we have designed a proxy architecture that enables seamless extensions by pre-processing of the input text and parameters, and post processing of the annotations. We have then implemented enhanced functionalities for annotating and indexing free text such as: scoring, detection of context (negation, experiencer, temporality), new output formats and coarse-grained concept recognition (with UMLS Semantic Groups). In this paper, we present the NCBO Annotator+, a Web service which incorporates these new functionalities as well as a small set of evaluation results for concept recognition and clinical context detection on two standard evaluation tasks (Clef eHealth 2017, SemEval 2014). The Annotator+ has been successfully integrated into the SIFR BioPortal platform-an implementation of NCBO BioPortal for French biomedical terminologies and ontologies-to annotate English text. A Web user interface is available for testing and ontology selection (http://bioportal.lirmm.fr/ncbo_annotatorplus); however the Annotator+ is meant to be used through the Web service application programming interface (http://services.bioportal.lirmm.fr/ncbo_annotatorplus). The code is openly available, and we also provide a Docker packaging to enable easy local deployment to process sensitive (e.g. clinical) data in-house (https://github.com/sifrproject). andon.tchechmedjiev@lirmm.fr. Supplementary data are available at Bioinformatics online.

Similarity-based prediction for Anatomical Therapeutic Chemical classification of drugs by integrating multiple data sources.

PubMed

Liu, Zhongyang; Guo, Feifei; Gu, Jiangyong; Wang, Yong; Li, Yang; Wang, Dan; Lu, Liang; Li, Dong; He, Fuchu

2015-06-01

Anatomical Therapeutic Chemical (ATC) classification system, widely applied in almost all drug utilization studies, is currently the most widely recognized classification system for drugs. Currently, new drug entries are added into the system only on users' requests, which leads to seriously incomplete drug coverage of the system, and bioinformatics prediction is helpful during this process. Here we propose a novel prediction model of drug-ATC code associations, using logistic regression to integrate multiple heterogeneous data sources including chemical structures, target proteins, gene expression, side-effects and chemical-chemical associations. The model obtains good performance for the prediction not only on ATC codes of unclassified drugs but also on new ATC codes of classified drugs assessed by cross-validation and independent test sets, and its efficacy exceeds previous methods. Further to facilitate the use, the model is developed into a user-friendly web service SPACE ( S: imilarity-based P: redictor of A: TC C: od E: ), which for each submitted compound, will give candidate ATC codes (ranked according to the decreasing probability_score predicted by the model) together with corresponding supporting evidence. This work not only contributes to knowing drugs' therapeutic, pharmacological and chemical properties, but also provides clues for drug repositioning and side-effect discovery. In addition, the construction of the prediction model also provides a general framework for similarity-based data integration which is suitable for other drug-related studies such as target, side-effect prediction etc. The web service SPACE is available at http://www.bprc.ac.cn/space. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

The price may not be right: the value of comparison shopping for prescription drugs.

PubMed

Arora, Sanjay; Sood, Neeraj; Terp, Sophie; Joyce, Geoffrey

2017-07-01

To measure variations in drug prices across and within zip codes that may reveal simple strategies to improve patients' access to prescribed medications. We compared drug prices at different types of pharmacies across and within local markets. In-store prices were compared with a Web-based service providing discount coupons for prescription medications. Prices were collected for 2 generic antibiotics because most patients have limited experience with them and are less likely to know the price ranges for them. Drug prices were obtained via telephone from 528 pharmacies in Los Angeles (LA) County, California, from July to August 2014. Online prices were collected from GoodRx, a popular Web-based service that aggregates available discounts and directly negotiates with retail outlets. Drug prices found at independent pharmacies and by using discount coupons available online were lower on average than at grocery, big-box, or chain drug stores for 2 widely prescribed antibiotics. The lowest-price prescription was offered at a grocery, big-box, or chain drug store in 6% of zip codes within the LA County area. Drug prices varied dramatically within a zip code, however, and were less expensive in lower-income areas. The average price difference within a zip code was $52 for levofloxacin and $17 for azithromycin. Price shopping for medications within a small geographic area can yield considerable cost savings for the uninsured and consumers in high-deductible health plans with high negotiated prices. Clinicians and patient advocates have an incentive to convey this information to patients to improve adherence to prescribed medicines and lower the financial burden of purchasing prescription drugs.

75 FR 384 - Event Problem Codes Web Site; Center for Devices and Radiological Health; Availability

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-05

...] Event Problem Codes Web Site; Center for Devices and Radiological Health; Availability AGENCY: Food and... the availability of a Web site where the Center for Devices and Radiological Health (CDRH) is posting... to all reporters (Sec. 803.21(b)). FDA is announcing the availability of a Web site that will make...

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

Argo_CUDA: Exhaustive GPU based approach for motif discovery in large DNA datasets.

PubMed

Vishnevsky, Oleg V; Bocharnikov, Andrey V; Kolchanov, Nikolay A

2018-02-01

The development of chromatin immunoprecipitation sequencing (ChIP-seq) technology has revolutionized the genetic analysis of the basic mechanisms underlying transcription regulation and led to accumulation of information about a huge amount of DNA sequences. There are a lot of web services which are currently available for de novo motif discovery in datasets containing information about DNA/protein binding. An enormous motif diversity makes their finding challenging. In order to avoid the difficulties, researchers use different stochastic approaches. Unfortunately, the efficiency of the motif discovery programs dramatically declines with the query set size increase. This leads to the fact that only a fraction of top "peak" ChIP-Seq segments can be analyzed or the area of analysis should be narrowed. Thus, the motif discovery in massive datasets remains a challenging issue. Argo_Compute Unified Device Architecture (CUDA) web service is designed to process the massive DNA data. It is a program for the detection of degenerate oligonucleotide motifs of fixed length written in 15-letter IUPAC code. Argo_CUDA is a full-exhaustive approach based on the high-performance GPU technologies. Compared with the existing motif discovery web services, Argo_CUDA shows good prediction quality on simulated sets. The analysis of ChIP-Seq sequences revealed the motifs which correspond to known transcription factor binding sites.

SP_Ace: Stellar Parameters And Chemical abundances Estimator

NASA Astrophysics Data System (ADS)

Boeche, C.; Grebel, E. K.

2018-05-01

SP_Ace (Stellar Parameters And Chemical abundances Estimator) estimates the stellar parameters Teff, log g, [M/H], and elemental abundances. It employs 1D stellar atmosphere models in Local Thermodynamic Equilibrium (LTE). The code is highly automated and suitable for analyzing the spectra of large spectroscopic surveys with low or medium spectral resolution (R = 2000-20 000). A web service for calculating these values with the software is also available.

Critical Infrastructure: Control Systems and the Terrorist Threat

DTIC Science & Technology

2004-01-20

Congressional Research Service ˜ The Library of Congress CRS Report for Congress Received through the CRS Web Order Code RL31534 Critical...http://www.pnl.gov/main/sectors/homeland.html]. 68 Rolf Carlson, “Sandia SCADA Program High-Security SCADA LDRD Final Report ,” Sandia Report SAND2002...and Industry Division Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the collection of information is estimated to

Critical Infrastructure: Control Systems and the Terrorist Threat

DTIC Science & Technology

2003-07-14

Congressional Research Service ˜ The Library of Congress CRS Report for Congress Received through the CRS Web Order Code RL31534 Critical...available online at [http://www.pnl.gov/main/sectors/homeland.html]. 56 Rolf Carlson, “Sandia SCADA Program High-Security SCADA LDRD Final Report ...Industry Division Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the collection of information is estimated to

Military Benefits for Former Spouses: Legislation and Policy Issues

DTIC Science & Technology

2004-12-09

Congressional Research Service ˜ The Library of Congress CRS Report for Congress Received through the CRS Web Order Code RL31663 Military Benefits ...REPORT DATE 09 DEC 2004 2. REPORT TYPE N/A 3. DATES COVERED - 4. TITLE AND SUBTITLE Military Benefits for Former Spouses: Leglislation...Military Benefits for Former Spouses: Legislation and Policy Issues Summary In 1981, the Supreme Court ruled that the former spouse of a military member

The Modern Research Data Portal: A Design Pattern for Networked, Data-Intensive Science

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

Chard, Kyle; Dart, Eli; Foster, Ian

Here we describe best practices for providing convenient, high-speed, secure access to large data via research data portals. We capture these best practices in a new design pattern, the Modern Research Data Portal, that disaggregates the traditional monolithic web-based data portal to achieve orders-of-magnitude increases in data transfer performance, support new deployment architectures that decouple control logic from data storage, and reduce development and operations costs. We introduce the design pattern; explain how it leverages high-performance Science DMZs and cloud-based data management services; review representative examples at research laboratories and universities, including both experimental facilities and supercomputer sites; describe howmore » to leverage Python APIs for authentication, authorization, data transfer, and data sharing; and use coding examples to demonstrate how these APIs can be used to implement a range of research data portal capabilities. Sample code at a companion web site, https://docs.globus.org/mrdp, provides application skeletons that readers can adapt to realize their own research data portals.« less

The Modern Research Data Portal: a design pattern for networked, data-intensive science

DOE PAGES

Chard, Kyle; Dart, Eli; Foster, Ian; ...

2018-01-15

We describe best practices for providing convenient, high-speed, secure access to large data via research data portals. Here, we capture these best practices in a new design pattern, the Modern Research Data Portal, that disaggregates the traditional monolithic web-based data portal to achieve orders-of-magnitude increases in data transfer performance, support new deployment architectures that decouple control logic from data storage, and reduce development and operations costs. We introduce the design pattern; explain how it leverages high-performance data enclaves and cloud-based data management services; review representative examples at research laboratories and universities, including both experimental facilities and supercomputer sites; describe howmore » to leverage Python APIs for authentication, authorization, data transfer, and data sharing; and use coding examples to demonstrate how these APIs can be used to implement a range of research data portal capabilities. Sample code at a companion web site,https://docs.globus.org/mrdp, provides application skeletons that readers can adapt to realize their own research data portals.« less

The Modern Research Data Portal: a design pattern for networked, data-intensive science

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

Chard, Kyle; Dart, Eli; Foster, Ian

We describe best practices for providing convenient, high-speed, secure access to large data via research data portals. Here, we capture these best practices in a new design pattern, the Modern Research Data Portal, that disaggregates the traditional monolithic web-based data portal to achieve orders-of-magnitude increases in data transfer performance, support new deployment architectures that decouple control logic from data storage, and reduce development and operations costs. We introduce the design pattern; explain how it leverages high-performance data enclaves and cloud-based data management services; review representative examples at research laboratories and universities, including both experimental facilities and supercomputer sites; describe howmore » to leverage Python APIs for authentication, authorization, data transfer, and data sharing; and use coding examples to demonstrate how these APIs can be used to implement a range of research data portal capabilities. Sample code at a companion web site,https://docs.globus.org/mrdp, provides application skeletons that readers can adapt to realize their own research data portals.« less

The International Solid Earth Research Virtual Observatory

NASA Astrophysics Data System (ADS)

Fox, G.; Pierce, M.; Rundle, J.; Donnellan, A.; Parker, J.; Granat, R.; Lyzenga, G.; McLeod, D.; Grant, L.

2004-12-01

We describe the architecture and initial implementation of the International Solid Earth Research Virtual Observatory (iSERVO). This has been prototyped within the USA as SERVOGrid and expansion is planned to Australia, China, Japan and other countries. We base our design on a globally scalable distributed "cyber-infrastructure" or Grid built around a Web Services-based approach consistent with the extended Web Service Interoperability approach. The Solid Earth Science Working Group of NASA has identified several challenges for Earth Science research. In order to investigate these, we need to couple numerical simulation codes and data mining tools to observational data sets. This observational data are now available on-line in internet-accessible forms, and the quantity of this data is expected to grow explosively over the next decade. We architect iSERVO as a loosely federated Grid of Grids with each country involved supporting a national Solid Earth Research Grid. The national Grid Operations, possibly with dedicated control centers, are linked together to support iSERVO where an International Grid control center may eventually be necessary. We address the difficult multi-administrative domain security and ownership issues by exposing capabilities as services for which the risk of abuse is minimized. We support large scale simulations within a single domain using service-hosted tools (mesh generation, data repository and sensor access, GIS, visualization). Simulations typically involve sequential or parallel machines in a single domain supported by cross-continent services. We use Web Services implement Service Oriented Architecture (SOA) using WSDL for service description and SOAP for message formats. These are augmented by UDDI, WS-Security, WS-Notification/Eventing and WS-ReliableMessaging in the WS-I+ approach. Support for the latter two capabilities will be available over the next 6 months from the NaradaBrokering messaging system. We augment these specifications with the powerful portlet architecture using WSRP and JSR168 supported by such portal containers as uPortal, WebSphere, and Apache JetSpeed2. The latter portal aggregates component user interfaces for each iSERVO service allowing flexible customization of the user interface. We exploit the portlets produced by the NSF NMI (Middleware initiative) OGCE activity. iSERVO also uses specifications from the Open Geographical Information Systems (GIS) Consortium (OGC) that defines a number of standards for modeling earth surface feature data and services for interacting with this data. The data models are expressed in the XML-based Geography Markup Language (GML), and the OGC service framework are being adapted to use the Web Service model. The SERVO prototype includes a GIS Grid that currently includes the core WMS and WFS (Map and Feature) services. We will follow the best practice in the Grid and Web Service field and will adapt our technology as appropriate. For example, we expect to support services built on WS-RF when is finalized and to make use of the database interfaces OGSA-DAI and its WS-I+ versions. Finally, we review advances in Web Service scripting (such as HPSearch) and workflow systems (such as GCF) and their applications to iSERVO.

An Automatic Web Service Composition Framework Using QoS-Based Web Service Ranking Algorithm.

PubMed

Mallayya, Deivamani; Ramachandran, Baskaran; Viswanathan, Suganya

2015-01-01

Web service has become the technology of choice for service oriented computing to meet the interoperability demands in web applications. In the Internet era, the exponential addition of web services nominates the "quality of service" as essential parameter in discriminating the web services. In this paper, a user preference based web service ranking (UPWSR) algorithm is proposed to rank web services based on user preferences and QoS aspect of the web service. When the user's request cannot be fulfilled by a single atomic service, several existing services should be composed and delivered as a composition. The proposed framework allows the user to specify the local and global constraints for composite web services which improves flexibility. UPWSR algorithm identifies best fit services for each task in the user request and, by choosing the number of candidate services for each task, reduces the time to generate the composition plans. To tackle the problem of web service composition, QoS aware automatic web service composition (QAWSC) algorithm proposed in this paper is based on the QoS aspects of the web services and user preferences. The proposed framework allows user to provide feedback about the composite service which improves the reputation of the services.

Flexible Web services integration: a novel personalised social approach

NASA Astrophysics Data System (ADS)

Metrouh, Abdelmalek; Mokhati, Farid

2018-05-01

Dynamic composition or integration remains one of the key objectives of Web services technology. This paper aims to propose an innovative approach of dynamic Web services composition based on functional and non-functional attributes and individual preferences. In this approach, social networks of Web services are used to maintain interactions between Web services in order to select and compose Web services that are more tightly related to user's preferences. We use the concept of Web services community in a social network of Web services to reduce considerably their search space. These communities are created by the direct involvement of Web services providers.

An Automatic Web Service Composition Framework Using QoS-Based Web Service Ranking Algorithm

PubMed Central

Mallayya, Deivamani; Ramachandran, Baskaran; Viswanathan, Suganya

2015-01-01

Web service has become the technology of choice for service oriented computing to meet the interoperability demands in web applications. In the Internet era, the exponential addition of web services nominates the “quality of service” as essential parameter in discriminating the web services. In this paper, a user preference based web service ranking (UPWSR) algorithm is proposed to rank web services based on user preferences and QoS aspect of the web service. When the user's request cannot be fulfilled by a single atomic service, several existing services should be composed and delivered as a composition. The proposed framework allows the user to specify the local and global constraints for composite web services which improves flexibility. UPWSR algorithm identifies best fit services for each task in the user request and, by choosing the number of candidate services for each task, reduces the time to generate the composition plans. To tackle the problem of web service composition, QoS aware automatic web service composition (QAWSC) algorithm proposed in this paper is based on the QoS aspects of the web services and user preferences. The proposed framework allows user to provide feedback about the composite service which improves the reputation of the services. PMID:26504894

A Different Web-Based Geocoding Service Using Fuzzy Techniques

NASA Astrophysics Data System (ADS)

Pahlavani, P.; Abbaspour, R. A.; Zare Zadiny, A.

2015-12-01

Geocoding - the process of finding position based on descriptive data such as address or postal code - is considered as one of the most commonly used spatial analyses. Many online map providers such as Google Maps, Bing Maps and Yahoo Maps present geocoding as one of their basic capabilities. Despite the diversity of geocoding services, users usually face some limitations when they use available online geocoding services. In existing geocoding services, proximity and nearness concept is not modelled appropriately as well as these services search address only by address matching based on descriptive data. In addition there are also some limitations in display searching results. Resolving these limitations can enhance efficiency of the existing geocoding services. This paper proposes the idea of integrating fuzzy technique with geocoding process to resolve these limitations. In order to implement the proposed method, a web-based system is designed. In proposed method, nearness to places is defined by fuzzy membership functions and multiple fuzzy distance maps are created. Then these fuzzy distance maps are integrated using fuzzy overlay technique for obtain the results. Proposed methods provides different capabilities for users such as ability to search multi-part addresses, searching places based on their location, non-point representation of results as well as displaying search results based on their priority.

G2S: a web-service for annotating genomic variants on 3D protein structures.

PubMed

Wang, Juexin; Sheridan, Robert; Sumer, S Onur; Schultz, Nikolaus; Xu, Dong; Gao, Jianjiong

2018-06-01

Accurately mapping and annotating genomic locations on 3D protein structures is a key step in structure-based analysis of genomic variants detected by recent large-scale sequencing efforts. There are several mapping resources currently available, but none of them provides a web API (Application Programming Interface) that supports programmatic access. We present G2S, a real-time web API that provides automated mapping of genomic variants on 3D protein structures. G2S can align genomic locations of variants, protein locations, or protein sequences to protein structures and retrieve the mapped residues from structures. G2S API uses REST-inspired design and it can be used by various clients such as web browsers, command terminals, programming languages and other bioinformatics tools for bringing 3D structures into genomic variant analysis. The webserver and source codes are freely available at https://g2s.genomenexus.org. g2s@genomenexus.org. Supplementary data are available at Bioinformatics online.

Menu-driven cloud computing and resource sharing for R and Bioconductor.

PubMed

Bolouri, Hamid; Dulepet, Rajiv; Angerman, Michael

2011-08-15

We report CRdata.org, a cloud-based, free, open-source web server for running analyses and sharing data and R scripts with others. In addition to using the free, public service, CRdata users can launch their own private Amazon Elastic Computing Cloud (EC2) nodes and store private data and scripts on Amazon's Simple Storage Service (S3) with user-controlled access rights. All CRdata services are provided via point-and-click menus. CRdata is open-source and free under the permissive MIT License (opensource.org/licenses/mit-license.php). The source code is in Ruby (ruby-lang.org/en/) and available at: github.com/seerdata/crdata. hbolouri@fhcrc.org.

Proposal for a Web Encoding Service (wes) for Spatial Data Transactio

NASA Astrophysics Data System (ADS)

Siew, C. B.; Peters, S.; Rahman, A. A.

2015-10-01

Web services utilizations in Spatial Data Infrastructure (SDI) have been well established and standardized by Open Geospatial Consortium (OGC). Similar web services for 3D SDI are also being established in recent years, with extended capabilities to handle 3D spatial data. The increasing popularity of using City Geographic Markup Language (CityGML) for 3D city modelling applications leads to the needs for large spatial data handling for data delivery. This paper revisits the available web services in OGC Web Services (OWS), and propose the background concepts and requirements for encoding spatial data via Web Encoding Service (WES). Furthermore, the paper discusses the data flow of the encoder within web service, e.g. possible integration with Web Processing Service (WPS) or Web 3D Services (W3DS). The integration with available web service could be extended to other available web services for efficient handling of spatial data, especially 3D spatial data.

Casemix Funding Optimisation: Working Together to Make the Most of Every Episode.

PubMed

Uzkuraitis, Carly; Hastings, Karen; Torney, Belinda

2010-10-01

Eastern Health, a large public Victorian Healthcare network, conducted a WIES optimisation audit across the casemix-funded sites for separations in the 2009/2010 financial year. The audit was conducted using existing staff resources and resulted in a significant increase in casemix funding at a minimal cost. The audit showcased the skill set of existing staff and resulted in enormous benefits to the coding and casemix team by demonstrating the value of the combination of skills that makes clinical coders unique. The development of an internal web-based application allowed accurate and timely reporting of the audit results, providing the basis for a restructure of the coding and casemix service, along with approval for additional staffing resources and inclusion of a regular auditing program to focus on the creation of high quality data for research, health services management and financial reimbursement.

Publicizing Your Web Resources for Maximum Exposure.

ERIC Educational Resources Information Center

Smith, Kerry J.

2001-01-01

Offers advice to librarians for marketing their Web sites on Internet search engines. Advises against relying solely on spiders and recommends adding metadata to the source code and delivering that information directly to the search engines. Gives an overview of metadata and typical coding for meta tags. Includes Web addresses for a number of…

Server-Side Includes Made Simple.

ERIC Educational Resources Information Center

Fagan, Jody Condit

2002-01-01

Describes server-side include (SSI) codes which allow Webmasters to insert content into Web pages without programming knowledge. Explains how to enable the codes on a Web server, provides a step-by-step process for implementing them, discusses tags and syntax errors, and includes examples of their use on the Web site for Southern Illinois…

Dynamic selection mechanism for quality of service aware web services

NASA Astrophysics Data System (ADS)

D'Mello, Demian Antony; Ananthanarayana, V. S.

2010-02-01

A web service is an interface of the software component that can be accessed by standard Internet protocols. The web service technology enables an application to application communication and interoperability. The increasing number of web service providers throughout the globe have produced numerous web services providing the same or similar functionality. This necessitates the use of tools and techniques to search the suitable services available over the Web. UDDI (universal description, discovery and integration) is the first initiative to find the suitable web services based on the requester's functional demands. However, the requester's requirements may also include non-functional aspects like quality of service (QoS). In this paper, the authors define a QoS model for QoS aware and business driven web service publishing and selection. The authors propose a QoS requirement format for the requesters, to specify their complex demands on QoS for the web service selection. The authors define a tree structure called quality constraint tree (QCT) to represent the requester's variety of requirements on QoS properties having varied preferences. The paper proposes a QoS broker based architecture for web service selection, which facilitates the requesters to specify their QoS requirements to select qualitatively optimal web service. A web service selection algorithm is presented, which ranks the functionally similar web services based on the degree of satisfaction of the requester's QoS requirements and preferences. The paper defines web service provider qualities to distinguish qualitatively competitive web services. The paper also presents the modelling and selection mechanism for the requester's alternative constraints defined on the QoS. The authors implement the QoS broker based system to prove the correctness of the proposed web service selection mechanism.

Second Generation Weather Impacts Decision Aid Applications and Web Services Overview

DTIC Science & Technology

2013-07-01

ABSTRACT Unclassified c . THIS PAGE Unclassified 19b. TELEPHONE NUMBER (Include area code) (575) 678-0634 Standard Form 298 (Rev. 8/98...Chesley, C . H.; Spillane, A. R.; Eure, S. L.; Shaw, P. J. Engineering Plan of the Integrated Weather Effects Decision Aids (IWEDA) Software Program...Planning Tool. Proceedings of the 1992 Battlefield Atmospherics Conference, 1992; pp. 501−509. 6. Chesley, C . H.; Johnson, J. S.; Maunz, W. G.; Spillane, A

Journalists’ Privilege to Withhold Information in Judicial and Other Proceedings: State Shield Statutes

DTIC Science & Technology

2005-03-08

Congressional Research Service ˜ The Library of Congress CRS Report for Congress Received through the CRS Web Order Code RL32806 Journalists ...currently valid OMB control number. 1. REPORT DATE 08 MAR 2005 2. REPORT TYPE N/A 3. DATES COVERED - 4. TITLE AND SUBTITLE Journalists ...State Shield Statutes Summary Absent a statutory or constitutional recognition of journalistic privilege, a reporter may be compelled to testify in legal

Mobile Code: The Future of the Internet

DTIC Science & Technology

1999-01-01

code ( mobile agents) to multiple proxies or servers " Customization " (e.g., re-formatting, filtering, metasearch) Information overload Diversified... Mobile code is necessary, rather than client-side code, since many customization features (such as information monitoring) do not work if the...economic foundation for Web sites, many Web sites earn money solely from advertisements . If these sites allow mobile agents to easily access the content

Incorporating Web 2.0 Technologies from an Organizational Perspective

NASA Astrophysics Data System (ADS)

Owens, R.

2009-12-01

The Arctic Research Consortium of the United States (ARCUS) provides support for the organization, facilitation, and dissemination of online educational and scientific materials and information to a wide range of stakeholders. ARCUS is currently weaving the fabric of Web 2.0 technologies—web development featuring interactive information sharing and user-centered design—into its structure, both as a tool for information management and for educational outreach. The importance of planning, developing, and maintaining a cohesive online platform in order to integrate data storage and dissemination will be discussed in this presentation, as well as some specific open source technologies and tools currently available, including: ○ Content Management: Any system set up to manage the content of web sites and services. Drupal is a content management system, built in a modular fashion allowing for a powerful set of features including, but not limited to weblogs, forums, event calendars, polling, and more. ○ Faceted Search: Combined with full text indexing, faceted searching allows site visitors to locate information quickly and then provides a set of 'filters' with which to narrow the search results. Apache Solr is a search server with a web-services like API (Application programming interface) that has built in support for faceted searching. ○ Semantic Web: The semantic web refers to the ongoing evolution of the World Wide Web as it begins to incorporate semantic components, which aid in processing requests. OpenCalais is a web service that uses natural language processing, along with other methods, in order to extract meaningful 'tags' from your content. This metadata can then be used to connect people, places, and things throughout your website, enriching the surfing experience for the end user. ○ Web Widgets: A web widget is a portable 'piece of code' that can be embedded easily into web pages by an end user. Timeline is a widget developed as part of the SIMILE project at MIT (Massachusetts Institute of Technology) for displaying time-based events in a clean, horizontal timeline display. Numerous standards, applications, and 3rd party integration services are also available for use in today's Web 2.0 environment. In addition to a cohesive online platform, the following tools can improve networking, information sharing, and increased scientific and educational collaboration: ○ Facebook (Fan pages, social networking, etc) ○ Twitter/Twitterfeed (Automatic updates in 3 steps) ○ Mobify.me (Mobile web) ○ Wimba, Adobe Connect, etc (real time conferencing) Increasingly, the scientific community is being asked to share data and information within and outside disciplines, with K-12 students, and with members of the public and policy-makers. Web 2.0 technologies can easily be set up and utilized to share data and other information to specific audiences in real time, and their simplicity ensures their increasing use by the science community in years to come.

Rolling Deck to Repository (R2R): Big Data and Standard Services for the Fleet Community

NASA Astrophysics Data System (ADS)

Arko, R. A.; Carbotte, S. M.; Chandler, C. L.; Smith, S. R.; Stocks, K. I.

2014-12-01

The Rolling Deck to Repository (R2R; http://rvdata.us/) program curates underway environmental sensor data from the U.S. academic oceanographic research fleet, ensuring data sets are routinely and consistently documented, preserved in long-term archives, and disseminated to the science community. Currently 25 in-service vessels contribute 7 terabytes of data to R2R each year, acquired from a full suite of geophysical, oceanographic, meteorological, and navigational sensors on over 400 cruises worldwide. To accommodate this large volume and variety of data, R2R has developed highly efficient stewardship procedures. These include scripted "break out" of cruise data packages from each vessel based on standard filename and directory patterns; automated harvest of cruise metadata from the UNOLS Office via Web Services and from OpenXML-based forms submitted by vessel operators; scripted quality assessment routines that calculate statistical summaries and standard ratings for selected data types; adoption of community-standard controlled vocabularies for vessel codes, instrument types, etc, provided by the NERC Vocabulary Server, in lieu of maintaining custom local term lists; and a standard package structure based on the IETF BagIt format for delivering data to long-term archives. Documentation and standard post-field products, including quality-controlled shiptrack navigation data for every cruise, are published in multiple services and formats to satisfy a diverse range of clients. These include Catalog Service for Web (CSW), GeoRSS, and OAI-PMH discovery services via a GeoNetwork portal; OGC Web Map and Feature Services for GIS clients; a citable Digital Object Identifier (DOI) for each dataset; ISO 19115-2 standard geospatial metadata records suitable for submission to long-term archives as well as the POGO global catalog; and Linked Open Data resources with a SPARQL query endpoint for Semantic Web clients. R2R participates in initiatives such as the Ocean Data Interoperability Platform (ODIP) and the NSF EarthCube OceanLink project to promote community-standard formats, vocabularies, and services among ocean data providers.

On transform coding tools under development for VP10

NASA Astrophysics Data System (ADS)

Parker, Sarah; Chen, Yue; Han, Jingning; Liu, Zoe; Mukherjee, Debargha; Su, Hui; Wang, Yongzhe; Bankoski, Jim; Li, Shunyao

2016-09-01

Google started the WebM Project in 2010 to develop open source, royaltyfree video codecs designed specifically for media on the Web. The second generation codec released by the WebM project, VP9, is currently served by YouTube, and enjoys billions of views per day. Realizing the need for even greater compression efficiency to cope with the growing demand for video on the web, the WebM team embarked on an ambitious project to develop a next edition codec, VP10, that achieves at least a generational improvement in coding efficiency over VP9. Starting from VP9, a set of new experimental coding tools have already been added to VP10 to achieve decent coding gains. Subsequently, Google joined a consortium of major tech companies called the Alliance for Open Media to jointly develop a new codec AV1. As a result, the VP10 effort is largely expected to merge with AV1. In this paper, we focus primarily on new tools in VP10 that improve coding of the prediction residue using transform coding techniques. Specifically, we describe tools that increase the flexibility of available transforms, allowing the codec to handle a more diverse range or residue structures. Results are presented on a standard test set.

Biographer: web-based editing and rendering of SBGN compliant biochemical networks.

PubMed

Krause, Falko; Schulz, Marvin; Ripkens, Ben; Flöttmann, Max; Krantz, Marcus; Klipp, Edda; Handorf, Thomas

2013-06-01

The rapid accumulation of knowledge in the field of Systems Biology during the past years requires advanced, but simple-to-use, methods for the visualization of information in a structured and easily comprehensible manner. We have developed biographer, a web-based renderer and editor for reaction networks, which can be integrated as a library into tools dealing with network-related information. Our software enables visualizations based on the emerging standard Systems Biology Graphical Notation. It is able to import networks encoded in various formats such as SBML, SBGN-ML and jSBGN, a custom lightweight exchange format. The core package is implemented in HTML5, CSS and JavaScript and can be used within any kind of web-based project. It features interactive graph-editing tools and automatic graph layout algorithms. In addition, we provide a standalone graph editor and a web server, which contains enhanced features like web services for the import and export of models and visualizations in different formats. The biographer tool can be used at and downloaded from the web page http://biographer.biologie.hu-berlin.de/. The different software packages, including a server-independent version as well as a web server for Windows and Linux based systems, are available at http://code.google.com/p/biographer/ under the open-source license LGPL

OntologyWidget – a reusable, embeddable widget for easily locating ontology terms

PubMed Central

Beauheim, Catherine C; Wymore, Farrell; Nitzberg, Michael; Zachariah, Zachariah K; Jin, Heng; Skene, JH Pate; Ball, Catherine A; Sherlock, Gavin

2007-01-01

Background Biomedical ontologies are being widely used to annotate biological data in a computer-accessible, consistent and well-defined manner. However, due to their size and complexity, annotating data with appropriate terms from an ontology is often challenging for experts and non-experts alike, because there exist few tools that allow one to quickly find relevant ontology terms to easily populate a web form. Results We have produced a tool, OntologyWidget, which allows users to rapidly search for and browse ontology terms. OntologyWidget can easily be embedded in other web-based applications. OntologyWidget is written using AJAX (Asynchronous JavaScript and XML) and has two related elements. The first is a dynamic auto-complete ontology search feature. As a user enters characters into the search box, the appropriate ontology is queried remotely for terms that match the typed-in text, and the query results populate a drop-down list with all potential matches. Upon selection of a term from the list, the user can locate this term within a generic and dynamic ontology browser, which comprises the second element of the tool. The ontology browser shows the paths from a selected term to the root as well as parent/child tree hierarchies. We have implemented web services at the Stanford Microarray Database (SMD), which provide the OntologyWidget with access to over 40 ontologies from the Open Biological Ontology (OBO) website [1]. Each ontology is updated weekly. Adopters of the OntologyWidget can either use SMD's web services, or elect to rely on their own. Deploying the OntologyWidget can be accomplished in three simple steps: (1) install Apache Tomcat [2] on one's web server, (2) download and install the OntologyWidget servlet stub that provides access to the SMD ontology web services, and (3) create an html (HyperText Markup Language) file that refers to the OntologyWidget using a simple, well-defined format. Conclusion We have developed OntologyWidget, an easy-to-use ontology search and display tool that can be used on any web page by creating a simple html description. OntologyWidget provides a rapid auto-complete search function paired with an interactive tree display. We have developed a web service layer that communicates between the web page interface and a database of ontology terms. We currently store 40 of the ontologies from the OBO website [1], as well as a several others. These ontologies are automatically updated on a weekly basis. OntologyWidget can be used in any web-based application to take advantage of the ontologies we provide via web services or any other ontology that is provided elsewhere in the correct format. The full source code for the JavaScript and description of the OntologyWidget is available from . PMID:17854506

OntologyWidget - a reusable, embeddable widget for easily locating ontology terms.

PubMed

Beauheim, Catherine C; Wymore, Farrell; Nitzberg, Michael; Zachariah, Zachariah K; Jin, Heng; Skene, J H Pate; Ball, Catherine A; Sherlock, Gavin

2007-09-13

Biomedical ontologies are being widely used to annotate biological data in a computer-accessible, consistent and well-defined manner. However, due to their size and complexity, annotating data with appropriate terms from an ontology is often challenging for experts and non-experts alike, because there exist few tools that allow one to quickly find relevant ontology terms to easily populate a web form. We have produced a tool, OntologyWidget, which allows users to rapidly search for and browse ontology terms. OntologyWidget can easily be embedded in other web-based applications. OntologyWidget is written using AJAX (Asynchronous JavaScript and XML) and has two related elements. The first is a dynamic auto-complete ontology search feature. As a user enters characters into the search box, the appropriate ontology is queried remotely for terms that match the typed-in text, and the query results populate a drop-down list with all potential matches. Upon selection of a term from the list, the user can locate this term within a generic and dynamic ontology browser, which comprises the second element of the tool. The ontology browser shows the paths from a selected term to the root as well as parent/child tree hierarchies. We have implemented web services at the Stanford Microarray Database (SMD), which provide the OntologyWidget with access to over 40 ontologies from the Open Biological Ontology (OBO) website 1. Each ontology is updated weekly. Adopters of the OntologyWidget can either use SMD's web services, or elect to rely on their own. Deploying the OntologyWidget can be accomplished in three simple steps: (1) install Apache Tomcat 2 on one's web server, (2) download and install the OntologyWidget servlet stub that provides access to the SMD ontology web services, and (3) create an html (HyperText Markup Language) file that refers to the OntologyWidget using a simple, well-defined format. We have developed OntologyWidget, an easy-to-use ontology search and display tool that can be used on any web page by creating a simple html description. OntologyWidget provides a rapid auto-complete search function paired with an interactive tree display. We have developed a web service layer that communicates between the web page interface and a database of ontology terms. We currently store 40 of the ontologies from the OBO website 1, as well as a several others. These ontologies are automatically updated on a weekly basis. OntologyWidget can be used in any web-based application to take advantage of the ontologies we provide via web services or any other ontology that is provided elsewhere in the correct format. The full source code for the JavaScript and description of the OntologyWidget is available from http://smd.stanford.edu/ontologyWidget/.

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.

MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services.

PubMed

Pratt, Brian; Howbert, J Jeffry; Tasman, Natalie I; Nilsson, Erik J

2012-01-01

MR-Tandem adapts the popular X!Tandem peptide search engine to work with Hadoop MapReduce for reliable parallel execution of large searches. MR-Tandem runs on any Hadoop cluster but offers special support for Amazon Web Services for creating inexpensive on-demand Hadoop clusters, enabling search volumes that might not otherwise be feasible with the compute resources a researcher has at hand. MR-Tandem is designed to drop in wherever X!Tandem is already in use and requires no modification to existing X!Tandem parameter files, and only minimal modification to X!Tandem-based workflows. MR-Tandem is implemented as a lightly modified X!Tandem C++ executable and a Python script that drives Hadoop clusters including Amazon Web Services (AWS) Elastic Map Reduce (EMR), using the modified X!Tandem program as a Hadoop Streaming mapper and reducer. The modified X!Tandem C++ source code is Artistic licensed, supports pluggable scoring, and is available as part of the Sashimi project at http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/extern/xtandem/. The MR-Tandem Python script is Apache licensed and available as part of the Insilicos Cloud Army project at http://ica.svn.sourceforge.net/viewvc/ica/trunk/mr-tandem/. Full documentation and a windows installer that configures MR-Tandem, Python and all necessary packages are available at this same URL. brian.pratt@insilicos.com

[Random Variable Read Me File

NASA Technical Reports Server (NTRS)

Teubert, Christopher; Sankararaman, Shankar; Cullo, Aiden

2017-01-01

Readme for the Random Variable Toolbox usable manner. is a Web-based Git version control repository hosting service. It is mostly used for computer code. It offers all of the distributed version control and source code management (SCM) functionality of Git as well as adding its own features. It provides access control and several collaboration features such as bug tracking, feature requests, task management, and wikis for every project.[3] GitHub offers both plans for private and free repositories on the same account[4] which are commonly used to host open-source software projects.[5] As of April 2017, GitHub reports having almost 20 million users and 57 million repositories,[6] making it the largest host of source code in the world.[7] GitHub has a mascot called Octocat, a cat with five tentacles and a human-like face

flexCloud: Deployment of the FLEXPART Atmospheric Transport Model as a Cloud SaaS Environment

NASA Astrophysics Data System (ADS)

Morton, Don; Arnold, Dèlia

2014-05-01

FLEXPART (FLEXible PARTicle dispersion model) is a Lagrangian transport and dispersion model used by a growing international community. We have used it to simulate and forecast the atmospheric transport of wildfire smoke, volcanic ash and radionuclides. Additionally, FLEXPART may be run in backwards mode to provide information for the determination of emission sources such as nuclear emissions and greenhouse gases. This open source software is distributed in source code form, and has several compiler and library dependencies that users need to address. Although well-documented, getting it compiled, set up, running, and post-processed is often tedious, making it difficult for the inexperienced user. Our interest is in moving scientific modeling and simulation activities from site-specific clusters and supercomputers to a cloud model as a service paradigm. Choosing FLEXPART for our prototyping, our vision is to construct customised IaaS images containing fully-compiled and configured FLEXPART codes, including pre-processing, execution and postprocessing components. In addition, with the inclusion of a small web server in the image, we introduce a web-accessible graphical user interface that drives the system. A further initiative being pursued is the deployment of multiple, simultaneous FLEXPART ensembles in the cloud. A single front-end web interface is used to define the ensemble members, and separate cloud instances are launched, on-demand, to run the individual models and to conglomerate the outputs into a unified display. The outcome of this work is a Software as a Service (Saas) deployment whereby the details of the underlying modeling systems are hidden, allowing modelers to perform their science activities without the burden of considering implementation details.

DNA barcode goes two-dimensions: DNA QR code web server.

PubMed

Liu, Chang; Shi, Linchun; Xu, Xiaolan; Li, Huan; Xing, Hang; Liang, Dong; Jiang, Kun; Pang, Xiaohui; Song, Jingyuan; Chen, Shilin

2012-01-01

The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, "DNA barcode" actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three different types of one-dimensional and ten two-dimensional barcode symbologies were compared based on different criteria, such as coding capacity, compression efficiency, and error detection ability. The quick response (QR) code was found to have the largest coding capacity and relatively high compression ratio. To facilitate the further usage of QR code-based DNA barcodes, a web server was developed and is accessible at http://qrfordna.dnsalias.org. The web server allows users to retrieve the QR code for a species of interests, convert a DNA sequence to and from a QR code, and perform species identification based on local and global sequence similarities. In summary, the first comprehensive evaluation of various barcode symbologies has been carried out. The QR code has been found to be the most appropriate symbology for DNA barcode sequences. A web server has also been constructed to allow biologists to utilize QR codes in practical DNA barcoding applications.

Personalization of Rule-based Web Services.

PubMed

Choi, Okkyung; Han, Sang Yong

2008-04-04

Nowadays Web users have clearly expressed their wishes to receive personalized services directly. Personalization is the way to tailor services directly to the immediate requirements of the user. However, the current Web Services System does not provide any features supporting this such as consideration of personalization of services and intelligent matchmaking. In this research a flexible, personalized Rule-based Web Services System to address these problems and to enable efficient search, discovery and construction across general Web documents and Semantic Web documents in a Web Services System is proposed. This system utilizes matchmaking among service requesters', service providers' and users' preferences using a Rule-based Search Method, and subsequently ranks search results. A prototype of efficient Web Services search and construction for the suggested system is developed based on the current work.

Moving code - Sharing geoprocessing logic on the Web

NASA Astrophysics Data System (ADS)

Müller, Matthias; Bernard, Lars; Kadner, Daniel

2013-09-01

Efficient data processing is a long-standing challenge in remote sensing. Effective and efficient algorithms are required for product generation in ground processing systems, event-based or on-demand analysis, environmental monitoring, and data mining. Furthermore, the increasing number of survey missions and the exponentially growing data volume in recent years have created demand for better software reuse as well as an efficient use of scalable processing infrastructures. Solutions that address both demands simultaneously have begun to slowly appear, but they seldom consider the possibility to coordinate development and maintenance efforts across different institutions, community projects, and software vendors. This paper presents a new approach to share, reuse, and possibly standardise geoprocessing logic in the field of remote sensing. Drawing from the principles of service-oriented design and distributed processing, this paper introduces moving-code packages as self-describing software components that contain algorithmic code and machine-readable descriptions of the provided functionality, platform, and infrastructure, as well as basic information about exploitation rights. Furthermore, the paper presents a lean publishing mechanism by which to distribute these packages on the Web and to integrate them in different processing environments ranging from monolithic workstations to elastic computational environments or "clouds". The paper concludes with an outlook toward community repositories for reusable geoprocessing logic and their possible impact on data-driven science in general.

The Exon-Florio National Security Test for Foreign Investment

DTIC Science & Technology

2006-03-15

Congressional Research Service ˜ The Library of Congress CRS Report for Congress Received through the CRS Web Order Code RL33312 The Exon- Florio ...number. 1. REPORT DATE 15 MAR 2006 2. REPORT TYPE N/A 3. DATES COVERED - 4. TITLE AND SUBTITLE The Exon- Florio National Security Test for...Z39-18 The Exon- Florio National Security Test for Foreign Investment Summary The proposed acquisitions of major operations in six major U.S. ports by

Distributed spatial information integration based on web service

NASA Astrophysics Data System (ADS)

Tong, Hengjian; Zhang, Yun; Shao, Zhenfeng

2008-10-01

Spatial information systems and spatial information in different geographic locations usually belong to different organizations. They are distributed and often heterogeneous and independent from each other. This leads to the fact that many isolated spatial information islands are formed, reducing the efficiency of information utilization. In order to address this issue, we present a method for effective spatial information integration based on web service. The method applies asynchronous invocation of web service and dynamic invocation of web service to implement distributed, parallel execution of web map services. All isolated information islands are connected by the dispatcher of web service and its registration database to form a uniform collaborative system. According to the web service registration database, the dispatcher of web services can dynamically invoke each web map service through an asynchronous delegating mechanism. All of the web map services can be executed at the same time. When each web map service is done, an image will be returned to the dispatcher. After all of the web services are done, all images are transparently overlaid together in the dispatcher. Thus, users can browse and analyze the integrated spatial information. Experiments demonstrate that the utilization rate of spatial information resources is significantly raised thought the proposed method of distributed spatial information integration.

