Using component technologies for web based wavelet enhanced mammographic image visualization.

PubMed

Sakellaropoulos, P; Costaridou, L; Panayiotakis, G

2000-01-01

The poor contrast detectability of mammography can be dealt with by domain specific software visualization tools. Remote desktop client access and time performance limitations of a previously reported visualization tool are addressed, aiming at more efficient visualization of mammographic image resources existing in web or PACS image servers. This effort is also motivated by the fact that at present, web browsers do not support domain-specific medical image visualization. To deal with desktop client access the tool was redesigned by exploring component technologies, enabling the integration of stand alone domain specific mammographic image functionality in a web browsing environment (web adaptation). The integration method is based on ActiveX Document Server technology. ActiveX Document is a part of Object Linking and Embedding (OLE) extensible systems object technology, offering new services in existing applications. The standard DICOM 3.0 part 10 compatible image-format specification Papyrus 3.0 is supported, in addition to standard digitization formats such as TIFF. The visualization functionality of the tool has been enhanced by including a fast wavelet transform implementation, which allows for real time wavelet based contrast enhancement and denoising operations. Initial use of the tool with mammograms of various breast structures demonstrated its potential in improving visualization of diagnostic mammographic features. Web adaptation and real time wavelet processing enhance the potential of the previously reported tool in remote diagnosis and education in mammography.

Web Instruction with the LBO Model.

ERIC Educational Resources Information Center

Agarwal, Rajshree; Day, A. Edward

2000-01-01

Presents a Web site that utilizes the Learning-by-Objective (LBO) model that integrates Internet tools for knowledge transmission, communication, and assessment of learning. Explains that the LBO model has been used in creating micro and macroeconomic course Web sites with WebCT software. (CMK)

Web Services Integration on the Fly

DTIC Science & Technology

2008-12-01

NETBEANS 6.1 AND VERSION CONTROL............................................28 1. NetBeans Integrated Development Environment (IDE) ................28 2...Forward and Reverse Engineering...................................................28 3. Implementation using NetBeans ...29 4. Subversion (SVN) for Version Control in NetBeans ......................29 O. PROTÉGÉ AUTHORING TOOL FOR SEMANTIC WEB

Lynx web services for annotations and systems analysis of multi-gene disorders.

PubMed

Sulakhe, Dinanath; Taylor, Andrew; Balasubramanian, Sandhya; Feng, Bo; Xie, Bingqing; Börnigen, Daniela; Dave, Utpal J; Foster, Ian T; Gilliam, T Conrad; Maltsev, Natalia

2014-07-01

Lynx is a web-based integrated systems biology platform that supports annotation and analysis of experimental data and generation of weighted hypotheses on molecular mechanisms contributing to human phenotypes and disorders of interest. Lynx has integrated multiple classes of biomedical data (genomic, proteomic, pathways, phenotypic, toxicogenomic, contextual and others) from various public databases as well as manually curated data from our group and collaborators (LynxKB). Lynx provides tools for gene list enrichment analysis using multiple functional annotations and network-based gene prioritization. Lynx provides access to the integrated database and the analytical tools via REST based Web Services (http://lynx.ci.uchicago.edu/webservices.html). This comprises data retrieval services for specific functional annotations, services to search across the complete LynxKB (powered by Lucene), and services to access the analytical tools built within the Lynx platform. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Integrating web 2.0 in clinical research education in a developing country.

PubMed

Amgad, Mohamed; AlFaar, Ahmad Samir

2014-09-01

The use of Web 2.0 tools in education and health care has received heavy attention over the past years. Over two consecutive years, Children's Cancer Hospital - Egypt 57357 (CCHE 57357), in collaboration with Egyptian universities, student bodies, and NGOs, conducted a summer course that supports undergraduate medical students to cross the gap between clinical practice and clinical research. This time, there was a greater emphasis on reaching out to the students using social media and other Web 2.0 tools, which were heavily used in the course, including Google Drive, Facebook, Twitter, YouTube, Mendeley, Google Hangout, Live Streaming, Research Electronic Data Capture (REDCap), and Dropbox. We wanted to investigate the usefulness of integrating Web 2.0 technologies into formal educational courses and modules. The evaluation survey was filled in by 156 respondents, 134 of whom were course candidates (response rate = 94.4 %) and 22 of whom were course coordinators (response rate = 81.5 %). The course participants came from 14 different universities throughout Egypt. Students' feedback was positive and supported the integration of Web 2.0 tools in academic courses and modules. Google Drive, Facebook, and Dropbox were found to be most useful.

War Gamers Handbook: A Guide for Professional War Gamers

DTIC Science & Technology

2015-11-01

more complex games led us to integrate knowledge management, web tools, and multitouch , multiuser technologies in order to more efficiently and... Multitouch multiuser (MTMU) and communications operating picture (COP) interfaces ◊ Web development—Web tools and player interfaces Now that the game...hurricane or flood scenario to provide a plausible backdrop to facilitate player interaction toward game objectives. Scenarios should include only the

Applying Web Usage Mining for Personalizing Hyperlinks in Web-Based Adaptive Educational Systems

ERIC Educational Resources Information Center

Romero, Cristobal; Ventura, Sebastian; Zafra, Amelia; de Bra, Paul

2009-01-01

Nowadays, the application of Web mining techniques in e-learning and Web-based adaptive educational systems is increasing exponentially. In this paper, we propose an advanced architecture for a personalization system to facilitate Web mining. A specific Web mining tool is developed and a recommender engine is integrated into the AHA! system in…

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. .

A Web simulation of medical image reconstruction and processing as an educational tool.

PubMed

Papamichail, Dimitrios; Pantelis, Evaggelos; Papagiannis, Panagiotis; Karaiskos, Pantelis; Georgiou, Evangelos

2015-02-01

Web educational resources integrating interactive simulation tools provide students with an in-depth understanding of the medical imaging process. The aim of this work was the development of a purely Web-based, open access, interactive application, as an ancillary learning tool in graduate and postgraduate medical imaging education, including a systematic evaluation of learning effectiveness. The pedagogic content of the educational Web portal was designed to cover the basic concepts of medical imaging reconstruction and processing, through the use of active learning and motivation, including learning simulations that closely resemble actual tomographic imaging systems. The user can implement image reconstruction and processing algorithms under a single user interface and manipulate various factors to understand the impact on image appearance. A questionnaire for pre- and post-training self-assessment was developed and integrated in the online application. The developed Web-based educational application introduces the trainee in the basic concepts of imaging through textual and graphical information and proceeds with a learning-by-doing approach. Trainees are encouraged to participate in a pre- and post-training questionnaire to assess their knowledge gain. An initial feedback from a group of graduate medical students showed that the developed course was considered as effective and well structured. An e-learning application on medical imaging integrating interactive simulation tools was developed and assessed in our institution.

Web Development Simplified

ERIC Educational Resources Information Center

Becker, Bernd W.

2010-01-01

The author has discussed the Multimedia Educational Resource for Teaching and Online Learning site, MERLOT, in a recent Electronic Roundup column. In this article, he discusses an entirely new Web page development tool that MERLOT has added for its members. The new tool is called the MERLOT Content Builder and is directly integrated into the…

Webbing and Orchestration. Two Interrelated Views on Digital Tools in Mathematics Education

ERIC Educational Resources Information Center

Trouche, Luc; Drijvers, Paul

2014-01-01

The integration of digital tools in mathematics education is considered both promising and problematic. To deal with this issue, notions of "webbing" and "instrumental orchestration" are developed. However, the two seemed to be disconnected, and having different cultural and theoretical roots. In this article, we investigate…

Integrating Thematic Web Portal Capabilities into the NASA Earthdata Web Infrastructure

NASA Technical Reports Server (NTRS)

Wong, Minnie; Baynes, Kathleen E.; Huang, Thomas; McLaughlin, Brett

2015-01-01

This poster will present the process of integrating thematic web portal capabilities into the NASA Earth data 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.

Network Computing Infrastructure to Share Tools and Data in Global Nuclear Energy Partnership

NASA Astrophysics Data System (ADS)

Kim, Guehee; Suzuki, Yoshio; Teshima, Naoya

CCSE/JAEA (Center for Computational Science and e-Systems/Japan Atomic Energy Agency) integrated a prototype system of a network computing infrastructure for sharing tools and data to support the U.S. and Japan collaboration in GNEP (Global Nuclear Energy Partnership). We focused on three technical issues to apply our information process infrastructure, which are accessibility, security, and usability. In designing the prototype system, we integrated and improved both network and Web technologies. For the accessibility issue, we adopted SSL-VPN (Security Socket Layer-Virtual Private Network) technology for the access beyond firewalls. For the security issue, we developed an authentication gateway based on the PKI (Public Key Infrastructure) authentication mechanism to strengthen the security. Also, we set fine access control policy to shared tools and data and used shared key based encryption method to protect tools and data against leakage to third parties. For the usability issue, we chose Web browsers as user interface and developed Web application to provide functions to support sharing tools and data. By using WebDAV (Web-based Distributed Authoring and Versioning) function, users can manipulate shared tools and data through the Windows-like folder environment. We implemented the prototype system in Grid infrastructure for atomic energy research: AEGIS (Atomic Energy Grid Infrastructure) developed by CCSE/JAEA. The prototype system was applied for the trial use in the first period of GNEP.

Web 2.0 and Marketing Education: Explanations and Experiential Applications

ERIC Educational Resources Information Center

Granitz, Neil; Koernig, Stephen K.

2011-01-01

Although both experiential learning and Web 2.0 tools focus on creativity, sharing, and collaboration, sparse research has been published integrating a Web 2.0 paradigm with experiential learning in marketing. In this article, Web 2.0 concepts are explained. Web 2.0 is then positioned as a philosophy that can advance experiential learning through…

Taverna: a tool for building and running workflows of services

PubMed Central

Hull, Duncan; Wolstencroft, Katy; Stevens, Robert; Goble, Carole; Pocock, Mathew R.; Li, Peter; Oinn, Tom

2006-01-01

Taverna is an application that eases the use and integration of the growing number of molecular biology tools and databases available on the web, especially web services. It allows bioinformaticians to construct workflows or pipelines of services to perform a range of different analyses, such as sequence analysis and genome annotation. These high-level workflows can integrate many different resources into a single analysis. Taverna is available freely under the terms of the GNU Lesser General Public License (LGPL) from . PMID:16845108

Enriching and improving the quality of linked data with GIS

NASA Astrophysics Data System (ADS)

Iwaniak, Adam; Kaczmarek, Iwona; Strzelecki, Marek; Lukowicz, Jaromar; Jankowski, Piotr

2016-06-01

Standardization of methods for data exchange in GIS has along history predating the creation of World Wide Web. The advent of World Wide Web brought the emergence of new solutions for data exchange and sharing including; more recently, standards proposed by the W3C for data exchange involving Semantic Web technologies and linked data. Despite the growing interest in integration, GIS and linked data are still two separate paradigms for describing and publishing spatial data on the Web. At the same time, both paradigms offer complementary ways of representing real world phenomena and means of analysis using different processing functions. The complementarity of linked data and GIS can be leveraged to synergize both paradigms resulting in richer data content and more powerful inferencing. The article presents an approach aimed at integrating linked data with GIS. The approach relies on the use of GIS tools for integration, verification and enrichment of linked data. The GIS tools are employed to enrich linked data by furnishing access to collection of data resources, defining relationship between data resources, and subsequently facilitating GIS data integration with linked data. The proposed approach is demonstrated with examples using data from DBpedia, OSM, and tools developed by the authors for standard GIS software.

Education 2.0 -- how has social media and Web 2.0 been integrated into medical education? A systematical literature review.

PubMed

Hollinderbäumer, Anke; Hartz, Tobias; Uckert, Frank

2013-01-01

Present-day students have grown up with considerable knowledge concerning multi-media. The communication modes they use are faster, more spontaneous, and independent of place and time. These new web-based forms of information and communication are used by students, educators, and patients in various ways. Universities which have already used these tools report many positive effects on the learning behaviour of the students. In a systematic literature review, we summarized the manner in which the integration of Social Media and Web 2.0 into education has taken place. A systematic literature search covering the last 5 years using MeSH terms was carried out via PubMed. Among the 20 chosen publications, there was only one German publication. Most of the publications are from the US and Great Britain. The latest publications report on the concrete usage of the tools in education, including social networking, podcasts, blogs, wikis, YouTube, Twitter and Skype. The integration of Web 2.0 and Social Media is the modern form of self-determined learning. It stimulates reflection and actively integrates the students in the construction of their knowledge. With these new tools, the students acquire skills which they need in both their social and professional lives.

Education 2.0 - How has social media and Web 2.0 been integrated into medical education? A systematical literature review

PubMed Central

Hollinderbäumer, Anke; Hartz, Tobias; Ückert, Frank

2013-01-01

Objective: Present-day students have grown up with considerable knowledge concerning multi-media. The communication modes they use are faster, more spontaneous, and independent of place and time. These new web-based forms of information and communication are used by students, educators, and patients in various ways. Universities which have already used these tools report many positive effects on the learning behaviour of the students. In a systematic literature review, we summarized the manner in which the integration of Social Media and Web 2.0 into education has taken place. Method: A systematic literature search covering the last 5 years using MeSH terms was carried out via PubMed. Result: Among the 20 chosen publications, there was only one German publication. Most of the publications are from the US and Great Britain. The latest publications report on the concrete usage of the tools in education, including social networking, podcasts, blogs, wikis, YouTube, Twitter and Skype. Conclusion: The integration of Web 2.0 and Social Media is the modern form of self-determined learning. It stimulates reflection and actively integrates the students in the construction of their knowledge. With these new tools, the students acquire skills which they need in both their social and professional lives. PMID:23467509

WIRM: An Open Source Toolkit for Building Biomedical Web Applications

PubMed Central

Jakobovits, Rex M.; Rosse, Cornelius; Brinkley, James F.

2002-01-01

This article describes an innovative software toolkit that allows the creation of web applications that facilitate the acquisition, integration, and dissemination of multimedia biomedical data over the web, thereby reducing the cost of knowledge sharing. There is a lack of high-level web application development tools suitable for use by researchers, clinicians, and educators who are not skilled programmers. Our Web Interfacing Repository Manager (WIRM) is a software toolkit that reduces the complexity of building custom biomedical web applications. WIRM’s visual modeling tools enable domain experts to describe the structure of their knowledge, from which WIRM automatically generates full-featured, customizable content management systems. PMID:12386108

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

Leveraging Web 2.0 in the Redesign of a Graduate-Level Technology Integration Course

ERIC Educational Resources Information Center

Oliver, Kevin

2007-01-01

In the emerging era of the "read-write" web, students can not only research and collect information from existing web resources, but also collaborate and create new information on the web in a surprising number of ways. Web 2.0 is an umbrella term for many individual tools that have been created with web collaboration, sharing, and/or new…

Library Web Site Administration: A Strategic Planning Model For the Smaller Academic Library

ERIC Educational Resources Information Center

Ryan, Susan M.

2003-01-01

Strategic planning provides a useful structure for creating and implementing library web sites. The planned integration of a library's web site into its mission and objectives ensures that the library's community of users will consider the web site one of the most important information tools the library offers.

Integrated Functional and Executional Modelling of Software Using Web-Based Databases

NASA Technical Reports Server (NTRS)

Kulkarni, Deepak; Marietta, Roberta

1998-01-01

NASA's software subsystems undergo extensive modification and updates over the operational lifetimes. It is imperative that modified software should satisfy safety goals. This report discusses the difficulties encountered in doing so and discusses a solution based on integrated modelling of software, use of automatic information extraction tools, web technology and databases.

EvalCOMIX®: A Web-Based Programme to Support Collaboration in Assessment

ERIC Educational Resources Information Center

Ibarra-Sáiz, María Soledad; Rodríguez-Gómez, Gregorio

2016-01-01

For many years assessment strategies and practices have emphasized on the one hand the importance of integrating assessment and learning and, secondly, the need to develop technological tools that facilitate this relationship and integration. In this paper, firstly we describe the EvalCOMIX® web service and then we present the opinions of…

Tailored and Integrated Web-Based Tools for Improving Psychosocial Outcomes of Cancer Patients: The DoTTI Development Framework

PubMed Central

Bryant, Jamie; Sanson-Fisher, Rob; Tzelepis, Flora; Henskens, Frans; Paul, Christine; Stevenson, William

2014-01-01

Background Effective communication with cancer patients and their families about their disease, treatment options, and possible outcomes may improve psychosocial outcomes. However, traditional approaches to providing information to patients, including verbal information and written booklets, have a number of shortcomings centered on their limited ability to meet patient preferences and literacy levels. New-generation Web-based technologies offer an innovative and pragmatic solution for overcoming these limitations by providing a platform for interactive information seeking, information sharing, and user-centered tailoring. Objective The primary goal of this paper is to discuss the advantages of comprehensive and iterative Web-based technologies for health information provision and propose a four-phase framework for the development of Web-based information tools. Methods The proposed framework draws on our experience of constructing a Web-based information tool for hematological cancer patients and their families. The framework is based on principles for the development and evaluation of complex interventions and draws on the Agile methodology of software programming that emphasizes collaboration and iteration throughout the development process. Results The DoTTI framework provides a model for a comprehensive and iterative approach to the development of Web-based informational tools for patients. The process involves 4 phases of development: (1) Design and development, (2) Testing early iterations, (3) Testing for effectiveness, and (4) Integration and implementation. At each step, stakeholders (including researchers, clinicians, consumers, and programmers) are engaged in consultations to review progress, provide feedback on versions of the Web-based tool, and based on feedback, determine the appropriate next steps in development. Conclusions This 4-phase framework is evidence-informed and consumer-centered and could be applied widely to develop Web-based programs for a diverse range of diseases. PMID:24641991

Tailored and integrated Web-based tools for improving psychosocial outcomes of cancer patients: the DoTTI development framework.