Distributed spatial information integration based on web service

NASA Astrophysics Data System (ADS)

Tong, Hengjian; Zhang, Yun; Shao, Zhenfeng

2009-10-01

Spatial information systems and spatial information in different geographic locations usually belong to different organizations. They are distributed and often heterogeneous and independent from each other. This leads to the fact that many isolated spatial information islands are formed, reducing the efficiency of information utilization. In order to address this issue, we present a method for effective spatial information integration based on web service. The method applies asynchronous invocation of web service and dynamic invocation of web service to implement distributed, parallel execution of web map services. All isolated information islands are connected by the dispatcher of web service and its registration database to form a uniform collaborative system. According to the web service registration database, the dispatcher of web services can dynamically invoke each web map service through an asynchronous delegating mechanism. All of the web map services can be executed at the same time. When each web map service is done, an image will be returned to the dispatcher. After all of the web services are done, all images are transparently overlaid together in the dispatcher. Thus, users can browse and analyze the integrated spatial information. Experiments demonstrate that the utilization rate of spatial information resources is significantly raised thought the proposed method of distributed spatial information integration.

Menu-driven cloud computing and resource sharing for R and Bioconductor

PubMed Central

Bolouri, Hamid; Angerman, Michael

2011-01-01

Summary: We report CRdata.org, a cloud-based, free, open-source web server for running analyses and sharing data and R scripts with others. In addition to using the free, public service, CRdata users can launch their own private Amazon Elastic Computing Cloud (EC2) nodes and store private data and scripts on Amazon's Simple Storage Service (S3) with user-controlled access rights. All CRdata services are provided via point-and-click menus. Availability and Implementation: CRdata is open-source and free under the permissive MIT License (opensource.org/licenses/mit-license.php). The source code is in Ruby (ruby-lang.org/en/) and available at: github.com/seerdata/crdata. Contact: hbolouri@fhcrc.org PMID:21685055

An overview of new video coding tools under consideration for VP10: the successor to VP9

NASA Astrophysics Data System (ADS)

Mukherjee, Debargha; Su, Hui; Bankoski, James; Converse, Alex; Han, Jingning; Liu, Zoe; Xu, Yaowu

2015-09-01

Google started an opensource project, entitled the WebM Project, in 2010 to develop royaltyfree video codecs for the web. The present generation codec developed in the WebM project called VP9 was finalized in mid2013 and is currently being served extensively by YouTube, resulting in billions of views per day. Even though adoption of VP9 outside Google is still in its infancy, the WebM project has already embarked on an ambitious project to develop a next edition codec VP10 that achieves at least a generational bitrate reduction over the current generation codec VP9. Although the project is still in early stages, a set of new experimental coding tools have already been added to baseline VP9 to achieve modest coding gains over a large enough test set. This paper provides a technical overview of these coding tools.

Providing Multi-Page Data Extraction Services with XWRAPComposer

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

Liu, Ling; Zhang, Jianjun; Han, Wei

2008-04-30

Dynamic Web data sources – sometimes known collectively as the Deep Web – increase the utility of the Web by providing intuitive access to data repositories anywhere that Web access is available. Deep Web services provide access to real-time information, like entertainment event listings, or present a Web interface to large databases or other data repositories. Recent studies suggest that the size and growth rate of the dynamic Web greatly exceed that of the static Web, yet dynamic content is often ignored by existing search engine indexers owing to the technical challenges that arise when attempting to search the Deepmore » Web. To address these challenges, we present DYNABOT, a service-centric crawler for discovering and clustering Deep Web sources offering dynamic content. DYNABOT has three unique characteristics. First, DYNABOT utilizes a service class model of the Web implemented through the construction of service class descriptions (SCDs). Second, DYNABOT employs a modular, self-tuning system architecture for focused crawling of the Deep Web using service class descriptions. Third, DYNABOT incorporates methods and algorithms for efficient probing of the Deep Web and for discovering and clustering Deep Web sources and services through SCD-based service matching analysis. Our experimental results demonstrate the effectiveness of the service class discovery, probing, and matching algorithms and suggest techniques for efficiently managing service discovery in the face of the immense scale of the Deep Web.« less

An Automated End-To Multi-Agent Qos Based Architecture for Selection of Geospatial Web Services

NASA Astrophysics Data System (ADS)

Shah, M.; Verma, Y.; Nandakumar, R.

2012-07-01

Over the past decade, Service-Oriented Architecture (SOA) and Web services have gained wide popularity and acceptance from researchers and industries all over the world. SOA makes it easy to build business applications with common services, and it provides like: reduced integration expense, better asset reuse, higher business agility, and reduction of business risk. Building of framework for acquiring useful geospatial information for potential users is a crucial problem faced by the GIS domain. Geospatial Web services solve this problem. With the help of web service technology, geospatial web services can provide useful geospatial information to potential users in a better way than traditional geographic information system (GIS). A geospatial Web service is a modular application designed to enable the discovery, access, and chaining of geospatial information and services across the web that are often both computation and data-intensive that involve diverse sources of data and complex processing functions. With the proliferation of web services published over the internet, multiple web services may provide similar functionality, but with different non-functional properties. Thus, Quality of Service (QoS) offers a metric to differentiate the services and their service providers. In a quality-driven selection of web services, it is important to consider non-functional properties of the web service so as to satisfy the constraints or requirements of the end users. The main intent of this paper is to build an automated end-to-end multi-agent based solution to provide the best-fit web service to service requester based on QoS.

MedlinePlus Connect: Web Service

MedlinePlus

... https://medlineplus.gov/connect/service.html MedlinePlus Connect: Web Service To use the sharing features on this ... if you implement MedlinePlus Connect by contacting us . Web Service Overview The parameters for the Web service ...

Focused Crawling of the Deep Web Using Service Class Descriptions

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

Rocco, D; Liu, L; Critchlow, T

2004-06-21

Dynamic Web data sources--sometimes known collectively as the Deep Web--increase the utility of the Web by providing intuitive access to data repositories anywhere that Web access is available. Deep Web services provide access to real-time information, like entertainment event listings, or present a Web interface to large databases or other data repositories. Recent studies suggest that the size and growth rate of the dynamic Web greatly exceed that of the static Web, yet dynamic content is often ignored by existing search engine indexers owing to the technical challenges that arise when attempting to search the Deep Web. To address thesemore » challenges, we present DynaBot, a service-centric crawler for discovering and clustering Deep Web sources offering dynamic content. DynaBot has three unique characteristics. First, DynaBot utilizes a service class model of the Web implemented through the construction of service class descriptions (SCDs). Second, DynaBot employs a modular, self-tuning system architecture for focused crawling of the DeepWeb using service class descriptions. Third, DynaBot incorporates methods and algorithms for efficient probing of the Deep Web and for discovering and clustering Deep Web sources and services through SCD-based service matching analysis. Our experimental results demonstrate the effectiveness of the service class discovery, probing, and matching algorithms and suggest techniques for efficiently managing service discovery in the face of the immense scale of the Deep Web.« less

Secure web-based invocation of large-scale plasma simulation codes

NASA Astrophysics Data System (ADS)

Dimitrov, D. A.; Busby, R.; Exby, J.; Bruhwiler, D. L.; Cary, J. R.

2004-12-01

We present our design and initial implementation of a web-based system for running, both in parallel and serial, Particle-In-Cell (PIC) codes for plasma simulations with automatic post processing and generation of visual diagnostics.

Provenance-Based Approaches to Semantic Web Service Discovery and Usage

ERIC Educational Resources Information Center

Narock, Thomas William

2012-01-01

The World Wide Web Consortium defines a Web Service as "a software system designed to support interoperable machine-to-machine interaction over a network." Web Services have become increasingly important both within and across organizational boundaries. With the recent advent of the Semantic Web, web services have evolved into semantic…

BISQUE: locus- and variant-specific conversion of genomic, transcriptomic and proteomic database identifiers.

PubMed

Meyer, Michael J; Geske, Philip; Yu, Haiyuan

2016-05-15

Biological sequence databases are integral to efforts to characterize and understand biological molecules and share biological data. However, when analyzing these data, scientists are often left holding disparate biological currency-molecular identifiers from different databases. For downstream applications that require converting the identifiers themselves, there are many resources available, but analyzing associated loci and variants can be cumbersome if data is not given in a form amenable to particular analyses. Here we present BISQUE, a web server and customizable command-line tool for converting molecular identifiers and their contained loci and variants between different database conventions. BISQUE uses a graph traversal algorithm to generalize the conversion process for residues in the human genome, genes, transcripts and proteins, allowing for conversion across classes of molecules and in all directions through an intuitive web interface and a URL-based web service. BISQUE is freely available via the web using any major web browser (http://bisque.yulab.org/). Source code is available in a public GitHub repository (https://github.com/hyulab/BISQUE). haiyuan.yu@cornell.edu 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.

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

deFUME: Dynamic exploration of functional metagenomic sequencing data.

PubMed

van der Helm, Eric; Geertz-Hansen, Henrik Marcus; Genee, Hans Jasper; Malla, Sailesh; Sommer, Morten Otto Alexander

2015-07-31

Functional metagenomic selections represent a powerful technique that is widely applied for identification of novel genes from complex metagenomic sources. However, whereas hundreds to thousands of clones can be easily generated and sequenced over a few days of experiments, analyzing the data is time consuming and constitutes a major bottleneck for experimental researchers in the field. Here we present the deFUME web server, an easy-to-use web-based interface for processing, annotation and visualization of functional metagenomics sequencing data, tailored to meet the requirements of non-bioinformaticians. The web-server integrates multiple analysis steps into one single workflow: read assembly, open reading frame prediction, and annotation with BLAST, InterPro and GO classifiers. Analysis results are visualized in an online dynamic web-interface. The deFUME webserver provides a fast track from raw sequence to a comprehensive visual data overview that facilitates effortless inspection of gene function, clustering and distribution. The webserver is available at cbs.dtu.dk/services/deFUME/and the source code is distributed at github.com/EvdH0/deFUME.

Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry.

PubMed

Wandy, Joe; Zhu, Yunfeng; van der Hooft, Justin J J; Daly, Rónán; Barrett, Michael P; Rogers, Simon

2017-09-14

We recently published MS2LDA, a method for the decomposition of sets of molecular fragment data derived from large metabolomics experiments. To make the method more widely available to the community, here we present ms2lda.org, a web application that allows users to upload their data, run MS2LDA analyses and explore the results through interactive visualisations. Ms2lda.org takes tandem mass spectrometry data in many standard formats and allows the user to infer the sets of fragment and neutral loss features that co-occur together (Mass2Motifs). As an alternative workflow, the user can also decompose a dataset onto predefined Mass2Motifs. This is accomplished through the web interface or programmatically from our web service. The website can be found at http://ms2lda.org , while the source code is available at https://github.com/sdrogers/ms2ldaviz under the MIT license. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

DNA Barcode Goes Two-Dimensions: DNA QR Code Web Server

PubMed Central

Li, Huan; Xing, Hang; Liang, Dong; Jiang, Kun; Pang, Xiaohui; Song, Jingyuan; Chen, Shilin

2012-01-01

The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, “DNA barcode” actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three different types of one-dimensional and ten two-dimensional barcode symbologies were compared based on different criteria, such as coding capacity, compression efficiency, and error detection ability. The quick response (QR) code was found to have the largest coding capacity and relatively high compression ratio. To facilitate the further usage of QR code-based DNA barcodes, a web server was developed and is accessible at http://qrfordna.dnsalias.org. The web server allows users to retrieve the QR code for a species of interests, convert a DNA sequence to and from a QR code, and perform species identification based on local and global sequence similarities. In summary, the first comprehensive evaluation of various barcode symbologies has been carried out. The QR code has been found to be the most appropriate symbology for DNA barcode sequences. A web server has also been constructed to allow biologists to utilize QR codes in practical DNA barcoding applications. PMID:22574113

Process model-based atomic service discovery and composition of composite semantic web services using web ontology language for services (OWL-S)

NASA Astrophysics Data System (ADS)

Paulraj, D.; Swamynathan, S.; Madhaiyan, M.

2012-11-01

Web Service composition has become indispensable as a single web service cannot satisfy complex functional requirements. Composition of services has received much interest to support business-to-business (B2B) or enterprise application integration. An important component of the service composition is the discovery of relevant services. In Semantic Web Services (SWS), service discovery is generally achieved by using service profile of Ontology Web Languages for Services (OWL-S). The profile of the service is a derived and concise description but not a functional part of the service. The information contained in the service profile is sufficient for atomic service discovery, but it is not sufficient for the discovery of composite semantic web services (CSWS). The purpose of this article is two-fold: first to prove that the process model is a better choice than the service profile for service discovery. Second, to facilitate the composition of inter-organisational CSWS by proposing a new composition method which uses process ontology. The proposed service composition approach uses an algorithm which performs a fine grained match at the level of atomic process rather than at the level of the entire service in a composite semantic web service. Many works carried out in this area have proposed solutions only for the composition of atomic services and this article proposes a solution for the composition of composite semantic web services.

Automatic geospatial information Web service composition based on ontology interface matching

NASA Astrophysics Data System (ADS)

Xu, Xianbin; Wu, Qunyong; Wang, Qinmin

2008-10-01

With Web services technology the functions of WebGIS can be presented as a kind of geospatial information service, and helped to overcome the limitation of the information-isolated situation in geospatial information sharing field. Thus Geospatial Information Web service composition, which conglomerates outsourced services working in tandem to offer value-added service, plays the key role in fully taking advantage of geospatial information services. This paper proposes an automatic geospatial information web service composition algorithm that employed the ontology dictionary WordNet to analyze semantic distances among the interfaces. Through making matching between input/output parameters and the semantic meaning of pairs of service interfaces, a geospatial information web service chain can be created from a number of candidate services. A practice of the algorithm is also proposed and the result of it shows the feasibility of this algorithm and the great promise in the emerging demand for geospatial information web service composition.

Graph-Based Semantic Web Service Composition for Healthcare Data Integration.

PubMed

Arch-Int, Ngamnij; Arch-Int, Somjit; Sonsilphong, Suphachoke; Wanchai, Paweena

2017-01-01

Within the numerous and heterogeneous web services offered through different sources, automatic web services composition is the most convenient method for building complex business processes that permit invocation of multiple existing atomic services. The current solutions in functional web services composition lack autonomous queries of semantic matches within the parameters of web services, which are necessary in the composition of large-scale related services. In this paper, we propose a graph-based Semantic Web Services composition system consisting of two subsystems: management time and run time. The management-time subsystem is responsible for dependency graph preparation in which a dependency graph of related services is generated automatically according to the proposed semantic matchmaking rules. The run-time subsystem is responsible for discovering the potential web services and nonredundant web services composition of a user's query using a graph-based searching algorithm. The proposed approach was applied to healthcare data integration in different health organizations and was evaluated according to two aspects: execution time measurement and correctness measurement.

Graph-Based Semantic Web Service Composition for Healthcare Data Integration

PubMed Central

2017-01-01

Within the numerous and heterogeneous web services offered through different sources, automatic web services composition is the most convenient method for building complex business processes that permit invocation of multiple existing atomic services. The current solutions in functional web services composition lack autonomous queries of semantic matches within the parameters of web services, which are necessary in the composition of large-scale related services. In this paper, we propose a graph-based Semantic Web Services composition system consisting of two subsystems: management time and run time. The management-time subsystem is responsible for dependency graph preparation in which a dependency graph of related services is generated automatically according to the proposed semantic matchmaking rules. The run-time subsystem is responsible for discovering the potential web services and nonredundant web services composition of a user's query using a graph-based searching algorithm. The proposed approach was applied to healthcare data integration in different health organizations and was evaluated according to two aspects: execution time measurement and correctness measurement. PMID:29065602

CrossTalk: The Journal of Defense Software Engineering. Volume 20, Number 9, September 2007

DTIC Science & Technology

2007-09-01

underlying application framework, e.g., Java Enter- prise Edition or .NET. This increases the risk that consumer Web services not based on the same...weaknesses and vulnera- bilities that are targeted by attackers and malicious code. For example, Apache Axis 2 enables a Java devel- oper to simply...load his/her Java objects into the Axis SOAP engine. At runtime, it is the SOAP engine that determines which incoming SOAP request messages should be

Reliable Execution Based on CPN and Skyline Optimization for Web Service Composition

PubMed Central

Ha, Weitao; Zhang, Guojun

2013-01-01

With development of SOA, the complex problem can be solved by combining available individual services and ordering them to best suit user's requirements. Web services composition is widely used in business environment. With the features of inherent autonomy and heterogeneity for component web services, it is difficult to predict the behavior of the overall composite service. Therefore, transactional properties and nonfunctional quality of service (QoS) properties are crucial for selecting the web services to take part in the composition. Transactional properties ensure reliability of composite Web service, and QoS properties can identify the best candidate web services from a set of functionally equivalent services. In this paper we define a Colored Petri Net (CPN) model which involves transactional properties of web services in the composition process. To ensure reliable and correct execution, unfolding processes of the CPN are followed. The execution of transactional composition Web service (TCWS) is formalized by CPN properties. To identify the best services of QoS properties from candidate service sets formed in the TCSW-CPN, we use skyline computation to retrieve dominant Web service. It can overcome that the reduction of individual scores to an overall similarity leads to significant information loss. We evaluate our approach experimentally using both real and synthetically generated datasets. PMID:23935431

Reliable execution based on CPN and skyline optimization for Web service composition.

PubMed

Chen, Liping; Ha, Weitao; Zhang, Guojun

2013-01-01

With development of SOA, the complex problem can be solved by combining available individual services and ordering them to best suit user's requirements. Web services composition is widely used in business environment. With the features of inherent autonomy and heterogeneity for component web services, it is difficult to predict the behavior of the overall composite service. Therefore, transactional properties and nonfunctional quality of service (QoS) properties are crucial for selecting the web services to take part in the composition. Transactional properties ensure reliability of composite Web service, and QoS properties can identify the best candidate web services from a set of functionally equivalent services. In this paper we define a Colored Petri Net (CPN) model which involves transactional properties of web services in the composition process. To ensure reliable and correct execution, unfolding processes of the CPN are followed. The execution of transactional composition Web service (TCWS) is formalized by CPN properties. To identify the best services of QoS properties from candidate service sets formed in the TCSW-CPN, we use skyline computation to retrieve dominant Web service. It can overcome that the reduction of individual scores to an overall similarity leads to significant information loss. We evaluate our approach experimentally using both real and synthetically generated datasets.

UNH Data Cooperative: A Cyber Infrastructure for Earth System Studies

NASA Astrophysics Data System (ADS)

Braswell, B. H.; Fekete, B. M.; Prusevich, A.; Gliden, S.; Magill, A.; Vorosmarty, C. J.

2007-12-01

Earth system scientists and managers have a continuously growing demand for a wide array of earth observations derived from various data sources including (a) modern satellite retrievals, (b) "in-situ" records, (c) various simulation outputs, and (d) assimilated data products combining model results with observational records. The sheer quantity of data, and formatting inconsistencies make it difficult for users to take full advantage of this important information resource. Thus the system could benefit from a thorough retooling of our current data processing procedures and infrastructure. Emerging technologies, like OPeNDAP and OGC map services, open standard data formats (NetCDF, HDF) data cataloging systems (NASA-Echo, Global Change Master Directory, etc.) are providing the basis for a new approach in data management and processing, where web- services are increasingly designed to serve computer-to-computer communications without human interactions and complex analysis can be carried out over distributed computer resources interconnected via cyber infrastructure. The UNH Earth System Data Collaborative is designed to utilize the aforementioned emerging web technologies to offer new means of access to earth system data. While the UNH Data Collaborative serves a wide array of data ranging from weather station data (Climate Portal) to ocean buoy records and ship tracks (Portsmouth Harbor Initiative) to land cover characteristics, etc. the underlaying data architecture shares common components for data mining and data dissemination via web-services. Perhaps the most unique element of the UNH Data Cooperative's IT infrastructure is its prototype modeling environment for regional ecosystem surveillance over the Northeast corridor, which allows the integration of complex earth system model components with the Cooperative's data services. While the complexity of the IT infrastructure to perform complex computations is continuously increasing, scientists are often forced to spend considerable amount of time to solve basic data management and preprocessing tasks and deal with low level computational design problems like parallelization of model codes. Our modeling infrastructure is designed to take care the bulk of the common tasks found in complex earth system models like I/O handling, computational domain and time management, parallel execution of the modeling tasks, etc. The modeling infrastructure allows scientists to focus on the numerical implementation of the physical processes on a single computational objects(typically grid cells) while the framework takes care of the preprocessing of input data, establishing of the data exchange between computation objects and the execution of the science code. In our presentation, we will discuss the key concepts of our modeling infrastructure. We will demonstrate integration of our modeling framework with data services offered by the UNH Earth System Data Collaborative via web interfaces. We will layout the road map to turn our prototype modeling environment into a truly community framework for wide range of earth system scientists and environmental managers.

PharmARTS: terminology web services for drug safety data coding and retrieval.

PubMed

Alecu, Iulian; Bousquet, Cédric; Degoulet, Patrice; Jaulent, Marie-Christine

2007-01-01

MedDRA and WHO-ART are the terminologies used to encode drug safety reports. The standardisation achieved with these terminologies facilitates: 1) The sharing of safety databases; 2) Data mining for the continuous reassessment of benefit-risk ratio at national or international level or in the pharmaceutical industry. There is some debate about the capacity of these terminologies for retrieving case reports related to similar medical conditions. We have developed a resource that allows grouping similar medical conditions more effectively than WHO-ART and MedDRA. We describe here a software tool facilitating the use of this terminological resource thanks to an RDF framework with support for RDF Schema inferencing and querying. This tool eases coding and data retrieval in drug safety.

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.

Biographer: web-based editing and rendering of SBGN compliant biochemical networks

PubMed Central

Krause, Falko; Schulz, Marvin; Ripkens, Ben; Flöttmann, Max; Krantz, Marcus; Klipp, Edda; Handorf, Thomas

2013-01-01

Motivation: The rapid accumulation of knowledge in the field of Systems Biology during the past years requires advanced, but simple-to-use, methods for the visualization of information in a structured and easily comprehensible manner. Results: We have developed biographer, a web-based renderer and editor for reaction networks, which can be integrated as a library into tools dealing with network-related information. Our software enables visualizations based on the emerging standard Systems Biology Graphical Notation. It is able to import networks encoded in various formats such as SBML, SBGN-ML and jSBGN, a custom lightweight exchange format. The core package is implemented in HTML5, CSS and JavaScript and can be used within any kind of web-based project. It features interactive graph-editing tools and automatic graph layout algorithms. In addition, we provide a standalone graph editor and a web server, which contains enhanced features like web services for the import and export of models and visualizations in different formats. Availability: The biographer tool can be used at and downloaded from the web page http://biographer.biologie.hu-berlin.de/. The different software packages, including a server-indepenent version as well as a web server for Windows and Linux based systems, are available at http://code.google.com/p/biographer/ under the open-source license LGPL. Contact: edda.klipp@biologie.hu-berlin.de or handorf@physik.hu-berlin.de PMID:23574737

GISMO: A MATLAB toolbox for seismic research, monitoring, & education

NASA Astrophysics Data System (ADS)

Thompson, G.; Reyes, C. G.; Kempler, L. A.

2017-12-01

GISMO is an open-source MATLAB toolbox which provides an object-oriented framework to build workflows and applications that read, process, visualize and write seismic waveform, catalog and instrument response data. GISMO can retrieve data from a variety of sources (e.g. FDSN web services, Earthworm/Winston servers) and data formats (SAC, Seisan, etc.). It can handle waveform data that crosses file boundaries. All this alleviates one of the most time consuming part for scientists developing their own codes. GISMO simplifies seismic data analysis by providing a common interface for your data, regardless of its source. Several common plots are built-in to GISMO, such as record section plots, spectrograms, depth-time sections, event count per unit time, energy release per unit time, etc. Other visualizations include map views and cross-sections of hypocentral data. Several common processing methods are also included, such as an extensive set of tools for correlation analysis. Support is being added to interface GISMO with ObsPy. GISMO encourages community development of an integrated set of codes and accompanying documentation, eliminating the need for seismologists to "reinvent the wheel". By sharing code the consistency and repeatability of results can be enhanced. GISMO is hosted on GitHub with documentation both within the source code and in the project wiki. GISMO has been used at the University of South Florida and University of Alaska Fairbanks in graduate-level courses including Seismic Data Analysis, Time Series Analysis and Computational Seismology. GISMO has also been tailored to interface with the common seismic monitoring software and data formats used by volcano observatories in the US and elsewhere. As an example, toolbox training was delivered to researchers at INETER (Nicaragua). Applications built on GISMO include IceWeb (e.g. web-based spectrograms), which has been used by Alaska Volcano Observatory since 1998 and became the prototype for the USGS Pensive system.

Web service module for access to g-Lite

NASA Astrophysics Data System (ADS)

Goranova, R.; Goranov, G.

2012-10-01

G-Lite is a lightweight grid middleware for grid computing installed on all clusters of the European Grid Infrastructure (EGI). The middleware is partially service-oriented and does not provide well-defined Web services for job management. The existing Web services in the environment cannot be directly used by grid users for building service compositions in the EGI. In this article we present a module of well-defined Web services for job management in the EGI. We describe the architecture of the module and the design of the developed Web services. The presented Web services are composable and can participate in service compositions (workflows). An example of usage of the module with tools for service compositions in g-Lite is shown.

Web3DMol: interactive protein structure visualization based on WebGL.

PubMed

Shi, Maoxiang; Gao, Juntao; Zhang, Michael Q

2017-07-03

A growing number of web-based databases and tools for protein research are being developed. There is now a widespread need for visualization tools to present the three-dimensional (3D) structure of proteins in web browsers. Here, we introduce our 3D modeling program-Web3DMol-a web application focusing on protein structure visualization in modern web browsers. Users submit a PDB identification code or select a PDB archive from their local disk, and Web3DMol will display and allow interactive manipulation of the 3D structure. Featured functions, such as sequence plot, fragment segmentation, measure tool and meta-information display, are offered for users to gain a better understanding of protein structure. Easy-to-use APIs are available for developers to reuse and extend Web3DMol. Web3DMol can be freely accessed at http://web3dmol.duapp.com/, and the source code is distributed under the MIT license. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

From GCode to STL: Reconstruct Models from 3D Printing as a Service

NASA Astrophysics Data System (ADS)

Baumann, Felix W.; Schuermann, Martin; Odefey, Ulrich; Pfeil, Markus

2017-12-01

The authors present a method to reverse engineer 3D printer specific machine instructions (GCode) to a point cloud representation and then a STL (Stereolithography) file format. GCode is a machine code that is used for 3D printing among other applications, such as CNC routers. Such code files contain instructions for the 3D printer to move and control its actuator, in case of Fused Deposition Modeling (FDM), the printhead that extrudes semi-molten plastics. The reverse engineering method presented here is based on the digital simulation of the extrusion process of FDM type 3D printing. The reconstructed models and pointclouds do not accommodate for hollow structures, such as holes or cavities. The implementation is performed in Python and relies on open source software and libraries, such as Matplotlib and OpenCV. The reconstruction is performed on the model’s extrusion boundary and considers mechanical imprecision. The complete reconstruction mechanism is available as a RESTful (Representational State Transfer) Web service.

BOWS (bioinformatics open web services) to centralize bioinformatics tools in web services.

PubMed

Velloso, Henrique; Vialle, Ricardo A; Ortega, J Miguel

2015-06-02

Bioinformaticians face a range of difficulties to get locally-installed tools running and producing results; they would greatly benefit from a system that could centralize most of the tools, using an easy interface for input and output. Web services, due to their universal nature and widely known interface, constitute a very good option to achieve this goal. Bioinformatics open web services (BOWS) is a system based on generic web services produced to allow programmatic access to applications running on high-performance computing (HPC) clusters. BOWS intermediates the access to registered tools by providing front-end and back-end web services. Programmers can install applications in HPC clusters in any programming language and use the back-end service to check for new jobs and their parameters, and then to send the results to BOWS. Programs running in simple computers consume the BOWS front-end service to submit new processes and read results. BOWS compiles Java clients, which encapsulate the front-end web service requisitions, and automatically creates a web page that disposes the registered applications and clients. Bioinformatics open web services registered applications can be accessed from virtually any programming language through web services, or using standard java clients. The back-end can run in HPC clusters, allowing bioinformaticians to remotely run high-processing demand applications directly from their machines.

PiCO QL: A software library for runtime interactive queries on program data

NASA Astrophysics Data System (ADS)

Fragkoulis, Marios; Spinellis, Diomidis; Louridas, Panos

PiCO QL is an open source C/C++ software whose scientific scope is real-time interactive analysis of in-memory data through SQL queries. It exposes a relational view of a system's or application's data structures, which is queryable through SQL. While the application or system is executing, users can input queries through a web-based interface or issue web service requests. Queries execute on the live data structures through the respective relational views. PiCO QL makes a good candidate for ad-hoc data analysis in applications and for diagnostics in systems settings. Applications of PiCO QL include the Linux kernel, the Valgrind instrumentation framework, a GIS application, a virtual real-time observatory of stellar objects, and a source code analyser.

A Java API for working with PubChem datasets.

PubMed

Southern, Mark R; Griffin, Patrick R

2011-03-01

PubChem is a public repository of chemical structures and associated biological activities. The PubChem BioAssay database contains assay descriptions, conditions and readouts and biological screening results that have been submitted by the biomedical research community. The PubChem web site and Power User Gateway (PUG) web service allow users to interact with the data and raw files are available via FTP. These resources are helpful to many but there can also be great benefit by using a software API to manipulate the data. Here, we describe a Java API with entity objects mapped to the PubChem Schema and with wrapper functions for calling the NCBI eUtilities and PubChem PUG web services. PubChem BioAssays and associated chemical compounds can then be queried and manipulated in a local relational database. Features include chemical structure searching and generation and display of curve fits from stored dose-response experiments, something that is not yet available within PubChem itself. The aim is to provide researchers with a fast, consistent, queryable local resource from which to manipulate PubChem BioAssays in a database agnostic manner. It is not intended as an end user tool but to provide a platform for further automation and tools development. http://code.google.com/p/pubchemdb.

MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services

PubMed Central

Pratt, Brian; Howbert, J. Jeffry; Tasman, Natalie I.; Nilsson, Erik J.

2012-01-01

Summary: MR-Tandem adapts the popular X!Tandem peptide search engine to work with Hadoop MapReduce for reliable parallel execution of large searches. MR-Tandem runs on any Hadoop cluster but offers special support for Amazon Web Services for creating inexpensive on-demand Hadoop clusters, enabling search volumes that might not otherwise be feasible with the compute resources a researcher has at hand. MR-Tandem is designed to drop in wherever X!Tandem is already in use and requires no modification to existing X!Tandem parameter files, and only minimal modification to X!Tandem-based workflows. Availability and implementation: MR-Tandem is implemented as a lightly modified X!Tandem C++ executable and a Python script that drives Hadoop clusters including Amazon Web Services (AWS) Elastic Map Reduce (EMR), using the modified X!Tandem program as a Hadoop Streaming mapper and reducer. The modified X!Tandem C++ source code is Artistic licensed, supports pluggable scoring, and is available as part of the Sashimi project at http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/extern/xtandem/. The MR-Tandem Python script is Apache licensed and available as part of the Insilicos Cloud Army project at http://ica.svn.sourceforge.net/viewvc/ica/trunk/mr-tandem/. Full documentation and a windows installer that configures MR-Tandem, Python and all necessary packages are available at this same URL. Contact: brian.pratt@insilicos.com PMID:22072385

Web Services--A Buzz Word with Potentials

Treesearch

János T. Füstös

2006-01-01

The simplest definition of a web service is an application that provides a web API. The web API exposes the functionality of the solution to other applications. The web API relies on other Internet-based technologies to manage communications. The resulting web services are pervasive, vendor-independent, language-neutral, and very low-cost. The main purpose of a web API...

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/).

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.

Research on the development and preliminary application of Beijing agricultural sci-tech service hotline WebApp in agricultural consulting services

NASA Astrophysics Data System (ADS)

Yu, Weishui; Luo, Changshou; Zheng, Yaming; Wei, Qingfeng; Cao, Chengzhong

2017-09-01

To deal with the “last kilometer” problem during the agricultural science and technology information service, we analyzed the feasibility, necessity and advantages of WebApp applied to agricultural information service and discussed the modes of WebApp used in agricultural information service based on the requirements analysis and the function of WebApp. To overcome the existing App’s defects of difficult installation and weak compatibility between the mobile operating systems, the Beijing Agricultural Sci-tech Service Hotline WebApp was developed based on the HTML and JAVA technology. The WebApp has greater compatibility and simpler operation than the Native App, what’s more, it can be linked to the WeChat public platform making it spread easily and run directly without setup process. The WebApp was used to provide agricultural expert consulting services and agriculture information push, obtained a good preliminary application achievement. Finally, we concluded the creative application of WebApp in agricultural consulting services and prospected the development of WebApp in agricultural information service.

CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison

PubMed Central

Castrignanò, Tiziana; Canali, Alessandro; Grillo, Giorgio; Liuni, Sabino; Mignone, Flavio; Pesole, Graziano

2004-01-01

The identification and characterization of genome tracts that are highly conserved across species during evolution may contribute significantly to the functional annotation of whole-genome sequences. Indeed, such sequences are likely to correspond to known or unknown coding exons or regulatory motifs. Here, we present a web server implementing a previously developed algorithm that, by comparing user-submitted genome sequences, is able to identify statistically significant conserved blocks and assess their coding or noncoding nature through the measure of a coding potential score. The web tool, available at http://www.caspur.it/CSTminer/, is dynamically interconnected with the Ensembl genome resources and produces a graphical output showing a map of detected conserved sequences and annotated gene features. PMID:15215464

WeBIAS: a web server for publishing bioinformatics applications.

PubMed

Daniluk, Paweł; Wilczyński, Bartek; Lesyng, Bogdan

2015-11-02

One of the requirements for a successful scientific tool is its availability. Developing a functional web service, however, is usually considered a mundane and ungratifying task, and quite often neglected. When publishing bioinformatic applications, such attitude puts additional burden on the reviewers who have to cope with poorly designed interfaces in order to assess quality of presented methods, as well as impairs actual usefulness to the scientific community at large. In this note we present WeBIAS-a simple, self-contained solution to make command-line programs accessible through web forms. It comprises a web portal capable of serving several applications and backend schedulers which carry out computations. The server handles user registration and authentication, stores queries and results, and provides a convenient administrator interface. WeBIAS is implemented in Python and available under GNU Affero General Public License. It has been developed and tested on GNU/Linux compatible platforms covering a vast majority of operational WWW servers. Since it is written in pure Python, it should be easy to deploy also on all other platforms supporting Python (e.g. Windows, Mac OS X). Documentation and source code, as well as a demonstration site are available at http://bioinfo.imdik.pan.pl/webias . WeBIAS has been designed specifically with ease of installation and deployment of services in mind. Setting up a simple application requires minimal effort, yet it is possible to create visually appealing, feature-rich interfaces for query submission and presentation of results.

The taxonomic name resolution service: an online tool for automated standardization of plant names

PubMed Central

2013-01-01

Background The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous scientific conclusions and faulty policy decisions. The lack of tools for correcting this ‘names problem’ has become a fundamental obstacle to integrating disparate data sources and advancing the progress of biodiversity science. Results The TNRS, or Taxonomic Name Resolution Service, is an online application for automated and user-supervised standardization of plant scientific names. The TNRS builds upon and extends existing open-source applications for name parsing and fuzzy matching. Names are standardized against multiple reference taxonomies, including the Missouri Botanical Garden's Tropicos database. Capable of processing thousands of names in a single operation, the TNRS parses and corrects misspelled names and authorities, standardizes variant spellings, and converts nomenclatural synonyms to accepted names. Family names can be included to increase match accuracy and resolve many types of homonyms. Partial matching of higher taxa combined with extraction of annotations, accession numbers and morphospecies allows the TNRS to standardize taxonomy across a broad range of active and legacy datasets. Conclusions We show how the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names. As a result, the TNRS can aid the integration of disparate biological datasets. Although the TNRS was developed to aid in standardizing plant names, its underlying algorithms and design can be extended to all organisms and nomenclatural codes. The TNRS is accessible via a web interface at http://tnrs.iplantcollaborative.org/ and as a RESTful web service and application programming interface. Source code is available at https://github.com/iPlantCollaborativeOpenSource/TNRS/. PMID:23324024

Web-based data collection: detailed methods of a questionnaire and data gathering tool

PubMed Central

Cooper, Charles J; Cooper, Sharon P; del Junco, Deborah J; Shipp, Eva M; Whitworth, Ryan; Cooper, Sara R

2006-01-01

There have been dramatic advances in the development of web-based data collection instruments. This paper outlines a systematic web-based approach to facilitate this process through locally developed code and to describe the results of using this process after two years of data collection. We provide a detailed example of a web-based method that we developed for a study in Starr County, Texas, assessing high school students' work and health status. This web-based application includes data instrument design, data entry and management, and data tables needed to store the results that attempt to maximize the advantages of this data collection method. The software also efficiently produces a coding manual, web-based statistical summary and crosstab reports, as well as input templates for use by statistical packages. Overall, web-based data entry using a dynamic approach proved to be a very efficient and effective data collection system. This data collection method expedited data processing and analysis and eliminated the need for cumbersome and expensive transfer and tracking of forms, data entry, and verification. The code has been made available for non-profit use only to the public health research community as a free download [1]. PMID:16390556

An Interactive and Comprehensive Working Environment for High-Energy Physics Software with Python and Jupyter Notebooks

NASA Astrophysics Data System (ADS)

Braun, N.; Hauth, T.; Pulvermacher, C.; Ritter, M.

2017-10-01

Today’s analyses for high-energy physics (HEP) experiments involve processing a large amount of data with highly specialized algorithms. The contemporary workflow from recorded data to final results is based on the execution of small scripts - often written in Python or ROOT macros which call complex compiled algorithms in the background - to perform fitting procedures and generate plots. During recent years interactive programming environments, such as Jupyter, became popular. Jupyter allows to develop Python-based applications, so-called notebooks, which bundle code, documentation and results, e.g. plots. Advantages over classical script-based approaches is the feature to recompute only parts of the analysis code, which allows for fast and iterative development, and a web-based user frontend, which can be hosted centrally and only requires a browser on the user side. In our novel approach, Python and Jupyter are tightly integrated into the Belle II Analysis Software Framework (basf2), currently being developed for the Belle II experiment in Japan. This allows to develop code in Jupyter notebooks for every aspect of the event simulation, reconstruction and analysis chain. These interactive notebooks can be hosted as a centralized web service via jupyterhub with docker and used by all scientists of the Belle II Collaboration. Because of its generality and encapsulation, the setup can easily be scaled to large installations.

Assessing primary care data quality.

PubMed

Lim, Yvonne Mei Fong; Yusof, Maryati; Sivasampu, Sheamini

2018-04-16

Purpose The purpose of this paper is to assess National Medical Care Survey data quality. Design/methodology/approach Data completeness and representativeness were computed for all observations while other data quality measures were assessed using a 10 per cent sample from the National Medical Care Survey database; i.e., 12,569 primary care records from 189 public and private practices were included in the analysis. Findings Data field completion ranged from 69 to 100 per cent. Error rates for data transfer from paper to web-based application varied between 0.5 and 6.1 per cent. Error rates arising from diagnosis and clinical process coding were higher than medication coding. Data fields that involved free text entry were more prone to errors than those involving selection from menus. The authors found that completeness, accuracy, coding reliability and representativeness were generally good, while data timeliness needs to be improved. Research limitations/implications Only data entered into a web-based application were examined. Data omissions and errors in the original questionnaires were not covered. Practical implications Results from this study provided informative and practicable approaches to improve primary health care data completeness and accuracy especially in developing nations where resources are limited. Originality/value Primary care data quality studies in developing nations are limited. Understanding errors and missing data enables researchers and health service administrators to prevent quality-related problems in primary care data.

Open NASA Earth Exchange (OpenNEX): Strategies for enabling cross organization collaboration in the earth sciences

NASA Astrophysics Data System (ADS)

Michaelis, A.; Ganguly, S.; Nemani, R. R.; Votava, P.; Wang, W.; Lee, T. J.; Dungan, J. L.

2014-12-01

Sharing community-valued codes, intermediary datasets and results from individual efforts with others that are not in a direct funded collaboration can be a challenge. Cross organization collaboration is often impeded due to infrastructure security constraints, rigid financial controls, bureaucracy, and workforce nationalities, etc., which can force groups to work in a segmented fashion and/or through awkward and suboptimal web services. We show how a focused community may come together, share modeling and analysis codes, computing configurations, scientific results, knowledge and expertise on a public cloud platform; diverse groups of researchers working together at "arms length". Through the OpenNEX experimental workshop, users can view short technical "how-to" videos and explore encapsulated working environment. Workshop participants can easily instantiate Amazon Machine Images (AMI) or launch full cluster and data processing configurations within minutes. Enabling users to instantiate computing environments from configuration templates on large public cloud infrastructures, such as Amazon Web Services, may provide a mechanism for groups to easily use each others work and collaborate indirectly. Moreover, using the public cloud for this workshop allowed a single group to host a large read only data archive, making datasets of interest to the community widely available on the public cloud, enabling other groups to directly connect to the data and reduce the costs of the collaborative work by freeing other individual groups from redundantly retrieving, integrating or financing the storage of the datasets of interest.

Creation and utilization of a World Wide Web based space radiation effects code: SIREST

NASA Technical Reports Server (NTRS)

Singleterry, R. C. Jr; Wilson, J. W.; Shinn, J. L.; Tripathi, R. K.; Thibeault, S. A.; Noor, A. K.; Cucinotta, F. A.; Badavi, F. F.; Chang, C. K.; Qualls, G. D.;

Methodology of decreasing software complexity using ontology

NASA Astrophysics Data System (ADS)

DÄ browska-Kubik, Katarzyna

2015-09-01

In this paper a model of web application`s source code, based on the OSD ontology (Ontology for Software Development), is proposed. This model is applied to implementation and maintenance phase of software development process through the DevOntoCreator tool [5]. The aim of this solution is decreasing software complexity of that source code, using many different maintenance techniques, like creation of documentation, elimination dead code, cloned code or bugs, which were known before [1][2]. Due to this approach saving on software maintenance costs of web applications will be possible.

IT Security: Target: The Web

ERIC Educational Resources Information Center

Waters, John K.

2009-01-01

In December, Microsoft announced a major security flaw affecting its Internet Explorer web browser. The flaw allowed hackers to use hidden computer code they had already injected into legitimate websites to steal the passwords of visitors to those sites. Reportedly, more than 10,000 websites were infected with the destructive code by the time…

Novel inter and intra prediction tools under consideration for the emerging AV1 video codec

NASA Astrophysics Data System (ADS)

Joshi, Urvang; Mukherjee, Debargha; Han, Jingning; Chen, Yue; Parker, Sarah; Su, Hui; Chiang, Angie; Xu, Yaowu; Liu, Zoe; Wang, Yunqing; Bankoski, Jim; Wang, Chen; Keyder, Emil

2017-09-01

Google started the WebM Project in 2010 to develop open source, royalty- free video codecs designed specifically for media on the Web. The second generation codec released by the WebM project, VP9, is currently served by YouTube, and enjoys billions of views per day. Realizing the need for even greater compression efficiency to cope with the growing demand for video on the web, the WebM team embarked on an ambitious project to develop a next edition codec AV1, in a consortium of major tech companies called the Alliance for Open Media, that achieves at least a generational improvement in coding efficiency over VP9. In this paper, we focus primarily on new tools in AV1 that improve the prediction of pixel blocks before transforms, quantization and entropy coding are invoked. Specifically, we describe tools and coding modes that improve intra, inter and combined inter-intra prediction. Results are presented on standard test sets.

The EMBRACE web service collection

PubMed Central

Pettifer, Steve; Ison, Jon; Kalaš, Matúš; Thorne, Dave; McDermott, Philip; Jonassen, Inge; Liaquat, Ali; Fernández, José M.; Rodriguez, Jose M.; Partners, INB-; Pisano, David G.; Blanchet, Christophe; Uludag, Mahmut; Rice, Peter; Bartaseviciute, Edita; Rapacki, Kristoffer; Hekkelman, Maarten; Sand, Olivier; Stockinger, Heinz; Clegg, Andrew B.; Bongcam-Rudloff, Erik; Salzemann, Jean; Breton, Vincent; Attwood, Teresa K.; Cameron, Graham; Vriend, Gert

2010-01-01

The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences. The project concluded that in order for web services to achieve widespread adoption, standards must be defined for the choice of web service technology, for semantically annotating both service function and the data exchanged, and a mechanism for discovering services must be provided. Building on this, the project developed: EDAM, an ontology for describing life science web services; BioXSD, a schema for exchanging data between services; and a centralized registry (http://www.embraceregistry.net) that collects together around 1000 services developed by the consortium partners. This article presents the current status of the collection and its associated recommendations and standards definitions. PMID:20462862

Climate Model Diagnostic Analyzer Web Service System

NASA Astrophysics Data System (ADS)

Lee, S.; Pan, L.; Zhai, C.; Tang, B.; Jiang, J. H.