PubMed

Smits, Rochelle; Bryant, Jamie; Sanson-Fisher, Rob; Tzelepis, Flora; Henskens, Frans; Paul, Christine; Stevenson, William

2014-03-14

Effective communication with cancer patients and their families about their disease, treatment options, and possible outcomes may improve psychosocial outcomes. However, traditional approaches to providing information to patients, including verbal information and written booklets, have a number of shortcomings centered on their limited ability to meet patient preferences and literacy levels. New-generation Web-based technologies offer an innovative and pragmatic solution for overcoming these limitations by providing a platform for interactive information seeking, information sharing, and user-centered tailoring. The primary goal of this paper is to discuss the advantages of comprehensive and iterative Web-based technologies for health information provision and propose a four-phase framework for the development of Web-based information tools. The proposed framework draws on our experience of constructing a Web-based information tool for hematological cancer patients and their families. The framework is based on principles for the development and evaluation of complex interventions and draws on the Agile methodology of software programming that emphasizes collaboration and iteration throughout the development process. The DoTTI framework provides a model for a comprehensive and iterative approach to the development of Web-based informational tools for patients. The process involves 4 phases of development: (1) Design and development, (2) Testing early iterations, (3) Testing for effectiveness, and (4) Integration and implementation. At each step, stakeholders (including researchers, clinicians, consumers, and programmers) are engaged in consultations to review progress, provide feedback on versions of the Web-based tool, and based on feedback, determine the appropriate next steps in development. This 4-phase framework is evidence-informed and consumer-centered and could be applied widely to develop Web-based programs for a diverse range of diseases.

CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets.

PubMed

Schofield, E C; Carver, T; Achuthan, P; Freire-Pritchett, P; Spivakov, M; Todd, J A; Burren, O S

2016-08-15

Promoter capture Hi-C (PCHi-C) allows the genome-wide interrogation of physical interactions between distal DNA regulatory elements and gene promoters in multiple tissue contexts. Visual integration of the resultant chromosome interaction maps with other sources of genomic annotations can provide insight into underlying regulatory mechanisms. We have developed Capture HiC Plotter (CHiCP), a web-based tool that allows interactive exploration of PCHi-C interaction maps and integration with both public and user-defined genomic datasets. CHiCP is freely accessible from www.chicp.org and supports most major HTML5 compliant web browsers. Full source code and installation instructions are available from http://github.com/D-I-L/django-chicp ob219@cam.ac.uk. © The Author 2016. Published by Oxford University Press. All rights reserved.

Organizational Alignment Through Information Technology: A Web-Based Approach to Change

NASA Technical Reports Server (NTRS)

Heinrichs, W.; Smith, J.

1999-01-01

This paper reports on the effectiveness of web-based internet tools and databases to facilitate integration of technical organizations with interfaces that minimize modification of each technical organization.

Collaborative Writing with Web 2.0 Technologies: Education Students' Perceptions

ERIC Educational Resources Information Center

Brodahl, Cornelia; Hadjerrouit, Said; Hansen, Nils Kristian

2011-01-01

Web 2.0 technologies are becoming popular in teaching and learning environments. Among them several online collaborative writing tools, like wikis and blogs, have been integrated into educational settings. Research has been carried out on a wide range of subjects related to wikis, while other, comparable tools like Google Docs and EtherPad remain…

PathCase-SB architecture and database design

PubMed Central

2011-01-01

Background Integration of metabolic pathways resources and regulatory metabolic network models, and deploying new tools on the integrated platform can help perform more effective and more efficient systems biology research on understanding the regulation in metabolic networks. Therefore, the tasks of (a) integrating under a single database environment regulatory metabolic networks and existing models, and (b) building tools to help with modeling and analysis are desirable and intellectually challenging computational tasks. Description PathCase Systems Biology (PathCase-SB) is built and released. The PathCase-SB database provides data and API for multiple user interfaces and software tools. The current PathCase-SB system provides a database-enabled framework and web-based computational tools towards facilitating the development of kinetic models for biological systems. PathCase-SB aims to integrate data of selected biological data sources on the web (currently, BioModels database and KEGG), and to provide more powerful and/or new capabilities via the new web-based integrative framework. This paper describes architecture and database design issues encountered in PathCase-SB's design and implementation, and presents the current design of PathCase-SB's architecture and database. Conclusions PathCase-SB architecture and database provide a highly extensible and scalable environment with easy and fast (real-time) access to the data in the database. PathCase-SB itself is already being used by researchers across the world. PMID:22070889

WebQuest on Conic Sections as a Learning Tool for Prospective Teachers

ERIC Educational Resources Information Center

Kurtulus, Aytac; Ada, Tuba

2012-01-01

WebQuests incorporate technology with educational concepts through integrating online resources with student-centred and activity-based learning. In this study, we describe and evaluate a WebQuest based on conic sections, which we have used with a group of prospective mathematics teachers. The WebQuest entitled: "Creating a Carpet Design Using…

Quality Dashboards: Technical and Architectural Considerations of an Actionable Reporting Tool for Population Management

PubMed Central

Olsha-Yehiav, Maya; Einbinder, Jonathan S.; Jung, Eunice; Linder, Jeffrey A.; Greim, Julie; Li, Qi; Schnipper, Jeffrey L.; Middleton, Blackford

2006-01-01

Quality Dashboards (QD) is a condition-specific, actionable web-based application for quality reporting and population management that is integrated into the Electronic Health Record (EHR). Using server-based graphic web controls in a .Net environment to construct Quality Dashboards allows customization of the reporting tool without the need to rely on commercial business intelligence tool. Quality Dashboards will improve patient care and quality outcomes as clinicians utilize the reporting tool for population management. PMID:17238671

Integrating the hospital library with patient care, teaching and research: model and Web 2.0 tools to create a social and collaborative community of clinical research in a hospital setting.

PubMed

Montano, Blanca San José; Garcia Carretero, Rafael; Varela Entrecanales, Manuel; Pozuelo, Paz Martin

2010-09-01

Research in hospital settings faces several difficulties. Information technologies and certain Web 2.0 tools may provide new models to tackle these problems, allowing for a collaborative approach and bridging the gap between clinical practice, teaching and research. We aim to gather a community of researchers involved in the development of a network of learning and investigation resources in a hospital setting. A multi-disciplinary work group analysed the needs of the research community. We studied the opportunities provided by Web 2.0 tools and finally we defined the spaces that would be developed, describing their elements, members and different access levels. WIKINVESTIGACION is a collaborative web space with the aim of integrating the management of all the hospital's teaching and research resources. It is composed of five spaces, with different access privileges. The spaces are: Research Group Space 'wiki for each individual research group', Learning Resources Centre devoted to the Library, News Space, Forum and Repositories. The Internet, and most notably the Web 2.0 movement, is introducing some overwhelming changes in our society. Research and teaching in the hospital setting will join this current and take advantage of these tools to socialise and improve knowledge management.

Modeling Tools for Propulsion Analysis and Computational Fluid Dynamics on the Internet

NASA Technical Reports Server (NTRS)

Muss, J. A.; Johnson, C. W.; Gotchy, M. B.

2000-01-01

The existing RocketWeb(TradeMark) Internet Analysis System (httr)://www.iohnsonrockets.com/rocketweb) provides an integrated set of advanced analysis tools that can be securely accessed over the Internet. Since these tools consist of both batch and interactive analysis codes, the system includes convenient methods for creating input files and evaluating the resulting data. The RocketWeb(TradeMark) system also contains many features that permit data sharing which, when further developed, will facilitate real-time, geographically diverse, collaborative engineering within a designated work group. Adding work group management functionality while simultaneously extending and integrating the system's set of design and analysis tools will create a system providing rigorous, controlled design development, reducing design cycle time and cost.

Report Central: quality reporting tool in an electronic health record.

PubMed

Jung, Eunice; Li, Qi; Mangalampalli, Anil; Greim, Julie; Eskin, Michael S; Housman, Dan; Isikoff, Jeremy; Abend, Aaron H; Middleton, Blackford; Einbinder, Jonathan S

2006-01-01

Quality reporting tools, integrated with ambulatory electronic health records, can help clinicians and administrators understand performance, manage populations, and improve quality. Report Central is a secure web report delivery tool built on Crystal Reports XItrade mark and ASP.NET technologies. Pilot evaluation of Report Central indicates that clinicians prefer a quality reporting tool that is integrated with our home-grown EHR to support clinical workflow.

Program Management Tool

NASA Technical Reports Server (NTRS)

Gawadiak, Yuri; Wong, Alan; Maluf, David; Bell, David; Gurram, Mohana; Tran, Khai Peter; Hsu, Jennifer; Yagi, Kenji; Patel, Hemil

2007-01-01

The Program Management Tool (PMT) is a comprehensive, Web-enabled business intelligence software tool for assisting program and project managers within NASA enterprises in gathering, comprehending, and disseminating information on the progress of their programs and projects. The PMT provides planning and management support for implementing NASA programmatic and project management processes and requirements. It provides an online environment for program and line management to develop, communicate, and manage their programs, projects, and tasks in a comprehensive tool suite. The information managed by use of the PMT can include monthly reports as well as data on goals, deliverables, milestones, business processes, personnel, task plans, monthly reports, and budgetary allocations. The PMT provides an intuitive and enhanced Web interface to automate the tedious process of gathering and sharing monthly progress reports, task plans, financial data, and other information on project resources based on technical, schedule, budget, and management criteria and merits. The PMT is consistent with the latest Web standards and software practices, including the use of Extensible Markup Language (XML) for exchanging data and the WebDAV (Web Distributed Authoring and Versioning) protocol for collaborative management of documents. The PMT provides graphical displays of resource allocations in the form of bar and pie charts using Microsoft Excel Visual Basic for Application (VBA) libraries. The PMT has an extensible architecture that enables integration of PMT with other strategic-information software systems, including, for example, the Erasmus reporting system, now part of the NASA Integrated Enterprise Management Program (IEMP) tool suite, at NASA Marshall Space Flight Center (MSFC). The PMT data architecture provides automated and extensive software interfaces and reports to various strategic information systems to eliminate duplicative human entries and minimize data integrity issues among various NASA systems that impact schedules and planning.

Integration and Implementation of Web Simulators in Experimental e-Learning: An Application for Capacity Auctions

ERIC Educational Resources Information Center

Otamendi, Francisco Javier; Doncel, Luis Miguel

2013-01-01

Experimental teaching in general, and simulation in particular, have primarily been used in lecture rooms but in the future must also be adapted to e-learning. The integration of web simulators into virtual learning environments, coupled with specific supporting video documentation and the use of videoconference tools, results in robust…

Web-Based Tools for Designing and Developing Teaching Materials for Integration of Information Technology into Instruction

ERIC Educational Resources Information Center

Chang, Kuo-En; Sung, Yao-Ting; Hou, Huei-Tse

2006-01-01

Educational software for teachers is an important, yet usually ignored, link for integrating information technology into classroom instruction. This study builds a web-based teaching material design and development system. The process in the system is divided into four stages, analysis, design, development, and practice. Eight junior high school…

Web-Based Surveys Facilitate Undergraduate Research and Knowledge

ERIC Educational Resources Information Center

Grimes, Paul, Ed.; Steele, Scott R.

2008-01-01

The author presents Web-based surveying as a valuable tool for achieving quality undergraduate research in upper-level economics courses. Web-based surveys can be employed in efforts to integrate undergraduate research into the curriculum without overburdening students or faculty. The author discusses the value of undergraduate research, notes…

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

NASA Astrophysics Data System (ADS)

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

2014-03-01

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

LifeWatchGreece Portal development: architecture, implementation and challenges for a biodiversity research e-infrastructure.

PubMed

Gougousis, Alexandros; Bailly, Nicolas

2016-01-01

Biodiversity data is characterized by its cross-disciplinary character, the extremely broad range of data types and structures, and the plethora of different data sources providing resources for the same piece of information in a heterogeneous way. Since the web inception two decades ago, there are multiple initiatives to connect, aggregate, share, and publish biodiversity data, and to establish data and work flows in order to analyze them. The European program LifeWatch aims at establishing a distributed network of nodes implementing virtual research environment in Europe to facilitate the work of biodiversity researchers and managers. LifeWatchGreece is one of these nodes where a portal was developed offering access to a suite of virtual laboratories and e-services. Despite its strict definition in information technology, in practice "portal" is a fairly broad term that embraces many web architectures. In the biodiversity domain, the term "portal" is usually used to indicate either a web site that provides access to a single or an aggregation of data repositories (like: http://indiabiodiversity.org/, http://www.mountainbiodiversity.org/, http://data.freshwaterbiodiversity.eu), a web site that gathers information about various online biodiversity tools (like http://test-eubon.ebd.csic.es/, http://marine.lifewatch.eu/) or a web site that just gathers information and news about the biodiversity domain (like http://chm.moew.government.bg). LifeWatchGreece's portal takes the concept of a portal a step further. In strict IT terms, LifeWatchGreece's portal is partly a portal, partly a platform and partly an aggregator. It includes a number of biodiversity-related web tools integrated into a centrally-controlled software ecosystem. This ecosystem includes subsystems for access control, traffic monitoring, user notifications and web tool management. These subsystems are shared to all the web tools that have been integrated to the portal and thereby are part of this ecosystem. These web tools do not consist in external and completely independent web applications as it happens in most other portals. A quite obvious (to the user) indication of this is the Single-Sign-On (SSO) functionality for all tools and the common user interface wrapper that most of these tools use. Another example of a less obvious functionality is the common user profile that is shared and can be utilized by all tools (e.g user's timezone).

An Integrated Software Package to Enable Predictive Simulation Capabilities

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

Chen, Yousu; Fitzhenry, Erin B.; Jin, Shuangshuang

The power grid is increasing in complexity due to the deployment of smart grid technologies. Such technologies vastly increase the size and complexity of power grid systems for simulation and modeling. This increasing complexity necessitates not only the use of high-performance-computing (HPC) techniques, but a smooth, well-integrated interplay between HPC applications. This paper presents a new integrated software package that integrates HPC applications and a web-based visualization tool based on a middleware framework. This framework can support the data communication between different applications. Case studies with a large power system demonstrate the predictive capability brought by the integrated software package,more » as well as the better situational awareness provided by the web-based visualization tool in a live mode. Test results validate the effectiveness and usability of the integrated software package.« less

An Investigation of the Factors That Influence Preservice Teachers' Intentions and Integration of Web 2.0 Tools

ERIC Educational Resources Information Center

Sadaf, Ayesha; Newby, Timothy J.; Ertmer, Peggy A.

2016-01-01

The purpose of the study was to investigate factors that predict preservice teachers' intentions and actual uses of Web 2.0 tools in their classrooms. A two-phase, mixed method, sequential explanatory design was used. The first phase explored factors, based on the decomposed theory of planned behavior, that predict preservice teachers' intentions…

Progress on water data integration and distribution: a summary of select U.S. Geological Survey data systems

USGS Publications Warehouse

Blodgett, David L.; Lucido, Jessica M.; Kreft, James M.

2016-01-01

Critical water-resources issues ranging from flood response to water scarcity make access to integrated water information, services, tools, and models essential. Since 1995 when the first water data web pages went online, the U.S. Geological Survey has been at the forefront of water data distribution and integration. Today, real-time and historical streamflow observations are available via web pages and a variety of web service interfaces. The Survey has built partnerships with Federal and State agencies to integrate hydrologic data providing continuous observations of surface and groundwater, temporally discrete water quality data, groundwater well logs, aquatic biology data, water availability and use information, and tools to help characterize the landscape for modeling. In this paper, we summarize the status and design patterns implemented for selected data systems. We describe how these systems contribute to a U.S. Federal Open Water Data Initiative and present some gaps and lessons learned that apply to global hydroinformatics data infrastructure.

A Web-Based Monitoring System for Multidisciplinary Design Projects

NASA Technical Reports Server (NTRS)

Rogers, James L.; Salas, Andrea O.; Weston, Robert P.

1998-01-01

In today's competitive environment, both industry and government agencies are under pressure to reduce the time and cost of multidisciplinary design projects. New tools have been introduced to assist in this process by facilitating the integration of and communication among diverse disciplinary codes. One such tool, a framework for multidisciplinary computational environments, is defined as a hardware and software architecture that enables integration, execution, and communication among diverse disciplinary processes. An examination of current frameworks reveals weaknesses in various areas, such as sequencing, displaying, monitoring, and controlling the design process. The objective of this research is to explore how Web technology, integrated with an existing framework, can improve these areas of weakness. This paper describes a Web-based system that optimizes and controls the execution sequence of design processes; and monitors the project status and results. The three-stage evolution of the system with increasingly complex problems demonstrates the feasibility of this approach.

Report Central: Quality Reporting Tool in an Electronic Health Record

PubMed Central

Jung, Eunice; Li, Qi; Mangalampalli, Anil; Greim, Julie; Eskin, Michael S.; Housman, Dan; Isikoff, Jeremy; Abend, Aaron H.; Middleton, Blackford; Einbinder, Jonathan S.

2006-01-01

Quality reporting tools, integrated with ambulatory electronic health records, can help clinicians and administrators understand performance, manage populations, and improve quality. Report Central is a secure web report delivery tool built on Crystal Reports XI™ and ASP.NET technologies. Pilot evaluation of Report Central indicates that clinicians prefer a quality reporting tool that is integrated with our home-grown EHR to support clinical workflow. PMID:17238590

Web-based automation of green building rating index and life cycle cost analysis

NASA Astrophysics Data System (ADS)

Shahzaib Khan, Jam; Zakaria, Rozana; Aminuddin, Eeydzah; IzieAdiana Abidin, Nur; Sahamir, Shaza Rina; Ahmad, Rosli; Nafis Abas, Darul

2018-04-01

Sudden decline in financial markets and economic meltdown has slow down adaptation and lowered interest of investors towards green certified buildings due to their higher initial costs. Similarly, it is essential to fetch investor’s attention towards more development of green buildings through automated tools for the construction projects. Though, historical dearth is found on the automation of green building rating tools that brings up an essential gap to develop an automated analog computerized programming tool. This paper present a proposed research aim to develop an integrated web-based automated analog computerized programming that applies green building rating assessment tool, green technology and life cycle cost analysis. It also emphasizes to identify variables of MyCrest and LCC to be integrated and developed in a framework then transformed into automated analog computerized programming. A mix methodology of qualitative and quantitative survey and its development portray the planned to carry MyCrest-LCC integration to an automated level. In this study, the preliminary literature review enriches better understanding of Green Building Rating Tools (GBRT) integration to LCC. The outcome of this research is a pave way for future researchers to integrate other efficient tool and parameters that contributes towards green buildings and future agendas.

WARCProcessor: An Integrative Tool for Building and Management of Web Spam Corpora.

PubMed

Callón, Miguel; Fdez-Glez, Jorge; Ruano-Ordás, David; Laza, Rosalía; Pavón, Reyes; Fdez-Riverola, Florentino; Méndez, Jose Ramón

2017-12-22

In this work we present the design and implementation of WARCProcessor, a novel multiplatform integrative tool aimed to build scientific datasets to facilitate experimentation in web spam research. The developed application allows the user to specify multiple criteria that change the way in which new corpora are generated whilst reducing the number of repetitive and error prone tasks related with existing corpus maintenance. For this goal, WARCProcessor supports up to six commonly used data sources for web spam research, being able to store output corpus in standard WARC format together with complementary metadata files. Additionally, the application facilitates the automatic and concurrent download of web sites from Internet, giving the possibility of configuring the deep of the links to be followed as well as the behaviour when redirected URLs appear. WARCProcessor supports both an interactive GUI interface and a command line utility for being executed in background.