2013-12-01

The latest Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report stressed the need for the comprehensive and innovative evaluation of climate models with newly available global observations. The traditional approach to climate model evaluation, which compares a single parameter at a time, identifies symptomatic model biases and errors but fails to diagnose the model problems. The model diagnosis process requires physics-based multi-variable comparisons that typically involve large-volume and heterogeneous datasets, making them both computationally- and data-intensive. To address these challenges, we are developing a parallel, distributed web-service system that enables the physics-based multi-variable model performance evaluations and diagnoses through the comprehensive and synergistic use of multiple observational data, reanalysis data, and model outputs. We have developed a methodology to transform an existing science application code into a web service using a Python wrapper interface and Python web service frameworks (i.e., Flask, Gunicorn, and Tornado). The web-service system, called Climate Model Diagnostic Analyzer (CMDA), currently supports (1) all the datasets from Obs4MIPs and a few ocean datasets from NOAA and Argo, which can serve as observation-based reference data for model evaluation and (2) many of CMIP5 model outputs covering a broad range of atmosphere, ocean, and land variables from the CMIP5 specific historical runs and AMIP runs. Analysis capabilities currently supported by CMDA are (1) the calculation of annual and seasonal means of physical variables, (2) the calculation of time evolution of the means in any specified geographical region, (3) the calculation of correlation between two variables, and (4) the calculation of difference between two variables. A web user interface is chosen for CMDA because it not only lowers the learning curve and removes the adoption barrier of the tool but also enables instantaneous use, avoiding the hassle of local software installation and environment incompatibility. CMDA is planned to be used as an educational tool for the summer school organized by JPL's Center for Climate Science in 2014. The requirements of the educational tool are defined with the interaction with the school organizers, and CMDA is customized to meet the requirements accordingly. The tool needs to be production quality for 30+ simultaneous users. The summer school will thus serve as a valuable testbed for the tool development, preparing CMDA to serve the Earth-science modeling and model-analysis community at the end of the project. This work was funded by the NASA Earth Science Program called Computational Modeling Algorithms and Cyberinfrastructure (CMAC).

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.

Enhancing UCSF Chimera through web services

PubMed Central

Huang, Conrad C.; Meng, Elaine C.; Morris, John H.; Pettersen, Eric F.; Ferrin, Thomas E.

2014-01-01

Integrating access to web services with desktop applications allows for an expanded set of application features, including performing computationally intensive tasks and convenient searches of databases. We describe how we have enhanced UCSF Chimera (http://www.rbvi.ucsf.edu/chimera/), a program for the interactive visualization and analysis of molecular structures and related data, through the addition of several web services (http://www.rbvi.ucsf.edu/chimera/docs/webservices.html). By streamlining access to web services, including the entire job submission, monitoring and retrieval process, Chimera makes it simpler for users to focus on their science projects rather than data manipulation. Chimera uses Opal, a toolkit for wrapping scientific applications as web services, to provide scalable and transparent access to several popular software packages. We illustrate Chimera's use of web services with an example workflow that interleaves use of these services with interactive manipulation of molecular sequences and structures, and we provide an example Python program to demonstrate how easily Opal-based web services can be accessed from within an application. Web server availability: http://webservices.rbvi.ucsf.edu/opal2/dashboard?command=serviceList. PMID:24861624

Real-time GIS data model and sensor web service platform for environmental data management.

PubMed

Gong, Jianya; Geng, Jing; Chen, Zeqiang

2015-01-09

Effective environmental data management is meaningful for human health. In the past, environmental data management involved developing a specific environmental data management system, but this method often lacks real-time data retrieving and sharing/interoperating capability. With the development of information technology, a Geospatial Service Web method is proposed that can be employed for environmental data management. The purpose of this study is to determine a method to realize environmental data management under the Geospatial Service Web framework. A real-time GIS (Geographic Information System) data model and a Sensor Web service platform to realize environmental data management under the Geospatial Service Web framework are proposed in this study. The real-time GIS data model manages real-time data. The Sensor Web service platform is applied to support the realization of the real-time GIS data model based on the Sensor Web technologies. To support the realization of the proposed real-time GIS data model, a Sensor Web service platform is implemented. Real-time environmental data, such as meteorological data, air quality data, soil moisture data, soil temperature data, and landslide data, are managed in the Sensor Web service platform. In addition, two use cases of real-time air quality monitoring and real-time soil moisture monitoring based on the real-time GIS data model in the Sensor Web service platform are realized and demonstrated. The total time efficiency of the two experiments is 3.7 s and 9.2 s. The experimental results show that the method integrating real-time GIS data model and Sensor Web Service Platform is an effective way to manage environmental data under the Geospatial Service Web framework.

Similarity Based Semantic Web Service Match

NASA Astrophysics Data System (ADS)

Peng, Hui; Niu, Wenjia; Huang, Ronghuai

Semantic web service discovery aims at returning the most matching advertised services to the service requester by comparing the semantic of the request service with an advertised service. The semantic of a web service are described in terms of inputs, outputs, preconditions and results in Ontology Web Language for Service (OWL-S) which formalized by W3C. In this paper we proposed an algorithm to calculate the semantic similarity of two services by weighted averaging their inputs and outputs similarities. Case study and applications show the effectiveness of our algorithm in service match.

Integrating thematic web portal capabilities into the NASA Earthdata Web Infrastructure

NASA Astrophysics Data System (ADS)

Wong, M. M.; McLaughlin, B. D.; Huang, T.; Baynes, K.

2015-12-01

The National Aeronautics and Space Administration (NASA) acquires and distributes an abundance of Earth science data on a daily basis to a diverse user community worldwide. To assist the scientific community and general public in achieving a greater understanding of the interdisciplinary nature of Earth science and of key environmental and climate change topics, the NASA Earthdata web infrastructure is integrating new methods of presenting and providing access to Earth science information, data, research and results. This poster will present the process of integrating thematic web portal capabilities into the NASA Earthdata web infrastructure, with examples from the Sea Level Change Portal. The Sea Level Change Portal will be a source of current NASA research, data and information regarding sea level change. The portal will provide sea level change information through articles, graphics, videos and animations, an interactive tool to view and access sea level change data and a dashboard showing sea level change indicators. Earthdata is a part of the Earth Observing System Data and Information System (EOSDIS) project. EOSDIS is a key core capability in NASA's Earth Science Data Systems Program. It provides end-to-end capabilities for managing NASA's Earth science data from various sources - satellites, aircraft, field measurements, and various other programs. It is comprised of twelve Distributed Active Archive Centers (DAACs), Science Computing Facilities (SCFs), data discovery and service access client (Reverb and Earthdata Search), dataset directory (Global Change Master Directory - GCMD), near real-time data (Land Atmosphere Near real-time Capability for EOS - LANCE), Worldview (an imagery visualization interface), Global Imagery Browse Services, the Earthdata Code Collaborative and a host of other discipline specific data discovery, data access, data subsetting and visualization tools.

Boverhof's App Earns Honorable Mention in Amazon's Web Services

Science.gov Websites

» Boverhof's App Earns Honorable Mention in Amazon's Web Services Competition News & Publications News Publications Facebook Google+ Twitter Boverhof's App Earns Honorable Mention in Amazon's Web Services by Amazon Web Services (AWS). Amazon officially announced the winners of its EC2 Spotathon on Monday

Biological Web Service Repositories Review

PubMed Central

Urdidiales‐Nieto, David; Navas‐Delgado, Ismael

2016-01-01

Abstract Web services play a key role in bioinformatics enabling the integration of database access and analysis of algorithms. However, Web service repositories do not usually publish information on the changes made to their registered Web services. Dynamism is directly related to the changes in the repositories (services registered or unregistered) and at service level (annotation changes). Thus, users, software clients or workflow based approaches lack enough relevant information to decide when they should review or re‐execute a Web service or workflow to get updated or improved results. The dynamism of the repository could be a measure for workflow developers to re‐check service availability and annotation changes in the services of interest to them. This paper presents a review on the most well‐known Web service repositories in the life sciences including an analysis of their dynamism. Freshness is introduced in this paper, and has been used as the measure for the dynamism of these repositories. PMID:27783459

A Method for Transforming Existing Web Service Descriptions into an Enhanced Semantic Web Service Framework

NASA Astrophysics Data System (ADS)

Du, Xiaofeng; Song, William; Munro, Malcolm

Web Services as a new distributed system technology has been widely adopted by industries in the areas, such as enterprise application integration (EAI), business process management (BPM), and virtual organisation (VO). However, lack of semantics in the current Web Service standards has been a major barrier in service discovery and composition. In this chapter, we propose an enhanced context-based semantic service description framework (CbSSDF+) that tackles the problem and improves the flexibility of service discovery and the correctness of generated composite services. We also provide an agile transformation method to demonstrate how the various formats of Web Service descriptions on the Web can be managed and renovated step by step into CbSSDF+ based service description without large amount of engineering work. At the end of the chapter, we evaluate the applicability of the transformation method and the effectiveness of CbSSDF+ through a series of experiments.

Using RxNorm and NDF-RT to classify medication data extracted from electronic health records: experiences from the Rochester Epidemiology Project.

PubMed

Pathak, Jyotishman; Murphy, Sean P; Willaert, Brian N; Kremers, Hilal M; Yawn, Barbara P; Rocca, Walter A; Chute, Christopher G

2011-01-01

RxNorm and NDF-RT published by the National Library of Medicine (NLM) and Veterans Affairs (VA), respectively, are two publicly available federal medication terminologies. In this study, we evaluate the applicability of RxNorm and National Drug File-Reference Terminology (NDF-RT) for extraction and classification of medication data retrieved using structured querying and natural language processing techniques from electronic health records at two different medical centers within the Rochester Epidemiology Project (REP). Specifically, we explore how mappings between RxNorm concept codes and NDF-RT drug classes can be leveraged for hierarchical organization and grouping of REP medication data, identify gaps and coverage issues, and analyze the recently released NLM's NDF-RT Web service API. Our study concludes that RxNorm and NDF-RT can be applied together for classification of medication extracted from multiple EHR systems, although several issues and challenges remain to be addressed. We further conclude that the Web service APIs developed by the NLM provide useful functionalities for such activities.

Trident: scalable compute archives: workflows, visualization, and analysis

NASA Astrophysics Data System (ADS)

Gopu, Arvind; Hayashi, Soichi; Young, Michael D.; Kotulla, Ralf; Henschel, Robert; Harbeck, Daniel

2016-08-01

The Astronomy scientific community has embraced Big Data processing challenges, e.g. associated with time-domain astronomy, and come up with a variety of novel and efficient data processing solutions. However, data processing is only a small part of the Big Data challenge. Efficient knowledge discovery and scientific advancement in the Big Data era requires new and equally efficient tools: modern user interfaces for searching, identifying and viewing data online without direct access to the data; tracking of data provenance; searching, plotting and analyzing metadata; interactive visual analysis, especially of (time-dependent) image data; and the ability to execute pipelines on supercomputing and cloud resources with minimal user overhead or expertise even to novice computing users. The Trident project at Indiana University offers a comprehensive web and cloud-based microservice software suite that enables the straight forward deployment of highly customized Scalable Compute Archive (SCA) systems; including extensive visualization and analysis capabilities, with minimal amount of additional coding. Trident seamlessly scales up or down in terms of data volumes and computational needs, and allows feature sets within a web user interface to be quickly adapted to meet individual project requirements. Domain experts only have to provide code or business logic about handling/visualizing their domain's data products and about executing their pipelines and application work flows. Trident's microservices architecture is made up of light-weight services connected by a REST API and/or a message bus; a web interface elements are built using NodeJS, AngularJS, and HighCharts JavaScript libraries among others while backend services are written in NodeJS, PHP/Zend, and Python. The software suite currently consists of (1) a simple work flow execution framework to integrate, deploy, and execute pipelines and applications (2) a progress service to monitor work flows and sub-work flows (3) ImageX, an interactive image visualization service (3) an authentication and authorization service (4) a data service that handles archival, staging and serving of data products, and (5) a notification service that serves statistical collation and reporting needs of various projects. Several other additional components are under development. Trident is an umbrella project, that evolved from the One Degree Imager, Portal, Pipeline, and Archive (ODI-PPA) project which we had initially refactored toward (1) a powerful analysis/visualization portal for Globular Cluster System (GCS) survey data collected by IU researchers, 2) a data search and download portal for the IU Electron Microscopy Center's data (EMC-SCA), 3) a prototype archive for the Ludwig Maximilian University's Wide Field Imager. The new Trident software has been used to deploy (1) a metadata quality control and analytics portal (RADY-SCA) for DICOM formatted medical imaging data produced by the IU Radiology Center, 2) Several prototype work flows for different domains, 3) a snapshot tool within IU's Karst Desktop environment, 4) a limited component-set to serve GIS data within the IU GIS web portal. Trident SCA systems leverage supercomputing and storage resources at Indiana University but can be configured to make use of any cloud/grid resource, from local workstations/servers to (inter)national supercomputing facilities such as XSEDE.

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.

From Cues to Nudge: A Knowledge-Based Framework for Surveillance of Healthcare-Associated Infections.

PubMed

Shaban-Nejad, Arash; Mamiya, Hiroshi; Riazanov, Alexandre; Forster, Alan J; Baker, Christopher J O; Tamblyn, Robyn; Buckeridge, David L

2016-01-01

We propose an integrated semantic web framework consisting of formal ontologies, web services, a reasoner and a rule engine that together recommend appropriate level of patient-care based on the defined semantic rules and guidelines. The classification of healthcare-associated infections within the HAIKU (Hospital Acquired Infections - Knowledge in Use) framework enables hospitals to consistently follow the standards along with their routine clinical practice and diagnosis coding to improve quality of care and patient safety. The HAI ontology (HAIO) groups over thousands of codes into a consistent hierarchy of concepts, along with relationships and axioms to capture knowledge on hospital-associated infections and complications with focus on the big four types, surgical site infections (SSIs), catheter-associated urinary tract infection (CAUTI); hospital-acquired pneumonia, and blood stream infection. By employing statistical inferencing in our study we use a set of heuristics to define the rule axioms to improve the SSI case detection. We also demonstrate how the occurrence of an SSI is identified using semantic e-triggers. The e-triggers will be used to improve our risk assessment of post-operative surgical site infections (SSIs) for patients undergoing certain type of surgeries (e.g., coronary artery bypass graft surgery (CABG)).

A Comparison of Source Code Plagiarism Detection Engines

NASA Astrophysics Data System (ADS)

Lancaster, Thomas; Culwin, Fintan

2004-06-01

Automated techniques for finding plagiarism in student source code submissions have been in use for over 20 years and there are many available engines and services. This paper reviews the literature on the major modern detection engines, providing a comparison of them based upon the metrics and techniques they deploy. Generally the most common and effective techniques are seen to involve tokenising student submissions then searching pairs of submissions for long common substrings, an example of what is defined to be a paired structural metric. Computing academics are recommended to use one of the two Web-based detection engines, MOSS and JPlag. It is shown that whilst detection is well established there are still places where further research would be useful, particularly where visual support of the investigation process is possible.

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.

The impact of web services at the IRIS DMC

NASA Astrophysics Data System (ADS)

Weekly, R. T.; Trabant, C. M.; Ahern, T. K.; Stults, M.; Suleiman, Y. Y.; Van Fossen, M.; Weertman, B.

2015-12-01

The IRIS Data Management Center (DMC) has served the seismological community for nearly 25 years. In that time we have offered data and information from our archive using a variety of mechanisms ranging from email-based to desktop applications to web applications and web services. Of these, web services have quickly become the primary method for data extraction at the DMC. In 2011, the first full year of operation, web services accounted for over 40% of the data shipped from the DMC. In 2014, over ~450 TB of data was delivered directly to users through web services, representing nearly 70% of all shipments from the DMC that year. In addition to handling requests directly from users, the DMC switched all data extraction methods to use web services in 2014. On average the DMC now handles between 10 and 20 million requests per day submitted to web service interfaces. The rapid adoption of web services is attributed to the many advantages they bring. For users, they provide on-demand data using an interface technology, HTTP, that is widely supported in nearly every computing environment and language. These characteristics, combined with human-readable documentation and existing tools make integration of data access into existing workflows relatively easy. For the DMC, the web services provide an abstraction layer to internal repositories allowing for concentrated optimization of extraction workflow and easier evolution of those repositories. Lending further support to DMC's push in this direction, the core web services for station metadata, timeseries data and event parameters were adopted as standards by the International Federation of Digital Seismograph Networks (FDSN). We expect to continue enhancing existing services and building new capabilities for this platform. For example, the DMC has created a federation system and tools allowing researchers to discover and collect seismic data from data centers running the FDSN-standardized services. A future capability will leverage the DMC's MUSTANG project to select data based on data quality measurements. Within five years, the DMC's web services have proven to be a robust and flexible platform that enables continued growth for the DMC. We expect continued enhancements and adoption of web services.

So You Wanna Be a Web Author?

ERIC Educational Resources Information Center

Buchanan, Larry

1996-01-01

Defines HyperText Markup Language (HTML) as it relates to the World Wide Web (WWW). Describes steps needed to create HTML files on a UNIX system and to make them accessible via the WWW. Presents a list of basic HTML formatting codes and explains the coding used in the author's personal HTML file. (JMV)

Web service discovery among large service pools utilising semantic similarity and clustering

NASA Astrophysics Data System (ADS)

Chen, Fuzan; Li, Minqiang; Wu, Harris; Xie, Lingli

2017-03-01

With the rapid development of electronic business, Web services have attracted much attention in recent years. Enterprises can combine individual Web services to provide new value-added services. An emerging challenge is the timely discovery of close matches to service requests among large service pools. In this study, we first define a new semantic similarity measure combining functional similarity and process similarity. We then present a service discovery mechanism that utilises the new semantic similarity measure for service matching. All the published Web services are pre-grouped into functional clusters prior to the matching process. For a user's service request, the discovery mechanism first identifies matching services clusters and then identifies the best matching Web services within these matching clusters. Experimental results show that the proposed semantic discovery mechanism performs better than a conventional lexical similarity-based mechanism.

A verification strategy for web services composition using enhanced stacked automata model.

PubMed

Nagamouttou, Danapaquiame; Egambaram, Ilavarasan; Krishnan, Muthumanickam; Narasingam, Poonkuzhali

2015-01-01

Currently, Service-Oriented Architecture (SOA) is becoming the most popular software architecture of contemporary enterprise applications, and one crucial technique of its implementation is web services. Individual service offered by some service providers may symbolize limited business functionality; however, by composing individual services from different service providers, a composite service describing the intact business process of an enterprise can be made. Many new standards have been defined to decipher web service composition problem namely Business Process Execution Language (BPEL). BPEL provides an initial work for forming an Extended Markup Language (XML) specification language for defining and implementing business practice workflows for web services. The problems with most realistic approaches to service composition are the verification of composed web services. It has to depend on formal verification method to ensure the correctness of composed services. A few research works has been carried out in the literature survey for verification of web services for deterministic system. Moreover the existing models did not address the verification properties like dead transition, deadlock, reachability and safetyness. In this paper, a new model to verify the composed web services using Enhanced Stacked Automata Model (ESAM) has been proposed. The correctness properties of the non-deterministic system have been evaluated based on the properties like dead transition, deadlock, safetyness, liveness and reachability. Initially web services are composed using Business Process Execution Language for Web Service (BPEL4WS) and it is converted into ESAM (combination of Muller Automata (MA) and Push Down Automata (PDA)) and it is transformed into Promela language, an input language for Simple ProMeLa Interpreter (SPIN) tool. The model is verified using SPIN tool and the results revealed better recital in terms of finding dead transition and deadlock in contrast to the existing models.

Pragmatic Computing - A Semiotic Perspective to Web Services

NASA Astrophysics Data System (ADS)

Liu, Kecheng

The web seems to have evolved from a syntactic web, a semantic web to a pragmatic web. This evolution conforms to the study of information and technology from the theory of semiotics. The pragmatics, concerning with the use of information in relation to the context and intended purposes, is extremely important in web service and applications. Much research in pragmatics has been carried out; but in the same time, attempts and solutions have led to some more questions. After reviewing the current work in pragmatic web, the paper presents a semiotic approach to website services, particularly on request decomposition and service aggregation.

The web server of IBM's Bioinformatics and Pattern Discovery group.

PubMed

Huynh, Tien; Rigoutsos, Isidore; Parida, Laxmi; Platt, Daniel; Shibuya, Tetsuo

2003-07-01

We herein present and discuss the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server is operational around the clock and provides access to a variety of methods that have been published by the group's members and collaborators. The available tools correspond to applications ranging from the discovery of patterns in streams of events and the computation of multiple sequence alignments, to the discovery of genes in nucleic acid sequences and the interactive annotation of amino acid sequences. Additionally, annotations for more than 70 archaeal, bacterial, eukaryotic and viral genomes are available on-line and can be searched interactively. The tools and code bundles can be accessed beginning at http://cbcsrv.watson.ibm.com/Tspd.html whereas the genomics annotations are available at http://cbcsrv.watson.ibm.com/Annotations/.

The web server of IBM's Bioinformatics and Pattern Discovery group

PubMed Central

Huynh, Tien; Rigoutsos, Isidore; Parida, Laxmi; Platt, Daniel; Shibuya, Tetsuo

2003-01-01

We herein present and discuss the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server is operational around the clock and provides access to a variety of methods that have been published by the group's members and collaborators. The available tools correspond to applications ranging from the discovery of patterns in streams of events and the computation of multiple sequence alignments, to the discovery of genes in nucleic acid sequences and the interactive annotation of amino acid sequences. Additionally, annotations for more than 70 archaeal, bacterial, eukaryotic and viral genomes are available on-line and can be searched interactively. The tools and code bundles can be accessed beginning at http://cbcsrv.watson.ibm.com/Tspd.html whereas the genomics annotations are available at http://cbcsrv.watson.ibm.com/Annotations/. PMID:12824385

IRONSIDES: DNS With No Single Packet Denial of Service or Remote Code Execution Vulnerabilities

DTIC Science & Technology

2012-02-27

Caching DNSSEC TSIG 1Pv6 Wildcard S fi.. In terface y y Y * N __ mo e ---- o •• vare y y y N NN y m progress y y y NY N Web, Y command...Proceedings of the 2007 IEEE Aerospace Conference. [6) C. Heitmeyer, M . Archer, E. Leonard and J. Mclean, "Applying formal methods to a certifiably secure...2003). [1 5] DNSSEC-The DNS Security Extensions, http:// http://www.dnssec.net/ (16] S . Conchon, E. Contcjean and J. Kanig, "Ergo : A theorem prover

An audit of health products advertised for sale on chiropractic Web sites in Canada and consideration of these practices in the context of Canadian chiropractic codes of ethics and conduct.

PubMed

Page, Stacey A; Grod, Jaroslaw P

2009-01-01

This study describes the extent to which chiropractors with Web sites practicing in Canada advertise health products for sale and considers this practice in the context of chiropractic codes of ethics and conduct. Chiropractic Web sites in Canada were identified using a public online business directory (Canada 411). The Web sites were searched, and an inventory of the health products for sale was taken. The influences of type of practice and province of practice on the sale of health product were assessed. Textual comments about health product marketing were summarized. National and provincial codes of ethics were reviewed, and the content on health product advertising was summarized. Two hundred eighty-seven Web sites were reviewed. Just more than half of the Web sites contained information on health products for sale (n = 158, 54%). Orthotics were advertised most often (n = 136 practices, 47%), followed by vitamins/nutritional supplements (n = 53, 18%), pillows and supports (n = 40, 14%), and exercise/rehabilitation products (n = 20, 7%). Chiropractors in solo or group chiropractic practices were less likely to advertise health products than those in multidisciplinary practice (P < .001), whereas chiropractors in BC were less likely to advertise nutritional supplements (P < .01). Provincial codes of ethics and conduct varied in their guidelines regarding health product sales. Variations in codes of ethics and in the proportions of practitioners advertising health products for sales across the country suggest that opinions may be divided on the acceptability of health product sales. Such practices raise questions and considerations for the chiropractic profession.

QoS measurement of workflow-based web service compositions using Colored Petri net.

PubMed

Nematzadeh, Hossein; Motameni, Homayun; Mohamad, Radziah; Nematzadeh, Zahra

2014-01-01

Workflow-based web service compositions (WB-WSCs) is one of the main composition categories in service oriented architecture (SOA). Eflow, polymorphic process model (PPM), and business process execution language (BPEL) are the main techniques of the category of WB-WSCs. Due to maturity of web services, measuring the quality of composite web services being developed by different techniques becomes one of the most important challenges in today's web environments. Business should try to provide good quality regarding the customers' requirements to a composed web service. Thus, quality of service (QoS) which refers to nonfunctional parameters is important to be measured since the quality degree of a certain web service composition could be achieved. This paper tried to find a deterministic analytical method for dependability and performance measurement using Colored Petri net (CPN) with explicit routing constructs and application of theory of probability. A computer tool called WSET was also developed for modeling and supporting QoS measurement through simulation.

Enhancing UCSF Chimera through web services.

PubMed

Huang, Conrad C; Meng, Elaine C; Morris, John H; Pettersen, Eric F; Ferrin, Thomas E

2014-07-01

Integrating access to web services with desktop applications allows for an expanded set of application features, including performing computationally intensive tasks and convenient searches of databases. We describe how we have enhanced UCSF Chimera (http://www.rbvi.ucsf.edu/chimera/), a program for the interactive visualization and analysis of molecular structures and related data, through the addition of several web services (http://www.rbvi.ucsf.edu/chimera/docs/webservices.html). By streamlining access to web services, including the entire job submission, monitoring and retrieval process, Chimera makes it simpler for users to focus on their science projects rather than data manipulation. Chimera uses Opal, a toolkit for wrapping scientific applications as web services, to provide scalable and transparent access to several popular software packages. We illustrate Chimera's use of web services with an example workflow that interleaves use of these services with interactive manipulation of molecular sequences and structures, and we provide an example Python program to demonstrate how easily Opal-based web services can be accessed from within an application. Web server availability: http://webservices.rbvi.ucsf.edu/opal2/dashboard?command=serviceList. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Development of a Web Based Simulating System for Earthquake Modeling on the Grid

NASA Astrophysics Data System (ADS)

Seber, D.; Youn, C.; Kaiser, T.

2007-12-01

Existing cyberinfrastructure-based information, data and computational networks now allow development of state- of-the-art, user-friendly simulation environments that democratize access to high-end computational environments and provide new research opportunities for many research and educational communities. Within the Geosciences cyberinfrastructure network, GEON, we have developed the SYNSEIS (SYNthetic SEISmogram) toolkit to enable efficient computations of 2D and 3D seismic waveforms for a variety of research purposes especially for helping to analyze the EarthScope's USArray seismic data in a speedy and efficient environment. The underlying simulation software in SYNSEIS is a finite difference code, E3D, developed by LLNL (S. Larsen). The code is embedded within the SYNSEIS portlet environment and it is used by our toolkit to simulate seismic waveforms of earthquakes at regional distances (<1000km). Architecturally, SYNSEIS uses both Web Service and Grid computing resources in a portal-based work environment and has a built in access mechanism to connect to national supercomputer centers as well as to a dedicated, small-scale compute cluster for its runs. Even though Grid computing is well-established in many computing communities, its use among domain scientists still is not trivial because of multiple levels of complexities encountered. We grid-enabled E3D using our own dialect XML inputs that include geological models that are accessible through standard Web services within the GEON network. The XML inputs for this application contain structural geometries, source parameters, seismic velocity, density, attenuation values, number of time steps to compute, and number of stations. By enabling a portal based access to a such computational environment coupled with its dynamic user interface we enable a large user community to take advantage of such high end calculations in their research and educational activities. Our system can be used to promote an efficient and effective modeling environment to help scientists as well as educators in their daily activities and speed up the scientific discovery process.

User Needs of Digital Service Web Portals: A Case Study

ERIC Educational Resources Information Center

Heo, Misook; Song, Jung-Sook; Seol, Moon-Won

2013-01-01

The authors examined the needs of digital information service web portal users. More specifically, the needs of Korean cultural portal users were examined as a case study. The conceptual framework of a web-based portal is that it is a complex, web-based service application with characteristics of information systems and service agents. In…

Compression-based aggregation model for medical web services.

PubMed

Al-Shammary, Dhiah; Khalil, Ibrahim

2010-01-01

Many organizations such as hospitals have adopted Cloud Web services in applying their network services to avoid investing heavily computing infrastructure. SOAP (Simple Object Access Protocol) is the basic communication protocol of Cloud Web services that is XML based protocol. Generally,Web services often suffer congestions and bottlenecks as a result of the high network traffic that is caused by the large XML overhead size. At the same time, the massive load on Cloud Web services in terms of the large demand of client requests has resulted in the same problem. In this paper, two XML-aware aggregation techniques that are based on exploiting the compression concepts are proposed in order to aggregate the medical Web messages and achieve higher message size reduction.

A snapshot of 3649 Web-based services published between 1994 and 2017 shows a decrease in availability after 2 years.

PubMed

Osz, Ágnes; Pongor, Lorinc Sándor; Szirmai, Danuta; Gyorffy, Balázs

2017-12-08

The long-term availability of online Web services is of utmost importance to ensure reproducibility of analytical results. However, because of lack of maintenance following acceptance, many servers become unavailable after a short period of time. Our aim was to monitor the accessibility and the decay rate of published Web services as well as to determine the factors underlying trends changes. We searched PubMed to identify publications containing Web server-related terms published between 1994 and 2017. Automatic and manual screening was used to check the status of each Web service. Kruskall-Wallis, Mann-Whitney and Chi-square tests were used to evaluate various parameters, including availability, accessibility, platform, origin of authors, citation, journal impact factor and publication year. We identified 3649 publications in 375 journals of which 2522 (69%) were currently active. Over 95% of sites were running in the first 2 years, but this rate dropped to 84% in the third year and gradually sank afterwards (P < 1e-16). The mean half-life of Web services is 10.39 years. Working Web services were published in journals with higher impact factors (P = 4.8e-04). Services published before the year 2000 received minimal attention. The citation of offline services was less than for those online (P = 0.022). The majority of Web services provide analytical tools, and the proportion of databases is slowly decreasing. Conclusions. Almost one-third of Web services published to date went out of service. We recommend continued support of Web-based services to increase the reproducibility of published results. © The Author 2017. Published by Oxford University Press.

Analysis Tool Web Services from the EMBL-EBI.

PubMed

McWilliam, Hamish; Li, Weizhong; Uludag, Mahmut; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Cowley, Andrew Peter; Lopez, Rodrigo

2013-07-01

Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods.

Analysis Tool Web Services from the EMBL-EBI

PubMed Central

McWilliam, Hamish; Li, Weizhong; Uludag, Mahmut; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Cowley, Andrew Peter; Lopez, Rodrigo

2013-01-01

Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods. PMID:23671338

Biological Web Service Repositories Review.

PubMed

Urdidiales-Nieto, David; Navas-Delgado, Ismael; Aldana-Montes, José F

2017-05-01

Web services play a key role in bioinformatics enabling the integration of database access and analysis of algorithms. However, Web service repositories do not usually publish information on the changes made to their registered Web services. Dynamism is directly related to the changes in the repositories (services registered or unregistered) and at service level (annotation changes). Thus, users, software clients or workflow based approaches lack enough relevant information to decide when they should review or re-execute a Web service or workflow to get updated or improved results. The dynamism of the repository could be a measure for workflow developers to re-check service availability and annotation changes in the services of interest to them. This paper presents a review on the most well-known Web service repositories in the life sciences including an analysis of their dynamism. Freshness is introduced in this paper, and has been used as the measure for the dynamism of these repositories. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

The value of Web-based library services at Cedars-Sinai Health System.

PubMed

Halub, L P

1999-07-01

Cedars-Sinai Medical Library/Information Center has maintained Web-based services since 1995 on the Cedars-Sinai Health System network. In that time, the librarians have found the provision of Web-based services to be a very worthwhile endeavor. Library users value the services that they access from their desktops because the services save time. They also appreciate being able to access services at their convenience, without restriction by the library's hours of operation. The library values its Web site because it brings increased visibility within the health system, and it enables library staff to expand services when budget restrictions have forced reduced hours of operation. In creating and maintaining the information center Web site, the librarians have learned the following lessons: consider the design carefully; offer what services you can, but weigh the advantages of providing the services against the time required to maintain them; make the content as accessible as possible; promote your Web site; and make friends in other departments, especially information services.

The value of Web-based library services at Cedars-Sinai Health System.

PubMed Central

Halub, L P

1999-01-01

Cedars-Sinai Medical Library/Information Center has maintained Web-based services since 1995 on the Cedars-Sinai Health System network. In that time, the librarians have found the provision of Web-based services to be a very worthwhile endeavor. Library users value the services that they access from their desktops because the services save time. They also appreciate being able to access services at their convenience, without restriction by the library's hours of operation. The library values its Web site because it brings increased visibility within the health system, and it enables library staff to expand services when budget restrictions have forced reduced hours of operation. In creating and maintaining the information center Web site, the librarians have learned the following lessons: consider the design carefully; offer what services you can, but weigh the advantages of providing the services against the time required to maintain them; make the content as accessible as possible; promote your Web site; and make friends in other departments, especially information services. PMID:10427423

MedlinePlus Connect: How it Works

MedlinePlus

... it looks depends on how it is implemented. Web Application The Web application returns a formatted response ... for more examples of Web Application response pages. Web Service The MedlinePlus Connect REST-based Web service ...

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/.

A Privacy Access Control Framework for Web Services Collaboration with Role Mechanisms

NASA Astrophysics Data System (ADS)

Liu, Linyuan; Huang, Zhiqiu; Zhu, Haibin

With the popularity of Internet technology, web services are becoming the most promising paradigm for distributed computing. This increased use of web services has meant that more and more personal information of consumers is being shared with web service providers, leading to the need to guarantee the privacy of consumers. This paper proposes a role-based privacy access control framework for Web services collaboration, it utilizes roles to specify the privacy privileges of services, and considers the impact on the reputation degree of the historic experience of services in playing roles. Comparing to the traditional privacy access control approaches, this framework can make the fine-grained authorization decision, thus efficiently protecting consumers' privacy.

75 FR 15693 - Extension of Web-Based TRICARE Assistance Program Demonstration Project

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-30

... DEPARTMENT OF DEFENSE Office of the Secretary Extension of Web-Based TRICARE Assistance Program Demonstration Project AGENCY: Department of Defense (DoD). ACTION: Notice of a Web-Based TRICARE Assistance... States Code, Section 1092, entitled Web-Based TRICARE Assistance Program. This demonstration was...

A Java API for working with PubChem datasets

PubMed Central

Southern, Mark R.; Griffin, Patrick R.

2011-01-01

Summary: PubChem is a public repository of chemical structures and associated biological activities. The PubChem BioAssay database contains assay descriptions, conditions and readouts and biological screening results that have been submitted by the biomedical research community. The PubChem web site and Power User Gateway (PUG) web service allow users to interact with the data and raw files are available via FTP. These resources are helpful to many but there can also be great benefit by using a software API to manipulate the data. Here, we describe a Java API with entity objects mapped to the PubChem Schema and with wrapper functions for calling the NCBI eUtilities and PubChem PUG web services. PubChem BioAssays and associated chemical compounds can then be queried and manipulated in a local relational database. Features include chemical structure searching and generation and display of curve fits from stored dose–response experiments, something that is not yet available within PubChem itself. The aim is to provide researchers with a fast, consistent, queryable local resource from which to manipulate PubChem BioAssays in a database agnostic manner. It is not intended as an end user tool but to provide a platform for further automation and tools development. Availability: http://code.google.com/p/pubchemdb Contact: southern@scripps.edu PMID:21216779

SIDECACHE: Information access, management and dissemination framework for web services.

PubMed

Doderer, Mark S; Burkhardt, Cory; Robbins, Kay A

2011-06-14

Many bioinformatics algorithms and data sets are deployed using web services so that the results can be explored via the Internet and easily integrated into other tools and services. These services often include data from other sites that is accessed either dynamically or through file downloads. Developers of these services face several problems because of the dynamic nature of the information from the upstream services. Many publicly available repositories of bioinformatics data frequently update their information. When such an update occurs, the developers of the downstream service may also need to update. For file downloads, this process is typically performed manually followed by web service restart. Requests for information obtained by dynamic access of upstream sources is sometimes subject to rate restrictions. SideCache provides a framework for deploying web services that integrate information extracted from other databases and from web sources that are periodically updated. This situation occurs frequently in biotechnology where new information is being continuously generated and the latest information is important. SideCache provides several types of services including proxy access and rate control, local caching, and automatic web service updating. We have used the SideCache framework to automate the deployment and updating of a number of bioinformatics web services and tools that extract information from remote primary sources such as NCBI, NCIBI, and Ensembl. The SideCache framework also has been used to share research results through the use of a SideCache derived web service.

Design for Connecting Spatial Data Infrastructures with Sensor Web (sensdi)

NASA Astrophysics Data System (ADS)

Bhattacharya, D.; M., M.

2016-06-01

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. It is about research to harness the sensed environment by utilizing domain specific sensor data to create a generalized sensor webframework. The challenges being semantic enablement for Spatial Data Infrastructures, and connecting the interfaces of SDI with interfaces of Sensor Web. The proposed research plan is to Identify sensor data sources, Setup an open source SDI, Match the APIs and functions between Sensor Web and SDI, and Case studies like hazard applications, urban applications etc. We take up co-operative development of SDI best practices to enable a new realm of a location enabled and semantically enriched World Wide Web - the "Geospatial Web" or "Geosemantic Web" by setting up one to one correspondence between WMS, WFS, WCS, Metadata and 'Sensor Observation Service' (SOS); 'Sensor Planning Service' (SPS); 'Sensor Alert Service' (SAS); a service that facilitates asynchronous message interchange between users and services, and between two OGC-SWE services, called the 'Web Notification Service' (WNS). Hence in conclusion, it is of importance to geospatial studies to integrate SDI with Sensor Web. The integration can be done through merging the common OGC interfaces of SDI and Sensor Web. Multi-usability studies to validate integration has to be undertaken as future research.

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.

QR Codes: Outlook for Food Science and Nutrition.

PubMed

Sanz-Valero, Javier; Álvarez Sabucedo, Luis M; Wanden-Berghe, Carmina; Santos Gago, Juan M

2016-01-01

QR codes opens up the possibility to develop simple-to-use, cost-effective-cost, and functional systems based on the optical recognition of inexpensive tags attached to physical objects. These systems, combined with Web platforms, can provide us with advanced services that are already currently broadly used on many contexts of the common life. Due to its philosophy, based on the automatic recognition of messages embedded on simple graphics by means of common devices such as mobile phones, QR codes are very convenient for the average user. Regretfully, its potential has not yet been fully exploited in the domains of food science and nutrition. This paper points out some applications to make the most of this technology for these domains in a straightforward manner. For its characteristics, we are addressing systems with low barriers to entry and high scalability for its deployment. Therefore, its launching among professional and final users is quite simple. The paper also provides high-level indications for the evaluation of the technological frame required to implement the identified possibilities of use.

Dynamic Generation of Reduced Ontologies to Support Resource Constraints of Mobile Devices

ERIC Educational Resources Information Center

Schrimpsher, Dan

2011-01-01

As Web Services and the Semantic Web become more important, enabling technologies such as web service ontologies will grow larger. At the same time, use of mobile devices to access web services has doubled in the last year. The ability of these resource constrained devices to download and reason across these ontologies to support service discovery…

A Smart Modeling Framework for Integrating BMI-enabled Models as Web Services

NASA Astrophysics Data System (ADS)

Jiang, P.; Elag, M.; Kumar, P.; Peckham, S. D.; Liu, R.; Marini, L.; Hsu, L.

2015-12-01

Serviced-oriented computing provides an opportunity to couple web service models using semantic web technology. Through this approach, models that are exposed as web services can be conserved in their own local environment, thus making it easy for modelers to maintain and update the models. In integrated modeling, the serviced-oriented loose-coupling approach requires (1) a set of models as web services, (2) the model metadata describing the external features of a model (e.g., variable name, unit, computational grid, etc.) and (3) a model integration framework. We present the architecture of coupling web service models that are self-describing by utilizing a smart modeling framework. We expose models that are encapsulated with CSDMS (Community Surface Dynamics Modeling System) Basic Model Interfaces (BMI) as web services. The BMI-enabled models are self-describing by uncovering models' metadata through BMI functions. After a BMI-enabled model is serviced, a client can initialize, execute and retrieve the meta-information of the model by calling its BMI functions over the web. Furthermore, a revised version of EMELI (Peckham, 2015), an Experimental Modeling Environment for Linking and Interoperability, is chosen as the framework for coupling BMI-enabled web service models. EMELI allows users to combine a set of component models into a complex model by standardizing model interface using BMI as well as providing a set of utilities smoothing the integration process (e.g., temporal interpolation). We modify the original EMELI so that the revised modeling framework is able to initialize, execute and find the dependencies of the BMI-enabled web service models. By using the revised EMELI, an example will be presented on integrating a set of topoflow model components that are BMI-enabled and exposed as web services. Reference: Peckham, S.D. (2014) EMELI 1.0: An experimental smart modeling framework for automatic coupling of self-describing models, Proceedings of HIC 2014, 11th International Conf. on Hydroinformatics, New York, NY.

Farm Mapping to Assist, Protect, and Prepare Emergency Responders: Farm MAPPER.

PubMed

Reyes, Iris; Rollins, Tami; Mahnke, Andrea; Kadolph, Christopher; Minor, Gerald; Keifer, Matthew

2014-01-01

Responders such as firefighters and emergency medical technicians who respond to farm emergencies often face complex and unknown environments. They may encounter hazards such as fuels, solvents, pesticides, caustics, and exploding gas storage cylinders. Responders may be unaware of dirt roads within the farm that can expedite their arrival at critical sites or snow-covered manure pits that act as hidden hazards. A response to a farm, unless guided by someone familiar with the operation, may present a risk to responders and post a challenge in locating the victim. This project explored the use of a Web-based farm-mapping application optimized for tablets and accessible via easily accessible on-site matrix barcodes, or quick response codes (QR codes), to provide emergency responders with hazard and resource information to agricultural operations. Secured portals were developed for both farmers and responders, allowing both parties to populate and customize farm maps with icons. Data were stored online and linked to QR codes attached to mailbox posts where emergency responders may read them with a mobile device. Mock responses were conducted on dairy farms to test QR code linking efficacy, Web site security, and field usability. Findings from farmer usability tests showed willingness to enter data as well as ease of Web site navigation and data entry even with farmers who had limited computer knowledge. Usability tests with emergency responders showed ease of QR code connectivity to the farm maps and ease of Web site navigation. Further research is needed to improve data security as well as assess the program's applicability to nonfarm environments and integration with existing emergency response systems. The next phases of this project will expand the program for regional and national use, develop QR code-linked, Web-based extrication guidance for farm machinery for victim entrapment rescue, and create QR code-linked online training videos and materials for limited English proficient immigrant farm workers.

Managing the Web-Enhanced Geographic Information Service.

ERIC Educational Resources Information Center

Stephens, Denise

1997-01-01

Examines key management issues involved in delivering geographic information services on the World Wide Web, using the Geographic Information Center (GIC) program at the University of Virginia Library as a reference. Highlights include integrating the Web into services; building collections for Web delivery; and evaluating spatial information…

Automated geospatial Web Services composition based on geodata quality requirements

NASA Astrophysics Data System (ADS)

Cruz, Sérgio A. B.; Monteiro, Antonio M. V.; Santos, Rafael

2012-10-01

Service-Oriented Architecture and Web Services technologies improve the performance of activities involved in geospatial analysis with a distributed computing architecture. However, the design of the geospatial analysis process on this platform, by combining component Web Services, presents some open issues. The automated construction of these compositions represents an important research topic. Some approaches to solving this problem are based on AI planning methods coupled with semantic service descriptions. This work presents a new approach using AI planning methods to improve the robustness of the produced geospatial Web Services composition. For this purpose, we use semantic descriptions of geospatial data quality requirements in a rule-based form. These rules allow the semantic annotation of geospatial data and, coupled with the conditional planning method, this approach represents more precisely the situations of nonconformities with geodata quality that may occur during the execution of the Web Service composition. The service compositions produced by this method are more robust, thus improving process reliability when working with a composition of chained geospatial Web Services.

Code AI Personal Web Pages

NASA Technical Reports Server (NTRS)

Garcia, Joseph A.; Smith, Charles A. (Technical Monitor)

1998-01-01

The document consists of a publicly available web site (george.arc.nasa.gov) for Joseph A. Garcia's personal web pages in the AI division. Only general information will be posted and no technical material. All the information is unclassified.

Data near processing support for climate data analysis

NASA Astrophysics Data System (ADS)

Kindermann, Stephan; Ehbrecht, Carsten; Hempelmann, Nils

2016-04-01

Climate data repositories grow in size exponentially. Scalable data near processing capabilities are required to meet future data analysis requirements and to replace current "data download and process at home" workflows and approaches. On one hand side, these processing capabilities should be accessible via standardized interfaces (e.g. OGC WPS), on the other side a large variety of processing tools, toolboxes and deployment alternatives have to be supported and maintained at the data/processing center. We present a community approach of a modular and flexible system supporting the development, deployment and maintenace of OGC-WPS based web processing services. This approach is organized in an open source github project (called "bird-house") supporting individual processing services ("birds", e.g. climate index calculations, model data ensemble calculations), which rely on basic common infrastructural components (e.g. installation and deployment recipes, analysis code dependencies management). To support easy deployment at data centers as well as home institutes (e.g. for testing and development) the system supports the management of the often very complex package dependency chain of climate data analysis packages as well as docker based packaging and installation. We present a concrete deployment scenario at the German Climate Computing Center (DKRZ). The DKRZ one hand side hosts a multi-petabyte climate archive which is integrated e.g. into the european ENES and worldwide ESGF data infrastructure, and on the other hand hosts an HPC center supporting (model) data production and data analysis. The deployment scenario also includes openstack based data cloud services to support data import and data distribution for bird-house based WPS web processing services. Current challenges for inter-institutionnal deployments of web processing services supporting the european and international climate modeling community as well as the climate impact community are highlighted. Also aspects supporting future WPS based cross community usage scenarios supporting data reuse and data provenance aspects are reflected.

BioCatalogue: a universal catalogue of web services for the life sciences

PubMed Central

Bhagat, Jiten; Tanoh, Franck; Nzuobontane, Eric; Laurent, Thomas; Orlowski, Jerzy; Roos, Marco; Wolstencroft, Katy; Aleksejevs, Sergejs; Stevens, Robert; Pettifer, Steve; Lopez, Rodrigo; Goble, Carole A.

2010-01-01

The use of Web Services to enable programmatic access to on-line bioinformatics is becoming increasingly important in the Life Sciences. However, their number, distribution and the variable quality of their documentation can make their discovery and subsequent use difficult. A Web Services registry with information on available services will help to bring together service providers and their users. The BioCatalogue (http://www.biocatalogue.org/) provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Services in the BioCatalogue can be described and searched in multiple ways based upon their technical types, bioinformatics categories, user tags, service providers or data inputs and outputs. They are also subject to constant monitoring, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. The system is accessible via a human-readable ‘Web 2.0’-style interface and a programmatic Web Service interface. The BioCatalogue follows a community approach in which all services can be registered, browsed and incrementally documented with annotations by any member of the scientific community. PMID:20484378

BioCatalogue: a universal catalogue of web services for the life sciences.

PubMed

Bhagat, Jiten; Tanoh, Franck; Nzuobontane, Eric; Laurent, Thomas; Orlowski, Jerzy; Roos, Marco; Wolstencroft, Katy; Aleksejevs, Sergejs; Stevens, Robert; Pettifer, Steve; Lopez, Rodrigo; Goble, Carole A

2010-07-01

The use of Web Services to enable programmatic access to on-line bioinformatics is becoming increasingly important in the Life Sciences. However, their number, distribution and the variable quality of their documentation can make their discovery and subsequent use difficult. A Web Services registry with information on available services will help to bring together service providers and their users. The BioCatalogue (http://www.biocatalogue.org/) provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Services in the BioCatalogue can be described and searched in multiple ways based upon their technical types, bioinformatics categories, user tags, service providers or data inputs and outputs. They are also subject to constant monitoring, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. The system is accessible via a human-readable 'Web 2.0'-style interface and a programmatic Web Service interface. The BioCatalogue follows a community approach in which all services can be registered, browsed and incrementally documented with annotations by any member of the scientific community.

Customer Decision Making in Web Services with an Integrated P6 Model

NASA Astrophysics Data System (ADS)

Sun, Zhaohao; Sun, Junqing; Meredith, Grant

Customer decision making (CDM) is an indispensable factor for web services. This article examines CDM in web services with a novel P6 model, which consists of the 6 Ps: privacy, perception, propensity, preference, personalization and promised experience. This model integrates the existing 6 P elements of marketing mix as the system environment of CDM in web services. The new integrated P6 model deals with the inner world of the customer and incorporates what the customer think during the DM process. The proposed approach will facilitate the research and development of web services and decision support systems.

The HydroServer Platform for Sharing Hydrologic Data

NASA Astrophysics Data System (ADS)

Tarboton, D. G.; Horsburgh, J. S.; Schreuders, K.; Maidment, D. R.; Zaslavsky, I.; Valentine, D. W.

2010-12-01

The CUAHSI Hydrologic Information System (HIS) is an internet based system that supports sharing of hydrologic data. HIS consists of databases connected using the Internet through Web services, as well as software for data discovery, access, and publication. The HIS system architecture is comprised of servers for publishing and sharing data, a centralized catalog to support cross server data discovery and a desktop client to access and analyze data. This paper focuses on HydroServer, the component developed for sharing and publishing space-time hydrologic datasets. A HydroServer is a computer server that contains a collection of databases, web services, tools, and software applications that allow data producers to store, publish, and manage the data from an experimental watershed or project site. HydroServer is designed to permit publication of data as part of a distributed national/international system, while still locally managing access to the data. We describe the HydroServer architecture and software stack, including tools for managing and publishing time series data for fixed point monitoring sites as well as spatially distributed, GIS datasets that describe a particular study area, watershed, or region. HydroServer adopts a standards based approach to data publication, relying on accepted and emerging standards for data storage and transfer. CUAHSI developed HydroServer code is free with community code development managed through the codeplex open source code repository and development system. There is some reliance on widely used commercial software for general purpose and standard data publication capability. The sharing of data in a common format is one way to stimulate interdisciplinary research and collaboration. It is anticipated that the growing, distributed network of HydroServers will facilitate cross-site comparisons and large scale studies that synthesize information from diverse settings, making the network as a whole greater than the sum of its parts in advancing hydrologic research. Details of the CUAHSI HIS can be found at http://his.cuahsi.org, and HydroServer codeplex site http://hydroserver.codeplex.com.

Ubiquitous Computing Services Discovery and Execution Using a Novel Intelligent Web Services Algorithm

PubMed Central

Choi, Okkyung; Han, SangYong

2007-01-01

Ubiquitous Computing makes it possible to determine in real time the location and situations of service requesters in a web service environment as it enables access to computers at any time and in any place. Though research on various aspects of ubiquitous commerce is progressing at enterprises and research centers, both domestically and overseas, analysis of a customer's personal preferences based on semantic web and rule based services using semantics is not currently being conducted. This paper proposes a Ubiquitous Computing Services System that enables a rule based search as well as semantics based search to support the fact that the electronic space and the physical space can be combined into one and the real time search for web services and the construction of efficient web services thus become possible.

Some Programs Should Not Run on Laptops - Providing Programmatic Access to Applications Via Web Services

NASA Astrophysics Data System (ADS)

Gupta, V.; Gupta, N.; Gupta, S.; Field, E.; Maechling, P.

2003-12-01

Modern laptop computers, and personal computers, can provide capabilities that are, in many ways, comparable to workstations or departmental servers. However, this doesn't mean we should run all computations on our local computers. We have identified several situations in which it preferable to implement our seismological application programs in a distributed, server-based, computing model. In this model, application programs on the user's laptop, or local computer, invoke programs that run on an organizational server, and the results are returned to the invoking system. Situations in which a server-based architecture may be preferred include: (a) a program is written in a language, or written for an operating environment, that is unsupported on the local computer, (b) software libraries or utilities required to execute a program are not available on the users computer, (c) a computational program is physically too large, or computationally too expensive, to run on a users computer, (d) a user community wants to enforce a consistent method of performing a computation by standardizing on a single implementation of a program, and (e) the computational program may require current information, that is not available to all client computers. Until recently, distributed, server-based, computational capabilities were implemented using client/server architectures. In these architectures, client programs were often written in the same language, and they executed in the same computing environment, as the servers. Recently, a new distributed computational model, called Web Services, has been developed. Web Services are based on Internet standards such as XML, SOAP, WDSL, and UDDI. Web Services offer the promise of platform, and language, independent distributed computing. To investigate this new computational model, and to provide useful services to the SCEC Community, we have implemented several computational and utility programs using a Web Service architecture. We have hosted these Web Services as a part of the SCEC Community Modeling Environment (SCEC/CME) ITR Project (http://www.scec.org/cme). We have implemented Web Services for several of the reasons sited previously. For example, we implemented a FORTRAN-based Earthquake Rupture Forecast (ERF) as a Web Service for use by client computers that don't support a FORTRAN runtime environment. We implemented a Generic Mapping Tool (GMT) Web Service for use by systems that don't have local access to GMT. We implemented a Hazard Map Calculator Web Service to execute Hazard calculations that are too computationally intensive to run on a local system. We implemented a Coordinate Conversion Web Service to enforce a standard and consistent method for converting between UTM and Lat/Lon. Our experience developing these services indicates both strengths and weakness in current Web Service technology. Client programs that utilize Web Services typically need network access, a significant disadvantage at times. Programs with simple input and output parameters were the easiest to implement as Web Services, while programs with complex parameter-types required a significant amount of additional development. We also noted that Web services are very data-oriented, and adapting object-oriented software into the Web Service model proved problematic. Also, the Web Service approach of converting data types into XML format for network transmission has significant inefficiencies for some data sets.

The Organizational Role of Web Services

ERIC Educational Resources Information Center

Mitchell, Erik

2011-01-01

The workload of Web librarians is already split between Web-related and other library tasks. But today's technological environment has created new implications for existing services and new demands for staff time. It is time to reconsider how libraries can best allocate resources to provide effective Web services. Delivering high-quality services…

78 FR 60303 - Agency Information Collection Activities: Online Survey of Web Services Employers; New...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-01

...-NEW] Agency Information Collection Activities: Online Survey of Web Services Employers; New... Web site at http://www.Regulations.gov under e-Docket ID number USCIS-2013- 0003. When submitting... information collection. (2) Title of the Form/Collection: Online Survey of Web Services Employers. (3) Agency...

78 FR 42537 - Agency Information Collection Activities: Online Survey of Web Services Employers; New...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-16

...-NEW] Agency Information Collection Activities: Online Survey of Web Services Employers; New... Information Collection: New information collection. (2) Title of the Form/Collection: Online Survey of Web... sector. It is necessary that USCIS obtains data on the E-Verify Program Web Services. Gaining an...

A Web service substitution method based on service cluster nets

NASA Astrophysics Data System (ADS)

Du, YuYue; Gai, JunJing; Zhou, MengChu

2017-11-01

Service substitution is an important research topic in the fields of Web services and service-oriented computing. This work presents a novel method to analyse and substitute Web services. A new concept, called a Service Cluster Net Unit, is proposed based on Web service clusters. A service cluster is converted into a Service Cluster Net Unit. Then it is used to analyse whether the services in the cluster can satisfy some service requests. Meanwhile, the substitution methods of an atomic service and a composite service are proposed. The correctness of the proposed method is proved, and the effectiveness is shown and compared with the state-of-the-art method via an experiment. It can be readily applied to e-commerce service substitution to meet the business automation needs.

Tomcat, Oracle & XML Web Archive

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

Cothren, D. C.

2008-01-01

The TOX (Tomcat Oracle & XML) web archive is a foundation for development of HTTP-based applications using Tomcat (or some other servlet container) and an Oracle RDBMS. Use of TOX requires coding primarily in PL/SQL, JavaScript, and XSLT, but also in HTML, CSS and potentially Java. Coded in Java and PL/SQL itself, TOX provides the foundation for more complex applications to be built.

deepTools2: a next generation web server for deep-sequencing data analysis.

PubMed

Ramírez, Fidel; Ryan, Devon P; Grüning, Björn; Bhardwaj, Vivek; Kilpert, Fabian; Richter, Andreas S; Heyne, Steffen; Dündar, Friederike; Manke, Thomas

2016-07-08

We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data. Its core tool set, deepTools, allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. Since we first described our deepTools Galaxy server in 2014, we have implemented new solutions for many requests from the community and our users. Here, we introduce significant enhancements and new tools to further improve data visualization and interpretation. deepTools continue to be open to all users and freely available as a web service at deeptools.ie-freiburg.mpg.de The new deepTools2 suite can be easily deployed within any Galaxy framework via the toolshed repository, and we also provide source code for command line usage under Linux and Mac OS X. A public and documented API for access to deepTools functionality is also available. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Model-driven methodology for rapid deployment of smart spaces based on resource-oriented architectures.

PubMed

Corredor, Iván; Bernardos, Ana M; Iglesias, Josué; Casar, José R

2012-01-01

Advances in electronics nowadays facilitate the design of smart spaces based on physical mash-ups of sensor and actuator devices. At the same time, software paradigms such as Internet of Things (IoT) and Web of Things (WoT) are motivating the creation of technology to support the development and deployment of web-enabled embedded sensor and actuator devices with two major objectives: (i) to integrate sensing and actuating functionalities into everyday objects, and (ii) to easily allow a diversity of devices to plug into the Internet. Currently, developers who are applying this Internet-oriented approach need to have solid understanding about specific platforms and web technologies. In order to alleviate this development process, this research proposes a Resource-Oriented and Ontology-Driven Development (ROOD) methodology based on the Model Driven Architecture (MDA). This methodology aims at enabling the development of smart spaces through a set of modeling tools and semantic technologies that support the definition of the smart space and the automatic generation of code at hardware level. ROOD feasibility is demonstrated by building an adaptive health monitoring service for a Smart Gym.

Web Services as Public Services: Are We Supporting Our Busiest Service Point?

ERIC Educational Resources Information Center

Riley-Huff, Debra A.

2009-01-01

This article is an analysis of academic library organizational culture, patterns, and processes as they relate to Web services. Data gathered in a research survey is examined in an attempt to reveal current departmental and administrative attitudes, practices, and support for Web services in the library research environment. (Contains 10 tables.)

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

PubMed Central

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

2015-01-01

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

An Architecture for Autonomic Web Service Process Planning

NASA Astrophysics Data System (ADS)

Moore, Colm; Xue Wang, Ming; Pahl, Claus

Web service composition is a technology that has received considerable attention in the last number of years. Languages and tools to aid in the process of creating composite Web services have been received specific attention. Web service composition is the process of linking single Web services together in order to accomplish more complex tasks. One area of Web service composition that has not received as much attention is the area of dynamic error handling and re-planning, enabling autonomic composition. Given a repository of service descriptions and a task to complete, it is possible for AI planners to automatically create a plan that will achieve this goal. If however a service in the plan is unavailable or erroneous the plan will fail. Motivated by this problem, this paper suggests autonomous re-planning as a means to overcome dynamic problems. Our solution involves automatically recovering from faults and creating a context-dependent alternate plan. We present an architecture that serves as a basis for the central activities autonomous composition, monitoring and fault handling.

Domain-specific Web Service Discovery with Service Class Descriptions

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

Rocco, D; Caverlee, J; Liu, L

2005-02-14

This paper presents DynaBot, a domain-specific web service discovery system. The core idea of the DynaBot service discovery system is to use domain-specific service class descriptions powered by an intelligent Deep Web crawler. In contrast to current registry-based service discovery systems--like the several available UDDI registries--DynaBot promotes focused crawling of the Deep Web of services and discovers candidate services that are relevant to the domain of interest. It uses intelligent filtering algorithms to match services found by focused crawling with the domain-specific service class descriptions. We demonstrate the capability of DynaBot through the BLAST service discovery scenario and describe ourmore » initial experience with DynaBot.« less

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

DOE PAGES

Wilke, Andreas; Bischof, Jared; Harrison, Travis; ...

2015-01-08

Metagenomic sequencing has produced significant amounts of data in recent years. For example, as of summer 2013, MGRAST 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, asmore » 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.« less

A RESTful API for Accessing Microbial Community Data for MG-RAST

PubMed Central

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. PMID:25569221

BioRuby: bioinformatics software for the Ruby programming language.

PubMed

Goto, Naohisa; Prins, Pjotr; Nakao, Mitsuteru; Bonnal, Raoul; Aerts, Jan; Katayama, Toshiaki

2010-10-15

The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser. BioRuby is free and open source software, made available under the Ruby license. BioRuby runs on all platforms that support Ruby, including Linux, Mac OS X and Windows. And, with JRuby, BioRuby runs on the Java Virtual Machine. The source code is available from http://www.bioruby.org/. katayama@bioruby.org

QMachine: commodity supercomputing in web browsers.

PubMed

Wilkinson, Sean R; Almeida, Jonas S

2014-06-09

Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for querying, processing, and visualizing genomics' "Big Data" from sources like The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) without local software installation or configuration. The design of QMachine (QM) was driven by the opportunity to use this pervasive computing model in the context of the Web of Linked Data in Biomedicine. QM is an open-sourced, publicly available web service that acts as a messaging system for posting tasks and retrieving results over HTTP. The illustrative application described here distributes the analyses of 20 Streptococcus pneumoniae genomes for shared suffixes. Because all analytical and data retrieval tasks are executed by volunteer machines, few server resources are required. Any modern web browser can submit those tasks and/or volunteer to execute them without installing any extra plugins or programs. A client library provides high-level distribution templates including MapReduce. This stark departure from the current reliance on expensive server hardware running "download and install" software has already gathered substantial community interest, as QM received more than 2.2 million API calls from 87 countries in 12 months. QM was found adequate to deliver the sort of scalable bioinformatics solutions that computation- and data-intensive workflows require. Paradoxically, the sandboxed execution of code by web browsers was also found to enable them, as compute nodes, to address critical privacy concerns that characterize biomedical environments.

Available, intuitive and free! Building e-learning modules using web 2.0 services.

PubMed

Tam, Chun Wah Michael; Eastwood, Anne

2012-01-01

E-learning is part of the mainstream in medical education and often provides the most efficient and effective means of engaging learners in a particular topic. However, translating design and content ideas into a useable product can be technically challenging, especially in the absence of information technology (IT) support. There is little published literature on the use of web 2.0 services to build e-learning activities. To describe the web 2.0 tools and solutions employed to build the GP Synergy evidence-based medicine and critical appraisal online course. We used and integrated a number of free web 2.0 services including: Prezi, a web-based presentation platform; YouTube, a video sharing service; Google Docs, a online document platform; Tiny.cc, a URL shortening service; and Wordpress, a blogging platform. The course consisting of five multimedia-rich, tutorial-like modules was built without IT specialist assistance or specialised software. The web 2.0 services used were free. The course can be accessed with a modern web browser. Modern web 2.0 services remove many of the technical barriers for creating and sharing content on the internet. When used synergistically, these services can be a flexible and low-cost platform for building e-learning activities. They were a pragmatic solution in our context.

76 FR 28439 - Submission for OMB Review; Comment Request; NCI Cancer Genetics Services Directory Web-Based...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-17

...; Comment Request; NCI Cancer Genetics Services Directory Web-Based Application Form and Update Mailer... currently valid OMB control number. Proposed Collection: Title: NCI Cancer Genetics Services Directory Web... application form and the Web-based update mailer is to collect information about genetics professionals to be...

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.

Discectomy-related information on the internet: does the quality follow the surge?

PubMed

Elhassan, Yahya; Sheridan, Gerard; Nassiri, Mujtaba; Osman, Mugtaba; Kiely, Pat; Noel, Jacques

2015-01-15

A quality-control Internet-based study using recognized quality-scoring systems. To evaluate the quality of information available on the Internet. Quality of health information on the Internet is of much concern and the emphasis for appraisal of Internet Web sites is needed. This study is to determine if it has improved with the surge in Internet usage. The 3 most commonly used search engines were identified and a search for "Discectomy" was performed on each. Two reviewers categorized the Web sites according to their types and the quality of each was assessed using recognized scoring systems including the Journal of the American Medical Association (JAMA) benchmark, DISCERN score, and discectomy-specific content score. The quality of the information was also assessed according to the presence and absence of the Health on the Net code. Fifty-three Web sites were identified, and analyzed. Commercial Web sites were predominant, 24 of them were identified, 7 were governmental, 6 were produced by physicians, none were produced by allied health professionals, 3 were academic, 4 were public health information Web sites, 4 were attached to social media and discussion groups, 3 were related to media, and 2 were unspecified. Internet sites with a Health on the Net code demonstrated significantly higher quality than those without the code (P < 0.0001). Public health information Web sites attained the highest overall DISCERN and discectomy-specific scores followed by Web sites of the government and nonprofit organizations. The overall quality of information regarding discectomy remains poor and variable despite an exponential increase in the number of users and Web sites, with a slight trend toward improvement, only 20% to 30% are of good quality, compared with that 10 years ago (<10%). Presence of Health on the Net code is a very reliable marker for health information quality.

76 FR 14034 - Proposed Collection; Comment Request; NCI Cancer Genetics Services Directory Web-Based...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-15

... Request; NCI Cancer Genetics Services Directory Web-Based Application Form and Update Mailer Summary: In... Cancer Genetics Services Directory Web-based Application Form and Update Mailer. [[Page 14035

Web Application Software for Ground Operations Planning Database (GOPDb) Management

NASA Technical Reports Server (NTRS)

Lanham, Clifton; Kallner, Shawn; Gernand, Jeffrey

2013-01-01

A Web application facilitates collaborative development of the ground operations planning document. This will reduce costs and development time for new programs by incorporating the data governance, access control, and revision tracking of the ground operations planning data. Ground Operations Planning requires the creation and maintenance of detailed timelines and documentation. The GOPDb Web application was created using state-of-the-art Web 2.0 technologies, and was deployed as SaaS (Software as a Service), with an emphasis on data governance and security needs. Application access is managed using two-factor authentication, with data write permissions tied to user roles and responsibilities. Multiple instances of the application can be deployed on a Web server to meet the robust needs for multiple, future programs with minimal additional cost. This innovation features high availability and scalability, with no additional software that needs to be bought or installed. For data governance and security (data quality, management, business process management, and risk management for data handling), the software uses NAMS. No local copy/cloning of data is permitted. Data change log/tracking is addressed, as well as collaboration, work flow, and process standardization. The software provides on-line documentation and detailed Web-based help. There are multiple ways that this software can be deployed on a Web server to meet ground operations planning needs for future programs. The software could be used to support commercial crew ground operations planning, as well as commercial payload/satellite ground operations planning. The application source code and database schema are owned by NASA.

Virtual machine provisioning, code management, and data movement design for the Fermilab HEPCloud Facility

NASA Astrophysics Data System (ADS)

Timm, S.; Cooper, G.; Fuess, S.; Garzoglio, G.; Holzman, B.; Kennedy, R.; Grassano, D.; Tiradani, A.; Krishnamurthy, R.; Vinayagam, S.; Raicu, I.; Wu, H.; Ren, S.; Noh, S.-Y.

2017-10-01

The Fermilab HEPCloud Facility Project has as its goal to extend the current Fermilab facility interface to provide transparent access to disparate resources including commercial and community clouds, grid federations, and HPC centers. This facility enables experiments to perform the full spectrum of computing tasks, including data-intensive simulation and reconstruction. We have evaluated the use of the commercial cloud to provide elasticity to respond to peaks of demand without overprovisioning local resources. Full scale data-intensive workflows have been successfully completed on Amazon Web Services for two High Energy Physics Experiments, CMS and NOνA, at the scale of 58000 simultaneous cores. This paper describes the significant improvements that were made to the virtual machine provisioning system, code caching system, and data movement system to accomplish this work. The virtual image provisioning and contextualization service was extended to multiple AWS regions, and to support experiment-specific data configurations. A prototype Decision Engine was written to determine the optimal availability zone and instance type to run on, minimizing cost and job interruptions. We have deployed a scalable on-demand caching service to deliver code and database information to jobs running on the commercial cloud. It uses the frontiersquid server and CERN VM File System (CVMFS) clients on EC2 instances and utilizes various services provided by AWS to build the infrastructure (stack). We discuss the architecture and load testing benchmarks on the squid servers. We also describe various approaches that were evaluated to transport experimental data to and from the cloud, and the optimal solutions that were used for the bulk of the data transport. Finally, we summarize lessons learned from this scale test, and our future plans to expand and improve the Fermilab HEP Cloud Facility.

Virtual Machine Provisioning, Code Management, and Data Movement Design for the Fermilab HEPCloud Facility

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

Timm, S.; Cooper, G.; Fuess, S.

The Fermilab HEPCloud Facility Project has as its goal to extend the current Fermilab facility interface to provide transparent access to disparate resources including commercial and community clouds, grid federations, and HPC centers. This facility enables experiments to perform the full spectrum of computing tasks, including data-intensive simulation and reconstruction. We have evaluated the use of the commercial cloud to provide elasticity to respond to peaks of demand without overprovisioning local resources. Full scale data-intensive workflows have been successfully completed on Amazon Web Services for two High Energy Physics Experiments, CMS and NOνA, at the scale of 58000 simultaneous cores.more » This paper describes the significant improvements that were made to the virtual machine provisioning system, code caching system, and data movement system to accomplish this work. The virtual image provisioning and contextualization service was extended to multiple AWS regions, and to support experiment-specific data configurations. A prototype Decision Engine was written to determine the optimal availability zone and instance type to run on, minimizing cost and job interruptions. We have deployed a scalable on-demand caching service to deliver code and database information to jobs running on the commercial cloud. It uses the frontiersquid server and CERN VM File System (CVMFS) clients on EC2 instances and utilizes various services provided by AWS to build the infrastructure (stack). We discuss the architecture and load testing benchmarks on the squid servers. We also describe various approaches that were evaluated to transport experimental data to and from the cloud, and the optimal solutions that were used for the bulk of the data transport. Finally, we summarize lessons learned from this scale test, and our future plans to expand and improve the Fermilab HEP Cloud Facility.« less

Database Resources of the BIG Data Center in 2018

PubMed Central

Xu, Xingjian; Hao, Lili; Zhu, Junwei; Tang, Bixia; Zhou, Qing; Song, Fuhai; Chen, Tingting; Zhang, Sisi; Dong, Lili; Lan, Li; Wang, Yanqing; Sang, Jian; Hao, Lili; Liang, Fang; Cao, Jiabao; Liu, Fang; Liu, Lin; Wang, Fan; Ma, Yingke; Xu, Xingjian; Zhang, Lijuan; Chen, Meili; Tian, Dongmei; Li, Cuiping; Dong, Lili; Du, Zhenglin; Yuan, Na; Zeng, Jingyao; Zhang, Zhewen; Wang, Jinyue; Shi, Shuo; Zhang, Yadong; Pan, Mengyu; Tang, Bixia; Zou, Dong; Song, Shuhui; Sang, Jian; Xia, Lin; Wang, Zhennan; Li, Man; Cao, Jiabao; Niu, Guangyi; Zhang, Yang; Sheng, Xin; Lu, Mingming; Wang, Qi; Xiao, Jingfa; Zou, Dong; Wang, Fan; Hao, Lili; Liang, Fang; Li, Mengwei; Sun, Shixiang; Zou, Dong; Li, Rujiao; Yu, Chunlei; Wang, Guangyu; Sang, Jian; Liu, Lin; Li, Mengwei; Li, Man; Niu, Guangyi; Cao, Jiabao; Sun, Shixiang; Xia, Lin; Yin, Hongyan; Zou, Dong; Xu, Xingjian; Ma, Lina; Chen, Huanxin; Sun, Yubin; Yu, Lei; Zhai, Shuang; Sun, Mingyuan; Zhang, Zhang; Zhao, Wenming; Xiao, Jingfa; Bao, Yiming; Song, Shuhui; Hao, Lili; Li, Rujiao; Ma, Lina; Sang, Jian; Wang, Yanqing; Tang, Bixia; Zou, Dong; Wang, Fan

2018-01-01

Abstract The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. PMID:29036542

OneGeology Web Services and Portal as a global geological SDI - latest standards and technology

NASA Astrophysics Data System (ADS)

Duffy, Tim; Tellez-Arenas, Agnes

2014-05-01

The global coverage of OneGeology Web Services (www.onegeology.org and portal.onegeology.org) achieved since 2007 from the 120 participating geological surveys will be reviewed and issues arising discussed. Recent enhancements to the OneGeology Web Services capabilities will be covered including new up to 5 star service accreditation scheme utilising the ISO/OGC Web Mapping Service standard version 1.3, core ISO 19115 metadata additions and Version 2.0 Web Feature Services (WFS) serving the new IUGS-CGI GeoSciML V3.2 geological web data exchange language standard (http://www.geosciml.org/) with its associated 30+ IUGS-CGI available vocabularies (http://resource.geosciml.org/ and http://srvgeosciml.brgm.fr/eXist2010/brgm/client.html). Use of the CGI simpelithology and timescale dictionaries now allow those who wish to do so to offer data harmonisation to query their GeoSciML 3.2 based Web Feature Services and their GeoSciML_Portrayal V2.0.1 (http://www.geosciml.org/) Web Map Services in the OneGeology portal (http://portal.onegeology.org). Contributing to OneGeology involves offering to serve ideally 1:1000,000 scale geological data (in practice any scale now is warmly welcomed) as an OGC (Open Geospatial Consortium) standard based WMS (Web Mapping Service) service from an available WWW server. This may either be hosted within the Geological Survey or a neighbouring, regional or elsewhere institution that offers to serve that data for them i.e. offers to help technically by providing the web serving IT infrastructure as a 'buddy'. OneGeology is a standards focussed Spatial Data Infrastructure (SDI) and works to ensure that these standards work together and it is now possible for European Geological Surveys to register their INSPIRE web services within the OneGeology SDI (e.g. see http://www.geosciml.org/geosciml/3.2/documentation/cookbook/INSPIRE_GeoSciML_Cookbook%20_1.0.pdf). The Onegeology portal (http://portal.onegeology.org) is the first port of call for anyone wishing to discover the availability of global geological web services and has new functionality to view and use such services including multiple projection support. KEYWORDS : OneGeology; GeoSciML V 3.2; Data exchange; Portal; INSPIRE; Standards; OGC; Interoperability; GeoScience information; WMS; WFS; Cookbook.

Web Services and Other Enhancements at the Northern California Earthquake Data Center

NASA Astrophysics Data System (ADS)

Neuhauser, D. S.; Zuzlewski, S.; Allen, R. M.

2012-12-01

The Northern California Earthquake Data Center (NCEDC) provides data archive and distribution services for seismological and geophysical data sets that encompass northern California. The NCEDC is enhancing its ability to deliver rapid information through Web Services. NCEDC Web Services use well-established web server and client protocols and REST software architecture to allow users to easily make queries using web browsers or simple program interfaces and to receive the requested data in real-time rather than through batch or email-based requests. Data are returned to the user in the appropriate format such as XML, RESP, or MiniSEED depending on the service, and are compatible with the equivalent IRIS DMC web services. The NCEDC is currently providing the following Web Services: (1) Station inventory and channel response information delivered in StationXML format, (2) Channel response information delivered in RESP format, (3) Time series availability delivered in text and XML formats, (4) Single channel and bulk data request delivered in MiniSEED format. The NCEDC is also developing a rich Earthquake Catalog Web Service to allow users to query earthquake catalogs based on selection parameters such as time, location or geographic region, magnitude, depth, azimuthal gap, and rms. It will return (in QuakeML format) user-specified results that can include simple earthquake parameters, as well as observations such as phase arrivals, codas, amplitudes, and computed parameters such as first motion mechanisms, moment tensors, and rupture length. The NCEDC will work with both IRIS and the International Federation of Digital Seismograph Networks (FDSN) to define a uniform set of web service specifications that can be implemented by multiple data centers to provide users with a common data interface across data centers. The NCEDC now hosts earthquake catalogs and waveforms from the US Department of Energy (DOE) Enhanced Geothermal Systems (EGS) monitoring networks. These data can be accessed through the above web services and through special NCEDC web pages.

The use of quality benchmarking in assessing web resources for the dermatology virtual branch library of the National electronic Library for Health (NeLH).

PubMed

Kamel Boulos, M N; Roudsari, A V; Gordon, C; Muir Gray, J A

2001-01-01

In 1998, the U.K. National Health Service Information for Health Strategy proposed the implementation of a National electronic Library for Health to provide clinicians, healthcare managers and planners, patients and the public with easy, round the clock access to high quality, up-to-date electronic information on health and healthcare. The Virtual Branch Libraries are among the most important components of the National electronic Library for Health. They aim at creating online knowledge based communities, each concerned with some specific clinical and other health-related topics. This study is about the envisaged Dermatology Virtual Branch Libraries of the National electronic Library for Health. It aims at selecting suitable dermatology Web resources for inclusion in the forthcoming Virtual Branch Libraries after establishing preliminary quality benchmarking rules for this task. Psoriasis, being a common dermatological condition, has been chosen as a starting point. Because quality is a principal concern of the National electronic Library for Health, the study includes a review of the major quality benchmarking systems available today for assessing health-related Web sites. The methodology of developing a quality benchmarking system has been also reviewed. Aided by metasearch Web tools, candidate resources were hand-selected in light of the reviewed benchmarking systems and specific criteria set by the authors. Over 90 professional and patient-oriented Web resources on psoriasis and dermatology in general are suggested for inclusion in the forthcoming Dermatology Virtual Branch Libraries. The idea of an all-in knowledge-hallmarking instrument for the National electronic Library for Health is also proposed based on the reviewed quality benchmarking systems. Skilled, methodical, organized human reviewing, selection and filtering based on well-defined quality appraisal criteria seems likely to be the key ingredient in the envisaged National electronic Library for Health service. Furthermore, by promoting the application of agreed quality guidelines and codes of ethics by all health information providers and not just within the National electronic Library for Health, the overall quality of the Web will improve with time and the Web will ultimately become a reliable and integral part of the care space.

Research of three level match method about semantic web service based on ontology

NASA Astrophysics Data System (ADS)

Xiao, Jie; Cai, Fang

2011-10-01

An important step of Web service Application is the discovery of useful services. Keywords are used in service discovery in traditional technology like UDDI and WSDL, with the disadvantage of user intervention, lack of semantic description and low accuracy. To cope with these problems, OWL-S is introduced and extended with QoS attributes to describe the attribute and functions of Web Services. A three-level service matching algorithm based on ontology and QOS in proposed in this paper. Our algorithm can match web service by utilizing the service profile, QoS parameters together with input and output of the service. Simulation results shows that it greatly enhanced the speed of service matching while high accuracy is also guaranteed.

Interoperability And Value Added To Earth Observation Data

NASA Astrophysics Data System (ADS)

Gasperi, J.

2012-04-01

Geospatial web services technology has provided a new means for geospatial data interoperability. Open Geospatial Consortium (OGC) services such as Web Map Service (WMS) to request maps on the Internet, Web Feature Service (WFS) to exchange vectors or Catalog Service for the Web (CSW) to search for geospatialized data have been widely adopted in the Geosciences community in general and in the remote sensing community in particular. These services make Earth Observation data available to a wider range of public users than ever before. The mapshup web client offers an innovative and efficient user interface that takes advantage of the power of interoperability. This presentation will demonstrate how mapshup can be effectively used in the context of natural disasters management.

SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services

PubMed Central

Gessler, Damian DG; Schiltz, Gary S; May, Greg D; Avraham, Shulamit; Town, Christopher D; Grant, David; Nelson, Rex T

2009-01-01

Background SSWAP (Simple Semantic Web Architecture and Protocol; pronounced "swap") is an architecture, protocol, and platform for using reasoning to semantically integrate heterogeneous disparate data and services on the web. SSWAP was developed as a hybrid semantic web services technology to overcome limitations found in both pure web service technologies and pure semantic web technologies. Results There are currently over 2400 resources published in SSWAP. Approximately two dozen are custom-written services for QTL (Quantitative Trait Loci) and mapping data for legumes and grasses (grains). The remaining are wrappers to Nucleic Acids Research Database and Web Server entries. As an architecture, SSWAP establishes how clients (users of data, services, and ontologies), providers (suppliers of data, services, and ontologies), and discovery servers (semantic search engines) interact to allow for the description, querying, discovery, invocation, and response of semantic web services. As a protocol, SSWAP provides the vocabulary and semantics to allow clients, providers, and discovery servers to engage in semantic web services. The protocol is based on the W3C-sanctioned first-order description logic language OWL DL. As an open source platform, a discovery server running at (as in to "swap info") uses the description logic reasoner Pellet to integrate semantic resources. The platform hosts an interactive guide to the protocol at , developer tools at , and a portal to third-party ontologies at (a "swap meet"). Conclusion SSWAP addresses the three basic requirements of a semantic web services architecture (i.e., a common syntax, shared semantic, and semantic discovery) while addressing three technology limitations common in distributed service systems: i.e., i) the fatal mutability of traditional interfaces, ii) the rigidity and fragility of static subsumption hierarchies, and iii) the confounding of content, structure, and presentation. SSWAP is novel by establishing the concept of a canonical yet mutable OWL DL graph that allows data and service providers to describe their resources, to allow discovery servers to offer semantically rich search engines, to allow clients to discover and invoke those resources, and to allow providers to respond with semantically tagged data. SSWAP allows for a mix-and-match of terms from both new and legacy third-party ontologies in these graphs. PMID:19775460

39 CFR 3001.12 - Service of documents.

Code of Federal Regulations, 2010 CFR

2010-07-01

... or presiding officer has determined is unable to receive service through the Commission's Web site... presiding officer has determined is unable to receive service through the Commission Web site shall be by... service list for each current proceeding will be available on the Commission's Web site http://www.prc.gov...

New Web Server - the Java Version of Tempest - Produced

NASA Technical Reports Server (NTRS)

York, David W.; Ponyik, Joseph G.

2000-01-01

A new software design and development effort has produced a Java (Sun Microsystems, Inc.) version of the award-winning Tempest software (refs. 1 and 2). In 1999, the Embedded Web Technology (EWT) team received a prestigious R&D 100 Award for Tempest, Java Version. In this article, "Tempest" will refer to the Java version of Tempest, a World Wide Web server for desktop or embedded systems. Tempest was designed at the NASA Glenn Research Center at Lewis Field to run on any platform for which a Java Virtual Machine (JVM, Sun Microsystems, Inc.) exists. The JVM acts as a translator between the native code of the platform and the byte code of Tempest, which is compiled in Java. These byte code files are Java executables with a ".class" extension. Multiple byte code files can be zipped together as a "*.jar" file for more efficient transmission over the Internet. Today's popular browsers, such as Netscape (Netscape Communications Corporation) and Internet Explorer (Microsoft Corporation) have built-in Virtual Machines to display Java applets.

ChemCalc: a building block for tomorrow's chemical infrastructure.

PubMed

Patiny, Luc; Borel, Alain

2013-05-24

Web services, as an aspect of cloud computing, are becoming an important part of the general IT infrastructure, and scientific computing is no exception to this trend. We propose a simple approach to develop chemical Web services, through which servers could expose the essential data manipulation functionality that students and researchers need for chemical calculations. These services return their results as JSON (JavaScript Object Notation) objects, which facilitates their use for Web applications. The ChemCalc project http://www.chemcalc.org demonstrates this approach: we present three Web services related with mass spectrometry, namely isotopic distribution simulation, peptide fragmentation simulation, and molecular formula determination. We also developed a complete Web application based on these three Web services, taking advantage of modern HTML5 and JavaScript libraries (ChemDoodle and jQuery).

User-driven Cloud Implementation of environmental models and data for all

NASA Astrophysics Data System (ADS)

Gurney, R. J.; Percy, B. J.; Elkhatib, Y.; Blair, G. S.

2014-12-01

Environmental data and models come from disparate sources over a variety of geographical and temporal scales with different resolutions and data standards, often including terabytes of data and model simulations. Unfortunately, these data and models tend to remain solely within the custody of the private and public organisations which create the data, and the scientists who build models and generate results. Although many models and datasets are theoretically available to others, the lack of ease of access tends to keep them out of reach of many. We have developed an intuitive web-based tool that utilises environmental models and datasets located in a cloud to produce results that are appropriate to the user. Storyboards showing the interfaces and visualisations have been created for each of several exemplars. A library of virtual machine images has been prepared to serve these exemplars. Each virtual machine image has been tailored to run computer models appropriate to the end user. Two approaches have been used; first as RESTful web services conforming to the Open Geospatial Consortium (OGC) Web Processing Service (WPS) interface standard using the Python-based PyWPS; second, a MySQL database interrogated using PHP code. In all cases, the web client sends the server an HTTP GET request to execute the process with a number of parameter values and, once execution terminates, an XML or JSON response is sent back and parsed at the client side to extract the results. All web services are stateless, i.e. application state is not maintained by the server, reducing its operational overheads and simplifying infrastructure management tasks such as load balancing and failure recovery. A hybrid cloud solution has been used with models and data sited on both private and public clouds. The storyboards have been transformed into intuitive web interfaces at the client side using HTML, CSS and JavaScript, utilising plug-ins such as jQuery and Flot (for graphics), and Google Maps APIs. We have demonstrated that a cloud infrastructure can be used to assemble a virtual research environment that, coupled with a user-driven development approach, is able to cater to the needs of a wide range of user groups, from domain experts to concerned members of the general public.

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.

Real-time Shakemap implementation in Austria

NASA Astrophysics Data System (ADS)

Weginger, Stefan; Jia, Yan; Papi Isaba, Maria; Horn, Nikolaus

2017-04-01

ShakeMaps provide near-real-time maps of ground motion and shaking intensity following significant earthquakes. They are automatically generated within a few minutes after occurrence of an earthquake. We tested and included the USGS ShakeMap 4.0 (experimental code) based on python in the Antelope real-time system with local modified GMPE and Site Effects based on the conditions in Austria. The ShakeMaps are provided in terms of Intensity, PGA, PGV and PSA. Future presentation of ShakeMap contour lines and Ground Motion Parameter with interactive maps and data exchange over Web-Services are shown.

Mobile Cloud Computing with SOAP and REST Web Services

NASA Astrophysics Data System (ADS)

Ali, Mushtaq; Fadli Zolkipli, Mohamad; Mohamad Zain, Jasni; Anwar, Shahid

2018-05-01

Mobile computing in conjunction with Mobile web services drives a strong approach where the limitations of mobile devices may possibly be tackled. Mobile Web Services are based on two types of technologies; SOAP and REST, which works with the existing protocols to develop Web services. Both the approaches carry their own distinct features, yet to keep the constraint features of mobile devices in mind, the better in two is considered to be the one which minimize the computation and transmission overhead while offloading. The load transferring of mobile device to remote servers for execution called computational offloading. There are numerous approaches to implement computational offloading a viable solution for eradicating the resources constraints of mobile device, yet a dynamic method of computational offloading is always required for a smooth and simple migration of complex tasks. The intention of this work is to present a distinctive approach which may not engage the mobile resources for longer time. The concept of web services utilized in our work to delegate the computational intensive tasks for remote execution. We tested both SOAP Web services approach and REST Web Services for mobile computing. Two parameters considered in our lab experiments to test; Execution Time and Energy Consumption. The results show that RESTful Web services execution is far better than executing the same application by SOAP Web services approach, in terms of execution time and energy consumption. Conducting experiments with the developed prototype matrix multiplication app, REST execution time is about 200% better than SOAP execution approach. In case of energy consumption REST execution is about 250% better than SOAP execution approach.

Adopting and adapting a commercial view of web services for the Navy

NASA Astrophysics Data System (ADS)

Warner, Elizabeth; Ladner, Roy; Katikaneni, Uday; Petry, Fred

2005-05-01

Web Services are being adopted as the enabling technology to provide net-centric capabilities for many Department of Defense operations. The Navy Enterprise Portal, for example, is Web Services-based, and the Department of the Navy is promulgating guidance for developing Web Services. Web Services, however, only constitute a baseline specification that provides the foundation on which users, under current approaches, write specialized applications in order to retrieve data over the Internet. Application development may increase dramatically as the number of different available Web Services increases. Reasons for specialized application development include XML schema versioning differences, adoption/use of diverse business rules, security access issues, and time/parameter naming constraints, among others. We are currently developing for the US Navy a system which will improve delivery of timely and relevant meteorological and oceanographic (MetOc) data to the warfighter. Our objective is to develop an Advanced MetOc Broker (AMB) that leverages Web Services technology to identify, retrieve and integrate relevant MetOc data in an automated manner. The AMB will utilize a Mediator, which will be developed by applying ontological research and schema matching techniques to MetOc forms of data. The AMB, using the Mediator, will support a new, advanced approach to the use of Web Services; namely, the automated identification, retrieval and integration of MetOc data. Systems based on this approach will then not require extensive end-user application development for each Web Service from which data can be retrieved. Users anywhere on the globe will be able to receive timely environmental data that fits their particular needs.