WARCProcessor: An Integrative Tool for Building and Management of Web Spam Corpora

PubMed Central

Callón, Miguel; Fdez-Glez, Jorge; Ruano-Ordás, David; Laza, Rosalía; Pavón, Reyes; Méndez, Jose Ramón

2017-01-01

In this work we present the design and implementation of WARCProcessor, a novel multiplatform integrative tool aimed to build scientific datasets to facilitate experimentation in web spam research. The developed application allows the user to specify multiple criteria that change the way in which new corpora are generated whilst reducing the number of repetitive and error prone tasks related with existing corpus maintenance. For this goal, WARCProcessor supports up to six commonly used data sources for web spam research, being able to store output corpus in standard WARC format together with complementary metadata files. Additionally, the application facilitates the automatic and concurrent download of web sites from Internet, giving the possibility of configuring the deep of the links to be followed as well as the behaviour when redirected URLs appear. WARCProcessor supports both an interactive GUI interface and a command line utility for being executed in background. PMID:29271913

Taking Open Innovation to the Molecular Level - Strengths and Limitations.

PubMed

Zdrazil, Barbara; Blomberg, Niklas; Ecker, Gerhard F

2012-08-01

The ever-growing availability of large-scale open data and its maturation is having a significant impact on industrial drug-discovery, as well as on academic and non-profit research. As industry is changing to an 'open innovation' business concept, precompetitive initiatives and strong public-private partnerships including academic research cooperation partners are gaining more and more importance. Now, the bioinformatics and cheminformatics communities are seeking for web tools which allow the integration of this large volume of life science datasets available in the public domain. Such a data exploitation tool would ideally be able to answer complex biological questions by formulating only one search query. In this short review/perspective, we outline the use of semantic web approaches for data and knowledge integration. Further, we discuss strengths and current limitations of public available data retrieval tools and integrated platforms.

Cytoscape: the network visualization tool for GenomeSpace workflows.

PubMed

Demchak, Barry; Hull, Tim; Reich, Michael; Liefeld, Ted; Smoot, Michael; Ideker, Trey; Mesirov, Jill P

2014-01-01

Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded over 850 times since the release of its first version in September, 2013.

Cytoscape: the network visualization tool for GenomeSpace workflows

PubMed Central

Demchak, Barry; Hull, Tim; Reich, Michael; Liefeld, Ted; Smoot, Michael; Ideker, Trey; Mesirov, Jill P.

2014-01-01

Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded over 850 times since the release of its first version in September, 2013. PMID:25165537

Language Learning on the World Wide Web: An Investigation of EFL Learners' Attitudes and Perceptions.

ERIC Educational Resources Information Center

Yang, Shu Ching

2001-01-01

Describes the integration of Web resources as instructional and learning tools in an EFL (English as a Foreign Language) class in Taiwan. Highlights include challenges and advantages of using the Web; learners' perceptions; intentional and incidental learning; disorientation and cognitive overload; and information seeking as problem-solving. A…

NMRPro: an integrated web component for interactive processing and visualization of NMR spectra.

PubMed

Mohamed, Ahmed; Nguyen, Canh Hao; Mamitsuka, Hiroshi

2016-07-01

The popularity of using NMR spectroscopy in metabolomics and natural products has driven the development of an array of NMR spectral analysis tools and databases. Particularly, web applications are well used recently because they are platform-independent and easy to extend through reusable web components. Currently available web applications provide the analysis of NMR spectra. However, they still lack the necessary processing and interactive visualization functionalities. To overcome these limitations, we present NMRPro, a web component that can be easily incorporated into current web applications, enabling easy-to-use online interactive processing and visualization. NMRPro integrates server-side processing with client-side interactive visualization through three parts: a python package to efficiently process large NMR datasets on the server-side, a Django App managing server-client interaction, and SpecdrawJS for client-side interactive visualization. Demo and installation instructions are available at http://mamitsukalab.org/tools/nmrpro/ mohamed@kuicr.kyoto-u.ac.jp 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.

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

NASA Technical Reports Server (NTRS)

Ashish, Naveen; Goforth, Andre

2005-01-01

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

Web-site evaluation tools: a case study in reproductive health information.

PubMed

Aslani, Azam; Pournik, Omid; Abu-Hanna, Ameen; Eslami, Saeid

2014-01-01

Internet forms an opportunity to inform, teach, and connect professionals and patients. However, much information on Internet is incomplete, inaccurate, or misleading, and not only in the medical domain. Because of the potential for damage from misleading and inaccurate health information, many organizations and individuals have published or implemented scoring tools for evaluating the appropriateness or quality of these resources. The objective of this study is to identify and summarize scoring tools that have evaluated web-sites providing reproductive health information in order to compare them and recommend an overarching evaluation tool. We searched Ovid MEDLINE(R) (1946 to July 2013) and OVID Embase (1980 to July 2013); and included English language studies that have evaluated the quality of websites providing reproductive health information. Studies only assessing the content of websites were excluded. We identified 5 scoring tools: 1-The HON (health on the net) Code of Conduct for medical and health Web sites, 2-Silberg scores, 3-Hogne Sandvik scale, 4-Jim Kapoun's Criteria for Evaluating Web Pages, and 5-The Health Information Technology Institute (HITI) criteria. We have compared these scales and identified 14 criteria: authorship, ownership, currency, objectivity/content, transparency/source, interactivity, privacy/ethics, financial disclosure, navigability/links, complementarity, advertising policy, design, quantity, and accessibility. We integrated these criteria and introduced a new tool with 10 criteria. Website evaluation tools differ in their evaluation criteria and there is a lack of consensus about which to use; therefore, an integrated easy to use set of criteria is needed.

REopt Lite Web Tool Evaluates Photovoltaics and Battery Storage

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

Building on the success of the REopt renewable energy integration and optimization platform, NREL has developed a free, publicly available web version of REopt called REopt Lite. REopt Lite evaluates the economics of grid-connected photovoltaics (PV) and battery storage at a site. It allows building owners to identify the system sizes and battery dispatch strategy that minimize their life cycle cost of energy. This web tool also estimates the amount of time a PV and storage system can sustain the site's critical load during a grid outage.

Integrated Functional and Executional Modelling of Software Using Web-Based Databases

NASA Technical Reports Server (NTRS)

Kulkarni, Deepak; Marietta, Roberta

1998-01-01

NASA's software subsystems undergo extensive modification and updates over the operational lifetimes. It is imperative that modified software should satisfy safety goals. This report discusses the difficulties encountered in doing so and discusses a solution based on integrated modelling of software, use of automatic information extraction tools, web technology and databases. To appear in an article of Journal of Database Management.

Googling DNA sequences on the World Wide Web.

PubMed

Hajibabaei, Mehrdad; Singer, Gregory A C

2009-11-10

New web-based technologies provide an excellent opportunity for sharing and accessing information and using web as a platform for interaction and collaboration. Although several specialized tools are available for analyzing DNA sequence information, conventional web-based tools have not been utilized for bioinformatics applications. We have developed a novel algorithm and implemented it for searching species-specific genomic sequences, DNA barcodes, by using popular web-based methods such as Google. We developed an alignment independent character based algorithm based on dividing a sequence library (DNA barcodes) and query sequence to words. The actual search is conducted by conventional search tools such as freely available Google Desktop Search. We implemented our algorithm in two exemplar packages. We developed pre and post-processing software to provide customized input and output services, respectively. Our analysis of all publicly available DNA barcode sequences shows a high accuracy as well as rapid results. Our method makes use of conventional web-based technologies for specialized genetic data. It provides a robust and efficient solution for sequence search on the web. The integration of our search method for large-scale sequence libraries such as DNA barcodes provides an excellent web-based tool for accessing this information and linking it to other available categories of information on the web.

MAPI: towards the integrated exploitation of bioinformatics Web Services.

PubMed

Ramirez, Sergio; Karlsson, Johan; Trelles, Oswaldo

2011-10-27

Bioinformatics is commonly featured as a well assorted list of available web resources. Although diversity of services is positive in general, the proliferation of tools, their dispersion and heterogeneity complicate the integrated exploitation of such data processing capacity. To facilitate the construction of software clients and make integrated use of this variety of tools, we present a modular programmatic application interface (MAPI) that provides the necessary functionality for uniform representation of Web Services metadata descriptors including their management and invocation protocols of the services which they represent. This document describes the main functionality of the framework and how it can be used to facilitate the deployment of new software under a unified structure of bioinformatics Web Services. A notable feature of MAPI is the modular organization of the functionality into different modules associated with specific tasks. This means that only the modules needed for the client have to be installed, and that the module functionality can be extended without the need for re-writing the software client. The potential utility and versatility of the software library has been demonstrated by the implementation of several currently available clients that cover different aspects of integrated data processing, ranging from service discovery to service invocation with advanced features such as workflows composition and asynchronous services calls to multiple types of Web Services including those registered in repositories (e.g. GRID-based, SOAP, BioMOBY, R-bioconductor, and others).

An Empirical Study of Instructor Adoption of Web-Based Learning Systems

ERIC Educational Resources Information Center

Wang, Wei-Tsong; Wang, Chun-Chieh

2009-01-01

For years, web-based learning systems have been widely employed in both educational and non-educational institutions. Although web-based learning systems are emerging as a useful tool for facilitating teaching and learning activities, the number of users is not increasing as fast as expected. This study develops an integrated model of instructor…

Evaluating Web 2.0 Technologies in Higher Education Using Students' Perceptions and Performance

ERIC Educational Resources Information Center

Karvounidis, T.; Chimos, K.; Bersimis, S.; Douligeris, C.

2014-01-01

In this work, Web 2.0 technologies in higher education are evaluated using students' perceptions, satisfaction, performance and behaviour. The study evaluates the Web 2.0 tools as stand-alone entities as well in terms of their cross-operability and integration (confluence) to synergistic contributions towards the enhancement of student…

BUSCA: an integrative web server to predict subcellular localization of proteins.

PubMed

Savojardo, Castrense; Martelli, Pier Luigi; Fariselli, Piero; Profiti, Giuseppe; Casadio, Rita

2018-04-30

Here, we present BUSCA (http://busca.biocomp.unibo.it), a novel web server that integrates different computational tools for predicting protein subcellular localization. BUSCA combines methods for identifying signal and transit peptides (DeepSig and TPpred3), GPI-anchors (PredGPI) and transmembrane domains (ENSEMBLE3.0 and BetAware) with tools for discriminating subcellular localization of both globular and membrane proteins (BaCelLo, MemLoci and SChloro). Outcomes from the different tools are processed and integrated for annotating subcellular localization of both eukaryotic and bacterial protein sequences. We benchmark BUSCA against protein targets derived from recent CAFA experiments and other specific data sets, reporting performance at the state-of-the-art. BUSCA scores better than all other evaluated methods on 2732 targets from CAFA2, with a F1 value equal to 0.49 and among the best methods when predicting targets from CAFA3. We propose BUSCA as an integrated and accurate resource for the annotation of protein subcellular localization.

Web-TCGA: an online platform for integrated analysis of molecular cancer data sets.

PubMed

Deng, Mario; Brägelmann, Johannes; Schultze, Joachim L; Perner, Sven

2016-02-06

The Cancer Genome Atlas (TCGA) is a pool of molecular data sets publicly accessible and freely available to cancer researchers anywhere around the world. However, wide spread use is limited since an advanced knowledge of statistics and statistical software is required. In order to improve accessibility we created Web-TCGA, a web based, freely accessible online tool, which can also be run in a private instance, for integrated analysis of molecular cancer data sets provided by TCGA. In contrast to already available tools, Web-TCGA utilizes different methods for analysis and visualization of TCGA data, allowing users to generate global molecular profiles across different cancer entities simultaneously. In addition to global molecular profiles, Web-TCGA offers highly detailed gene and tumor entity centric analysis by providing interactive tables and views. As a supplement to other already available tools, such as cBioPortal (Sci Signal 6:pl1, 2013, Cancer Discov 2:401-4, 2012), Web-TCGA is offering an analysis service, which does not require any installation or configuration, for molecular data sets available at the TCGA. Individual processing requests (queries) are generated by the user for mutation, methylation, expression and copy number variation (CNV) analyses. The user can focus analyses on results from single genes and cancer entities or perform a global analysis (multiple cancer entities and genes simultaneously).

ePlant and the 3D data display initiative: integrative systems biology on the world wide web.

PubMed

Fucile, Geoffrey; Di Biase, David; Nahal, Hardeep; La, Garon; Khodabandeh, Shokoufeh; Chen, Yani; Easley, Kante; Christendat, Dinesh; Kelley, Lawrence; Provart, Nicholas J

2011-01-10

Visualization tools for biological data are often limited in their ability to interactively integrate data at multiple scales. These computational tools are also typically limited by two-dimensional displays and programmatic implementations that require separate configurations for each of the user's computing devices and recompilation for functional expansion. Towards overcoming these limitations we have developed "ePlant" (http://bar.utoronto.ca/eplant) - a suite of open-source world wide web-based tools for the visualization of large-scale data sets from the model organism Arabidopsis thaliana. These tools display data spanning multiple biological scales on interactive three-dimensional models. Currently, ePlant consists of the following modules: a sequence conservation explorer that includes homology relationships and single nucleotide polymorphism data, a protein structure model explorer, a molecular interaction network explorer, a gene product subcellular localization explorer, and a gene expression pattern explorer. The ePlant's protein structure explorer module represents experimentally determined and theoretical structures covering >70% of the Arabidopsis proteome. The ePlant framework is accessed entirely through a web browser, and is therefore platform-independent. It can be applied to any model organism. To facilitate the development of three-dimensional displays of biological data on the world wide web we have established the "3D Data Display Initiative" (http://3ddi.org).

The BioExtract Server: a web-based bioinformatic workflow platform

PubMed Central

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

2011-01-01

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

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.

A semantic problem solving environment for integrative parasite research: identification of intervention targets for Trypanosoma cruzi.

PubMed

Parikh, Priti P; Minning, Todd A; Nguyen, Vinh; Lalithsena, Sarasi; Asiaee, Amir H; Sahoo, Satya S; Doshi, Prashant; Tarleton, Rick; Sheth, Amit P

2012-01-01

Research on the biology of parasites requires a sophisticated and integrated computational platform to query and analyze large volumes of data, representing both unpublished (internal) and public (external) data sources. Effective analysis of an integrated data resource using knowledge discovery tools would significantly aid biologists in conducting their research, for example, through identifying various intervention targets in parasites and in deciding the future direction of ongoing as well as planned projects. A key challenge in achieving this objective is the heterogeneity between the internal lab data, usually stored as flat files, Excel spreadsheets or custom-built databases, and the external databases. Reconciling the different forms of heterogeneity and effectively integrating data from disparate sources is a nontrivial task for biologists and requires a dedicated informatics infrastructure. Thus, we developed an integrated environment using Semantic Web technologies that may provide biologists the tools for managing and analyzing their data, without the need for acquiring in-depth computer science knowledge. We developed a semantic problem-solving environment (SPSE) that uses ontologies to integrate internal lab data with external resources in a Parasite Knowledge Base (PKB), which has the ability to query across these resources in a unified manner. The SPSE includes Web Ontology Language (OWL)-based ontologies, experimental data with its provenance information represented using the Resource Description Format (RDF), and a visual querying tool, Cuebee, that features integrated use of Web services. We demonstrate the use and benefit of SPSE using example queries for identifying gene knockout targets of Trypanosoma cruzi for vaccine development. Answers to these queries involve looking up multiple sources of data, linking them together and presenting the results. The SPSE facilitates parasitologists in leveraging the growing, but disparate, parasite data resources by offering an integrative platform that utilizes Semantic Web techniques, while keeping their workload increase minimal.

Teaching Tectonics to Undergraduates with Web GIS

NASA Astrophysics Data System (ADS)

Anastasio, D. J.; Bodzin, A.; Sahagian, D. L.; Rutzmoser, S.

2013-12-01

Geospatial reasoning skills provide a means for manipulating, interpreting, and explaining structured information and are involved in higher-order cognitive processes that include problem solving and decision-making. Appropriately designed tools, technologies, and curriculum can support spatial learning. We present Web-based visualization and analysis tools developed with Javascript APIs to enhance tectonic curricula while promoting geospatial thinking and scientific inquiry. The Web GIS interface integrates graphics, multimedia, and animations that allow users to explore and discover geospatial patterns that are not easily recognized. Features include a swipe tool that enables users to see underneath layers, query tools useful in exploration of earthquake and volcano data sets, a subduction and elevation profile tool which facilitates visualization between map and cross-sectional views, drafting tools, a location function, and interactive image dragging functionality on the Web GIS. The Web GIS platform is independent and can be implemented on tablets or computers. The GIS tool set enables learners to view, manipulate, and analyze rich data sets from local to global scales, including such data as geology, population, heat flow, land cover, seismic hazards, fault zones, continental boundaries, and elevation using two- and three- dimensional visualization and analytical software. Coverages which allow users to explore plate boundaries and global heat flow processes aided learning in a Lehigh University Earth and environmental science Structural Geology and Tectonics class and are freely available on the Web.

Mining and integration of pathway diagrams from imaging data.

PubMed

Kozhenkov, Sergey; Baitaluk, Michael

2012-03-01

Pathway diagrams from PubMed and World Wide Web (WWW) contain valuable highly curated information difficult to reach without tools specifically designed and customized for the biological semantics and high-content density of the images. There is currently no search engine or tool that can analyze pathway images, extract their pathway components (molecules, genes, proteins, organelles, cells, organs, etc.) and indicate their relationships. Here, we describe a resource of pathway diagrams retrieved from article and web-page images through optical character recognition, in conjunction with data mining and data integration methods. The recognized pathways are integrated into the BiologicalNetworks research environment linking them to a wealth of data available in the BiologicalNetworks' knowledgebase, which integrates data from >100 public data sources and the biomedical literature. Multiple search and analytical tools are available that allow the recognized cellular pathways, molecular networks and cell/tissue/organ diagrams to be studied in the context of integrated knowledge, experimental data and the literature. BiologicalNetworks software and the pathway repository are freely available at www.biologicalnetworks.org. Supplementary data are available at Bioinformatics online.

Web tools for predictive toxicology model building.