Discovery Mechanisms for the Sensor Web

PubMed Central

Jirka, Simon; Bröring, Arne; Stasch, Christoph

2009-01-01

This paper addresses the discovery of sensors within the OGC Sensor Web Enablement framework. Whereas services like the OGC Web Map Service or Web Coverage Service are already well supported through catalogue services, the field of sensor networks and the according discovery mechanisms is still a challenge. The focus within this article will be on the use of existing OGC Sensor Web components for realizing a discovery solution. After discussing the requirements for a Sensor Web discovery mechanism, an approach will be presented that was developed within the EU funded project “OSIRIS”. This solution offers mechanisms to search for sensors, exploit basic semantic relationships, harvest sensor metadata and integrate sensor discovery into already existing catalogues. PMID:22574038

AdaFF: Adaptive Failure-Handling Framework for Composite Web Services

NASA Astrophysics Data System (ADS)

Kim, Yuna; Lee, Wan Yeon; Kim, Kyong Hoon; Kim, Jong

In this paper, we propose a novel Web service composition framework which dynamically accommodates various failure recovery requirements. In the proposed framework called Adaptive Failure-handling Framework (AdaFF), failure-handling submodules are prepared during the design of a composite service, and some of them are systematically selected and automatically combined with the composite Web service at service instantiation in accordance with the requirement of individual users. In contrast, existing frameworks cannot adapt the failure-handling behaviors to user's requirements. AdaFF rapidly delivers a composite service supporting the requirement-matched failure handling without manual development, and contributes to a flexible composite Web service design in that service architects never care about failure handling or variable requirements of users. For proof of concept, we implement a prototype system of the AdaFF, which automatically generates a composite service instance with Web Services Business Process Execution Language (WS-BPEL) according to the users' requirement specified in XML format and executes the generated instance on the ActiveBPEL engine.

A New Approach for Semantic Web Matching

NASA Astrophysics Data System (ADS)

Zamanifar, Kamran; Heidary, Golsa; Nematbakhsh, Naser; Mardukhi, Farhad

In this work we propose a new approach for semantic web matching to improve the performance of Web Service replacement. Because in automatic systems we should ensure the self-healing, self-configuration, self-optimization and self-management, all services should be always available and if one of them crashes, it should be replaced with the most similar one. Candidate services are advertised in Universal Description, Discovery and Integration (UDDI) all in Web Ontology Language (OWL). By the help of bipartite graph, we did the matching between the crashed service and a Candidate one. Then we chose the best service, which had the maximum rate of matching. In fact we compare two services' functionalities and capabilities to see how much they match. We found that the best way for matching two web services, is comparing the functionalities of them.

Climatological Data Option in My Weather Impacts Decision Aid (MyWIDA) Overview

DTIC Science & Technology

2017-07-18

rules. It consists of 2 databases, a data service server, a collection of web service, and web applications that show weather impacts on selected...3.1.2 ClimoDB 5 3.2 Data Service 5 3.2.1 Data Requestor 5 3.2.2 Data Decoder 6 3.2.3 Post Processor 6 3.2.4 Job Scheduler 6 3.3 Web Service 6...6.1 Additional Data Option 9 6.2 Impact Overlay Web Service 9 6.3 Graphical User Interface 9 7. References 10 List of Symbols, Abbreviations, and

Alignment-Annotator web server: rendering and annotating sequence alignments.

PubMed

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-07-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Alignment-Annotator web server: rendering and annotating sequence alignments

PubMed Central

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-01-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. Availability: http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. PMID:24813445

Using QR Codes to Differentiate Learning for Gifted and Talented Students

ERIC Educational Resources Information Center

Siegle, Del

2015-01-01

QR codes are two-dimensional square patterns that are capable of coding information that ranges from web addresses to links to YouTube video. The codes save time typing and eliminate errors in entering addresses incorrectly. These codes make learning with technology easier for students and motivationally engage them in news ways.

[Study of efficiancy of teleconsultation: the Telepathology Consultation Service of the Professional Assoziation of German Pathologists for the screening program of breast carcinoma].

PubMed

Schrader, T; Hufnagl, P; Schlake, W; Dietel, M

2005-01-01

In the autumn a German screening program was started for detecting breast cancer in the population of women fifty and above. For the first time in this program, quality assurance rules were established: All statements of the radiologists and pathologists have to be confirmed by a second opinion. This improvement in quality is combined with a delay in time and additional expence. A new Telepathology Consultation Service was developed based on the experiences of the Telepathology Consultation Center of the UICC to speed up the second opinion process. The complete web-based service is operated under MS Windows 2003 Server, as web server the Internet Information Server, and the SQL-Server (both Microsoft) as the database. The websites, forms and control mechanism have been coded in by ASP scripts and JavaScript. A study to evaluate the effectiveness of telepathological consultation in comparison to conventional consultation has been carried out. Pathologists of the Professional Association of German Pathologists took part as well as requesting pathologists and as consultants for other participants. The quality of telepathological diagnosis was comparable to the conventional diagnosis. Telepathology allows a faster respond of 1 to 2 day (conventional postal delay). The time to prepare a telepathology request is about twice as conventional. This ratio may be inverted by an interface between the Pathology Information System and the Telepathology Server and the use of virtual microscopy. The Telepathology Consultation Service of the Professional Association of German Pathologists is a fast and effective German-language, internet-based service for obtaining a second opinion.

Managing World Wide Web Information in a Frames Environment: A Guide to Constructing Web Pages Using Frames.

ERIC Educational Resources Information Center

Gilstrap, Donald L.

1998-01-01

Explains how to build World Wide Web home pages using frames-based HTML so that librarians can manage Web-based information and improve their home pages. Provides descriptions and 15 examples for writing frames-HTML code, including advanced concepts and additional techniques for home-page design. (Author/LRW)

Design and implementation of CUAHSI WaterML and WaterOneFlow Web Services

NASA Astrophysics Data System (ADS)

Valentine, D. W.; Zaslavsky, I.; Whitenack, T.; Maidment, D.

2007-12-01

WaterOneFlow is a term for a group of web services created by and for the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) community. CUAHSI web services facilitate the retrieval of hydrologic observations information from online data sources using the SOAP protocol. CUAHSI Water Markup Language (below referred to as WaterML) is an XML schema defining the format of messages returned by the WaterOneFlow web services. \

Processing biological literature with customizable Web services supporting interoperable formats.

PubMed

Rak, Rafal; Batista-Navarro, Riza Theresa; Carter, Jacob; Rowley, Andrew; Ananiadou, Sophia

2014-01-01

Web services have become a popular means of interconnecting solutions for processing a body of scientific literature. This has fuelled research on high-level data exchange formats suitable for a given domain and ensuring the interoperability of Web services. In this article, we focus on the biological domain and consider four interoperability formats, BioC, BioNLP, XMI and RDF, that represent domain-specific and generic representations and include well-established as well as emerging specifications. We use the formats in the context of customizable Web services created in our Web-based, text-mining workbench Argo that features an ever-growing library of elementary analytics and capabilities to build and deploy Web services straight from a convenient graphical user interface. We demonstrate a 2-fold customization of Web services: by building task-specific processing pipelines from a repository of available analytics, and by configuring services to accept and produce a combination of input and output data interchange formats. We provide qualitative evaluation of the formats as well as quantitative evaluation of automatic analytics. The latter was carried out as part of our participation in the fourth edition of the BioCreative challenge. Our analytics built into Web services for recognizing biochemical concepts in BioC collections achieved the highest combined scores out of 10 participating teams. Database URL: http://argo.nactem.ac.uk. © The Author(s) 2014. Published by Oxford University Press.

Data partitioning enables the use of standard SOAP Web Services in genome-scale workflows.

PubMed

Sztromwasser, Pawel; Puntervoll, Pål; Petersen, Kjell

2011-07-26

Biological databases and computational biology tools are provided by research groups around the world, and made accessible on the Web. Combining these resources is a common practice in bioinformatics, but integration of heterogeneous and often distributed tools and datasets can be challenging. To date, this challenge has been commonly addressed in a pragmatic way, by tedious and error-prone scripting. Recently however a more reliable technique has been identified and proposed as the platform that would tie together bioinformatics resources, namely Web Services. In the last decade the Web Services have spread wide in bioinformatics, and earned the title of recommended technology. However, in the era of high-throughput experimentation, a major concern regarding Web Services is their ability to handle large-scale data traffic. We propose a stream-like communication pattern for standard SOAP Web Services, that enables efficient flow of large data traffic between a workflow orchestrator and Web Services. We evaluated the data-partitioning strategy by comparing it with typical communication patterns on an example pipeline for genomic sequence annotation. The results show that data-partitioning lowers resource demands of services and increases their throughput, which in consequence allows to execute in-silico experiments on genome-scale, using standard SOAP Web Services and workflows. As a proof-of-principle we annotated an RNA-seq dataset using a plain BPEL workflow engine.

Processing biological literature with customizable Web services supporting interoperable formats

PubMed Central

Rak, Rafal; Batista-Navarro, Riza Theresa; Carter, Jacob; Rowley, Andrew; Ananiadou, Sophia

2014-01-01

Web services have become a popular means of interconnecting solutions for processing a body of scientific literature. This has fuelled research on high-level data exchange formats suitable for a given domain and ensuring the interoperability of Web services. In this article, we focus on the biological domain and consider four interoperability formats, BioC, BioNLP, XMI and RDF, that represent domain-specific and generic representations and include well-established as well as emerging specifications. We use the formats in the context of customizable Web services created in our Web-based, text-mining workbench Argo that features an ever-growing library of elementary analytics and capabilities to build and deploy Web services straight from a convenient graphical user interface. We demonstrate a 2-fold customization of Web services: by building task-specific processing pipelines from a repository of available analytics, and by configuring services to accept and produce a combination of input and output data interchange formats. We provide qualitative evaluation of the formats as well as quantitative evaluation of automatic analytics. The latter was carried out as part of our participation in the fourth edition of the BioCreative challenge. Our analytics built into Web services for recognizing biochemical concepts in BioC collections achieved the highest combined scores out of 10 participating teams. Database URL: http://argo.nactem.ac.uk. PMID:25006225

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.

Development of web-based services for an ensemble flood forecasting and risk assessment system

NASA Astrophysics Data System (ADS)

Yaw Manful, Desmond; He, Yi; Cloke, Hannah; Pappenberger, Florian; Li, Zhijia; Wetterhall, Fredrik; Huang, Yingchun; Hu, Yuzhong

2010-05-01

Flooding is a wide spread and devastating natural disaster worldwide. Floods that took place in the last decade in China were ranked the worst amongst recorded floods worldwide in terms of the number of human fatalities and economic losses (Munich Re-Insurance). Rapid economic development and population expansion into low lying flood plains has worsened the situation. Current conventional flood prediction systems in China are neither suited to the perceptible climate variability nor the rapid pace of urbanization sweeping the country. Flood prediction, from short-term (a few hours) to medium-term (a few days), needs to be revisited and adapted to changing socio-economic and hydro-climatic realities. The latest technology requires implementation of multiple numerical weather prediction systems. The availability of twelve global ensemble weather prediction systems through the ‘THORPEX Interactive Grand Global Ensemble' (TIGGE) offers a good opportunity for an effective state-of-the-art early forecasting system. A prototype of a Novel Flood Early Warning System (NEWS) using the TIGGE database is tested in the Huai River basin in east-central China. It is the first early flood warning system in China that uses the massive TIGGE database cascaded with river catchment models, the Xinanjiang hydrologic model and a 1-D hydraulic model, to predict river discharge and flood inundation. The NEWS algorithm is also designed to provide web-based services to a broad spectrum of end-users. The latter presents challenges as both databases and proprietary codes reside in different locations and converge at dissimilar times. NEWS will thus make use of a ready-to-run grid system that makes distributed computing and data resources available in a seamless and secure way. An ability to run or function on different operating systems and provide an interface or front that is accessible to broad spectrum of end-users is additional requirement. The aim is to achieve robust interoperability through strong security and workflow capabilities. A physical network diagram and a work flow scheme of all the models, codes and databases used to achieve the NEWS algorithm are presented. They constitute a first step in the development of a platform for providing real time flood forecasting services on the web to mitigate 21st century weather phenomena.

31 CFR 515.578 - Exportation of certain services incident to Internet-based communications.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Internet, such as instant messaging, chat and email, social networking, sharing of photos and movies, web... direct or indirect exportation of web-hosting services that are for purposes other than personal communications (e.g., web-hosting services for commercial endeavors) or of domain name registration services. (4...

31 CFR 515.578 - Exportation of certain services incident to Internet-based communications.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Internet, such as instant messaging, chat and email, social networking, sharing of photos and movies, web... direct or indirect exportation of web-hosting services that are for purposes other than personal communications (e.g., web-hosting services for commercial endeavors) or of domain name registration services. (4...

REMORA: a pilot in the ocean of BioMoby web-services.

PubMed

Carrere, Sébastien; Gouzy, Jérôme

2006-04-01

Emerging web-services technology allows interoperability between multiple distributed architectures. Here, we present REMORA, a web server implemented according to the BioMoby web-service specifications, providing life science researchers with an easy-to-use workflow generator and launcher, a repository of predefined workflows and a survey system. Jerome.Gouzy@toulouse.inra.fr The REMORA web server is freely available at http://bioinfo.genopole-toulouse.prd.fr/remora, sources are available upon request from the authors.

jORCA: easily integrating bioinformatics Web Services.

PubMed

Martín-Requena, Victoria; Ríos, Javier; García, Maximiliano; Ramírez, Sergio; Trelles, Oswaldo

2010-02-15

Web services technology is becoming the option of choice to deploy bioinformatics tools that are universally available. One of the major strengths of this approach is that it supports machine-to-machine interoperability over a network. However, a weakness of this approach is that various Web Services differ in their definition and invocation protocols, as well as their communication and data formats-and this presents a barrier to service interoperability. jORCA is a desktop client aimed at facilitating seamless integration of Web Services. It does so by making a uniform representation of the different web resources, supporting scalable service discovery, and automatic composition of workflows. Usability is at the top of the jORCA agenda; thus it is a highly customizable and extensible application that accommodates a broad range of user skills featuring double-click invocation of services in conjunction with advanced execution-control, on the fly data standardization, extensibility of viewer plug-ins, drag-and-drop editing capabilities, plus a file-based browsing style and organization of favourite tools. The integration of bioinformatics Web Services is made easier to support a wider range of users. .

National Centers for Environmental Prediction

Science.gov Websites

. Government's official Web portal to all Federal, state and local government Web resources and services. MISSION Web Page [scroll down to "Verification" Section] HRRR Verification at NOAA ESRL HRRR Web Verification Web Page NOAA / National Weather Service National Centers for Environmental Prediction

Component, Context, and Manufacturing Model Library (C2M2L)

DTIC Science & Technology

2012-11-01

123 5.1 MML Population and Web Service Interface...104 Table 41. Relevant Questions with Associated Web Services...the models, and implementing web services that provide semantically aware programmatic access to the models, including implementing the MS&T

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.

WebGLORE: a web service for Grid LOgistic REgression.

PubMed

Jiang, Wenchao; Li, Pinghao; Wang, Shuang; Wu, Yuan; Xue, Meng; Ohno-Machado, Lucila; Jiang, Xiaoqian

2013-12-15

WebGLORE is a free web service that enables privacy-preserving construction of a global logistic regression model from distributed datasets that are sensitive. It only transfers aggregated local statistics (from participants) through Hypertext Transfer Protocol Secure to a trusted server, where the global model is synthesized. WebGLORE seamlessly integrates AJAX, JAVA Applet/Servlet and PHP technologies to provide an easy-to-use web service for biomedical researchers to break down policy barriers during information exchange. http://dbmi-engine.ucsd.edu/webglore3/. WebGLORE can be used under the terms of GNU general public license as published by the Free Software Foundation.

The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation

PubMed Central

2011-01-01

Background The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community. Description SADI - Semantic Automated Discovery and Integration - is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services "stack", SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers. Conclusions SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behaviour we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies. PMID:22024447

The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation.

PubMed

Wilkinson, Mark D; Vandervalk, Benjamin; McCarthy, Luke

2011-10-24

The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community. SADI - Semantic Automated Discovery and Integration - is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services "stack", SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers. SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behaviour we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies.

Semantic Web Services Challenge, Results from the First Year. Series: Semantic Web And Beyond, Volume 8.

NASA Astrophysics Data System (ADS)

Petrie, C.; Margaria, T.; Lausen, H.; Zaremba, M.

Explores trade-offs among existing approaches. Reveals strengths and weaknesses of proposed approaches, as well as which aspects of the problem are not yet covered. Introduces software engineering approach to evaluating semantic web services. Service-Oriented Computing is one of the most promising software engineering trends because of the potential to reduce the programming effort for future distributed industrial systems. However, only a small part of this potential rests on the standardization of tools offered by the web services stack. The larger part of this potential rests upon the development of sufficient semantics to automate service orchestration. Currently there are many different approaches to semantic web service descriptions and many frameworks built around them. A common understanding, evaluation scheme, and test bed to compare and classify these frameworks in terms of their capabilities and shortcomings, is necessary to make progress in developing the full potential of Service-Oriented Computing. The Semantic Web Services Challenge is an open source initiative that provides a public evaluation and certification of multiple frameworks on common industrially-relevant problem sets. This edited volume reports on the first results in developing common understanding of the various technologies intended to facilitate the automation of mediation, choreography and discovery for Web Services using semantic annotations. Semantic Web Services Challenge: Results from the First Year is designed for a professional audience composed of practitioners and researchers in industry. Professionals can use this book to evaluate SWS technology for their potential practical use. The book is also suitable for advanced-level students in computer science.

HealthCyberMap: a semantic visual browser of medical Internet resources based on clinical codes and the human body metaphor.

PubMed

Kamel Boulos, Maged N; Roudsari, Abdul V; Carso N, Ewart R

2002-12-01

HealthCyberMap (HCM-http://healthcybermap.semanticweb.org) is a web-based service for healthcare professionals and librarians, patients and the public in general that aims at mapping parts of the health information resources in cyberspace in novel ways to improve their retrieval and navigation. HCM adopts a clinical metadata framework built upon a clinical coding ontology for the semantic indexing, classification and browsing of Internet health information resources. A resource metadata base holds information about selected resources. HCM then uses GIS (Geographic Information Systems) spatialization methods to generate interactive navigational cybermaps from the metadata base. These visual cybermaps are based on familiar medical metaphors. HCM cybermaps can be considered as semantically spatialized, ontology-based browsing views of the underlying resource metadata base. Using a clinical coding scheme as a metric for spatialization ('semantic distance') is unique to HCM and is very much suited for the semantic categorization and navigation of Internet health information resources. Clinical codes ensure reliable and unambiguous topical indexing of these resources. HCM also introduces a useful form of cyberspatial analysis for the detection of topical coverage gaps in the resource metadata base using choropleth (shaded) maps of human body systems.

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

NASA Astrophysics Data System (ADS)

Huang, L. Xinglai; Sheng, Grant

2006-10-01

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

Detection And Classification Of Web Robots With Honeypots

DTIC Science & Technology

2016-03-01

CLASSIFICATION OF WEB ROBOTS WITH HONEYPOTS by Sean F. McKenna March 2016 Thesis Advisor: Neil Rowe Second Reader: Justin P. Rohrer THIS...Master’s thesis 4. TITLE AND SUBTITLE DETECTION AND CLASSIFICATION OF WEB ROBOTS WITH HONEYPOTS 5. FUNDING NUMBERS 6. AUTHOR(S) Sean F. McKenna 7...DISTRIBUTION CODE 13. ABSTRACT (maximum 200 words) Web robots are automated programs that systematically browse the Web , collecting information. Although

The Virtual Watershed Observatory: Cyberinfrastructure for Model-Data Integration and Access

NASA Astrophysics Data System (ADS)

Duffy, C.; Leonard, L. N.; Giles, L.; Bhatt, G.; Yu, X.

2011-12-01

The Virtual Watershed Observatory (VWO) is a concept where scientists, water managers, educators and the general public can create a virtual observatory from integrated hydrologic model results, national databases and historical or real-time observations via web services. In this paper, we propose a prototype for automated and virtualized web services software using national data products for climate reanalysis, soils, geology, terrain and land cover. The VWO has the broad purpose of making accessible water resource simulations, real-time data assimilation, calibration and archival at the scale of HUC 12 watersheds (Hydrologic Unit Code) anywhere in the continental US. Our prototype for model-data integration focuses on creating tools for fast data storage from selected national databases, as well as the computational resources necessary for a dynamic, distributed watershed simulation. The paper will describe cyberinfrastructure tools and workflow that attempts to resolve the problem of model-data accessibility and scalability such that individuals, research teams, managers and educators can create a WVO in a desired context. Examples are given for the NSF-funded Shale Hills Critical Zone Observatory and the European Critical Zone Observatories within the SoilTrEC project. In the future implementation of WVO services will benefit from the development of a cloud cyber infrastructure as the prototype evolves to data and model intensive computation for continental scale water resource predictions.

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.

Seahawk: moving beyond HTML in Web-based bioinformatics analysis.

PubMed

Gordon, Paul M K; Sensen, Christoph W

2007-06-18

Traditional HTML interfaces for input to and output from Bioinformatics analysis on the Web are highly variable in style, content and data formats. Combining multiple analyses can therefore be an onerous task for biologists. Semantic Web Services allow automated discovery of conceptual links between remote data analysis servers. A shared data ontology and service discovery/execution framework is particularly attractive in Bioinformatics, where data and services are often both disparate and distributed. Instead of biologists copying, pasting and reformatting data between various Web sites, Semantic Web Service protocols such as MOBY-S hold out the promise of seamlessly integrating multi-step analysis. We have developed a program (Seahawk) that allows biologists to intuitively and seamlessly chain together Web Services using a data-centric, rather than the customary service-centric approach. The approach is illustrated with a ferredoxin mutation analysis. Seahawk concentrates on lowering entry barriers for biologists: no prior knowledge of the data ontology, or relevant services is required. In stark contrast to other MOBY-S clients, in Seahawk users simply load Web pages and text files they already work with. Underlying the familiar Web-browser interaction is an XML data engine based on extensible XSLT style sheets, regular expressions, and XPath statements which import existing user data into the MOBY-S format. As an easily accessible applet, Seahawk moves beyond standard Web browser interaction, providing mechanisms for the biologist to concentrate on the analytical task rather than on the technical details of data formats and Web forms. As the MOBY-S protocol nears a 1.0 specification, we expect more biologists to adopt these new semantic-oriented ways of doing Web-based analysis, which empower them to do more complicated, ad hoc analysis workflow creation without the assistance of a programmer.

Seahawk: moving beyond HTML in Web-based bioinformatics analysis

PubMed Central

Gordon, Paul MK; Sensen, Christoph W

2007-01-01

Background Traditional HTML interfaces for input to and output from Bioinformatics analysis on the Web are highly variable in style, content and data formats. Combining multiple analyses can therfore be an onerous task for biologists. Semantic Web Services allow automated discovery of conceptual links between remote data analysis servers. A shared data ontology and service discovery/execution framework is particularly attractive in Bioinformatics, where data and services are often both disparate and distributed. Instead of biologists copying, pasting and reformatting data between various Web sites, Semantic Web Service protocols such as MOBY-S hold out the promise of seamlessly integrating multi-step analysis. Results We have developed a program (Seahawk) that allows biologists to intuitively and seamlessly chain together Web Services using a data-centric, rather than the customary service-centric approach. The approach is illustrated with a ferredoxin mutation analysis. Seahawk concentrates on lowering entry barriers for biologists: no prior knowledge of the data ontology, or relevant services is required. In stark contrast to other MOBY-S clients, in Seahawk users simply load Web pages and text files they already work with. Underlying the familiar Web-browser interaction is an XML data engine based on extensible XSLT style sheets, regular expressions, and XPath statements which import existing user data into the MOBY-S format. Conclusion As an easily accessible applet, Seahawk moves beyond standard Web browser interaction, providing mechanisms for the biologist to concentrate on the analytical task rather than on the technical details of data formats and Web forms. As the MOBY-S protocol nears a 1.0 specification, we expect more biologists to adopt these new semantic-oriented ways of doing Web-based analysis, which empower them to do more complicated, ad hoc analysis workflow creation without the assistance of a programmer. PMID:17577405

Piloting a Collaborative Web-Based System for Testing ICD-11.

PubMed

Donada, Marc; Kostanjsek, Nenad; Della Mea, Vincenzo; Celik, Can; Jakob, Robert

2017-01-01

The 11^th revision of the International Classification of Diseases (ICD-11), for the first time in ICD history, deployed web-based collaboration of experts and ICT tools. To ensure that ICD-11 is working well, it needs to be systematically field tested in different settings, across the world. This will be done by means of a number of experiments. In order to support its implementation, a web-based system (ICDfit) has been designed and developed. The present paper illustrates the current prototype of the system and its technical testing. the system has been designed according to WHO requirements, and implemented using PHP and MySQL. Then, a preliminary technical test has been designed and run in January 2016, involving 8 users. They had to carry out double coding, that is, coding case summaries with both ICD-10 and ICD-11, and answering quick questions on the coding difficulty. the 8 users coded 632 cases each, spending an average of 163 seconds per case. While we found an issue in the mechanism used to record coding times, no further issues were found. the proposed system seems to be technically adequate for supporting future ICD-11 testing.

Maintenance and Exchange of Learning Objects in a Web Services Based e-Learning System

ERIC Educational Resources Information Center

Vossen, Gottfried; Westerkamp, Peter

2004-01-01

"Web services" enable partners to exploit applications via the Internet. Individual services can be composed to build new and more complex ones with additional and more comprehensive functionality. In this paper, we apply the Web service paradigm to electronic learning, and show how to exchange and maintain learning objects is a…

Developer Network

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

2012-08-21

NREL's Developer Network, developer.nrel.gov, provides data that users can access to provide data to their own analyses, mobile and web applications. Developers can retrieve the data through a Web services API (application programming interface). The Developer Network handles overhead of serving up web services such as key management, authentication, analytics, reporting, documentation standards, and throttling in a common architecture, while allowing web services and APIs to be maintained and managed independently.

API REST Web service and backend system Of Lecturer’s Assessment Information System on Politeknik Negeri Bali

NASA Astrophysics Data System (ADS)

Manuaba, I. B. P.; Rudiastini, E.

2018-01-01

Assessment of lecturers is a tool used to measure lecturer performance. Lecturer’s assessment variable can be measured from three aspects : teaching activities, research and community service. Broad aspect to measure the performance of lecturers requires a special framework, so that the system can be developed in a sustainable manner. Issues of this research is to create a API web service data tool, so the lecturer assessment system can be developed in various frameworks. The research was developed with web service and php programming language with the output of json extension data. The conclusion of this research is API web service data application can be developed using several platforms such as web, mobile application

Utilization of services in a randomized trial testing phone- and web-based interventions for smoking cessation.

PubMed

Zbikowski, Susan M; Jack, Lisa M; McClure, Jennifer B; Deprey, Mona; Javitz, Harold S; McAfee, Timothy A; Catz, Sheryl L; Richards, Julie; Bush, Terry; Swan, Gary E

2011-05-01

Phone counseling has become standard for behavioral smoking cessation treatment. Newer options include Web and integrated phone-Web treatment. No prior research, to our knowledge, has systematically compared the effectiveness of these three treatment modalities in a randomized trial. Understanding how utilization varies by mode, the impact of utilization on outcomes, and predictors of utilization across each mode could lead to improved treatments. One thousand two hundred and two participants were randomized to phone, Web, or combined phone-Web cessation treatment. Services varied by modality and were tracked using automated systems. All participants received 12 weeks of varenicline, printed guides, an orientation call, and access to a phone supportline. Self-report data were collected at baseline and 6-month follow-up. Overall, participants utilized phone services more often than the Web-based services. Among treatment groups with Web access, a significant proportion logged in only once (37% phone-Web, 41% Web), and those in the phone-Web group logged in less often than those in the Web group (mean = 2.4 vs. 3.7, p = .0001). Use of the phone also was correlated with increased use of the Web. In multivariate analyses, greater use of the phone- or Web-based services was associated with higher cessation rates. Finally, older age and the belief that certain treatments could improve success were consistent predictors of greater utilization across groups. Other predictors varied by treatment group. Opportunities for enhancing treatment utilization exist, particularly for Web-based programs. Increasing utilization more broadly could result in better overall treatment effectiveness for all intervention modalities.

Implementation of Sensor Twitter Feed Web Service Server and Client

DTIC Science & Technology

2016-12-01

ARL-TN-0807 ● DEC 2016 US Army Research Laboratory Implementation of Sensor Twitter Feed Web Service Server and Client by...Implementation of Sensor Twitter Feed Web Service Server and Client by Bhagyashree V Kulkarni University of Maryland Michael H Lee Computational...

AWSCS-A System to Evaluate Different Approaches for the Automatic Composition and Execution of Web Services Flows

PubMed Central

Tardiole Kuehne, Bruno; Estrella, Julio Cezar; Nunes, Luiz Henrique; Martins de Oliveira, Edvard; Hideo Nakamura, Luis; Gomes Ferreira, Carlos Henrique; Carlucci Santana, Regina Helena; Reiff-Marganiec, Stephan; Santana, Marcos José

2015-01-01

This paper proposes a system named AWSCS (Automatic Web Service Composition System) to evaluate different approaches for automatic composition of Web services, based on QoS parameters that are measured at execution time. The AWSCS is a system to implement different approaches for automatic composition of Web services and also to execute the resulting flows from these approaches. Aiming at demonstrating the results of this paper, a scenario was developed, where empirical flows were built to demonstrate the operation of AWSCS, since algorithms for automatic composition are not readily available to test. The results allow us to study the behaviour of running composite Web services, when flows with the same functionality but different problem-solving strategies were compared. Furthermore, we observed that the influence of the load applied on the running system as the type of load submitted to the system is an important factor to define which approach for the Web service composition can achieve the best performance in production. PMID:26068216

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

PubMed

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

2015-11-01

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

AWSCS-A System to Evaluate Different Approaches for the Automatic Composition and Execution of Web Services Flows.

PubMed

Tardiole Kuehne, Bruno; Estrella, Julio Cezar; Nunes, Luiz Henrique; Martins de Oliveira, Edvard; Hideo Nakamura, Luis; Gomes Ferreira, Carlos Henrique; Carlucci Santana, Regina Helena; Reiff-Marganiec, Stephan; Santana, Marcos José

2015-01-01

This paper proposes a system named AWSCS (Automatic Web Service Composition System) to evaluate different approaches for automatic composition of Web services, based on QoS parameters that are measured at execution time. The AWSCS is a system to implement different approaches for automatic composition of Web services and also to execute the resulting flows from these approaches. Aiming at demonstrating the results of this paper, a scenario was developed, where empirical flows were built to demonstrate the operation of AWSCS, since algorithms for automatic composition are not readily available to test. The results allow us to study the behaviour of running composite Web services, when flows with the same functionality but different problem-solving strategies were compared. Furthermore, we observed that the influence of the load applied on the running system as the type of load submitted to the system is an important factor to define which approach for the Web service composition can achieve the best performance in production.

Web services as applications' integration tool: QikProp case study.

PubMed

Laoui, Abdel; Polyakov, Valery R

2011-07-15

Web services are a new technology that enables to integrate applications running on different platforms by using primarily XML to enable communication among different computers over the Internet. Large number of applications was designed as stand alone systems before the concept of Web services was introduced and it is a challenge to integrate them into larger computational networks. A generally applicable method of wrapping stand alone applications into Web services was developed and is described. To test the technology, it was applied to the QikProp for DOS (Windows). Although performance of the application did not change when it was delivered as a Web service, this form of deployment had offered several advantages like simplified and centralized maintenance, smaller number of licenses, and practically no training for the end user. Because by using the described approach almost any legacy application can be wrapped as a Web service, this form of delivery may be recommended as a global alternative to traditional deployment solutions. Copyright © 2011 Wiley Periodicals, Inc.

Using USNO's API to Obtain Data

NASA Astrophysics Data System (ADS)

Lesniak, Michael V.; Pozniak, Daniel; Punnoose, Tarun

2015-01-01

The U.S. Naval Observatory (USNO) is in the process of modernizing its publicly available web services into APIs (Application Programming Interfaces). Services configured as APIs offer greater flexibility to the user and allow greater usage. Depending on the particular service, users who implement our APIs will receive either a PNG (Portable Network Graphics) image or data in JSON (JavaScript Object Notation) format. This raw data can then be embedded in third-party web sites or in apps.Part of the USNO's mission is to provide astronomical and timing data to government agencies and the general public. To this end, the USNO provides accurate computations of astronomical phenomena such as dates of lunar phases, rise and set times of the Moon and Sun, and lunar and solar eclipse times. Users who navigate to our web site and select one of our 18 services are prompted to complete a web form, specifying parameters such as date, time, location, and object. Many of our services work for years between 1700 and 2100, meaning that past, present, and future events can be computed. Upon form submission, our web server processes the request, computes the data, and outputs it to the user.Over recent years, the use of the web by the general public has vastly changed. In response to this, the USNO is modernizing its web-based data services. This includes making our computed data easier to embed within third-party web sites as well as more easily querying from apps running on tablets and smart phones. To facilitate this, the USNO has begun converting its services into APIs. In addition to the existing web forms for the various services, users are able to make direct URL requests that return either an image or numerical data.To date, four of our web services have been configured to run with APIs. Two are image-producing services: "Apparent Disk of a Solar System Object" and "Day and Night Across the Earth." Two API data services are "Complete Sun and Moon Data for One Day" and "Dates of Primary Phases of the Moon." Instructions for how to use our API services as well as examples of their use can be found on one of our explanatory web pages and will be discussed here.

SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services.

PubMed

Gessler, Damian D G; Schiltz, Gary S; May, Greg D; Avraham, Shulamit; Town, Christopher D; Grant, David; Nelson, Rex T

2009-09-23

SSWAP (Simple Semantic Web Architecture and Protocol; pronounced "swap") is an architecture, protocol, and platform for using reasoning to semantically integrate heterogeneous disparate data and services on the web. SSWAP was developed as a hybrid semantic web services technology to overcome limitations found in both pure web service technologies and pure semantic web technologies. There are currently over 2400 resources published in SSWAP. Approximately two dozen are custom-written services for QTL (Quantitative Trait Loci) and mapping data for legumes and grasses (grains). The remaining are wrappers to Nucleic Acids Research Database and Web Server entries. As an architecture, SSWAP establishes how clients (users of data, services, and ontologies), providers (suppliers of data, services, and ontologies), and discovery servers (semantic search engines) interact to allow for the description, querying, discovery, invocation, and response of semantic web services. As a protocol, SSWAP provides the vocabulary and semantics to allow clients, providers, and discovery servers to engage in semantic web services. The protocol is based on the W3C-sanctioned first-order description logic language OWL DL. As an open source platform, a discovery server running at http://sswap.info (as in to "swap info") uses the description logic reasoner Pellet to integrate semantic resources. The platform hosts an interactive guide to the protocol at http://sswap.info/protocol.jsp, developer tools at http://sswap.info/developer.jsp, and a portal to third-party ontologies at http://sswapmeet.sswap.info (a "swap meet"). SSWAP addresses the three basic requirements of a semantic web services architecture (i.e., a common syntax, shared semantic, and semantic discovery) while addressing three technology limitations common in distributed service systems: i.e., i) the fatal mutability of traditional interfaces, ii) the rigidity and fragility of static subsumption hierarchies, and iii) the confounding of content, structure, and presentation. SSWAP is novel by establishing the concept of a canonical yet mutable OWL DL graph that allows data and service providers to describe their resources, to allow discovery servers to offer semantically rich search engines, to allow clients to discover and invoke those resources, and to allow providers to respond with semantically tagged data. SSWAP allows for a mix-and-match of terms from both new and legacy third-party ontologies in these graphs.

WebGIS based on semantic grid model and web services

NASA Astrophysics Data System (ADS)

Zhang, WangFei; Yue, CaiRong; Gao, JianGuo

2009-10-01

As the combination point of the network technology and GIS technology, WebGIS has got the fast development in recent years. With the restriction of Web and the characteristics of GIS, traditional WebGIS has some prominent problems existing in development. For example, it can't accomplish the interoperability of heterogeneous spatial databases; it can't accomplish the data access of cross-platform. With the appearance of Web Service and Grid technology, there appeared great change in field of WebGIS. Web Service provided an interface which can give information of different site the ability of data sharing and inter communication. The goal of Grid technology was to make the internet to a large and super computer, with this computer we can efficiently implement the overall sharing of computing resources, storage resource, data resource, information resource, knowledge resources and experts resources. But to WebGIS, we only implement the physically connection of data and information and these is far from the enough. Because of the different understanding of the world, following different professional regulations, different policies and different habits, the experts in different field will get different end when they observed the same geographic phenomenon and the semantic heterogeneity produced. Since these there are large differences to the same concept in different field. If we use the WebGIS without considering of the semantic heterogeneity, we will answer the questions users proposed wrongly or we can't answer the questions users proposed. To solve this problem, this paper put forward and experienced an effective method of combing semantic grid and Web Services technology to develop WebGIS. In this paper, we studied the method to construct ontology and the method to combine Grid technology and Web Services and with the detailed analysis of computing characteristics and application model in the distribution of data, we designed the WebGIS query system driven by ontology based on Grid technology and Web Services.

Failure Analysis for Composition of Web Services Represented as Labeled Transition Systems

NASA Astrophysics Data System (ADS)

Nadkarni, Dinanath; Basu, Samik; Honavar, Vasant; Lutz, Robyn

The Web service composition problem involves the creation of a choreographer that provides the interaction between a set of component services to realize a goal service. Several methods have been proposed and developed to address this problem. In this paper, we consider those scenarios where the composition process may fail due to incomplete specification of goal service requirements or due to the fact that the user is unaware of the functionality provided by the existing component services. In such cases, it is desirable to have a composition algorithm that can provide feedback to the user regarding the cause of failure in the composition process. Such feedback will help guide the user to re-formulate the goal service and iterate the composition process. We propose a failure analysis technique for composition algorithms that views Web service behavior as multiple sequences of input/output events. Our technique identifies the possible cause of composition failure and suggests possible recovery options to the user. We discuss our technique using a simple e-Library Web service in the context of the MoSCoE Web service composition framework.

WebGLORE: a Web service for Grid LOgistic REgression

PubMed Central

Jiang, Wenchao; Li, Pinghao; Wang, Shuang; Wu, Yuan; Xue, Meng; Ohno-Machado, Lucila; Jiang, Xiaoqian

2013-01-01

WebGLORE is a free web service that enables privacy-preserving construction of a global logistic regression model from distributed datasets that are sensitive. It only transfers aggregated local statistics (from participants) through Hypertext Transfer Protocol Secure to a trusted server, where the global model is synthesized. WebGLORE seamlessly integrates AJAX, JAVA Applet/Servlet and PHP technologies to provide an easy-to-use web service for biomedical researchers to break down policy barriers during information exchange. Availability and implementation: http://dbmi-engine.ucsd.edu/webglore3/. WebGLORE can be used under the terms of GNU general public license as published by the Free Software Foundation. Contact: x1jiang@ucsd.edu PMID:24072732

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

PubMed

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

2011-11-29

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

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

PubMed Central

2011-01-01

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

Modern Technologies aspects for Oceanographic Data Management and Dissemination : The HNODC Implementation

NASA Astrophysics Data System (ADS)

Lykiardopoulos, A.; Iona, A.; Lakes, V.; Batis, A.; Balopoulos, E.

2009-04-01

The development of new technologies for the aim of enhancing Web Applications with Dynamically data access was the starting point for Geospatial Web Applications to developed at the same time as well. By the means of these technologies the Web Applications embed the capability of presenting Geographical representations of the Geo Information. The induction in nowadays, of the state of the art technologies known as Web Services, enforce the Web Applications to have interoperability among them i.e. to be able to process requests from each other via a network. In particular throughout the Oceanographic Community, modern Geographical Information systems based on Geospatial Web Services are now developed or will be developed shortly in the near future, with capabilities of managing the information itself fully through Web Based Geographical Interfaces. The exploitation of HNODC Data Base, through a Web Based Application enhanced with Web Services by the use of open source tolls may be consider as an ideal case of such implementation. Hellenic National Oceanographic Data Center (HNODC) as a National Public Oceanographic Data provider and at the same time a member of the International Net of Oceanographic Data Centers( IOC/IODE), owns a very big volume of Data and Relevant information about the Marine Ecosystem. For the efficient management and exploitation of these Data, a relational Data Base has been constructed with a storage of over 300.000 station data concerning, physical, chemical and biological Oceanographic information. The development of a modern Web Application for the End User worldwide to be able to explore and navigate throughout HNODC data via the use of an interface with the capability of presenting Geographical representations of the Geo Information, is today a fact. The application is constituted with State of the art software components and tools such as: • Geospatial and no Spatial Web Services mechanisms • Geospatial open source tools for the creation of Dynamic Geographical Representations. • Communication protocols (messaging mechanisms) in all Layers such as XML and GML together with SOAP protocol via Apache/Axis. At the same time the application may interact with any other SOA application either in sending or receiving Geospatial Data through Geographical Layers, since it inherits the big advantage of interoperability between Web Services systems. Roughly the Architecture can denoted as follows: • At the back End Open source PostgreSQL DBMS stands as the data storage mechanism with more than one Data Base Schemas cause of the separation of the Geospatial Data and the non Geospatial Data. • UMN Map Server and Geoserver are the mechanisms for: Represent Geospatial Data via Web Map Service (WMS) Querying and Navigating in Geospatial and Meta Data Information via Web Feature Service (WFS) oAnd in the near future Transacting and processing new or existing Geospatial Data via Web Processing Service (WPS) • Map Bender, a geospatial portal site management software for OGC and OWS architectures acts as the integration module between the Geospatial Mechanisms. Mapbender comes with an embedded data model capable to manage interfaces for displaying, navigating and querying OGC compliant web map and feature services (WMS and transactional WFS). • Apache and Tomcat stand again as the Web Service middle Layers • Apache Axis with it's embedded implementation of the SOAP protocol ("Simple Object Access Protocol") acts as the No spatial data Mechanism of Web Services. These modules of the platform are still under development but their implementation will be fulfilled in the near future. • And a new Web user Interface for the end user based on enhanced and customized version of a MapBender GUI, a powerful Web Services client. For HNODC the interoperability of Web Services is the big advantage of the developed platform since it is capable to act in the future as provider and consumer of Web Services in both ways: • Either as data products provider for external SOA platforms. • Or as consumer of data products from external SOA platforms for new applications to be developed or for existing applications to be enhanced. A great paradigm of Data Managenet integration and dissemination via the use of such technologies is the European's Union Research Project Seadatanet, with the main objective to develop a standardized distributed system for managing and disseminating the large and diverse data sets and to enhance the currently existing infrastructures with Web Services Further more and when the technology of Web Processing Service (WPS), will be mature enough and applicable for development, the derived data products will be able to have any kind of GIS functionality for consumers across the network. From this point of view HNODC, joins the global scientific community by providing and consuming application Independent data products.

Pragmatic service development and customisation with the CEDA OGC Web Services framework

NASA Astrophysics Data System (ADS)

Pascoe, Stephen; Stephens, Ag; Lowe, Dominic

2010-05-01

The CEDA OGC Web Services framework (COWS) emphasises rapid service development by providing a lightweight layer of OGC web service logic on top of Pylons, a mature web application framework for the Python language. This approach gives developers a flexible web service development environment without compromising access to the full range of web application tools and patterns: Model-View-Controller paradigm, XML templating, Object-Relational-Mapper integration and authentication/authorization. We have found this approach useful for exploring evolving standards and implementing protocol extensions to meet the requirements of operational deployments. This paper outlines how COWS is being used to implement customised WMS, WCS, WFS and WPS services in a variety of web applications from experimental prototypes to load-balanced cluster deployments serving 10-100 simultaneous users. In particular we will cover 1) The use of Climate Science Modeling Language (CSML) in complex-feature aware WMS, WCS and WFS services, 2) Extending WMS to support applications with features specific to earth system science and 3) A cluster-enabled Web Processing Service (WPS) supporting asynchronous data processing. The COWS WPS underpins all backend services in the UK Climate Projections User Interface where users can extract, plot and further process outputs from a multi-dimensional probabilistic climate model dataset. The COWS WPS supports cluster job execution, result caching, execution time estimation and user management. The COWS WMS and WCS components drive the project-specific NCEO and QESDI portals developed by the British Atmospheric Data Centre. These portals use CSML as a backend description format and implement features such as multiple WMS layer dimensions and climatology axes that are beyond the scope of general purpose GIS tools and yet vital for atmospheric science applications.