PubMed

Jeliazkova, Nina

2012-07-01

The development and use of web tools in chemistry has accumulated more than 15 years of history already. Powered by the advances in the Internet technologies, the current generation of web systems are starting to expand into areas, traditional for desktop applications. The web platforms integrate data storage, cheminformatics and data analysis tools. The ease of use and the collaborative potential of the web is compelling, despite the challenges. The topic of this review is a set of recently published web tools that facilitate predictive toxicology model building. The focus is on software platforms, offering web access to chemical structure-based methods, although some of the frameworks could also provide bioinformatics or hybrid data analysis functionalities. A number of historical and current developments are cited. In order to provide comparable assessment, the following characteristics are considered: support for workflows, descriptor calculations, visualization, modeling algorithms, data management and data sharing capabilities, availability of GUI or programmatic access and implementation details. The success of the Web is largely due to its highly decentralized, yet sufficiently interoperable model for information access. The expected future convergence between cheminformatics and bioinformatics databases provides new challenges toward management and analysis of large data sets. The web tools in predictive toxicology will likely continue to evolve toward the right mix of flexibility, performance, scalability, interoperability, sets of unique features offered, friendly user interfaces, programmatic access for advanced users, platform independence, results reproducibility, curation and crowdsourcing utilities, collaborative sharing and secure access.

Toward a More Flexible Web-Based Framework for Multidisciplinary Design

NASA Technical Reports Server (NTRS)

Rogers, J. L.; Salas, A. O.

1999-01-01

In today's competitive environment, both industry and government agencies are under pressure to reduce the time and cost of multidisciplinary design projects. New tools have been introduced to assist in this process by facilitating the integration of and communication among diverse disciplinary codes. One such tool, a framework for multidisciplinary design, is defined as a hardware-software architecture that enables integration, execution, and communication among diverse disciplinary processes. An examination of current frameworks reveals weaknesses in various areas, such as sequencing, monitoring, controlling, and displaying the design process. The objective of this research is to explore how Web technology can improve these areas of weakness and lead toward a more flexible framework. This article describes a Web-based system that optimizes and controls the execution sequence of design processes in addition to monitoring the project status and displaying the design results.

Integrated Modeling Environment

NASA Technical Reports Server (NTRS)

Mosier, Gary; Stone, Paul; Holtery, Christopher

2006-01-01

The Integrated Modeling Environment (IME) is a software system that establishes a centralized Web-based interface for integrating people (who may be geographically dispersed), processes, and data involved in a common engineering project. The IME includes software tools for life-cycle management, configuration management, visualization, and collaboration.

Capitalizing on Web 2.0 in the Social Studies Context

ERIC Educational Resources Information Center

Holcomb, Lori B.; Beal, Candy M.

2010-01-01

This paper focuses primarily on the integration of Web 2.0 technologies into social studies education. It documents how various Web 2.0 tools can be utilized in the social studies context to support and enhance teaching and learning. For the purposes of focusing on one specific topic, global connections at the middle school level will be the…

Making Web3D Less Scary: Toward Easy-to-Use Web3D e-Learning Content Development Tools for Educators

ERIC Educational Resources Information Center

de Byl, Penny

2009-01-01

Penny de Byl argues that one of the biggest challenges facing educators today is the integration of rich and immersive three-dimensional environments with existing teaching and learning materials. To empower educators with the ability to embrace emerging Web3D technologies, the Advanced Learning and Immersive Virtual Environment (ALIVE) research…

Open source software integrated into data services of Japanese planetary explorations

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Toward Technology Integration in Mathematics Education: A Technology-Integration Course Planning Assignment

ERIC Educational Resources Information Center

Kersaint, Gladis

2007-01-01

This article describes a technology integration course planning assignment that was developed to enhance preservice teachers' technological pedagogical content knowledge (TPCK). This assignment required preservice teachers work with peers to integrate various technological tools (e.g., graphing calculators, web-based mathematics applets, etc) in a…

WebProtégé: A Collaborative Ontology Editor and Knowledge Acquisition Tool for the Web

PubMed Central

Tudorache, Tania; Nyulas, Csongor; Noy, Natalya F.; Musen, Mark A.

2012-01-01

In this paper, we present WebProtégé—a lightweight ontology editor and knowledge acquisition tool for the Web. With the wide adoption of Web 2.0 platforms and the gradual adoption of ontologies and Semantic Web technologies in the real world, we need ontology-development tools that are better suited for the novel ways of interacting, constructing and consuming knowledge. Users today take Web-based content creation and online collaboration for granted. WebProtégé integrates these features as part of the ontology development process itself. We tried to lower the entry barrier to ontology development by providing a tool that is accessible from any Web browser, has extensive support for collaboration, and a highly customizable and pluggable user interface that can be adapted to any level of user expertise. The declarative user interface enabled us to create custom knowledge-acquisition forms tailored for domain experts. We built WebProtégé using the existing Protégé infrastructure, which supports collaboration on the back end side, and the Google Web Toolkit for the front end. The generic and extensible infrastructure allowed us to easily deploy WebProtégé in production settings for several projects. We present the main features of WebProtégé and its architecture and describe briefly some of its uses for real-world projects. WebProtégé is free and open source. An online demo is available at http://webprotege.stanford.edu. PMID:23807872

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.

Public health, GIS, and the internet.

PubMed

Croner, Charles M

2003-01-01

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

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.

The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis

PubMed Central

Rampp, Markus; Soddemann, Thomas; Lederer, Hermann

2006-01-01

We describe a versatile and extensible integrated bioinformatics toolkit for the analysis of biological sequences over the Internet. The web portal offers convenient interactive access to a growing pool of chainable bioinformatics software tools and databases that are centrally installed and maintained by the RZG. Currently, supported tasks comprise sequence similarity searches in public or user-supplied databases, computation and validation of multiple sequence alignments, phylogenetic analysis and protein–structure prediction. Individual tools can be seamlessly chained into pipelines allowing the user to conveniently process complex workflows without the necessity to take care of any format conversions or tedious parsing of intermediate results. The toolkit is part of the Max-Planck Integrated Gene Analysis System (MIGenAS) of the Max Planck Society available at (click ‘Start Toolkit’). PMID:16844980

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.

Reusable science tools for analog exploration missions: xGDS Web Tools, VERVE, and Gigapan Voyage

NASA Astrophysics Data System (ADS)

Lee, Susan Y.; Lees, David; Cohen, Tamar; Allan, Mark; Deans, Matthew; Morse, Theodore; Park, Eric; Smith, Trey

2013-10-01

The Exploration Ground Data Systems (xGDS) project led by the Intelligent Robotics Group (IRG) at NASA Ames Research Center creates software tools to support multiple NASA-led planetary analog field experiments. The two primary tools that fall under the xGDS umbrella are the xGDS Web Tools (xGDS-WT) and Visual Environment for Remote Virtual Exploration (VERVE). IRG has also developed a hardware and software system that is closely integrated with our xGDS tools and is used in multiple field experiments called Gigapan Voyage. xGDS-WT, VERVE, and Gigapan Voyage are examples of IRG projects that improve the ratio of science return versus development effort by creating generic and reusable tools that leverage existing technologies in both hardware and software. xGDS Web Tools provides software for gathering and organizing mission data for science and engineering operations, including tools for planning traverses, monitoring autonomous or piloted vehicles, visualization, documentation, analysis, and search. VERVE provides high performance three dimensional (3D) user interfaces used by scientists, robot operators, and mission planners to visualize robot data in real time. Gigapan Voyage is a gigapixel image capturing and processing tool that improves situational awareness and scientific exploration in human and robotic analog missions. All of these technologies emphasize software reuse and leverage open source and/or commercial-off-the-shelf tools to greatly improve the utility and reduce the development and operational cost of future similar technologies. Over the past several years these technologies have been used in many NASA-led robotic field campaigns including the Desert Research and Technology Studies (DRATS), the Pavilion Lake Research Project (PLRP), the K10 Robotic Follow-Up tests, and most recently we have become involved in the NASA Extreme Environment Mission Operations (NEEMO) field experiments. A major objective of these joint robot and crew experiments is to improve NASAs understanding of how to most effectively execute and increase science return from exploration missions. This paper focuses on an integrated suite of xGDS software and compatible hardware tools: xGDS Web Tools, VERVE, and Gigapan Voyage, how they are used, and the design decisions that were made to allow them to be easily developed, integrated, tested, and reused by multiple NASA field experiments and robotic platforms.

WebPrInSeS: automated full-length clone sequence identification and verification using high-throughput sequencing data.

PubMed

Massouras, Andreas; Decouttere, Frederik; Hens, Korneel; Deplancke, Bart

2010-07-01

High-throughput sequencing (HTS) is revolutionizing our ability to obtain cheap, fast and reliable sequence information. Many experimental approaches are expected to benefit from the incorporation of such sequencing features in their pipeline. Consequently, software tools that facilitate such an incorporation should be of great interest. In this context, we developed WebPrInSeS, a web server tool allowing automated full-length clone sequence identification and verification using HTS data. WebPrInSeS encompasses two separate software applications. The first is WebPrInSeS-C which performs automated sequence verification of user-defined open-reading frame (ORF) clone libraries. The second is WebPrInSeS-E, which identifies positive hits in cDNA or ORF-based library screening experiments such as yeast one- or two-hybrid assays. Both tools perform de novo assembly using HTS data from any of the three major sequencing platforms. Thus, WebPrInSeS provides a highly integrated, cost-effective and efficient way to sequence-verify or identify clones of interest. WebPrInSeS is available at http://webprinses.epfl.ch/ and is open to all users.