Standardized mappings--a framework to combine different semantic mappers into a standardized web-API.

PubMed

Neuhaus, Philipp; Doods, Justin; Dugas, Martin

2015-01-01

Automatic coding of medical terms is an important, but highly complicated and laborious task. To compare and evaluate different strategies a framework with a standardized web-interface was created. Two UMLS mapping strategies are compared to demonstrate the interface. The framework is a Java Spring application running on a Tomcat application server. It accepts different parameters and returns results in JSON format. To demonstrate the framework, a list of medical data items was mapped by two different methods: similarity search in a large table of terminology codes versus search in a manually curated repository. These mappings were reviewed by a specialist. The evaluation shows that the framework is flexible (due to standardized interfaces like HTTP and JSON), performant and reliable. Accuracy of automatically assigned codes is limited (up to 40%). Combining different semantic mappers into a standardized Web-API is feasible. This framework can be easily enhanced due to its modular design.

Technical Services and the World Wide Web.

ERIC Educational Resources Information Center

Scheschy, Virginia M.

The World Wide Web and browsers such as Netscape and Mosaic have simplified access to electronic resources. Today, technical services librarians can share in the wealth of information available on the Web. One of the premier Web sites for acquisitions librarians is AcqWeb, a cousin of the AcqNet listserv. In addition to interesting news items,…

QMachine: commodity supercomputing in web browsers

PubMed Central

2014-01-01

Background Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for querying, processing, and visualizing genomics’ “Big Data” from sources like The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) without local software installation or configuration. The design of QMachine (QM) was driven by the opportunity to use this pervasive computing model in the context of the Web of Linked Data in Biomedicine. Results QM is an open-sourced, publicly available web service that acts as a messaging system for posting tasks and retrieving results over HTTP. The illustrative application described here distributes the analyses of 20 Streptococcus pneumoniae genomes for shared suffixes. Because all analytical and data retrieval tasks are executed by volunteer machines, few server resources are required. Any modern web browser can submit those tasks and/or volunteer to execute them without installing any extra plugins or programs. A client library provides high-level distribution templates including MapReduce. This stark departure from the current reliance on expensive server hardware running “download and install” software has already gathered substantial community interest, as QM received more than 2.2 million API calls from 87 countries in 12 months. Conclusions QM was found adequate to deliver the sort of scalable bioinformatics solutions that computation- and data-intensive workflows require. Paradoxically, the sandboxed execution of code by web browsers was also found to enable them, as compute nodes, to address critical privacy concerns that characterize biomedical environments. PMID:24913605

Dumbing Down the Net

NASA Astrophysics Data System (ADS)

Jamison, Mark A.; Hauge, Janice A.

It is commonplace for sellers of goods and services to enhance the value of their products by paying extra for premium delivery service. For example, package delivery services such as Federal Express and the US Postal Service offer shippers a variety of delivery speeds and insurance programs. Web content providers such as Yahoo! and MSN Live Earth can purchase web-enhancing services from companies such as Akamai to speed the delivery of their web content to customers.1

Determinants of Corporate Web Services Adoption: A Survey of Companies in Korea

ERIC Educational Resources Information Center

Kim, Daekil

2010-01-01

Despite the growing interest and attention from Information Technology researchers and practitioners, empirical research on factors that influence an organization's likelihood of adoption of Web Services has been limited. This study identified the factors influencing Web Services adoption from the perspective of 151 South Korean firms. The…

Web 2.0 Strategy in Libraries and Information Services

ERIC Educational Resources Information Center

Byrne, Alex

2008-01-01

Web 2.0 challenges libraries to change from their predominantly centralised service models with integrated library management systems at the hub. Implementation of Web 2.0 technologies and the accompanying attitudinal shifts will demand reconceptualisation of the nature of library and information service around a dynamic, ever changing, networked,…

WIWS: a protein structure bioinformatics Web service collection.

PubMed

Hekkelman, M L; Te Beek, T A H; Pettifer, S R; Thorne, D; Attwood, T K; Vriend, G

2010-07-01

The WHAT IF molecular-modelling and drug design program is widely distributed in the world of protein structure bioinformatics. Although originally designed as an interactive application, its highly modular design and inbuilt control language have recently enabled its deployment as a collection of programmatically accessible web services. We report here a collection of WHAT IF-based protein structure bioinformatics web services: these relate to structure quality, the use of symmetry in crystal structures, structure correction and optimization, adding hydrogens and optimizing hydrogen bonds and a series of geometric calculations. The freely accessible web services are based on the industry standard WS-I profile and the EMBRACE technical guidelines, and are available via both REST and SOAP paradigms. The web services run on a dedicated computational cluster; their function and availability is monitored daily.

Using EMBL-EBI services via Web interface and programmatically via Web Services

PubMed Central

Lopez, Rodrigo; Cowley, Andrew; Li, Weizhong; McWilliam, Hamish

2015-01-01

The European Bioinformatics Institute (EMBL-EBI) provides access to a wide range of databases and analysis tools that are of key importance in bioinformatics. As well as providing Web interfaces to these resources, Web Services are available using SOAP and REST protocols that enable programmatic access to our resources and allow their integration into other applications and analytical workflows. This unit describes the various options available to a typical researcher or bioinformatician who wishes to use our resources via Web interface or programmatically via a range of programming languages. PMID:25501941

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.

OPserver: opacities and radiative accelerations on demand

NASA Astrophysics Data System (ADS)

Mendoza, C.; González, J.; Seaton, M. J.; Buerger, P.; Bellorín, A.; Meléndez, M.; Rodríguez, L. S.; Delahaye, F.; Zeippen, C. J.; Palacios, E.; Pradhan, A. K.

2009-05-01

We report on developments carried out within the Opacity Project (OP) to upgrade atomic database services to comply with e-infrastructure requirements. We give a detailed description of an interactive, online server for astrophysical opacities, referred to as OPserver, to be used in sophisticated stellar modelling where Rosseland mean opacities and radiative accelerations are computed at every depth point and each evolution cycle. This is crucial, for instance, in chemically peculiar stars and in the exploitation of the new asteroseismological data. OPserver, downloadable with the new OPCD_3.0 release from the Centre de Données Astronomiques de Strasbourg, France, computes mean opacities and radiative data for arbitrary chemical mixtures from the OP monochromatic opacities. It is essentially a client-server network restructuring and optimization of the suite of codes included in the earlier OPCD_2.0 release. The server can be installed locally or, alternatively, accessed remotely from the Ohio Supercomputer Center, Columbus, Ohio, USA. The client is an interactive web page or a subroutine library that can be linked to the user code. The suitability of this scheme in grid computing environments is emphasized, and its extension to other atomic database services for astrophysical purposes is discussed.

SSWAP: A Simple Semantic Web Architecture and Protocol for Semantic Web Services

USDA-ARS?s Scientific Manuscript database

SSWAP (Simple Semantic Web Architecture and Protocol) is an architecture, protocol, and platform for using reasoning to semantically integrate heterogeneous disparate data and services on the web. SSWAP is the driving technology behind the Virtual Plant Information Network, an NSF-funded semantic w...

Utilization of Services in a Randomized Trial Testing Phone- and Web-Based Interventions for Smoking Cessation

PubMed Central

Jack, Lisa M.; McClure, Jennifer B.; Deprey, Mona; Javitz, Harold S.; McAfee, Timothy A.; Catz, Sheryl L.; Richards, Julie; Bush, Terry; Swan, Gary E.

2011-01-01

Introduction: Phone counseling has become standard for behavioral smoking cessation treatment. Newer options include Web and integrated phone–Web treatment. No prior research, to our knowledge, has systematically compared the effectiveness of these three treatment modalities in a randomized trial. Understanding how utilization varies by mode, the impact of utilization on outcomes, and predictors of utilization across each mode could lead to improved treatments. Methods: One thousand two hundred and two participants were randomized to phone, Web, or combined phone–Web cessation treatment. Services varied by modality and were tracked using automated systems. All participants received 12 weeks of varenicline, printed guides, an orientation call, and access to a phone supportline. Self-report data were collected at baseline and 6-month follow-up. Results: Overall, participants utilized phone services more often than the Web-based services. Among treatment groups with Web access, a significant proportion logged in only once (37% phone–Web, 41% Web), and those in the phone–Web group logged in less often than those in the Web group (mean = 2.4 vs. 3.7, p = .0001). Use of the phone also was correlated with increased use of the Web. In multivariate analyses, greater use of the phone- or Web-based services was associated with higher cessation rates. Finally, older age and the belief that certain treatments could improve success were consistent predictors of greater utilization across groups. Other predictors varied by treatment group. Conclusions: Opportunities for enhancing treatment utilization exist, particularly for Web-based programs. Increasing utilization more broadly could result in better overall treatment effectiveness for all intervention modalities. PMID:21330267

Web Services Implementations at Land Process and Goddard Earth Sciences Distributed Active Archive Centers

NASA Astrophysics Data System (ADS)

Cole, M.; Bambacus, M.; Lynnes, C.; Sauer, B.; Falke, S.; Yang, W.

2007-12-01

NASA's vast array of scientific data within its Distributed Active Archive Centers (DAACs) is especially valuable to both traditional research scientists as well as the emerging market of Earth Science Information Partners. For example, the air quality science and management communities are increasingly using satellite derived observations in their analyses and decision making. The Air Quality Cluster in the Federation of Earth Science Information Partners (ESIP) uses web infrastructures of interoperability, or Service Oriented Architecture (SOA), to extend data exploration, use, and analysis and provides a user environment for DAAC products. In an effort to continually offer these NASA data to the broadest research community audience, and reusing emerging technologies, both NASA's Goddard Earth Science (GES) and Land Process (LP) DAACs have engaged in a web services pilot project. Through these projects both GES and LP have exposed data through the Open Geospatial Consortiums (OGC) Web Services standards. Reusing several different existing applications and implementation techniques, GES and LP successfully exposed a variety data, through distributed systems to be ingested into multiple end-user systems. The results of this project will enable researchers world wide to access some of NASA's GES & LP DAAC data through OGC protocols. This functionality encourages inter-disciplinary research while increasing data use through advanced technologies. This paper will concentrate on the implementation and use of OGC Web Services, specifically Web Map and Web Coverage Services (WMS, WCS) at GES and LP DAACs, and the value of these services within scientific applications, including integration with the DataFed air quality web infrastructure and in the development of data analysis web applications.

Database Resources of the BIG Data Center in 2018.

PubMed

2018-01-04

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Proof of Concept Integration of a Single-Level Service-Oriented Architecture into a Multi-Domain Secure Environment

DTIC Science & Technology

2008-03-01

Machine [29]. OC4J applications support Java Servlets , Web services, and the following J2EE specific standards: Extensible Markup Language (XML...IMAP Internet Message Access Protocol IP Internet Protocol IT Information Technology xviii J2EE Java Enterprise Environment JSR 168 Java ...LDAP), World Wide Web Distributed Authoring and Versioning (WebDav), Java Specification Request 168 (JSR 168), and Web Services for Remote

Persistent identifiers for web service requests relying on a provenance ontology design pattern

NASA Astrophysics Data System (ADS)

Car, Nicholas; Wang, Jingbo; Wyborn, Lesley; Si, Wei

2016-04-01

Delivering provenance information for datasets produced from static inputs is relatively straightforward: we represent the processing actions and data flow using provenance ontologies and link to stored copies of the inputs stored in repositories. If appropriate detail is given, the provenance information can then describe what actions have occurred (transparency) and enable reproducibility. When web service-generated data is used by a process to create a dataset instead of a static inputs, we need to use sophisticated provenance representations of the web service request as we can no longer just link to data stored in a repository. A graph-based provenance representation, such as the W3C's PROV standard, can be used to model the web service request as a single conceptual dataset and also as a small workflow with a number of components within the same provenance report. This dual representation does more than just allow simplified or detailed views of a dataset's production to be used where appropriate. It also allow persistent identifiers to be assigned to instances of a web service requests, thus enabling one form of dynamic data citation, and for those identifiers to resolve to whatever level of detail implementers think appropriate in order for that web service request to be reproduced. In this presentation we detail our reasoning in representing web service requests as small workflows. In outline, this stems from the idea that web service requests are perdurant things and in order to most easily persist knowledge of them for provenance, we should represent them as a nexus of relationships between endurant things, such as datasets and knowledge of particular system types, as these endurant things are far easier to persist. We also describe the ontology design pattern that we use to represent workflows in general and how we apply it to different types of web service requests. We give examples of specific web service requests instances that were made by systems at Australia's National Computing Infrastructure and show how one can 'click' through provenance interfaces to see the dual representations of the requests using provenance management tooling we have built.

WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions

PubMed Central

Karr, Jonathan R.; Phillips, Nolan C.; Covert, Markus W.

2014-01-01

Mechanistic ‘whole-cell’ models are needed to develop a complete understanding of cell physiology. However, extracting biological insights from whole-cell models requires running and analyzing large numbers of simulations. We developed WholeCellSimDB, a database for organizing whole-cell simulations. WholeCellSimDB was designed to enable researchers to search simulation metadata to identify simulations for further analysis, and quickly slice and aggregate simulation results data. In addition, WholeCellSimDB enables users to share simulations with the broader research community. The database uses a hybrid relational/hierarchical data format architecture to efficiently store and retrieve both simulation setup metadata and results data. WholeCellSimDB provides a graphical Web-based interface to search, browse, plot and export simulations; a JavaScript Object Notation (JSON) Web service to retrieve data for Web-based visualizations; a command-line interface to deposit simulations; and a Python API to retrieve data for advanced analysis. Overall, we believe WholeCellSimDB will help researchers use whole-cell models to advance basic biological science and bioengineering. Database URL: http://www.wholecellsimdb.org Source code repository URL: http://github.com/CovertLab/WholeCellSimDB PMID:25231498

Model-Driven Methodology for Rapid Deployment of Smart Spaces Based on Resource-Oriented Architectures

PubMed Central

Corredor, Iván; Bernardos, Ana M.; Iglesias, Josué; Casar, José R.

2012-01-01

Advances in electronics nowadays facilitate the design of smart spaces based on physical mash-ups of sensor and actuator devices. At the same time, software paradigms such as Internet of Things (IoT) and Web of Things (WoT) are motivating the creation of technology to support the development and deployment of web-enabled embedded sensor and actuator devices with two major objectives: (i) to integrate sensing and actuating functionalities into everyday objects, and (ii) to easily allow a diversity of devices to plug into the Internet. Currently, developers who are applying this Internet-oriented approach need to have solid understanding about specific platforms and web technologies. In order to alleviate this development process, this research proposes a Resource-Oriented and Ontology-Driven Development (ROOD) methodology based on the Model Driven Architecture (MDA). This methodology aims at enabling the development of smart spaces through a set of modeling tools and semantic technologies that support the definition of the smart space and the automatic generation of code at hardware level. ROOD feasibility is demonstrated by building an adaptive health monitoring service for a Smart Gym. PMID:23012544

MAPI: a software framework for distributed biomedical applications

PubMed Central

2013-01-01

Background The amount of web-based resources (databases, tools etc.) in biomedicine has increased, but the integrated usage of those resources is complex due to differences in access protocols and data formats. However, distributed data processing is becoming inevitable in several domains, in particular in biomedicine, where researchers face rapidly increasing data sizes. This big data is difficult to process locally because of the large processing, memory and storage capacity required. Results This manuscript describes a framework, called MAPI, which provides a uniform representation of resources available over the Internet, in particular for Web Services. The framework enhances their interoperability and collaborative use by enabling a uniform and remote access. The framework functionality is organized in modules that can be combined and configured in different ways to fulfil concrete development requirements. Conclusions The framework has been tested in the biomedical application domain where it has been a base for developing several clients that are able to integrate different web resources. The MAPI binaries and documentation are freely available at http://www.bitlab-es.com/mapi under the Creative Commons Attribution-No Derivative Works 2.5 Spain License. The MAPI source code is available by request (GPL v3 license). PMID:23311574

A flexible geospatial sensor observation service for diverse sensor data based on Web service

NASA Astrophysics Data System (ADS)

Chen, Nengcheng; Di, Liping; Yu, Genong; Min, Min

Achieving a flexible and efficient geospatial Sensor Observation Service (SOS) is difficult, given the diversity of sensor networks, the heterogeneity of sensor data storage, and the differing requirements of users. This paper describes development of a service-oriented multi-purpose SOS framework. The goal is to create a single method of access to the data by integrating the sensor observation service with other Open Geospatial Consortium (OGC) services — Catalogue Service for the Web (CSW), Transactional Web Feature Service (WFS-T) and Transactional Web Coverage Service (WCS-T). The framework includes an extensible sensor data adapter, an OGC-compliant geospatial SOS, a geospatial catalogue service, a WFS-T, and a WCS-T for the SOS, and a geospatial sensor client. The extensible sensor data adapter finds, stores, and manages sensor data from live sensors, sensor models, and simulation systems. Abstract factory design patterns are used during design and implementation. A sensor observation service compatible with the SWE is designed, following the OGC "core" and "transaction" specifications. It is implemented using Java servlet technology. It can be easily deployed in any Java servlet container and automatically exposed for discovery using Web Service Description Language (WSDL). Interaction sequences between a Sensor Web data consumer and an SOS, between a producer and an SOS, and between an SOS and a CSW are described in detail. The framework has been successfully demonstrated in application scenarios for EO-1 observations, weather observations, and water height gauge observations.

The impact of a state-sponsored mass media campaign on use of telephone quitline and web-based cessation services.

PubMed

Duke, Jennifer C; Mann, Nathan; Davis, Kevin C; MacMonegle, Anna; Allen, Jane; Porter, Lauren

2014-12-24

Most US smokers do not use evidence-based interventions as part of their quit attempts. Quitlines and Web-based treatments may contribute to reductions in population-level tobacco use if successfully promoted. Currently, few states implement sustained media campaigns to promote services and increase adult smoking cessation. This study examines the effects of Florida's tobacco cessation media campaign and a nationally funded media campaign on telephone quitline and Web-based registrations for cessation services from November 2010 through September 2013. We conducted multivariable analyses of weekly media-market-level target rating points (TRPs) and weekly registrations for cessation services through the Florida Quitline (1-877-U-CAN-NOW) or its Web-based cessation service, Web Coach (www.quitnow.net/florida). During 35 months, 141,221 tobacco users registered for cessation services through the Florida Quitline, and 53,513 registered through Web Coach. An increase in 100 weekly TRPs was associated with an increase of 7 weekly Florida Quitline registrants (β = 6.8, P < .001) and 2 Web Coach registrants (β = 1.7, P = .003) in an average media market. An increase in TRPs affected registrants from multiple demographic subgroups similarly. When state and national media campaigns aired simultaneously, approximately one-fifth of Florida's Quitline registrants came from the nationally advertised portal (1-800-QUIT-NOW). Sustained, state-sponsored media can increase the number of registrants to telephone quitlines and Web-based cessation services. Federally funded media campaigns can further increase the reach of state-sponsored cessation services.

The Impact of a State-Sponsored Mass Media Campaign on Use of Telephone Quitline and Web-Based Cessation Services

PubMed Central

Mann, Nathan; Davis, Kevin C.; MacMonegle, Anna; Allen, Jane; Porter, Lauren

2014-01-01

Introduction Most US smokers do not use evidence-based interventions as part of their quit attempts. Quitlines and Web-based treatments may contribute to reductions in population-level tobacco use if successfully promoted. Currently, few states implement sustained media campaigns to promote services and increase adult smoking cessation. This study examines the effects of Florida’s tobacco cessation media campaign and a nationally funded media campaign on telephone quitline and Web-based registrations for cessation services from November 2010 through September 2013. Methods We conducted multivariable analyses of weekly media-market–level target rating points (TRPs) and weekly registrations for cessation services through the Florida Quitline (1-877-U-CAN-NOW) or its Web-based cessation service, Web Coach (www.quitnow.net/florida). Results During 35 months, 141,221 tobacco users registered for cessation services through the Florida Quitline, and 53,513 registered through Web Coach. An increase in 100 weekly TRPs was associated with an increase of 7 weekly Florida Quitline registrants (β = 6.8, P < .001) and 2 Web Coach registrants (β = 1.7, P = .003) in an average media market. An increase in TRPs affected registrants from multiple demographic subgroups similarly. When state and national media campaigns aired simultaneously, approximately one-fifth of Florida’s Quitline registrants came from the nationally advertised portal (1-800-QUIT-NOW). Conclusion Sustained, state-sponsored media can increase the number of registrants to telephone quitlines and Web-based cessation services. Federally funded media campaigns can further increase the reach of state-sponsored cessation services. PMID:25539129

Occupational self-coding and automatic recording (OSCAR): a novel web-based tool to collect and code lifetime job histories in large population-based studies.

PubMed

De Matteis, Sara; Jarvis, Deborah; Young, Heather; Young, Alan; Allen, Naomi; Potts, James; Darnton, Andrew; Rushton, Lesley; Cullinan, Paul

2017-03-01

Objectives The standard approach to the assessment of occupational exposures is through the manual collection and coding of job histories. This method is time-consuming and costly and makes it potentially unfeasible to perform high quality analyses on occupational exposures in large population-based studies. Our aim was to develop a novel, efficient web-based tool to collect and code lifetime job histories in the UK Biobank, a population-based cohort of over 500 000 participants. Methods We developed OSCAR (occupations self-coding automatic recording) based on the hierarchical structure of the UK Standard Occupational Classification (SOC) 2000, which allows individuals to collect and automatically code their lifetime job histories via a simple decision-tree model. Participants were asked to find each of their jobs by selecting appropriate job categories until they identified their job title, which was linked to a hidden 4-digit SOC code. For each occupation a job title in free text was also collected to estimate Cohen's kappa (κ) inter-rater agreement between SOC codes assigned by OSCAR and an expert manual coder. Results OSCAR was administered to 324 653 UK Biobank participants with an existing email address between June and September 2015. Complete 4-digit SOC-coded lifetime job histories were collected for 108 784 participants (response rate: 34%). Agreement between the 4-digit SOC codes assigned by OSCAR and the manual coder for a random sample of 400 job titles was moderately good [κ=0.45, 95% confidence interval (95% CI) 0.42-0.49], and improved when broader job categories were considered (κ=0.64, 95% CI 0.61-0.69 at a 1-digit SOC-code level). Conclusions OSCAR is a novel, efficient, and reasonably reliable web-based tool for collecting and automatically coding lifetime job histories in large population-based studies. Further application in other research projects for external validation purposes is warranted.

Development of XML Schema for Broadband Digital Seismograms and Data Center Portal

NASA Astrophysics Data System (ADS)

Takeuchi, N.; Tsuboi, S.; Ishihara, Y.; Nagao, H.; Yamagishi, Y.; Watanabe, T.; Yanaka, H.; Yamaji, H.

2008-12-01

There are a number of data centers around the globe, where the digital broadband seismograms are opened to researchers. Those centers use their own user interfaces and there are no standard to access and retrieve seismograms from different data centers using unified interface. One of the emergent technologies to realize unified user interface for different data centers is the concept of WebService and WebService portal. Here we have developed a prototype of data center portal for digital broadband seismograms. This WebService portal uses WSDL (Web Services Description Language) to accommodate differences among the different data centers. By using the WSDL, alteration and addition of data center user interfaces can be easily managed. This portal, called NINJA Portal, assumes three WebServices: (1) database Query service, (2) Seismic event data request service, and (3) Seismic continuous data request service. Current system supports both station search of database Query service and seismic continuous data request service. Data centers supported by this NINJA portal will be OHP data center in ERI and Pacific21 data center in IFREE/JAMSTEC in the beginning. We have developed metadata standard for seismological data based on QuakeML for parametric data, which has been developed by ETH Zurich, and XML-SEED for waveform data, which was developed by IFREE/JAMSTEC. The prototype of NINJA portal is now released through IFREE web page (http://www.jamstec.go.jp/pacific21/).

75 FR 75170 - APHIS User Fee Web Site

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-02

...] APHIS User Fee Web Site AGENCY: Animal and Plant Health Inspection Service, USDA. ACTION: Notice... recover the costs of providing certain services. This notice announces the availability of a Web site that contains information about the Agency's user fees. ADDRESSES: The Agency's user fee Web site is located at...

MedlinePlus Connect: Technical Information

MedlinePlus

... Service Technical Information Page MedlinePlus Connect Implementation Options Web Application How does it work? Responds to requests ... examples of MedlinePlus Connect Web Application response pages. Web Service How does it work? Responds to requests ...

A Web 2.0 Interface to Ion Stopping Power and Other Physics Routines for High Energy Density Physics Applications

NASA Astrophysics Data System (ADS)

Stoltz, Peter; Veitzer, Seth

2008-04-01

We present a new Web 2.0-based interface to physics routines for High Energy Density Physics applications. These routines include models for ion stopping power, sputtering, secondary electron yields and energies, impact ionization cross sections, and atomic radiated power. The Web 2.0 interface allows users to easily explore the results of the models before using the routines within other codes or to analyze experimental results. We discuss how we used various Web 2.0 tools, including the Python 2.5, Django, and the Yahoo User Interface library. Finally, we demonstrate the interface by showing as an example the stopping power algorithms researchers are currently using within the Hydra code to analyze warm, dense matter experiments underway at the Neutralized Drift Compression Experiment facility at Lawrence Berkeley National Laboratory.

Developing Web Services for Technology Education. The Graphic Communication Electronic Publishing Project.

ERIC Educational Resources Information Center

Sanders, Mark

1999-01-01

Graphic Communication Electronic Publishing Project supports a Web site (http://TechEd.vt.edu/gcc/) for graphic communication teachers and students, providing links to Web materials, conversion of print materials to electronic formats, and electronic products and services including job listings, resume posting service, and a listserv. (SK)

Publication, discovery and interoperability of Clinical Decision Support Systems: A Linked Data approach.

PubMed

Marco-Ruiz, Luis; Pedrinaci, Carlos; Maldonado, J A; Panziera, Luca; Chen, Rong; Bellika, J Gustav

2016-08-01

The high costs involved in the development of Clinical Decision Support Systems (CDSS) make it necessary to share their functionality across different systems and organizations. Service Oriented Architectures (SOA) have been proposed to allow reusing CDSS by encapsulating them in a Web service. However, strong barriers in sharing CDS functionality are still present as a consequence of lack of expressiveness of services' interfaces. Linked Services are the evolution of the Semantic Web Services paradigm to process Linked Data. They aim to provide semantic descriptions over SOA implementations to overcome the limitations derived from the syntactic nature of Web services technologies. To facilitate the publication, discovery and interoperability of CDS services by evolving them into Linked Services that expose their interfaces as Linked Data. We developed methods and models to enhance CDS SOA as Linked Services that define a rich semantic layer based on machine interpretable ontologies that powers their interoperability and reuse. These ontologies provided unambiguous descriptions of CDS services properties to expose them to the Web of Data. We developed models compliant with Linked Data principles to create a semantic representation of the components that compose CDS services. To evaluate our approach we implemented a set of CDS Linked Services using a Web service definition ontology. The definitions of Web services were linked to the models developed in order to attach unambiguous semantics to the service components. All models were bound to SNOMED-CT and public ontologies (e.g. Dublin Core) in order to count on a lingua franca to explore them. Discovery and analysis of CDS services based on machine interpretable models was performed reasoning over the ontologies built. Linked Services can be used effectively to expose CDS services to the Web of Data by building on current CDS standards. This allows building shared Linked Knowledge Bases to provide machine interpretable semantics to the CDS service description alleviating the challenges on interoperability and reuse. Linked Services allow for building 'digital libraries' of distributed CDS services that can be hosted and maintained in different organizations. Copyright © 2016 Elsevier Inc. All rights reserved.

Automated Detection and Analysis of Interplanetary Shocks Running Real-Time on the Web

NASA Astrophysics Data System (ADS)

Vorotnikov, V.; Smith, C. W.; Hu, Q.; Szabo, A.; Skoug, R. M.; Cohen, C. M.; Davis, A. J.

2008-05-01

The ACE real-time data stream provides web-based now-casting capabilities for solar wind conditions upstream of Earth. We have built a fully automated code that finds and analyzes interplanetary shocks as they occur and posts their solutions on the Web for possible real-time application to space weather nowcasting. Shock analysis algorithms based on the Rankine-Hugoniot jump conditions exist and are in wide-spread use today for the interactive analysis of interplanetary shocks yielding parameters such as shock speed and propagation direction and shock strength in the form of compression ratios. At a previous meeting we reported on efforts to develop a fully automated code that used ACE Level-2 (science quality) data to prove the applicability and correctness of the code and the associated shock-finder. We have since adapted the code to run ACE RTSW data provided by NOAA. This data lacks the full 3-dimensional velocity vector for the solar wind and contains only a single component wind speed. We show that by assuming the wind velocity to be radial strong shock solutions remain essentially unchanged and the analysis performs as well as it would if 3-D velocity components were available. This is due, at least in part, to the fact that strong shocks tend to have nearly radial shock normals and it is the strong shocks that are most effective in space weather applications. Strong shocks are the only shocks that concern us in this application. The code is now running on the Web and the results are available to all.

Integrating geo web services for a user driven exploratory analysis

NASA Astrophysics Data System (ADS)

Moncrieff, Simon; Turdukulov, Ulanbek; Gulland, Elizabeth-Kate

2016-04-01

In data exploration, several online data sources may need to be dynamically aggregated or summarised over spatial region, time interval, or set of attributes. With respect to thematic data, web services are mainly used to present results leading to a supplier driven service model limiting the exploration of the data. In this paper we propose a user need driven service model based on geo web processing services. The aim of the framework is to provide a method for the scalable and interactive access to various geographic data sources on the web. The architecture combines a data query, processing technique and visualisation methodology to rapidly integrate and visually summarise properties of a dataset. We illustrate the environment on a health related use case that derives Age Standardised Rate - a dynamic index that needs integration of the existing interoperable web services of demographic data in conjunction with standalone non-spatial secure database servers used in health research. Although the example is specific to the health field, the architecture and the proposed approach are relevant and applicable to other fields that require integration and visualisation of geo datasets from various web services and thus, we believe is generic in its approach.

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.

Transformative Rendering of Internet Resources

DTIC Science & Technology

2012-10-01

4 Securing WiFi Connections...comes from legitimate web sites that have themselves been hacked . There is no way of anticipating which of these sites have been hacked and therefore...pose a security threat to visitors. The purpose of most of this web page hacking is to plant malicious code on the web site that will attack any

A Tutorial in Creating Web-Enabled Databases with Inmagic DB/TextWorks through ODBC.

ERIC Educational Resources Information Center

Breeding, Marshall

2000-01-01

Explains how to create Web-enabled databases. Highlights include Inmagic's DB/Text WebPublisher product called DB/TextWorks; ODBC (Open Database Connectivity) drivers; Perl programming language; HTML coding; Structured Query Language (SQL); Common Gateway Interface (CGI) programming; and examples of HTML pages and Perl scripts. (LRW)

A Semiotic Analysis of Icons on the World Wide Web.

ERIC Educational Resources Information Center

Ma, Yan

The World Wide Web allows users to interact with a graphic interface to search information in a hypermedia and multimedia environment. Graphics serve as reference points on the World Wide Web for searching and retrieving information. This study analyzed the culturally constructed syntax patterns, or codes, embedded in the icons of library…

The Ensembl REST API: Ensembl Data for Any Language.

PubMed

Yates, Andrew; Beal, Kathryn; Keenan, Stephen; McLaren, William; Pignatelli, Miguel; Ritchie, Graham R S; Ruffier, Magali; Taylor, Kieron; Vullo, Alessandro; Flicek, Paul

2015-01-01

We present a Web service to access Ensembl data using Representational State Transfer (REST). The Ensembl REST server enables the easy retrieval of a wide range of Ensembl data by most programming languages, using standard formats such as JSON and FASTA while minimizing client work. We also introduce bindings to the popular Ensembl Variant Effect Predictor tool permitting large-scale programmatic variant analysis independent of any specific programming language. The Ensembl REST API can be accessed at http://rest.ensembl.org and source code is freely available under an Apache 2.0 license from http://github.com/Ensembl/ensembl-rest. © The Author 2014. Published by Oxford University Press.

Accessing SDO data in a pipeline environment using the VSO WSDL/SOAP interface

NASA Astrophysics Data System (ADS)

Suarez Sola, F. I.; Hourcle, J. A.; Amezcua, A.; Bogart, R.; Davey, A. R.; Gurman, J. B.; Hill, F.; Hughitt, V. K.; Martens, P. C.; Spencer, J.; Vso Team

2010-12-01

As part of the Virtual Solar Observatory (VSO) effort to support the Solar Dynamics Observatory (SDO) data, the VSO has worked on bringing up to date its WSDL document and SOAP interface to make it compatible with most widely used web services core engines. (E.g. axis2, jws, etc.) In this presentation we will explore the possibilities available for searching and/or fetching data within pipeline code. We will explain some of the WSDL/VSO-SDO interface intricacies and show how the vast amount of data that is available via the VSO can be tapped via IDL, Java, Perl or C in an uncomplicated way.

Collaboratively Conceived, Designed and Implemented: Matching Visualization Tools with Geoscience Data Collections and Geoscience Data Collections with Visualization Tools via the ToolMatch Service.

NASA Astrophysics Data System (ADS)

Hoebelheinrich, N. J.; Lynnes, C.; West, P.; Ferritto, M.

2014-12-01

Two problems common to many geoscience domains are the difficulties in finding tools to work with a given dataset collection, and conversely, the difficulties in finding data for a known tool. A collaborative team from the Earth Science Information Partnership (ESIP) has gotten together to design and create a web service, called ToolMatch, to address these problems. The team began their efforts by defining an initial, relatively simple conceptual model that addressed the two uses cases briefly described above. The conceptual model is expressed as an ontology using OWL (Web Ontology Language) and DCterms (Dublin Core Terms), and utilizing standard ontologies such as DOAP (Description of a Project), FOAF (Friend of a Friend), SKOS (Simple Knowledge Organization System) and DCAT (Data Catalog Vocabulary). The ToolMatch service will be taking advantage of various Semantic Web and Web standards, such as OpenSearch, RESTful web services, SWRL (Semantic Web Rule Language) and SPARQL (Simple Protocol and RDF Query Language). The first version of the ToolMatch service was deployed in early fall 2014. While more complete testing is required, a number of communities besides ESIP member organizations have expressed interest in collaborating to create, test and use the service and incorporate it into their own web pages, tools and / or services including the USGS Data Catalog service, DataONE, the Deep Carbon Observatory, Virtual Solar Terrestrial Observatory (VSTO), and the U.S. Global Change Research Program. In this session, presenters will discuss the inception and development of the ToolMatch service, the collaborative process used to design, refine, and test the service, and future plans for the service.

Design Drivers of Water Data Services

NASA Astrophysics Data System (ADS)

Valentine, D.; Zaslavsky, I.

2008-12-01

The CUAHSI Hydrologic Information System (HIS) is being developed as a geographically distributed network of hydrologic data sources and functions that are integrated using web services so that they function as a connected whole. The core of the HIS service-oriented architecture is a collection of water web services, which provide uniform access to multiple repositories of observation data. These services use SOAP protocols communicating WaterML (Water Markup Language). When a client makes a data or metadata request using a CUAHSI HIS web service, these requests are made in standard manner, following the CUAHSI HIS web service signatures - regardless of how the underlying data source may be organized. Also, regardless of the format in which the data are returned by the source, the web services respond to requests by returning the data in a standard format of WaterML. The goal of WaterML design has been to capture semantics of hydrologic observations discovery and retrieval and express the point observations information model as an XML schema. To a large extent, it follows the representation of the information model as adopted by the CUASHI Observations Data Model (ODM) relational design. Another driver of WaterML design is specifications and metadata adopted by USGS NWIS, EPA STORET, and other federal agencies, as it seeks to provide a common foundation for exchanging both agency data and data collected in multiple academic projects. Another WaterML design principle was to create, in version 1 of HIS in particular, a fairly rigid and simple XML schema which is easy to generate and parse, thus creating the least barrier for adoption by hydrologists. WaterML includes a series of elements that reflect common notions used in describing hydrologic observations, such as site, variable, source, observation series, seriesCatalog, and data values. Each of the three main request methods in the water web services - GetSiteInfo, GetVariableInfo, and GetValues - has a corresponding response element in WaterML: SitesResponse, VariableResponse, and TimeSeriesResponse. The WaterML specification is being adopted by federal agencies. The experimental USGS NWIS Daily Values web service returns WaterML-compliant TImeSeriesResponse. The National Climatic Data Center is also prototyping WaterML for data delivery, and has developed a REST-based service that generates WaterML- compliant output for the NCDC ASOS network. Such agency-supported web services coming online provide a much more efficient way to deliver agency data compared to the web site scraper services that the CUAHSI HIS project has developed initially. The CUAHSI water data web services will continue to serve as the main communication mechanism within CUAHSI HIS, connecting a variety of data sources with a growing set of web service clients being developed in both academia and the commercial sector. The driving forces for the development of web services continue to be: - Application experience and needs of the growing number of CUAHSI HIS users, who experiment with additional data types, analysis modes, data browsing and searching strategies, and provide feedback to WaterML developers; - Data description requirements posed by various federal and state agencies; - Harmonization with standards being adopted or developed in neighboring communities, in particular the relevant standards being explored within the Open Geospatial Consortium. CUAHSI WaterML is a standard output schema for CUAHSI HIS water web services. Its formal specification is available as OGC discussion paper at www.opengeospatial.org/standards/dp/ class="ab'>

Operational Use of OGC Web Services at the Met Office

NASA Astrophysics Data System (ADS)

Wright, Bruce

2010-05-01

The Met Office has adopted the Service-Orientated Architecture paradigm to deliver services to a range of customers through Rich Internet Applications (RIAs). The approach uses standard Open Geospatial Consortium (OGC) web services to provide information to web-based applications through a range of generic data services. "Invent", the Met Office beta site, is used to showcase Met Office future plans for presenting web-based weather forecasts, product and information to the public. This currently hosts a freely accessible Weather Map Viewer, written in JavaScript, which accesses a Web Map Service (WMS), to deliver innovative web-based visualizations of weather and its potential impacts to the public. The intention is to engage the public in the development of new web-based services that more accurately meet their needs. As the service is intended for public use within the UK, it has been designed to support a user base of 5 million, the analysed level of UK web traffic reaching the Met Office's public weather information site. The required scalability has been realised through the use of multi-tier tile caching: - WMS requests are made for 256x256 tiles for fixed areas and zoom levels; - a Tile Cache, developed in house, efficiently serves tiles on demand, managing WMS request for the new tiles; - Edge Servers, externally hosted by Akamai, provide a highly scalable (UK-centric) service for pre-cached tiles, passing new requests to the Tile Cache; - the Invent Weather Map Viewer uses the Google Maps API to request tiles from Edge Servers. (We would expect to make use of the Web Map Tiling Service, when it becomes an OGC standard.) The Met Office delivers specialist commercial products to market sectors such as transport, utilities and defence, which exploit a Web Feature Service (WFS) for data relating forecasts and observations to specific geographic features, and a Web Coverage Service (WCS) for sub-selections of gridded data. These are locally rendered as maps or graphs, and combined with the WMS pre-rendered images and text, in a FLEX application, to provide sophisticated, user impact-based view of the weather. The OGC web services supporting these applications have been developed in collaboration with commercial companies. Visual Weather was originally a desktop application for forecasters, but IBL have developed it to expose the full range of forecast and observation data through standard web services (WCS and WMS). Forecasts and observations relating to specific locations and geographic features are held in an Oracle Database, and exposed as a WFS using Snowflake Software's GO-Publisher application. The Met Office has worked closely with both IBL and Snowflake Software to ensure that the web services provided strike a balance between conformance to the standards and performance in an operational environment. This has proved challenging in areas where the standards are rapidly evolving (e.g. WCS) or do not allow adequate description of the Met-Ocean domain (e.g. multiple time coordinates and parametric vertical coordinates). It has also become clear that careful selection of the features to expose, based on the way in which you expect users to query those features, in necessary in order to deliver adequate performance. These experiences are providing useful 'real-world' input in to the recently launched OGC MetOcean Domain Working Group and World Meteorological Organisation (WMO) initiatives in this area.

WebViz:A Web-based Collaborative Interactive Visualization System for large-Scale Data Sets

NASA Astrophysics Data System (ADS)

Yuen, D. A.; McArthur, E.; Weiss, R. M.; Zhou, J.; Yao, B.

2010-12-01

WebViz is a web-based application designed to conduct collaborative, interactive visualizations of large data sets for multiple users, allowing researchers situated all over the world to utilize the visualization services offered by the University of Minnesota’s Laboratory for Computational Sciences and Engineering (LCSE). This ongoing project has been built upon over the last 3 1/2 years .The motivation behind WebViz lies primarily with the need to parse through an increasing amount of data produced by the scientific community as a result of larger and faster multicore and massively parallel computers coming to the market, including the use of general purpose GPU computing. WebViz allows these large data sets to be visualized online by anyone with an account. The application allows users to save time and resources by visualizing data ‘on the fly’, wherever he or she may be located. By leveraging AJAX via the Google Web Toolkit (http://code.google.com/webtoolkit/), we are able to provide users with a remote, web portal to LCSE's (http://www.lcse.umn.edu) large-scale interactive visualization system already in place at the University of Minnesota. LCSE’s custom hierarchical volume rendering software provides high resolution visualizations on the order of 15 million pixels and has been employed for visualizing data primarily from simulations in astrophysics to geophysical fluid dynamics . In the current version of WebViz, we have implemented a highly extensible back-end framework built around HTTP "server push" technology. The web application is accessible via a variety of devices including netbooks, iPhones, and other web and javascript-enabled cell phones. Features in the current version include the ability for users to (1) securely login (2) launch multiple visualizations (3) conduct collaborative visualization sessions (4) delegate control aspects of a visualization to others and (5) engage in collaborative chats with other users within the user interface of the web application. These features are all in addition to a full range of essential visualization functions including 3-D camera and object orientation, position manipulation, time-stepping control, and custom color/alpha mapping.

Web Services and Data Enhancements at the Northern California Earthquake Data Center

NASA Astrophysics Data System (ADS)

Neuhauser, D. S.; Zuzlewski, S.; Lombard, P. N.; Allen, R. M.

2013-12-01

The Northern California Earthquake Data Center (NCEDC) provides data archive and distribution services for seismological and geophysical data sets that encompass northern California. The NCEDC is enhancing its ability to deliver rapid information through Web Services. NCEDC Web Services use well-established web server and client protocols and REST software architecture to allow users to easily make queries using web browsers or simple program interfaces and to receive the requested data in real-time rather than through batch or email-based requests. Data are returned to the user in the appropriate format such as XML, RESP, simple text, or MiniSEED depending on the service and selected output format. The NCEDC offers the following web services that are compliant with the International Federation of Digital Seismograph Networks (FDSN) web services specifications: (1) fdsn-dataselect: time series data delivered in MiniSEED format, (2) fdsn-station: station and channel metadata and time series availability delivered in StationXML format, (3) fdsn-event: earthquake event information delivered in QuakeML format. In addition, the NCEDC offers the the following IRIS-compatible web services: (1) sacpz: provide channel gains, poles, and zeros in SAC format, (2) resp: provide channel response information in RESP format, (3) dataless: provide station and channel metadata in Dataless SEED format. The NCEDC is also developing a web service to deliver timeseries from pre-assembled event waveform gathers. The NCEDC has waveform gathers for ~750,000 northern and central California events from 1984 to the present, many of which were created by the USGS NCSN prior to the establishment of the joint NCSS (Northern California Seismic System). We are currently adding waveforms to these older event gathers with time series from the UCB networks and other networks with waveforms archived at the NCEDC, and ensuring that the waveform for each channel in the event gathers have the highest quality waveform from the archive.

Factors that influence acceptance of web-based e-learning systems for the in-service education of junior high school teachers in Taiwan.

PubMed

Chen, Hong-Ren; Tseng, Hsiao-Fen

2012-08-01

Web-based e-learning is not restricted by time or place and can provide teachers with a learning environment that is flexible and convenient, enabling them to efficiently learn, quickly develop their professional expertise, and advance professionally. Many research reports on web-based e-learning have neglected the role of the teacher's perspective in the acceptance of using web-based e-learning systems for in-service education. We distributed questionnaires to 402 junior high school teachers in central Taiwan. This study used the Technology Acceptance Model (TAM) as our theoretical foundation and employed the Structure Equation Model (SEM) to examine factors that influenced intentions to use in-service training conducted through web-based e-learning. The results showed that motivation to use and Internet self-efficacy were significantly positively associated with behavioral intentions regarding the use of web-based e-learning for in-service training through the factors of perceived usefulness and perceived ease of use. The factor of computer anxiety had a significantly negative effect on behavioral intentions toward web-based e-learning in-service training through the factor of perceived ease of use. Perceived usefulness and motivation to use were the primary reasons for the acceptance by junior high school teachers of web-based e-learning systems for in-service training. Copyright © 2011 Elsevier Ltd. All rights reserved.

Service-based analysis of biological pathways

PubMed Central

Zheng, George; Bouguettaya, Athman

2009-01-01

Background Computer-based pathway discovery is concerned with two important objectives: pathway identification and analysis. Conventional mining and modeling approaches aimed at pathway discovery are often effective at achieving either objective, but not both. Such limitations can be effectively tackled leveraging a Web service-based modeling and mining approach. Results Inspired by molecular recognitions and drug discovery processes, we developed a Web service mining tool, named PathExplorer, to discover potentially interesting biological pathways linking service models of biological processes. The tool uses an innovative approach to identify useful pathways based on graph-based hints and service-based simulation verifying user's hypotheses. Conclusion Web service modeling of biological processes allows the easy access and invocation of these processes on the Web. Web service mining techniques described in this paper enable the discovery of biological pathways linking these process service models. Algorithms presented in this paper for automatically highlighting interesting subgraph within an identified pathway network enable the user to formulate hypothesis, which can be tested out using our simulation algorithm that are also described in this paper. PMID:19796403

Tobacco cessation among users of telephone and web-based interventions--four states, 2011-2012.

PubMed

Puckett, Mary; Neri, Antonio; Thompson, Trevor; Underwood, J Michael; Momin, Behnoosh; Kahende, Jennifer; Zhang, Lei; Stewart, Sherri L

2015-01-02

Smoking caused an average of 480,000 deaths per year in the United States from 2005 to 2009, and three in 10 cancer deaths in the United States are tobacco related. Tobacco cessation is a high public health priority, and all states offer some form of tobacco cessation service. Quitlines provide telephone-based counseling services and are an effective intervention for tobacco cessation. In addition to telephone services, 96% of all U.S. quitlines offer Web-based cessation services. Evidence is limited on the number of tobacco users who use more than one type of service, and studies report mixed results on whether combined telephone and Web-based counseling improves long-term cessation compared with telephone alone. CDC conducted a survey of users of telephone and Web-based cessation services in four states to determine the cessation success of users of these interventions. After adjusting for multiple variables, persons who used both telephone and Web-based services were more likely to report abstinence from smoking for 30 days at follow up (odds ratio = 1.3) compared with telephone-only users and with Web-only users (odds ratio = 1.5). These findings suggest that states might consider offering both types of cessation services to increase cessation success.

CASAS: A tool for composing automatically and semantically astrophysical services

NASA Astrophysics Data System (ADS)

Louge, T.; Karray, M. H.; Archimède, B.; Knödlseder, J.

2017-07-01

Multiple astronomical datasets are available through internet and the astrophysical Distributed Computing Infrastructure (DCI) called Virtual Observatory (VO). Some scientific workflow technologies exist for retrieving and combining data from those sources. However selection of relevant services, automation of the workflows composition and the lack of user-friendly platforms remain a concern. This paper presents CASAS, a tool for semantic web services composition in astrophysics. This tool proposes automatic composition of astrophysical web services and brings a semantics-based, automatic composition of workflows. It widens the services choice and eases the use of heterogeneous services. Semantic web services composition relies on ontologies for elaborating the services composition; this work is based on Astrophysical Services ONtology (ASON). ASON had its structure mostly inherited from the VO services capacities. Nevertheless, our approach is not limited to the VO and brings VO plus non-VO services together without the need for premade recipes. CASAS is available for use through a simple web interface.

XMM-Newton Mobile Web Application

NASA Astrophysics Data System (ADS)

Ibarra, A.; Kennedy, M.; Rodríguez, P.; Hernández, C.; Saxton, R.; Gabriel, C.

2013-10-01

We present the first XMM-Newton web mobile application, coded using new web technologies such as HTML5, the Query mobile framework, and D3 JavaScript data-driven library. This new web mobile application focuses on re-formatted contents extracted directly from the XMM-Newton web, optimizing the contents for mobile devices. The main goals of this development were to reach all kind of handheld devices and operating systems, while minimizing software maintenance. The application therefore has been developed as a web mobile implementation rather than a more costly native application. New functionality will be added regularly.

A Case Study in Web 2.0 Application Development

NASA Astrophysics Data System (ADS)

Marganian, P.; Clark, M.; Shelton, A.; McCarty, M.; Sessoms, E.

2010-12-01

Recent web technologies focusing on languages, frameworks, and tools are discussed, using the Robert C. Byrd Green Bank Telescopes (GBT) new Dynamic Scheduling System as the primary example. Within that example, we use a popular Python web framework, Django, to build the extensive web services for our users. We also use a second complimentary server, written in Haskell, to incorporate the core scheduling algorithms. We provide a desktop-quality experience across all the popular browsers for our users with the Google Web Toolkit and judicious use of JQuery in Django templates. Single sign-on and authentication throughout all NRAO web services is accomplished via the Central Authentication Service protocol, or CAS.

Using EMBL-EBI Services via Web Interface and Programmatically via Web Services.

PubMed

Lopez, Rodrigo; Cowley, Andrew; Li, Weizhong; McWilliam, Hamish

2014-12-12

The European Bioinformatics Institute (EMBL-EBI) provides access to a wide range of databases and analysis tools that are of key importance in bioinformatics. As well as providing Web interfaces to these resources, Web Services are available using SOAP and REST protocols that enable programmatic access to our resources and allow their integration into other applications and analytical workflows. This unit describes the various options available to a typical researcher or bioinformatician who wishes to use our resources via Web interface or programmatically via a range of programming languages. Copyright © 2014 John Wiley & Sons, Inc.

Development of Virtual Resource Based IoT Proxy for Bridging Heterogeneous Web Services in IoT Networks.

PubMed

Jin, Wenquan; Kim, DoHyeun

2018-05-26

The Internet of Things is comprised of heterogeneous devices, applications, and platforms using multiple communication technologies to connect the Internet for providing seamless services ubiquitously. With the requirement of developing Internet of Things products, many protocols, program libraries, frameworks, and standard specifications have been proposed. Therefore, providing a consistent interface to access services from those environments is difficult. Moreover, bridging the existing web services to sensor and actuator networks is also important for providing Internet of Things services in various industry domains. In this paper, an Internet of Things proxy is proposed that is based on virtual resources to bridge heterogeneous web services from the Internet to the Internet of Things network. The proxy enables clients to have transparent access to Internet of Things devices and web services in the network. The proxy is comprised of server and client to forward messages for different communication environments using the virtual resources which include the server for the message sender and the client for the message receiver. We design the proxy for the Open Connectivity Foundation network where the virtual resources are discovered by the clients as Open Connectivity Foundation resources. The virtual resources represent the resources which expose services in the Internet by web service providers. Although the services are provided by web service providers from the Internet, the client can access services using the consistent communication protocol in the Open Connectivity Foundation network. For discovering the resources to access services, the client also uses the consistent discovery interface to discover the Open Connectivity Foundation devices and virtual resources.

Security and Efficiency Concerns With Distributed Collaborative Networking Environments

DTIC Science & Technology

2003-09-01

have the ability to access Web communications services of the WebEx MediaTone Network from a single login. [24] WebEx provides a range of secure...Web. WebEx services enable secure data, voice and video communications through the browser and are supported by the WebEx MediaTone Network, a global...designed to host large-scale, structured events and conferences, featuring a Q&A Manager that allows multiple moderators to handle questions while

Accountable Information Flow for Java-Based Web Applications

DTIC Science & Technology

2010-01-01

runtime library Swift server runtime Java servlet framework HTTP Web server Web browser Figure 2: The Swift architecture introduced an open-ended...On the server, the Java application code links against Swift’s server-side run-time library, which in turn sits on top of the standard Java servlet ...AFRL-RI-RS-TR-2010-9 Final Technical Report January 2010 ACCOUNTABLE INFORMATION FLOW FOR JAVA -BASED WEB APPLICATIONS

Finding, Browsing and Getting Data Easily Using SPDF Web Services

NASA Technical Reports Server (NTRS)

Candey, R.; Chimiak, R.; Harris, B.; Johnson, R.; Kovalick, T.; Lal, N.; Leckner, H.; Liu, M.; McGuire, R.; Papitashvili, N.;

Web Services Security - Implementation and Evaluation Issues

NASA Astrophysics Data System (ADS)

Pimenidis, Elias; Georgiadis, Christos K.; Bako, Peter; Zorkadis, Vassilis

Web services development is a key theme in the utilization the commercial exploitation of the semantic web. Paramount to the development and offering of such services is the issue of security features and they way these are applied in instituting trust amongst participants and recipients of the service. Implementing such security features is a major challenge to developers as they need to balance these with performance and interoperability requirements. Being able to evaluate the level of security offered is a desirable feature for any prospective participant. The authors attempt to address the issues of security requirements and evaluation criteria, while they discuss the challenges of security implementation through a simple web service application case.

The Statistical Consulting Center for Astronomy (SCCA)

NASA Technical Reports Server (NTRS)

Akritas, Michael

2001-01-01

The process by which raw astronomical data acquisition is transformed into scientifically meaningful results and interpretation typically involves many statistical steps. Traditional astronomy limits itself to a narrow range of old and familiar statistical methods: means and standard deviations; least-squares methods like chi(sup 2) minimization; and simple nonparametric procedures such as the Kolmogorov-Smirnov tests. These tools are often inadequate for the complex problems and datasets under investigations, and recent years have witnessed an increased usage of maximum-likelihood, survival analysis, multivariate analysis, wavelet and advanced time-series methods. The Statistical Consulting Center for Astronomy (SCCA) assisted astronomers with the use of sophisticated tools, and to match these tools with specific problems. The SCCA operated with two professors of statistics and a professor of astronomy working together. Questions were received by e-mail, and were discussed in detail with the questioner. Summaries of those questions and answers leading to new approaches were posted on the Web (www.state.psu.edu/ mga/SCCA). In addition to serving individual astronomers, the SCCA established a Web site for general use that provides hypertext links to selected on-line public-domain statistical software and services. The StatCodes site (www.astro.psu.edu/statcodes) provides over 200 links in the areas of: Bayesian statistics; censored and truncated data; correlation and regression, density estimation and smoothing, general statistics packages and information; image analysis; interactive Web tools; multivariate analysis; multivariate clustering and classification; nonparametric analysis; software written by astronomers; spatial statistics; statistical distributions; time series analysis; and visualization tools. StatCodes has received a remarkable high and constant hit rate of 250 hits/week (over 10,000/year) since its inception in mid-1997. It is of interest to scientists both within and outside of astronomy. The most popular sections are multivariate techniques, image analysis, and time series analysis. Hundreds of copies of the ASURV, SLOPES and CENS-TAU codes developed by SCCA scientists were also downloaded from the StatCodes site. In addition to formal SCCA duties, SCCA scientists continued a variety of related activities in astrostatistics, including refereeing of statistically oriented papers submitted to the Astrophysical Journal, talks in meetings including Feigelson's talk to science journalists entitled "The reemergence of astrostatistics" at the American Association for the Advancement of Science meeting, and published papers of astrostatistical content.

RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps

PubMed Central

Drory Retwitzer, Matan; Polishchuk, Maya; Churkin, Elena; Kifer, Ilona; Yakhini, Zohar; Barash, Danny

2015-01-01

Searching for RNA sequence-structure patterns is becoming an essential tool for RNA practitioners. Novel discoveries of regulatory non-coding RNAs in targeted organisms and the motivation to find them across a wide range of organisms have prompted the use of computational RNA pattern matching as an enhancement to sequence similarity. State-of-the-art programs differ by the flexibility of patterns allowed as queries and by their simplicity of use. In particular—no existing method is available as a user-friendly web server. A general program that searches for RNA sequence-structure patterns is RNA Structator. However, it is not available as a web server and does not provide the option to allow flexible gap pattern representation with an upper bound of the gap length being specified at any position in the sequence. Here, we introduce RNAPattMatch, a web-based application that is user friendly and makes sequence/structure RNA queries accessible to practitioners of various background and proficiency. It also extends RNA Structator and allows a more flexible variable gaps representation, in addition to analysis of results using energy minimization methods. RNAPattMatch service is available at http://www.cs.bgu.ac.il/rnapattmatch. A standalone version of the search tool is also available to download at the site. PMID:25940619

Knowledge-driven enhancements for task composition in bioinformatics.

PubMed

Sutherland, Karen; McLeod, Kenneth; Ferguson, Gus; Burger, Albert

2009-10-01

A key application area of semantic technologies is the fast-developing field of bioinformatics. Sealife was a project within this field with the aim of creating semantics-based web browsing capabilities for the Life Sciences. This includes meaningfully linking significant terms from the text of a web page to executable web services. It also involves the semantic mark-up of biological terms, linking them to biomedical ontologies, then discovering and executing services based on terms that interest the user. A system was produced which allows a user to identify terms of interest on a web page and subsequently connects these to a choice of web services which can make use of these inputs. Elements of Artificial Intelligence Planning build on this to present a choice of higher level goals, which can then be broken down to construct a workflow. An Argumentation System was implemented to evaluate the results produced by three different gene expression databases. An evaluation of these modules was carried out on users from a variety of backgrounds. Users with little knowledge of web services were able to achieve tasks that used several services in much less time than they would have taken to do this manually. The Argumentation System was also considered a useful resource and feedback was collected on the best way to present results. Overall the system represents a move forward in helping users to both construct workflows and analyse results by incorporating specific domain knowledge into the software. It also provides a mechanism by which web pages can be linked to web services. However, this work covers a specific domain and much co-ordinated effort is needed to make all web services available for use in such a way, i.e. the integration of underlying knowledge is a difficult but essential task.

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases.

PubMed

Wollbrett, Julien; Larmande, Pierre; de Lamotte, Frédéric; Ruiz, Manuel

2013-04-15

In recent years, a large amount of "-omics" data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers. We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases. BioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic.

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases

PubMed Central

2013-01-01

Background In recent years, a large amount of “-omics” data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers. Results We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases. Conclusions BioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic. PMID:23586394

Selecting a Free Web-Hosted Survey Tool for Student Use

ERIC Educational Resources Information Center

Elbeck, Matt

2014-01-01

This study provides marketing educators a review of free web-based survey services and guidance for student use. A mixed methods approach started with online searches and metrics identifying 13 free web-hosted survey services, described as demonstration or project tools, and ranked using popularity and importance web-based metrics. For each…

About NOAA's National Weather Service

Science.gov Websites

official web portal to all federal, state and local government web resources and services. Follow the Field Offices are located across the country. Links to web sites of these components of the National that affect small businesses have established Web sites, e-mail addresses, and toll free phone numbers

Prediction of toxicity and comparison of alternatives using WebTEST (Web-services Toxicity Estimation Software Tool)

EPA Science Inventory

A Java-based web service is being developed within the US EPA’s Chemistry Dashboard to provide real time estimates of toxicity values and physical properties. WebTEST can generate toxicity predictions directly from a simple URL which includes the endpoint, QSAR method, and ...

Prediction of toxicity and comparison of alternatives using WebTEST (Web-services Toxicity Estimation Software Tool)(Bled Slovenia)

EPA Science Inventory

A Java-based web service is being developed within the US EPA’s Chemistry Dashboard to provide real time estimates of toxicity values and physical properties. WebTEST can generate toxicity predictions directly from a simple URL which includes the endpoint, QSAR method, and ...

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments.

PubMed

Burdick, David B; Cavnor, Chris C; Handcock, Jeremy; Killcoyne, Sarah; Lin, Jake; Marzolf, Bruz; Ramsey, Stephen A; Rovira, Hector; Bressler, Ryan; Shmulevich, Ilya; Boyle, John

2010-07-14

High throughput sequencing has become an increasingly important tool for biological research. However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires. Existing software solutions provide static and well-established algorithms in a restrictive package. However as high throughput sequencing is a rapidly evolving field, such static approaches lack the ability to readily adopt the latest advances and techniques which are often required by researchers. We have used a loosely coupled, service-oriented infrastructure to develop SeqAdapt. This system streamlines data management and allows for rapid integration of novel algorithms. Our approach also allows computational biologists to focus on developing and applying new methods instead of writing boilerplate infrastructure code. The system is based around the Addama service architecture and is available at our website as a demonstration web application, an installable single download and as a collection of individual customizable services.

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments

PubMed Central

2010-01-01

Background High throughput sequencing has become an increasingly important tool for biological research. However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires. Results Existing software solutions provide static and well-established algorithms in a restrictive package. However as high throughput sequencing is a rapidly evolving field, such static approaches lack the ability to readily adopt the latest advances and techniques which are often required by researchers. We have used a loosely coupled, service-oriented infrastructure to develop SeqAdapt. This system streamlines data management and allows for rapid integration of novel algorithms. Our approach also allows computational biologists to focus on developing and applying new methods instead of writing boilerplate infrastructure code. Conclusion The system is based around the Addama service architecture and is available at our website as a demonstration web application, an installable single download and as a collection of individual customizable services. PMID:20630057

A Community-Based Research Approach to Develop an Educational Web Portal

ERIC Educational Resources Information Center

Preiser-Houy, Lara; Navarrete, Carlos J.

2011-01-01

Service-learning projects are becoming more prevalent in Information Systems education. This study explores the use of community-based research, a special kind of a service-learning strategy, in an Information Systems web development course. The paper presents a case study of a service-learning project to develop an educational web portal for a…

The Business Information Services: Old-Line Online Moves to the Web.

ERIC Educational Resources Information Center

O'Leary, Mick

1997-01-01

Although the availability of free information on the World Wide Web has placed traditional, fee-based proprietary online services on the defensive, most major online business services are now on the Web. Highlights several business information providers: Profound, NewsNet and ProQuest Direct, Dow Jones and Wall Street Journal Interactive Edition,…

Vocabulary services to support scientific data interoperability

NASA Astrophysics Data System (ADS)

Cox, Simon; Mills, Katie; Tan, Florence

2013-04-01

Shared vocabularies are a core element in interoperable systems. Vocabularies need to be available at run-time, and where the vocabularies are shared by a distributed community this implies the use of web technology to provide vocabulary services. Given the ubiquity of vocabularies or classifiers in systems, vocabulary services are effectively the base of the interoperability stack. In contemporary knowledge organization systems, a vocabulary item is considered a concept, with the "terms" denoting it appearing as labels. The Simple Knowledge Organization System (SKOS) formalizes this as an RDF Schema (RDFS) application, with a bridge to formal logic in Web Ontology Language (OWL). For maximum utility, a vocabulary should be made available through the following interfaces: * the vocabulary as a whole - at an ontology URI corresponding to a vocabulary document * each item in the vocabulary - at the item URI * summaries, subsets, and resources derived by transformation * through the standard RDF web API - i.e. a SPARQL endpoint * through a query form for human users. However, the vocabulary data model may be leveraged directly in a standard vocabulary API that uses the semantics provided by SKOS. SISSvoc3 [1] accomplishes this as a standard set of URI templates for a vocabulary. Any URI comforming to the template selects a vocabulary subset based on the SKOS properties, including labels (skos:prefLabel, skos:altLabel, rdfs:label) and a subset of the semantic relations (skos:broader, skos:narrower, etc). SISSvoc3 thus provides a RESTFul SKOS API to query a vocabulary, but hiding the complexity of SPARQL. It has been implemented using the Linked Data API (LDA) [2], which connects to a SPARQL endpoint. By using LDA, we also get content-negotiation, alternative views, paging, metadata and other functionality provided in a standard way. A number of vocabularies have been formalized in SKOS and deployed by CSIRO, the Australian Bureau of Meteorology (BOM) and their collaborators using SISSvoc3, including: * geologic timescale (multiple versions) * soils classification * definitions from OGC standards * geosciml vocabularies * mining commodities * hyperspectral scalars Several other agencies in Australia have adopted SISSvoc3 for their vocabularies. SISSvoc3 differs from other SKOS-based vocabulary-access APIs such as GEMET [3] and NVS [4] in that (a) the service is decoupled from the content store, (b) the service URI is independent of the content URIs This means that a SISSvoc3 interface can be deployed over any SKOS vocabulary which is available at a SPARQL endpoint. As an example, a SISSvoc3 query and presentation interface has been deployed over the NERC vocabulary service hosted by the BODC, providing a search interface which is not available natively. We use vocabulary services to populate menus in user interfaces, to support data validation, and to configure data conversion routines. Related services built on LDA have also been used as a generic registry interface, and extended for serving gazetteer information. ACKNOWLEDGEMENTS The CSIRO SISSvoc3 implementation is built using the Epimorphics ELDA platform http://code.google.com/p/elda/. We thank Jacqui Githaiga and Terry Rankine for their contributions to SISSvoc design and implementation. REFERENCES 1. SISSvoc3 Specification https://www.seegrid.csiro.au/wiki/Siss/SISSvoc30Specification 2. Linked Data API http://code.google.com/p/linked-data-api/wiki/Specification 3. GEMET https://svn.eionet.europa.eu/projects/Zope/wiki/GEMETWebServiceAPI 4. NVS 2.0 http://vocab.nerc.ac.uk/

The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update

PubMed Central

Huynh, Tien; Rigoutsos, Isidore

2004-01-01

In this report, we provide an update on the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server, which is operational around the clock, provides access to a large number of methods that have been developed and published by the group's members. There is an increasing number of problems that these tools can help tackle; these problems range from the discovery of patterns in streams of events and the computation of multiple sequence alignments, to the discovery of genes in nucleic acid sequences, the identification—directly from sequence—of structural deviations from α-helicity and the annotation of amino acid sequences for antimicrobial activity. Additionally, annotations for more than 130 archaeal, bacterial, eukaryotic and viral genomes are now available on-line and can be searched interactively. The tools and code bundles continue to be accessible from http://cbcsrv.watson.ibm.com/Tspd.html whereas the genomics annotations are available at http://cbcsrv.watson.ibm.com/Annotations/. PMID:15215340

The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update.

PubMed

Huynh, Tien; Rigoutsos, Isidore

2004-07-01

In this report, we provide an update on the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server, which is operational around the clock, provides access to a large number of methods that have been developed and published by the group's members. There is an increasing number of problems that these tools can help tackle; these problems range from the discovery of patterns in streams of events and the computation of multiple sequence alignments, to the discovery of genes in nucleic acid sequences, the identification--directly from sequence--of structural deviations from alpha-helicity and the annotation of amino acid sequences for antimicrobial activity. Additionally, annotations for more than 130 archaeal, bacterial, eukaryotic and viral genomes are now available on-line and can be searched interactively. The tools and code bundles continue to be accessible from http://cbcsrv.watson.ibm.com/Tspd.html whereas the genomics annotations are available at http://cbcsrv.watson.ibm.com/Annotations/.

Pre-calculated protein structure alignments at the RCSB PDB website.

PubMed

Prlic, Andreas; Bliven, Spencer; Rose, Peter W; Bluhm, Wolfgang F; Bizon, Chris; Godzik, Adam; Bourne, Philip E

2010-12-01

With the continuous growth of the RCSB Protein Data Bank (PDB), providing an up-to-date systematic structure comparison of all protein structures poses an ever growing challenge. Here, we present a comparison tool for calculating both 1D protein sequence and 3D protein structure alignments. This tool supports various applications at the RCSB PDB website. First, a structure alignment web service calculates pairwise alignments. Second, a stand-alone application runs alignments locally and visualizes the results. Third, pre-calculated 3D structure comparisons for the whole PDB are provided and updated on a weekly basis. These three applications allow users to discover novel relationships between proteins available either at the RCSB PDB or provided by the user. A web user interface is available at http://www.rcsb.org/pdb/workbench/workbench.do. The source code is available under the LGPL license from http://www.biojava.org. A source bundle, prepared for local execution, is available from http://source.rcsb.org andreas@sdsc.edu; pbourne@ucsd.edu.

CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets.

PubMed

Flobak, Åsmund; Vazquez, Miguel; Lægreid, Astrid; Valencia, Alfonso

2017-08-01

Drug synergies are sought to identify combinations of drugs particularly beneficial. User-friendly software solutions that can assist analysis of large-scale datasets are required. CImbinator is a web-service that can aid in batch-wise and in-depth analyzes of data from small-scale and large-scale drug combination screens. CImbinator offers to quantify drug combination effects, using both the commonly employed median effect equation, as well as advanced experimental mathematical models describing dose response relationships. CImbinator is written in Ruby and R. It uses the R package drc for advanced drug response modeling. CImbinator is available at http://cimbinator.bioinfo.cnio.es , the source-code is open and available at https://github.com/Rbbt-Workflows/combination_index . A Docker image is also available at https://hub.docker.com/r/mikisvaz/rbbt-ci_mbinator/ . asmund.flobak@ntnu.no or miguel.vazquez@cnio.es. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

CHEMICAL STRUCTURE INDEXING OF TOXICITY DATA ON ...

EPA Pesticide Factsheets

Standardized chemical structure annotation of public toxicity databases and information resources is playing an increasingly important role in the 'flattening' and integration of diverse sets of biological activity data on the Internet. This review discusses public initiatives that are accelerating the pace of this transformation, with particular reference to toxicology-related chemical information. Chemical content annotators, structure locator services, large structure/data aggregator web sites, structure browsers, International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) codes, toxicity data models and public chemical/biological activity profiling initiatives are all playing a role in overcoming barriers to the integration of toxicity data, and are bringing researchers closer to the reality of a mineable chemical Semantic Web. An example of this integration of data is provided by the collaboration among researchers involved with the Distributed Structure-Searchable Toxicity (DSSTox) project, the Carcinogenic Potency Project, projects at the National Cancer Institute and the PubChem database. Standardizing chemical structure annotation of public toxicity databases

Implementation of Smart Metering based on Internet of Things

NASA Astrophysics Data System (ADS)

Kaur, Milanpreet; Mathew, Lini, Dr.; Alokdeep; Kumar, Ajay

2018-03-01

From the aspect of saving energy, there is a continuous modification in communication technology and information in order to satisfy all customers demand. Today customers are demanding for accurate energy measurement, timely data and for good customer services. The best solution is smart grid system with various communication technologies which can be cost effective and electrical section to have a bidirectional communication in which information about electrical energy consumption is shared between consumers as well as by utility for remote checking. This paper describes the monitoring of energy consumption with Arduino Uno board and Ethernet using IoT (Internet of Things) concept. This proposed design eliminates human inclusion in the conservation of electricity. The consumer can receive the information about consumption of energy by using IP address on their devices. The web client code is uploaded for checking the client information such as location, content, connection, and disconnection to the web server. This proposed system gives reliable and accurate information regarding electrical energy management system (EMS) through Internet of things (IoT).

BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts.

PubMed

Yang, Kun; Stracquadanio, Giovanni; Luo, Jingchuan; Boeke, Jef D; Bader, Joel S

2016-03-15

Combinatorial assembly of DNA elements is an efficient method for building large-scale synthetic pathways from standardized, reusable components. These methods are particularly useful because they enable assembly of multiple DNA fragments in one reaction, at the cost of requiring that each fragment satisfies design constraints. We developed BioPartsBuilder as a biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. It retrieves biological sequences, enforces compliance with assembly design standards and provides a fabrication plan for each fragment. BioPartsBuilder is accessible at http://public.biopartsbuilder.org and an Amazon Web Services image is available from the AWS Market Place (AMI ID: ami-508acf38). Source code is released under the MIT license, and available for download at https://github.com/baderzone/biopartsbuilder joel.bader@jhu.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Content Analysis of Vomit and Diarrhea Cleanup Procedures To Prevent Norovirus Infections in Retail and Food Service Operations.

PubMed

Chao, Morgan G; Dubé, Anne-Julie; Leone, Cortney M; Moore, Christina M; Fraser, Angela M

2016-11-01

Human noroviruses are the leading cause of foodborne disease in the United States, sickening 19 to 21 million Americans each year. Vomit and diarrhea are both highly concentrated sources of norovirus particles. For this reason, establishing appropriate cleanup procedures for these two substances is critical. Food service establishments in states that have adopted the 2009 or 2013 U.S. Food and Drug Administration Food Code are required to have a program detailing specific cleanup procedures. The aim of our study was to determine the alignment of existing vomit and diarrhea cleanup procedures with the 11 elements recommended in Annex 3 of the 2011 Supplement to the 2009 Food Code and to determine their readability and clarity of presentation. In July 2015, we located vomit and diarrhea cleanup procedures by asking Norovirus Collaborative for Outreach, Research, and Education stakeholders for procedures used by their constituency groups and by conducting a Google Advanced Search of the World Wide Web. We performed content analysis to determine alignment with the recommendations in Annex 3. Readability and clarity of presentation were also assessed. A total of 38 artifacts were analyzed. The mean alignment score was 7.0 ± 1.7 of 11 points; the mean clarity score was 6.7 ± 2.5 of 17 points. Only nine artifacts were classified as high clarity, high alignment. Vomit and diarrhea cleanup procedures should align with Annex 3 in the Food Code and should, as well, be clearly presented; yet, none of the artifacts completely met both conditions. To reduce the spread of norovirus infections in food service establishments, editable guidelines are needed that are aligned with Annex 3 and are clearly written, into which authors could insert their facility-specific information.

The Use of Quality Benchmarking in Assessing Web Resources for the Dermatology Virtual Branch Library of the National electronic Library for Health (NeLH)

PubMed Central

Roudsari, AV; Gordon, C; Gray, JA Muir

2001-01-01

Background In 1998, the U.K. National Health Service Information for Health Strategy proposed the implementation of a National electronic Library for Health to provide clinicians, healthcare managers and planners, patients and the public with easy, round the clock access to high quality, up-to-date electronic information on health and healthcare. The Virtual Branch Libraries are among the most important components of the National electronic Library for Health . They aim at creating online knowledge based communities, each concerned with some specific clinical and other health-related topics. Objectives This study is about the envisaged Dermatology Virtual Branch Libraries of the National electronic Library for Health . It aims at selecting suitable dermatology Web resources for inclusion in the forthcoming Virtual Branch Libraries after establishing preliminary quality benchmarking rules for this task. Psoriasis, being a common dermatological condition, has been chosen as a starting point. Methods Because quality is a principal concern of the National electronic Library for Health, the study includes a review of the major quality benchmarking systems available today for assessing health-related Web sites. The methodology of developing a quality benchmarking system has been also reviewed. Aided by metasearch Web tools, candidate resources were hand-selected in light of the reviewed benchmarking systems and specific criteria set by the authors. Results Over 90 professional and patient-oriented Web resources on psoriasis and dermatology in general are suggested for inclusion in the forthcoming Dermatology Virtual Branch Libraries. The idea of an all-in knowledge-hallmarking instrument for the National electronic Library for Health is also proposed based on the reviewed quality benchmarking systems. Conclusions Skilled, methodical, organized human reviewing, selection and filtering based on well-defined quality appraisal criteria seems likely to be the key ingredient in the envisaged National electronic Library for Health service. Furthermore, by promoting the application of agreed quality guidelines and codes of ethics by all health information providers and not just within the National electronic Library for Health, the overall quality of the Web will improve with time and the Web will ultimately become a reliable and integral part of the care space. PMID:11720947

Development of a Dynamic Web Mapping Service for Vegetation Productivity Using Earth Observation and in situ Sensors in a Sensor Web Based Approach

PubMed Central

Kooistra, Lammert; Bergsma, Aldo; Chuma, Beatus; de Bruin, Sytze

2009-01-01

This paper describes the development of a sensor web based approach which combines earth observation and in situ sensor data to derive typical information offered by a dynamic web mapping service (WMS). A prototype has been developed which provides daily maps of vegetation productivity for the Netherlands with a spatial resolution of 250 m. Daily available MODIS surface reflectance products and meteorological parameters obtained through a Sensor Observation Service (SOS) were used as input for a vegetation productivity model. This paper presents the vegetation productivity model, the sensor data sources and the implementation of the automated processing facility. Finally, an evaluation is made of the opportunities and limitations of sensor web based approaches for the development of web services which combine both satellite and in situ sensor sources. PMID:22574019

Web scraping technologies in an API world.

PubMed

Glez-Peña, Daniel; Lourenço, Anália; López-Fernández, Hugo; Reboiro-Jato, Miguel; Fdez-Riverola, Florentino

2014-09-01

Web services are the de facto standard in biomedical data integration. However, there are data integration scenarios that cannot be fully covered by Web services. A number of Web databases and tools do not support Web services, and existing Web services do not cover for all possible user data demands. As a consequence, Web data scraping, one of the oldest techniques for extracting Web contents, is still in position to offer a valid and valuable service to a wide range of bioinformatics applications, ranging from simple extraction robots to online meta-servers. This article reviews existing scraping frameworks and tools, identifying their strengths and limitations in terms of extraction capabilities. The main focus is set on showing how straightforward it is today to set up a data scraping pipeline, with minimal programming effort, and answer a number of practical needs. For exemplification purposes, we introduce a biomedical data extraction scenario where the desired data sources, well-known in clinical microbiology and similar domains, do not offer programmatic interfaces yet. Moreover, we describe the operation of WhichGenes and PathJam, two bioinformatics meta-servers that use scraping as means to cope with gene set enrichment analysis. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

An implementation of a security infrastructure compliant with the Italian Personal Data Protection Code in a web-based cooperative work system.

PubMed

Eccher, Claudio; Eccher, Lorenzo; Izzo, Umberto

2005-01-01

In this poster we describe the security solutions implemented in a web-based cooperative work frame-work for managing heart failure patients among different health care professionals involved in the care process. The solution, developed in close collaboration with the Law Department of the University of Trento, is compliant with the new Italian Personal Data Protection Code, issued in 2003, that regulates also the storing and processing of health data.

Bootstrapping and Maintaining Trust in the Cloud

DTIC Science & Technology

2016-03-16

of infrastructure-as-a- service (IaaS) cloud computing services such as Ama- zon Web Services, Google Compute Engine, Rackspace, et. al. means that...Implementation We implemented keylime in ∼3.2k lines of Python in four components: registrar, node, CV, and tenant. The registrar offers a REST-based web ...bootstrap key K. It provides an unencrypted REST-based web service for these two functions. As described earlier, the pro- tocols for exchanging data

MONTRA: An agile architecture for data publishing and discovery.

PubMed

Bastião Silva, Luís; Trifan, Alina; Luís Oliveira, José

2018-07-01

Data catalogues are a common form of capturing and presenting information about a specific kind of entity (e.g. products, services, professionals, datasets, etc.). However, the construction of a web-based catalogue for a particular scenario normally implies the development of a specific and dedicated solution. In this paper, we present MONTRA, a rapid-application development framework designed to facilitate the integration and discovery of heterogeneous objects, which may be characterized by distinct data structures. MONTRA was developed following a plugin-based architecture to allow dynamic composition of services over represented datasets. The core of MONTRA's functionalities resides in a flexible data skeleton used to characterize data entities, and from which a fully-fledged web data catalogue is automatically generated, ensuring access control and data privacy. MONTRA is being successfully used by several European projects to collect and manage biomedical databases. In this paper, we describe three of these applications scenarios. This work was motivated by the plethora of geographically scattered biomedical repositories, and by the role they can play altogether for the understanding of diseases and of the real-world effectiveness of treatments. Using metadata to expose datasets' characteristics, MONTRA greatly simplifies the task of building data catalogues. The source code is publicly available at https://github.com/bioinformatics-ua/montra. Copyright © 2018 Elsevier B.V. All rights reserved.

ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology[OPEN

PubMed Central

Waese, Jamie; Fan, Jim; Yu, Hans; Fucile, Geoffrey; Shi, Ruian; Cumming, Matthew; Town, Chris; Stuerzlinger, Wolfgang

2017-01-01

A big challenge in current systems biology research arises when different types of data must be accessed from separate sources and visualized using separate tools. The high cognitive load required to navigate such a workflow is detrimental to hypothesis generation. Accordingly, there is a need for a robust research platform that incorporates all data and provides integrated search, analysis, and visualization features through a single portal. Here, we present ePlant (http://bar.utoronto.ca/eplant), a visual analytic tool for exploring multiple levels of Arabidopsis thaliana data through a zoomable user interface. ePlant connects to several publicly available web services to download genome, proteome, interactome, transcriptome, and 3D molecular structure data for one or more genes or gene products of interest. Data are displayed with a set of visualization tools that are presented using a conceptual hierarchy from big to small, and many of the tools combine information from more than one data type. We describe the development of ePlant in this article and present several examples illustrating its integrative features for hypothesis generation. We also describe the process of deploying ePlant as an “app” on Araport. Building on readily available web services, the code for ePlant is freely available for any other biological species research. PMID:28808136

EnviroAtlas - Recreation, Culture, and Aesthetics Metrics for Conterminous United States

EPA Pesticide Factsheets

This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The Recreation, Culture, and Aesthetics category in this web service includes layers illustrating the ecosystems and natural resources that provide inherent cultural and aesthetic value or recreation opportunity, the need or demand for these amenities, the impacts associated with their presence and accessibility, and factors that place stress on the natural environment's capability to provide these benefits. EnviroAtlas allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the conterminous United States. Additional descriptive information about each attribute in this web service is located within each web service layer (see Full Metadata hyperlink) or can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

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.

User preference as quality markers of paediatric web sites.

PubMed

Hernández-Borges, Angel A; Macías-Cervi, Pablo; Gaspar-Guardado, Asunción; Torres-Alvarez De Arcaya, María Luisa; Ruíz-Rabaza, Ana; Jiménez-Sosa, Alejandro

2003-09-01

Little is known about the ability of internet users to distinguish the best medical resources online, and how their preferences, measured by usage and popularity indexes, correlate with established quality criteria. Our objective was to analyse whether the number of inbound links and/or daily visits to a sample of paediatric web pages are reliable quality markers of the pages. Two-year follow-up study of 363 web pages with paediatric information. The number of inbound links and the average number of daily visits to the pages were calculated on a yearly basis. In addition, their rates of compliance with the codes of conduct, guidelines and/or principles of three international organizations were evaluated. The quality code most widely met by the sample web pages was the Health on the Net Foundation Code of Conduct (overall rate, 60.2%). Sample pages showed a low degree of compliance with principles related to privacy, confidentiality and electronic commerce (overall rate less than 45%). Most importantly, we observed a moderate, significant correlation between compliance with quality criteria and the number of inbound links (p < 0.001). However, no correlation was found between the number of daily visits to a page and its degree of compliance with the principles. Some indexes derived from the analysis of webmasters' hyperlinks could be reliable quality markers of medical web resources.

StarScan: a web server for scanning small RNA targets from degradome sequencing data.

PubMed

Liu, Shun; Li, Jun-Hao; Wu, Jie; Zhou, Ke-Ren; Zhou, Hui; Yang, Jian-Hua; Qu, Liang-Hu

2015-07-01

Endogenous small non-coding RNAs (sRNAs), including microRNAs, PIWI-interacting RNAs and small interfering RNAs, play important gene regulatory roles in animals and plants by pairing to the protein-coding and non-coding transcripts. However, computationally assigning these various sRNAs to their regulatory target genes remains technically challenging. Recently, a high-throughput degradome sequencing method was applied to identify biologically relevant sRNA cleavage sites. In this study, an integrated web-based tool, StarScan (sRNA target Scan), was developed for scanning sRNA targets using degradome sequencing data from 20 species. Given a sRNA sequence from plants or animals, our web server performs an ultrafast and exhaustive search for potential sRNA-target interactions in annotated and unannotated genomic regions. The interactions between small RNAs and target transcripts were further evaluated using a novel tool, alignScore. A novel tool, degradomeBinomTest, was developed to quantify the abundance of degradome fragments located at the 9-11th nucleotide from the sRNA 5' end. This is the first web server for discovering potential sRNA-mediated RNA cleavage events in plants and animals, which affords mechanistic insights into the regulatory roles of sRNAs. The StarScan web server is available at http://mirlab.sysu.edu.cn/starscan/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Increasing the availability and usability of terrestrial ecology data through geospatial Web services and visualization tools (Invited)

NASA Astrophysics Data System (ADS)

Santhana Vannan, S.; Cook, R. B.; Wilson, B. E.; Wei, Y.

2010-12-01

Terrestrial ecology data sets are produced from diverse data sources such as model output, field data collection, laboratory analysis and remote sensing observation. These data sets can be created, distributed, and consumed in diverse ways as well. However, this diversity can hinder the usability of the data, and limit data users’ abilities to validate and reuse data for science and application purposes. Geospatial web services, such as those described in this paper, are an important means of reducing this burden. Terrestrial ecology researchers generally create the data sets in diverse file formats, with file and data structures tailored to the specific needs of their project, possibly as tabular data, geospatial images, or documentation in a report. Data centers may reformat the data to an archive-stable format and distribute the data sets through one or more protocols, such as FTP, email, and WWW. Because of the diverse data preparation, delivery, and usage patterns, users have to invest time and resources to bring the data into the format and structure most useful for their analysis. This time-consuming data preparation process shifts valuable resources from data analysis to data assembly. To address these issues, the ORNL DAAC, a NASA-sponsored terrestrial ecology data center, has utilized geospatial Web service technology, such as Open Geospatial Consortium (OGC) Web Map Service (WMS) and OGC Web Coverage Service (WCS) standards, to increase the usability and availability of terrestrial ecology data sets. Data sets are standardized into non-proprietary file formats and distributed through OGC Web Service standards. OGC Web services allow the ORNL DAAC to store data sets in a single format and distribute them in multiple ways and formats. Registering the OGC Web services through search catalogues and other spatial data tools allows for publicizing the data sets and makes them more available across the Internet. The ORNL DAAC has also created a Web-based graphical user interface called Spatial Data Access Tool (SDAT) that utilizes OGC Web services standards and allows data distribution and consumption for users not familiar with OGC standards. SDAT also allows for users to visualize the data set prior to download. Google Earth visualizations of the data set are also provided through SDAT. The use of OGC Web service standards at the ORNL DAAC has enabled an increase in data consumption. In one case, a data set had ~10 fold increase in download through OGC Web service in comparison to the conventional FTP and WWW method of access. The increase in download suggests that users are not only finding the data sets they need but also able to consume them readily in the format they need.

An Analysis of HTML and CSS Syntax Errors in a Web Development Course

ERIC Educational Resources Information Center

Park, Thomas H.; Dorn, Brian; Forte, Andrea

2015-01-01

Many people are first exposed to code through web development, yet little is known about the barriers beginners face in these formative experiences. In this article, we describe a study of undergraduate students enrolled in an introductory web development course taken by both computing majors and general education students. Using data collected…

Bottled SAFT: A Web App Providing SAFT-γ Mie Force Field Parameters for Thousands of Molecular Fluids.

PubMed

Ervik, Åsmund; Mejía, Andrés; Müller, Erich A

2016-09-26

Coarse-grained molecular simulation has become a popular tool for modeling simple and complex fluids alike. The defining aspects of a coarse grained model are the force field parameters, which must be determined for each particular fluid. Because the number of molecular fluids of interest in nature and in engineering processes is immense, constructing force field parameter tables by individually fitting to experimental data is a futile task. A step toward solving this challenge was taken recently by Mejía et al., who proposed a correlation that provides SAFT-γ Mie force field parameters for a fluid provided one knows the critical temperature, the acentric factor and a liquid density, all relatively accessible properties. Building on this, we have applied the correlation to more than 6000 fluids, and constructed a web application, called "Bottled SAFT", which makes this data set easily searchable by CAS number, name or chemical formula. Alternatively, the application allows the user to calculate parameters for components not present in the database. Once the intermolecular potential has been found through Bottled SAFT, code snippets are provided for simulating the desired substance using the "raaSAFT" framework, which leverages established molecular dynamics codes to run the simulations. The code underlying the web application is written in Python using the Flask microframework; this allows us to provide a modern high-performance web app while also making use of the scientific libraries available in Python. Bottled SAFT aims at taking the complexity out of obtaining force field parameters for a wide range of molecular fluids, and facilitates setting up and running coarse-grained molecular simulations. The web application is freely available at http://www.bottledsaft.org . The underlying source code is available on Bitbucket under a permissive license.

Global polar geospatial information service retrieval based on search engine and ontology reasoning

USGS Publications Warehouse

Chen, Nengcheng; E, Dongcheng; Di, Liping; Gong, Jianya; Chen, Zeqiang

2007-01-01

In order to improve the access precision of polar geospatial information service on web, a new methodology for retrieving global spatial information services based on geospatial service search and ontology reasoning is proposed, the geospatial service search is implemented to find the coarse service from web, the ontology reasoning is designed to find the refined service from the coarse service. The proposed framework includes standardized distributed geospatial web services, a geospatial service search engine, an extended UDDI registry, and a multi-protocol geospatial information service client. Some key technologies addressed include service discovery based on search engine and service ontology modeling and reasoning in the Antarctic geospatial context. Finally, an Antarctica multi protocol OWS portal prototype based on the proposed methodology is introduced.

Weaving Silos--A Leadership Challenge: A Cross-Functional Team Approach to Supporting Web-Based Student Services

ERIC Educational Resources Information Center

Kleemann, Gary L.

2005-01-01

The author reviews the evolution of Web services--from information sharing to transactional to relationship building--and the progression from first-generation to fourth-generation Web sites. (Contains 3 figures.)

Combining Domain-driven Design and Mashups for Service Development

NASA Astrophysics Data System (ADS)

Iglesias, Carlos A.; Fernández-Villamor, José Ignacio; Del Pozo, David; Garulli, Luca; García, Boni

This chapter presents the Romulus project approach to Service Development using Java-based web technologies. Romulus aims at improving productivity of service development by providing a tool-supported model to conceive Java-based web applications. This model follows a Domain Driven Design approach, which states that the primary focus of software projects should be the core domain and domain logic. Romulus proposes a tool-supported model, Roma Metaframework, that provides an abstraction layer on top of existing web frameworks and automates the application generation from the domain model. This metaframework follows an object centric approach, and complements Domain Driven Design by identifying the most common cross-cutting concerns (security, service, view, ...) of web applications. The metaframework uses annotations for enriching the domain model with these cross-cutting concerns, so-called aspects. In addition, the chapter presents the usage of mashup technology in the metaframework for service composition, using the web mashup editor MyCocktail. This approach is applied to a scenario of the Mobile Phone Service Portability case study for the development of a new service.

Web service activities at the IRIS DMC to support federated and multidisciplinary access

NASA Astrophysics Data System (ADS)

Trabant, Chad; Ahern, Timothy K.

2013-04-01

At the IRIS Data Management Center (DMC) we have developed a suite of web service interfaces to access our large archive of, primarily seismological, time series data and related metadata. The goals of these web services include providing: a) next-generation and easily used access interfaces for our current users, b) access to data holdings in a form usable for non-seismologists, c) programmatic access to facilitate integration into data processing workflows and d) a foundation for participation in federated data discovery and access systems. To support our current users, our services provide access to the raw time series data and metadata or conversions of the raw data to commonly used formats. Our services also support simple, on-the-fly signal processing options that are common first steps in many workflows. Additionally, high-level data products derived from raw data are available via service interfaces. To support data access by researchers unfamiliar with seismic data we offer conversion of the data to broadly usable formats (e.g. ASCII text) and data processing to convert the data to Earth units. By their very nature, web services are programmatic interfaces. Combined with ubiquitous support for web technologies in programming & scripting languages and support in many computing environments, web services are very well suited for integrating data access into data processing workflows. As programmatic interfaces that can return data in both discipline-specific and broadly usable formats, our services are also well suited for participation in federated and brokered systems either specific to seismology or multidisciplinary. Working within the International Federation of Digital Seismograph Networks, the DMC collaborated on the specification of standardized web service interfaces for use at any seismological data center. These data access interfaces, when supported by multiple data centers, will form a foundation on which to build discovery and access mechanisms for data sets spanning multiple centers. To promote the adoption of these standardized services the DMC has developed portable implementations of the software needed to host these interfaces, minimizing the work required at each data center. Within the COOPEUS project framework, the DMC is working with EU partners to install web services implementations at multiple data centers in Europe.

Architecture of a spatial data service system for statistical analysis and visualization of regional climate changes

NASA Astrophysics Data System (ADS)

Titov, A. G.; Okladnikov, I. G.; Gordov, E. P.

2017-11-01

The use of large geospatial datasets in climate change studies requires the development of a set of Spatial Data Infrastructure (SDI) elements, including geoprocessing and cartographical visualization web services. This paper presents the architecture of a geospatial OGC web service system as an integral part of a virtual research environment (VRE) general architecture for statistical processing and visualization of meteorological and climatic data. The architecture is a set of interconnected standalone SDI nodes with corresponding data storage systems. Each node runs a specialized software, such as a geoportal, cartographical web services (WMS/WFS), a metadata catalog, and a MySQL database of technical metadata describing geospatial datasets available for the node. It also contains geospatial data processing services (WPS) based on a modular computing backend realizing statistical processing functionality and, thus, providing analysis of large datasets with the results of visualization and export into files of standard formats (XML, binary, etc.). Some cartographical web services have been developed in a system’s prototype to provide capabilities to work with raster and vector geospatial data based on OGC web services. The distributed architecture presented allows easy addition of new nodes, computing and data storage systems, and provides a solid computational infrastructure for regional climate change studies based on modern Web and GIS technologies.

Enterprise Considerations for Ports and Protocols

DTIC Science & Technology

2016-10-21

selected communications. These protocols are restricted to specific ports or addresses in the receiving web service. HTTPS is familiarly restricted...in use by the web services and applications that are connected to the network are required for interoperability and security. Policies specify the...network or reside at the end-points (i.e., web services or clients). ____________________________ Manuscript received June 1, 2016; revised July

SOAP based web services and their future role in VO projects

NASA Astrophysics Data System (ADS)

Topf, F.; Jacquey, C.; Génot, V.; Cecconi, B.; André, N.; Zhang, T. L.; Kallio, E.; Lammer, H.; Facsko, G.; Stöckler, R.; Khodachenko, M.

2011-10-01

Modern state-of-the-art web services are from crucial importance for the interoperability of different VO tools existing in the planetary community. SOAP based web services assure the interconnectability between different data sources and tools by providing a common protocol for communication. This paper will point out a best practice approach with the Automated Multi-Dataset Analysis Tool (AMDA) developed by CDPP, Toulouse and the provision of VEX/MAG data from a remote database located at IWF, Graz. Furthermore a new FP7 project IMPEx will be introduced with a potential usage example of AMDA web services in conjunction with simulation models.

A Generic Evaluation Model for Semantic Web Services

NASA Astrophysics Data System (ADS)

Shafiq, Omair

Semantic Web Services research has gained momentum over the last few Years and by now several realizations exist. They are being used in a number of industrial use-cases. Soon software developers will be expected to use this infrastructure to build their B2B applications requiring dynamic integration. However, there is still a lack of guidelines for the evaluation of tools developed to realize Semantic Web Services and applications built on top of them. In normal software engineering practice such guidelines can already be found for traditional component-based systems. Also some efforts are being made to build performance models for servicebased systems. Drawing on these related efforts in component-oriented and servicebased systems, we identified the need for a generic evaluation model for Semantic Web Services applicable to any realization. The generic evaluation model will help users and customers to orient their systems and solutions towards using Semantic Web Services. In this chapter, we have presented the requirements for the generic evaluation model for Semantic Web Services and further discussed the initial steps that we took to sketch such a model. Finally, we discuss related activities for evaluating semantic technologies.

Adding Processing Functionality to the Sensor Web

NASA Astrophysics Data System (ADS)

Stasch, Christoph; Pross, Benjamin; Jirka, Simon; Gräler, Benedikt

2017-04-01

The Sensor Web allows discovering, accessing and tasking different kinds of environmental sensors in the Web, ranging from simple in-situ sensors to remote sensing systems. However, (geo-)processing functionality needs to be applied to integrate data from different sensor sources and to generate higher level information products. Yet, a common standardized approach for processing sensor data in the Sensor Web is still missing and the integration differs from application to application. Standardizing not only the provision of sensor data, but also the processing facilitates sharing and re-use of processing modules, enables reproducibility of processing results, and provides a common way to integrate external scalable processing facilities or legacy software. In this presentation, we provide an overview on on-going research projects that develop concepts for coupling standardized geoprocessing technologies with Sensor Web technologies. At first, different architectures for coupling sensor data services with geoprocessing services are presented. Afterwards, profiles for linear regression and spatio-temporal interpolation of the OGC Web Processing Services that allow consuming sensor data coming from and uploading predictions to Sensor Observation Services are introduced. The profiles are implemented in processing services for the hydrological domain. Finally, we illustrate how the R software can be coupled with existing OGC Sensor Web and Geoprocessing Services and present an example, how a Web app can be built that allows exploring the results of environmental models in an interactive way using the R Shiny framework. All of the software presented is available as Open Source Software.

OntoGene web services for biomedical text mining.

PubMed

Rinaldi, Fabio; Clematide, Simon; Marques, Hernani; Ellendorff, Tilia; Romacker, Martin; Rodriguez-Esteban, Raul

2014-01-01

Text mining services are rapidly becoming a crucial component of various knowledge management pipelines, for example in the process of database curation, or for exploration and enrichment of biomedical data within the pharmaceutical industry. Traditional architectures, based on monolithic applications, do not offer sufficient flexibility for a wide range of use case scenarios, and therefore open architectures, as provided by web services, are attracting increased interest. We present an approach towards providing advanced text mining capabilities through web services, using a recently proposed standard for textual data interchange (BioC). The web services leverage a state-of-the-art platform for text mining (OntoGene) which has been tested in several community-organized evaluation challenges,with top ranked results in several of them.

OntoGene web services for biomedical text mining

PubMed Central

2014-01-01

Text mining services are rapidly becoming a crucial component of various knowledge management pipelines, for example in the process of database curation, or for exploration and enrichment of biomedical data within the pharmaceutical industry. Traditional architectures, based on monolithic applications, do not offer sufficient flexibility for a wide range of use case scenarios, and therefore open architectures, as provided by web services, are attracting increased interest. We present an approach towards providing advanced text mining capabilities through web services, using a recently proposed standard for textual data interchange (BioC). The web services leverage a state-of-the-art platform for text mining (OntoGene) which has been tested in several community-organized evaluation challenges, with top ranked results in several of them. PMID:25472638

Integrating Multilevel Command and Control into a Service Oriented Architecture to Provide Cross Domain Capability

DTIC Science & Technology

2006-06-01

Horizontal Fusion, the JCDX team developed two web services, a Classification Policy Decision Service (cPDS), and a Federated Search Provider (FSP...The cPDS web service primarily provides other systems with methods for handling labeled data such as label comparison. The federated search provider...level domains. To provide defense-in-depth, cPDS and the Federated Search Provider are implemented on a separate server known as the JCDX Web

Designing Crop Simulation Web Service with Service Oriented Architecture Principle

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Web-based health services and clinical decision support.

PubMed

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

2004-01-01

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

Evaluation of Norwegian cancer hospitals' Web sites and explorative survey among cancer patients on their use of the Internet

PubMed Central

2001-01-01

Background Hospital homepages should provide comprehensive information on the hospital's services, such as departments and treatments available, prices, waiting time, leisure facilities, and other information important for patients and their relatives. Norway, with its population of approximately 4.3 million, ranks among the top countries globally for its ability to absorb and use technology. It is unclear to what degree Norwegian hospitals and patients use the Internet for information about health services. Objectives This study was undertaken to evaluate the quality of the biggest Norwegian cancer hospitals' Web sites and to gather some preliminary data on patients' use of the Internet. Methods In January 2001, we analyzed Web sites of 5 of the 7 biggest Norwegian hospitals treating cancer patients using a scoring system. The scoring instrument was based on recommendations developed by the Norwegian Central Information Service for Web sites and reflects the scope and depth of service information offered on hospital Web pages. In addition, 31 cancer patients visiting one hospital-based medical oncologist were surveyed about their use of the Internet. Results Of the 7 hospitals, 5 had a Web site. The Web sites differed markedly in quality. Types of information included - and number of Web sites that included each type of information - were, for example: search option, 1; interpreter service, 2; date of last update, 2; postal address, phone number, and e-mail service, 3; information in English, 2. None of the Web sites included information on waiting time or prices. Of the 31 patients surveyed, 12 had personal experience using the Internet and 4 had searched for medical information. The Internet users were significantly younger (mean age 47.8 years, range 28.4-66.8 years) than the nonusers (mean age 61.8 years, range 33.1-90.0 years) ( P= 0.007). Conclusions The hospitals' Web sites offer cancer patients and relatives useful information, but the Web sites were not impressive. PMID:11772545

New CPT codes: hospital, consultation, emergency and nursing facility services.

PubMed

Zuber, T J; Henley, D E

1992-03-01

New evaluation and management codes were created by the Current Procedural Terminology (CPT) Editorial Panel to ensure more accurate and consistent reporting of physician services. The new hospital inpatient codes describe three levels of service for both initial and subsequent care. Critical care services are reported according to the total time spent by a physician providing constant attention to a critically ill patient. Consultation codes are divided into four categories: office/outpatient, initial inpatient, follow-up inpatient and confirmatory. Emergency department services for both new and established patients are limited to five codes. In 1992, nursing facility services are described with either comprehensive-assessment codes or subsequent-care codes. Hospital discharge services may be reported in addition to the comprehensive nursing facility assessment. Since the 1992 CPT book will list only the new codes, and since all insurance carriers will not be using these codes in 1992, physicians are encouraged to keep their 1991 code books and contact their local insurance carriers to determine which codes will be used.

Building Interactive Simulations in Web Pages without Programming.

PubMed

Mailen Kootsey, J; McAuley, Grant; Bernal, Julie

2005-01-01

A software system is described for building interactive simulations and other numerical calculations in Web pages. The system is based on a new Java-based software architecture named NumberLinX (NLX) that isolates each function required to build the simulation so that a library of reusable objects could be assembled. The NLX objects are integrated into a commercial Web design program for coding-free page construction. The model description is entered through a wizard-like utility program that also functions as a model editor. The complete system permits very rapid construction of interactive simulations without coding. A wide range of applications are possible with the system beyond interactive calculations, including remote data collection and processing and collaboration over a network.

Quality and Business Offer Driven Selection of Web Services for Compositions

NASA Astrophysics Data System (ADS)

D'Mello, Demian Antony; Ananthanarayana, V. S.

The service composition makes use of the existing services to produce a new value added service to execute the complex business process. The service discovery finds the suitable services (candidates) for the various tasks of the composition based on the functionality. The service selection in composition assigns the best candidate for each tasks of the pre-structured composition plan based on the non-functional properties. In this paper, we propose the broker based architecture for the QoS and business offer aware Web service compositions. The broker architecture facilitates the registration of a new composite service into three different registries. The broker publishes service information into the service registry and QoS into the QoS registry. The business offers of the composite Web service are published into a separate repository called business offer (BO) registry. The broker employs the mechanism for the optimal assignment of the Web services to the individual tasks of the composition. The assignment is based on the composite service providers’s (CSP) variety of requirements defined on the QoS and business offers. The broker also computes the QoS of resulting composition and provides the useful information for the CSP to publish thier business offers.

Obtaining P3P privacy policies for composite services.

PubMed

Sun, Yi; Huang, Zhiqiu; Ke, Changbo

2014-01-01

With the development of web services technology, web services have changed from single to composite services. Privacy protection in composite services is becoming an important issue. P3P (platform for privacy preferences) is a privacy policy language which was designed for single web services. It enables service providers to express how they will deal with the privacy information of service consumers. In order to solve the problem that P3P cannot be applied to composite services directly, we propose a method to obtain P3P privacy policies for composite services. In this method, we present the definitions of Purpose, Recipient, and Retention elements as well as Optional and Required attributes for P3P policies of composite services. We also provide an instantiation to illustrate the feasibility of the method.

Geoinformatics in the public service: building a cyberinfrastructure across the geological surveys

USGS Publications Warehouse

Allison, M. Lee; Gundersen, Linda C.; Richard, Stephen M.; Keller, G. Randy; Baru, Chaitanya

2011-01-01

Advanced information technology infrastructure is increasingly being employed in the Earth sciences to provide researchers with efficient access to massive central databases and to integrate diversely formatted information from a variety of sources. These geoinformatics initiatives enable manipulation, modeling and visualization of data in a consistent way, and are helping to develop integrated Earth models at various scales, and from the near surface to the deep interior. This book uses a series of case studies to demonstrate computer and database use across the geosciences. Chapters are thematically grouped into sections that cover data collection and management; modeling and community computational codes; visualization and data representation; knowledge management and data integration; and web services and scientific workflows. Geoinformatics is a fascinating and accessible introduction to this emerging field for readers across the solid Earth sciences and an invaluable reference for researchers interested in initiating new cyberinfrastructure projects of their own.

Using secure web services to visualize poison center data for nationwide biosurveillance: a case study.

PubMed

Savel, Thomas G; Bronstein, Alvin; Duck, William; Rhodes, M Barry; Lee, Brian; Stinn, John; Worthen, Katherine

2010-01-01

Real-time surveillance systems are valuable for timely response to public health emergencies. It has been challenging to leverage existing surveillance systems in state and local communities, and, using a centralized architecture, add new data sources and analytical capacity. Because this centralized model has proven to be difficult to maintain and enhance, the US Centers for Disease Control and Prevention (CDC) has been examining the ability to use a federated model based on secure web services architecture, with data stewardship remaining with the data provider. As a case study for this approach, the American Association of Poison Control Centers and the CDC extended an existing data warehouse via a secure web service, and shared aggregate clinical effects and case counts data by geographic region and time period. To visualize these data, CDC developed a web browser-based interface, Quicksilver, which leveraged the Google Maps API and Flot, a javascript plotting library. Two iterations of the NPDS web service were completed in 12 weeks. The visualization client, Quicksilver, was developed in four months. This implementation of web services combined with a visualization client represents incremental positive progress in transitioning national data sources like BioSense and NPDS to a federated data exchange model. Quicksilver effectively demonstrates how the use of secure web services in conjunction with a lightweight, rapidly deployed visualization client can easily integrate isolated data sources for biosurveillance.

SeWeR: a customizable and integrated dynamic HTML interface to bioinformatics services.

PubMed

Basu, M K

2001-06-01

Sequence analysis using Web Resources (SeWeR) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser.

BPELPower—A BPEL execution engine for geospatial web services

NASA Astrophysics Data System (ADS)

Yu, Genong (Eugene); Zhao, Peisheng; Di, Liping; Chen, Aijun; Deng, Meixia; Bai, Yuqi

2012-10-01

The Business Process Execution Language (BPEL) has become a popular choice for orchestrating and executing workflows in the Web environment. As one special kind of scientific workflow, geospatial Web processing workflows are data-intensive, deal with complex structures in data and geographic features, and execute automatically with limited human intervention. To enable the proper execution and coordination of geospatial workflows, a specially enhanced BPEL execution engine is required. BPELPower was designed, developed, and implemented as a generic BPEL execution engine with enhancements for executing geospatial workflows. The enhancements are especially in its capabilities in handling Geography Markup Language (GML) and standard geospatial Web services, such as the Web Processing Service (WPS) and the Web Feature Service (WFS). BPELPower has been used in several demonstrations over the decade. Two scenarios were discussed in detail to demonstrate the capabilities of BPELPower. That study showed a standard-compliant, Web-based approach for properly supporting geospatial processing, with the only enhancement at the implementation level. Pattern-based evaluation and performance improvement of the engine are discussed: BPELPower directly supports 22 workflow control patterns and 17 workflow data patterns. In the future, the engine will be enhanced with high performance parallel processing and broad Web paradigms.

The design and implementation of web mining in web sites security

NASA Astrophysics Data System (ADS)

Li, Jian; Zhang, Guo-Yin; Gu, Guo-Chang; Li, Jian-Li

2003-06-01

The backdoor or information leak of Web servers can be detected by using Web Mining techniques on some abnormal Web log and Web application log data. The security of Web servers can be enhanced and the damage of illegal access can be avoided. Firstly, the system for discovering the patterns of information leakages in CGI scripts from Web log data was proposed. Secondly, those patterns for system administrators to modify their codes and enhance their Web site security were provided. The following aspects were described: one is to combine web application log with web log to extract more information, so web data mining could be used to mine web log for discovering the information that firewall and Information Detection System cannot find. Another approach is to propose an operation module of web site to enhance Web site security. In cluster server session, Density-Based Clustering technique is used to reduce resource cost and obtain better efficiency.

Customizable scientific web-portal for DIII-D nuclear fusion experiment

NASA Astrophysics Data System (ADS)

Abla, G.; Kim, E. N.; Schissel, D. P.

2010-04-01

Increasing utilization of the Internet and convenient web technologies has made the web-portal a major application interface for remote participation and control of scientific instruments. While web-portals have provided a centralized gateway for multiple computational services, the amount of visual output often is overwhelming due to the high volume of data generated by complex scientific instruments and experiments. Since each scientist may have different priorities and areas of interest in the experiment, filtering and organizing information based on the individual user's need can increase the usability and efficiency of a web-portal. DIII-D is the largest magnetic nuclear fusion device in the US. A web-portal has been designed to support the experimental activities of DIII-D researchers worldwide. It offers a customizable interface with personalized page layouts and list of services for users to select. Each individual user can create a unique working environment to fit his own needs and interests. Customizable services are: real-time experiment status monitoring, diagnostic data access, interactive data analysis and visualization. The web-portal also supports interactive collaborations by providing collaborative logbook, and online instant announcement services. The DIII-D web-portal development utilizes multi-tier software architecture, and Web 2.0 technologies and tools, such as AJAX and Django, to develop a highly-interactive and customizable user interface.

Reference Architecture for MNE 5 Technical System

DTIC Science & Technology

2007-05-30

of being available in most experiments. Core Services A core set of applications whi directories, web portal and collaboration applications etc. A...classifications Messages (xml, JMS, content level…) Meta data filtering, who can initiate services Web browsing Collaboration & messaging Border...Exchange Ref Architecture for MNE5 Tech System.doc 9 of 21 audit logging Person and machine Data lev objects, web services, messages rification el

Cauda equina syndrome: assessing the readability and quality of patient information on the Internet.

PubMed

O'Neill, Shane Ciaran; Baker, Joseph Frederick; Fitzgerald, Conall; Fleming, Christina; Rowan, Fiachra; Byrne, Damien; Synnott, Keith

2014-05-01

A readability and quality control Internet-based study using recognized quality scoring systems. To assess the readability and quality of Internet information relating to cauda equina syndrome accessed through common search engines. Access to health-related Internet information has increased dramatically during the past decade. A significant proportion of this information has been demonstrated to be set at too high a level for general comprehension. Despite this, searching for health-related information is now the third most popular online activity. A total of 125 cauda equina syndrome Web sites were analyzed from the 5 most popular Internet search engines: Google, Bing, Yahoo, Ask, and AOL. Web site authorship was classified: academic, physician, medico-legal, commercial, or discussion/social media. Readability of each Web site was assessed using the Flesch Reading Ease score, the Flesch-Kincaid grade level, and the Gunning Fog Index. Quality was calculated using the DISCERN instrument and The Journal of the American Medical Association benchmark criteria. The presence of HON-code certification was also assessed. Fifty-two individual Web sites were identified and assessed. The majority of Web sites were academic or physician compiled (53.8%; 28/52); however, a significant minority of Web sites were medico-legal related (19.2%; 10/52). Just 13.5% (7/52) of Web sites were at or below the recommended sixth-grade readability level. HON-code certified Web sites achieved significantly greater DISCERN (P = 0.0006) and The Journal of the American Medical Association (P = 0.0002) scores. Internet information relating to cauda equina syndrome is of variable quality and largely set at an inappropriate readability level. Given this variability in quality, health care providers should direct patients to known sources of reliable, readable online information. Identification of reliable sources may be aided by known markers of quality such as HON-code certification.

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.

PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories.

PubMed

Hanson-Smith, Victor; Johnson, Alexander

2016-07-01

The method of phylogenetic ancestral sequence reconstruction is a powerful approach for studying evolutionary relationships among protein sequence, structure, and function. In particular, this approach allows investigators to (1) reconstruct and "resurrect" (that is, synthesize in vivo or in vitro) extinct proteins to study how they differ from modern proteins, (2) identify key amino acid changes that, over evolutionary timescales, have altered the function of the protein, and (3) order historical events in the evolution of protein function. Widespread use of this approach has been slow among molecular biologists, in part because the methods require significant computational expertise. Here we present PhyloBot, a web-based software tool that makes ancestral sequence reconstruction easy. Designed for non-experts, it integrates all the necessary software into a single user interface. Additionally, PhyloBot provides interactive tools to explore evolutionary trajectories between ancestors, enabling the rapid generation of hypotheses that can be tested using genetic or biochemical approaches. Early versions of this software were used in previous studies to discover genetic mechanisms underlying the functions of diverse protein families, including V-ATPase ion pumps, DNA-binding transcription regulators, and serine/threonine protein kinases. PhyloBot runs in a web browser, and is available at the following URL: http://www.phylobot.com. The software is implemented in Python using the Django web framework, and runs on elastic cloud computing resources from Amazon Web Services. Users can create and submit jobs on our free server (at the URL listed above), or use our open-source code to launch their own PhyloBot server.

PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories

PubMed Central

Hanson-Smith, Victor; Johnson, Alexander

2016-01-01

The method of phylogenetic ancestral sequence reconstruction is a powerful approach for studying evolutionary relationships among protein sequence, structure, and function. In particular, this approach allows investigators to (1) reconstruct and “resurrect” (that is, synthesize in vivo or in vitro) extinct proteins to study how they differ from modern proteins, (2) identify key amino acid changes that, over evolutionary timescales, have altered the function of the protein, and (3) order historical events in the evolution of protein function. Widespread use of this approach has been slow among molecular biologists, in part because the methods require significant computational expertise. Here we present PhyloBot, a web-based software tool that makes ancestral sequence reconstruction easy. Designed for non-experts, it integrates all the necessary software into a single user interface. Additionally, PhyloBot provides interactive tools to explore evolutionary trajectories between ancestors, enabling the rapid generation of hypotheses that can be tested using genetic or biochemical approaches. Early versions of this software were used in previous studies to discover genetic mechanisms underlying the functions of diverse protein families, including V-ATPase ion pumps, DNA-binding transcription regulators, and serine/threonine protein kinases. PhyloBot runs in a web browser, and is available at the following URL: http://www.phylobot.com. The software is implemented in Python using the Django web framework, and runs on elastic cloud computing resources from Amazon Web Services. Users can create and submit jobs on our free server (at the URL listed above), or use our open-source code to launch their own PhyloBot server. PMID:27472806

Development of a web-based and mobile app to support physical activity in individuals with rheumatoid arthritis: results from the second step of a co-design process.

PubMed

Revenäs, Åsa; Opava, Christina H; Martin, Cathrin; Demmelmaier, Ingrid; Keller, Christina; Åsenlöf, Pernilla

2015-02-09

Long-term adherence to physical activity recommendations remains challenging for most individuals with rheumatoid arthritis (RA) despite evidence for its health benefits. The aim of this study was to provide basic data on system requirement specifications for a Web-based and mobile app to self-manage physical activity. More specifically, we explored the target user group, features of the future app, and correlations between the system requirements and the established behavior change techniques (BCTs). We used a participatory action research design. Qualitative data were collected using multiple methods in four workshops. Participants were 5 individuals with RA, a clinical physiotherapist, an officer from the Swedish Rheumatism Association, a Web designer, and 2 physiotherapy researchers. A taxonomy was used to determine the degree of correlation between the system requirements and established BCTs. Participants agreed that the future Web-based and mobile app should be based on two major components important for maintaining physical activity: (1) a calendar feature for goal setting, planning, and recording of physical activity performance and progress, and (2) a small community feature for positive feedback and support from peers. All system requirements correlated with established BCTs, which were coded as 24 different BCTs. To our knowledge, this study is the first to involve individuals with RA as co-designers, in collaboration with clinicians, researchers, and Web designers, to produce basic data to generate system requirement specifications for an eHealth service. The system requirements correlated to the BCTs, making specifications of content and future evaluation of effectiveness possible.

ASA24 enables multiple automatically coded self-administered 24-hour recalls and food records

Cancer.gov

A freely available web-based tool for epidemiologic, interventional, behavioral, or clinical research from NCI that enables multiple automatically coded self-administered 24-hour recalls and food records.

Web server for priority ordered multimedia services

NASA Astrophysics Data System (ADS)

Celenk, Mehmet; Godavari, Rakesh K.; Vetnes, Vermund

2001-10-01

In this work, our aim is to provide finer priority levels in the design of a general-purpose Web multimedia server with provisions of the CM services. The type of services provided include reading/writing a web page, downloading/uploading an audio/video stream, navigating the Web through browsing, and interactive video teleconferencing. The selected priority encoding levels for such operations follow the order of admin read/write, hot page CM and Web multicasting, CM read, Web read, CM write and Web write. Hot pages are the most requested CM streams (e.g., the newest movies, video clips, and HDTV channels) and Web pages (e.g., portal pages of the commercial Internet search engines). Maintaining a list of these hot Web pages and CM streams in a content addressable buffer enables a server to multicast hot streams with lower latency and higher system throughput. Cold Web pages and CM streams are treated as regular Web and CM requests. Interactive CM operations such as pause (P), resume (R), fast-forward (FF), and rewind (RW) have to be executed without allocation of extra resources. The proposed multimedia server model is a part of the distributed network with load balancing schedulers. The SM is connected to an integrated disk scheduler (IDS), which supervises an allocated disk manager. The IDS follows the same priority handling as the SM, and implements a SCAN disk-scheduling method for an improved disk access and a higher throughput. Different disks are used for the Web and CM services in order to meet the QoS requirements of CM services. The IDS ouput is forwarded to an Integrated Transmission Scheduler (ITS). The ITS creates a priority ordered buffering of the retrieved Web pages and CM data streams that are fed into an auto regressive moving average (ARMA) based traffic shaping circuitry before being transmitted through the network.

Web Survey Design in ASP.Net 2.0: A Simple Task with One Line of Code

ERIC Educational Resources Information Center

Liu, Chang

2007-01-01

Over the past few years, more and more companies have been investing in electronic commerce (EC) by designing and implementing Web-based applications. In the world of practice, the importance of using Web technology to reach individual customers has been presented by many researchers. This paper presents an easy way of conducting marketing…

What Teens Want to Know: Sexual Health Questions Submitted to a Teen Web Site

ERIC Educational Resources Information Center

Vickberg, Suzanne M. Johnson; Kohn, Julia E.; Franco, Lydia M.; Criniti, Shannon

2003-01-01

In 1999 Planned Parenthood[R] Federation of America (PPFA[R]) launched teenwire.com[SM], a Web site for young people. This study was designed to determine teens' reproductive health information needs. Selected for analysis were 1,219 submissions to the Ask the Experts section of the Web site. Each submission was independently coded by three of the…

Enabling Real-time Water Decision Support Services Using Model as a Service

NASA Astrophysics Data System (ADS)

Zhao, T.; Minsker, B. S.; Lee, J. S.; Salas, F. R.; Maidment, D. R.; David, C. H.

2014-12-01

Through application of computational methods and an integrated information system, data and river modeling services can help researchers and decision makers more rapidly understand river conditions under alternative scenarios. To enable this capability, workflows (i.e., analysis and model steps) are created and published as Web services delivered through an internet browser, including model inputs, a published workflow service, and visualized outputs. The RAPID model, which is a river routing model developed at University of Texas Austin for parallel computation of river discharge, has been implemented as a workflow and published as a Web application. This allows non-technical users to remotely execute the model and visualize results as a service through a simple Web interface. The model service and Web application has been prototyped in the San Antonio and Guadalupe River Basin in Texas, with input from university and agency partners. In the future, optimization model workflows will be developed to link with the RAPID model workflow to provide real-time water allocation decision support services.

Data Access Services that Make Remote Sensing Data Easier to Use

NASA Technical Reports Server (NTRS)

Lynnes, Christopher

2010-01-01

This slide presentation reviews some of the processes that NASA uses to make the remote sensing data easy to use over the World Wide Web. This work involves much research into data formats, geolocation structures and quality indicators, often to be followed by coding a preprocessing program. Only then are the data usable within the analysis tool of choice. The Goddard Earth Sciences Data and Information Services Center is deploying a variety of data access services that are designed to dramatically shorten the time consumed in the data preparation step. On-the-fly conversion to the standard network Common Data Form (netCDF) format with Climate-Forecast (CF) conventions imposes a standard coordinate system framework that makes data instantly readable through several tools, such as the Integrated Data Viewer, Gridded Analysis and Display System, Panoply and Ferret. A similar benefit is achieved by serving data through the Open Source Project for a Network Data Access Protocol (OPeNDAP), which also provides subsetting. The Data Quality Screening Service goes a step further in filtering out data points based on quality control flags, based on science team recommendations or user-specified criteria. Further still is the Giovanni online analysis system which goes beyond handling formatting and quality to provide visualization and basic statistics of the data. This general approach of automating the preparation steps has the important added benefit of enabling use of the data by non-human users (i.e., computer programs), which often make sub-optimal use of the available data due to the need to hard-code data preparation on the client side.

US Geoscience Information Network, Web Services for Geoscience Information Discovery and Access

NASA Astrophysics Data System (ADS)

Richard, S.; Allison, L.; Clark, R.; Coleman, C.; Chen, G.

2012-04-01

The US Geoscience information network has developed metadata profiles for interoperable catalog services based on ISO19139 and the OGC CSW 2.0.2. Currently data services are being deployed for the US Dept. of Energy-funded National Geothermal Data System. These services utilize OGC Web Map Services, Web Feature Services, and THREDDS-served NetCDF for gridded datasets. Services and underlying datasets (along with a wide variety of other information and non information resources are registered in the catalog system. Metadata for registration is produced by various workflows, including harvest from OGC capabilities documents, Drupal-based web applications, transformation from tabular compilations. Catalog search is implemented using the ESRI Geoportal open-source server. We are pursuing various client applications to demonstrated discovery and utilization of the data services. Currently operational applications allow catalog search and data acquisition from map services in an ESRI ArcMap extension, a catalog browse and search application built on openlayers and Django. We are developing use cases and requirements for other applications to utilize geothermal data services for resource exploration and evaluation.

Framework for Supporting Web-Based Collaborative Applications

NASA Astrophysics Data System (ADS)

Dai, Wei

The article proposes an intelligent framework for supporting Web-based applications. The framework focuses on innovative use of existing resources and technologies in the form of services and takes the leverage of theoretical foundation of services science and the research from services computing. The main focus of the framework is to deliver benefits to users with various roles such as service requesters, service providers, and business owners to maximize their productivity when engaging with each other via the Web. The article opens up with research motivations and questions, analyses the existing state of research in the field, and describes the approach in implementing the proposed framework. Finally, an e-health application is discussed to evaluate the effectiveness of the framework where participants such as general practitioners (GPs), patients, and health-care workers collaborate via the Web.

The anatomy of a World Wide Web library service: the BONES demonstration project. Biomedically Oriented Navigator of Electronic Services.

PubMed Central

Schnell, E H

1995-01-01

In 1994, the John A. Prior Health Sciences Library at Ohio State University began to develop a World Wide Web demonstration project, the Biomedically Oriented Navigator of Electronic Services (BONES). The initial intent of BONES was to facilitate the health professional's access to Internet resources by organizing them in a systematic manner. The project not only met this goal but also helped identify the resources needed to launch a full-scale Web library service. This paper discusses the tasks performed and resources used in the development of BONES and describes the creation and organization of documents on the BONES Web server. The paper also discusses the outcomes of the project and the impact on the library's staff and services. PMID:8547903

High-performance web services for querying gene and variant annotation.

PubMed

Xin, Jiwen; Mark, Adam; Afrasiabi, Cyrus; Tsueng, Ginger; Juchler, Moritz; Gopal, Nikhil; Stupp, Gregory S; Putman, Timothy E; Ainscough, Benjamin J; Griffith, Obi L; Torkamani, Ali; Whetzel, Patricia L; Mungall, Christopher J; Mooney, Sean D; Su, Andrew I; Wu, Chunlei

2016-05-06

Efficient tools for data management and integration are essential for many aspects of high-throughput biology. In particular, annotations of genes and human genetic variants are commonly used but highly fragmented across many resources. Here, we describe MyGene.info and MyVariant.info, high-performance web services for querying gene and variant annotation information. These web services are currently accessed more than three million times permonth. They also demonstrate a generalizable cloud-based model for organizing and querying biological annotation information. MyGene.info and MyVariant.info are provided as high-performance web services, accessible at http://mygene.info and http://myvariant.info . Both are offered free of charge to the research community.

Library Services through the World Wide Web.

ERIC Educational Resources Information Center

Xiao, Daniel; Mosley, Pixey Anne; Cornish, Alan

1997-01-01

Provides an overview of the services offered by Texas A&M University's Sterling C. Evans Library via the World Wide Web. Included are public relations, instruction, searching capabilities, enhanced communications, and exhibit options. Future applications of the Web in academic libraries are also addressed. (AEF)

Web services in the U.S. geological survey streamstats web application

USGS Publications Warehouse

Guthrie, J.D.; Dartiguenave, C.; Ries, Kernell G.

2009-01-01

StreamStats is a U.S. Geological Survey Web-based GIS application developed as a tool for waterresources planning and management, engineering design, and other applications. StreamStats' primary functionality allows users to obtain drainage-basin boundaries, basin characteristics, and streamflow statistics for gaged and ungaged sites. Recently, Web services have been developed that provide the capability to remote users and applications to access comprehensive GIS tools that are available in StreamStats, including delineating drainage-basin boundaries, computing basin characteristics, estimating streamflow statistics for user-selected locations, and determining point features that coincide with a National Hydrography Dataset (NHD) reach address. For the state of Kentucky, a web service also has been developed that provides users the ability to estimate daily time series of drainage-basin average values of daily precipitation and temperature. The use of web services allows the user to take full advantage of the datasets and processes behind the Stream Stats application without having to develop and maintain them. ?? 2009 IEEE.

New Interfaces to Web Documents and Services

NASA Technical Reports Server (NTRS)

Carlisle, W. H.

1996-01-01

This paper reports on investigations into how to extend capabilities of the Virtual Research Center (VRC) for NASA's Advanced Concepts Office. The work was performed as part of NASA's 1996 Summer Faculty Fellowship program, and involved research into and prototype development of software components that provide documents and services for the World Wide Web (WWW). The WWW has become a de-facto standard for sharing resources over the internet, primarily because web browsers are freely available for the most common hardware platforms and their operating systems. As a consequence of the popularity of the internet, tools, and techniques associated with web browsers are changing rapidly. New capabilities are offered by companies that support web browsers in order to achieve or remain a dominant participant in internet services. Because a goal of the VRC is to build an environment for NASA centers, universities, and industrial partners to share information associated with Advanced Concepts Office activities, the VRC tracks new techniques and services associated with the web in order to determine the their usefulness for distributed and collaborative engineering research activities. Most recently, Java has emerged as a new tool for providing internet services. Because the major web browser providers have decided to include Java in their software, investigations into Java were conducted this summer.

Exploring weight loss services in primary care and staff views on using a web-based programme.

PubMed

Ware, Lisa J; Williams, Sarah; Bradbury, Katherine; Brant, Catherine; Little, Paul; Hobbs, F D Richard; Yardley, Lucy

2012-01-01

Demand is increasing for primary care to deliver effective weight management services to patients, but research suggests that staff feel inadequately resourced for such a role. Supporting service delivery with a free and effective web-based weight management programme could maximise primary care resource and provide cost-effective support for patients. However, integration of e-health into primary care may face challenges. To explore primary care staff experiences of delivering weight management services and their perceptions of a web-based weight management programme to aid service delivery. Focus groups were conducted with primary care physicians, nurses and healthcare assistants (n = 36) involved in delivering weight loss services. Data were analysed using inductive thematic analysis. Participants thought that primary care should be involved in delivering weight management, especially when weight was aggravating health problems. However, they felt under-resourced to deliver these services and unsure as to the effectiveness of their input, as routine services were not evaluated. Beliefs that current services were ineffective resulted in staff reluctance to allocate more resources. Participants were hopeful that supplementing practice with a web-based weight management programme would enhance patient services and promote service evaluation. Although primary care staff felt they should deliver weight loss services, low levels of faith in the efficacy of current treatments resulted in provision of under-resourced and 'ad hoc' services. Integration of a web-based weight loss programme that promotes service evaluation and provides a cost-effective option for supporting patients may encourage practices to invest more in weight management services.

Making Spatial Statistics Service Accessible On Cloud Platform

NASA Astrophysics Data System (ADS)

Mu, X.; Wu, J.; Li, T.; Zhong, Y.; Gao, X.

2014-04-01

Web service can bring together applications running on diverse platforms, users can access and share various data, information and models more effectively and conveniently from certain web service platform. Cloud computing emerges as a paradigm of Internet computing in which dynamical, scalable and often virtualized resources are provided as services. With the rampant growth of massive data and restriction of net, traditional web services platforms have some prominent problems existing in development such as calculation efficiency, maintenance cost and data security. In this paper, we offer a spatial statistics service based on Microsoft cloud. An experiment was carried out to evaluate the availability and efficiency of this service. The results show that this spatial statistics service is accessible for the public conveniently with high processing efficiency.

Using ESO Reflex with Web Services

NASA Astrophysics Data System (ADS)

Järveläinen, P.; Savolainen, V.; Oittinen, T.; Maisala, S.; Ullgrén, M. Hook, R.

2008-08-01

ESO Reflex is a prototype graphical workflow system, based on Taverna, and primarily intended to be a flexible way of running ESO data reduction recipes along with other legacy applications and user-written tools. ESO Reflex can also readily use the Taverna Web Services features that are based on the Apache Axis SOAP implementation. Taverna is a general purpose Web Service client, and requires no programming to use such services. However, Taverna also has some restrictions: for example, no numerical types such integers. In addition the preferred binding style is document/literal wrapped, but most astronomical services publish the Axis default WSDL using RPC/encoded style. Despite these minor limitations we have created simple but very promising test VO workflow using the Sesame name resolver service at CDS Strasbourg, the Hubble SIAP server at the Multi-Mission Archive at Space Telescope (MAST) and the WESIX image cataloging and catalogue cross-referencing service at the University of Pittsburgh. ESO Reflex can also pass files and URIs via the PLASTIC protocol to visualisation tools and has its own viewer for VOTables. We picked these three Web Services to try to set up a realistic and useful ESO Reflex workflow. They also demonstrate ESO Reflex abilities to use many kind of Web Services because each of them requires a different interface. We describe each of these services in turn and comment on how it was used

KBWS: an EMBOSS associated package for accessing bioinformatics web services.

PubMed

Oshita, Kazuki; Arakawa, Kazuharu; Tomita, Masaru

2011-04-29

The availability of bioinformatics web-based services is rapidly proliferating, for their interoperability and ease of use. The next challenge is in the integration of these services in the form of workflows, and several projects are already underway, standardizing the syntax, semantics, and user interfaces. In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular Biology Open Software Suite (EMBOSS) UNIX command-line tools. EMBOSS provides sophisticated means for discoverability and interoperability for hundreds of tools, and our package, named the Keio Bioinformatics Web Service (KBWS), adds functionalities of local and multiple alignment of sequences, phylogenetic analyses, and prediction of cellular localization of proteins and RNA secondary structures. This software implemented in C is available under GPL from http://www.g-language.org/kbws/ and GitHub repository http://github.com/cory-ko/KBWS. Users can utilize the SOAP services implemented in Perl directly via WSDL file at http://soap.g-language.org/kbws.wsdl (RPC Encoded) and http://soap.g-language.org/kbws_dl.wsdl (Document/literal).

Large-area sheet task advanced dendritic web growth development

NASA Technical Reports Server (NTRS)

Duncan, C. S.; Seidensticker, R. G.; Mchugh, J. P.; Hopkins, R. H.; Meier, D.; Schruben, J.

1982-01-01

The computer code for calculating web temperature distribution was expanded to provide a graphics output in addition to numerical and punch card output. The new code was used to examine various modifications of the J419 configuration and, on the basis of the results, a new growth geometry was designed. Additionally, several mathematically defined temperature profiles were evaluated for the effects of the free boundary (growth front) on the thermal stress generation. Experimental growth runs were made with modified J419 configurations to complement the modeling work. A modified J435 configuration was evaluated.

Towards a global IT system for personalized medicine: the Medicine Safety Code initiative.

PubMed

Samwald, Matthias; Minarro-Giménez, José Antonio; Blagec, Kathrin; Adlassnig, Klaus-Peter

2014-01-01

The availability of pharmacogenomic data of individual patients can significantly improve physicians' prescribing behavior, lead to a reduced incidence of adverse drug events and an improvement of effectiveness of treatment. The Medicine Safety Code (MSC) initiative is an effort to improve the ability of clinicians and patients to share pharmacogenomic data and to use it at the point of care. The MSC is a standardized two-dimensional barcode that captures individual pharmacogenomic data. The system is backed by a web service that allows the decoding and interpretation of anonymous MSCs without requiring the installation of dedicated software. The system is based on a curated, ontology-based knowledge base representing pharmacogenomic definitions and clinical guidelines. The MSC system performed well in preliminary tests. To evaluate the system in realistic health care settings and to translate it into practical applications, the future participation of stakeholders in clinical institutions, researchers, pharmaceutical companies, genetic testing providers, health IT companies and health insurance organizations will be essential.