WebPrInSeS: automated full-length clone sequence identification and verification using high-throughput sequencing data

PubMed Central

Massouras, Andreas; Decouttere, Frederik; Hens, Korneel; Deplancke, Bart

2010-01-01

High-throughput sequencing (HTS) is revolutionizing our ability to obtain cheap, fast and reliable sequence information. Many experimental approaches are expected to benefit from the incorporation of such sequencing features in their pipeline. Consequently, software tools that facilitate such an incorporation should be of great interest. In this context, we developed WebPrInSeS, a web server tool allowing automated full-length clone sequence identification and verification using HTS data. WebPrInSeS encompasses two separate software applications. The first is WebPrInSeS-C which performs automated sequence verification of user-defined open-reading frame (ORF) clone libraries. The second is WebPrInSeS-E, which identifies positive hits in cDNA or ORF-based library screening experiments such as yeast one- or two-hybrid assays. Both tools perform de novo assembly using HTS data from any of the three major sequencing platforms. Thus, WebPrInSeS provides a highly integrated, cost-effective and efficient way to sequence-verify or identify clones of interest. WebPrInSeS is available at http://webprinses.epfl.ch/ and is open to all users. PMID:20501601

Using the World Wide Web and Creating Home Pages. A How-To-Do-It Manual. How-To-Do-It Manuals for Librarieans, Number 67.

ERIC Educational Resources Information Center

Metz, Ray E.; Junion-Metz, Gail

This book provides basic information about the World Wide Web and serves as a guide to the tools and techniques needed to browse the Web, integrate it into library services, or build an attractive, user-friendly home page for the library. Chapter 1 provides an overview of Web basics and chapter 2 discusses some of the big issues related to…

Overcoming Learning Time and Space Constraints through Technological Tool

ERIC Educational Resources Information Center

Zarei, Nafiseh; Hussin, Supyan; Rashid, Taufik

2015-01-01

Today the use of technological tools has become an evolution in language learning and language acquisition. Many instructors and lecturers believe that integrating Web-based learning tools into language courses allows pupils to become active learners during learning process. This study investigates how the Learning Management Blog (LMB) overcomes…

Teaching Bioinformatics and Neuroinformatics by Using Free Web-Based Tools

ERIC Educational Resources Information Center

Grisham, William; Schottler, Natalie A.; Valli-Marill, Joanne; Beck, Lisa; Beatty, Jackson

2010-01-01

This completely computer-based module's purpose is to introduce students to bioinformatics resources. We present an easy-to-adopt module that weaves together several important bioinformatic tools so students can grasp how these tools are used in answering research questions. Students integrate information gathered from websites dealing with…

Web 2.0 and internet social networking: a new tool for disaster management?--lessons from Taiwan.

PubMed

Huang, Cheng-Min; Chan, Edward; Hyder, Adnan A

2010-10-06

Internet social networking tools and the emerging web 2.0 technologies are providing a new way for web users and health workers in information sharing and knowledge dissemination. Based on the characters of immediate, two-way and large scale of impact, the internet social networking tools have been utilized as a solution in emergency response during disasters. This paper highlights the use of internet social networking in disaster emergency response and public health management of disasters by focusing on a case study of the typhoon Morakot disaster in Taiwan. In the case of typhoon disaster in Taiwan, internet social networking and mobile technology were found to be helpful for community residents, professional emergency rescuers, and government agencies in gathering and disseminating real-time information, regarding volunteer recruitment and relief supplies allocation. We noted that if internet tools are to be integrated in the development of emergency response system, the accessibility, accuracy, validity, feasibility, privacy and the scalability of itself should be carefully considered especially in the effort of applying it in resource poor settings. This paper seeks to promote an internet-based emergency response system by integrating internet social networking and information communication technology into central government disaster management system. Web-based networking provides two-way communication which establishes a reliable and accessible tunnel for proximal and distal users in disaster preparedness and management.

A web-based rapid assessment tool for production publishing solutions

NASA Astrophysics Data System (ADS)

Sun, Tong

2010-02-01

Solution assessment is a critical first-step in understanding and measuring the business process efficiency enabled by an integrated solution package. However, assessing the effectiveness of any solution is usually a very expensive and timeconsuming task which involves lots of domain knowledge, collecting and understanding the specific customer operational context, defining validation scenarios and estimating the expected performance and operational cost. This paper presents an intelligent web-based tool that can rapidly assess any given solution package for production publishing workflows via a simulation engine and create a report for various estimated performance metrics (e.g. throughput, turnaround time, resource utilization) and operational cost. By integrating the digital publishing workflow ontology and an activity based costing model with a Petri-net based workflow simulation engine, this web-based tool allows users to quickly evaluate any potential digital publishing solutions side-by-side within their desired operational contexts, and provides a low-cost and rapid assessment for organizations before committing any purchase. This tool also benefits the solution providers to shorten the sales cycles, establishing a trustworthy customer relationship and supplement the professional assessment services with a proven quantitative simulation and estimation technology.

Mendeley: Creating Communities of Scholarly Inquiry through Research Collaboration

ERIC Educational Resources Information Center

Zaugg, Holt; West, Richard E.; Tateishi, Isaku; Randall, Daniel L.

2010-01-01

Mendeley is a free, web-based tool for organizing research citations and annotating their accompanying PDF articles. Adapting Web 2.0 principles for academic scholarship, Mendeley integrates the management of the research articles with features for collaborating with researchers locally and worldwide. In this article the features of Mendeley are…

Lifelong Learning: Web-Based Information Literacy Module for Merchandisers

ERIC Educational Resources Information Center

Hines, Jean D.; Frey, Diane K.; Swinker, Mary E.

2005-01-01

Universities are strategically positioned to serve as a vital impetus in developing pre-professionals' lifelong learning skills. The development of a Web portal, InfoWIZARD, a tool for integrating information literacy and information technology in problem-based research assignments is described in this article. InfoWIZARD includes 20 modules in…

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Web-Based Learning Information System for Web 3.0

NASA Astrophysics Data System (ADS)

Rego, Hugo; Moreira, Tiago; García-Peñalvo, Francisco Jose

With the emergence of Web/eLearning 3.0 we have been developing/adjusting AHKME in order to face this great challenge. One of our goals is to allow the instructional designer and teacher to access standardized resources and evaluate the possibility of integration and reuse in eLearning systems, not only content but also the learning strategy. We have also integrated some collaborative tools for the adaptation of resources, as well as the collection of feedback from users to provide feedback to the system. We also provide tools for the instructional designer to create/customize specifications/ontologies to give structure and meaning to resources, manual and automatic search with recommendation of resources and instructional design based on the context, as well as recommendation of adaptations in learning resources. We also consider the concept of mobility and mobile technology applied to eLearning, allowing access by teachers and students to learning resources, regardless of time and space.

Large scale healthcare data integration and analysis using the semantic web.

PubMed

Timm, John; Renly, Sondra; Farkash, Ariel

2011-01-01

Healthcare data interoperability can only be achieved when the semantics of the content is well defined and consistently implemented across heterogeneous data sources. Achieving these objectives of interoperability requires the collaboration of experts from several domains. This paper describes tooling that integrates Semantic Web technologies with common tools to facilitate cross-domain collaborative development for the purposes of data interoperability. Our approach is divided into stages of data harmonization and representation, model transformation, and instance generation. We applied our approach on Hypergenes, an EU funded project, where we use our method to the Essential Hypertension disease model using a CDA template. Our domain expert partners include clinical providers, clinical domain researchers, healthcare information technology experts, and a variety of clinical data consumers. We show that bringing Semantic Web technologies into the healthcare interoperability toolkit increases opportunities for beneficial collaboration thus improving patient care and clinical research outcomes.

The value of the Semantic Web in the laboratory.

PubMed

Frey, Jeremy G

2009-06-01

The Semantic Web is beginning to impact on the wider chemical and physical sciences, beyond the earlier adopted bio-informatics. While useful in large-scale data driven science with automated processing, these technologies can also help integrate the work of smaller scale laboratories producing diverse data. The semantics aid the discovery, reliable re-use of data, provide improved provenance and facilitate automated processing by increased resilience to changes in presentation and reduced ambiguity. The Semantic Web, its tools and collections are not yet competitive with well-established solutions to current problems. It is in the reduced cost of instituting solutions to new problems that the versatility of Semantic Web-enabled data and resources will make their mark once the more general-purpose tools are more available.

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

Using Web Ontology Language to Integrate Heterogeneous Databases in the Neurosciences

PubMed Central

Lam, Hugo Y.K.; Marenco, Luis; Shepherd, Gordon M.; Miller, Perry L.; Cheung, Kei-Hoi

2006-01-01

Integrative neuroscience involves the integration and analysis of diverse types of neuroscience data involving many different experimental techniques. This data will increasingly be distributed across many heterogeneous databases that are web-accessible. Currently, these databases do not expose their schemas (database structures) and their contents to web applications/agents in a standardized, machine-friendly way. This limits database interoperation. To address this problem, we describe a pilot project that illustrates how neuroscience databases can be expressed using the Web Ontology Language, which is a semantically-rich ontological language, as a common data representation language to facilitate complex cross-database queries. In this pilot project, an existing tool called “D2RQ” was used to translate two neuroscience databases (NeuronDB and CoCoDat) into OWL, and the resulting OWL ontologies were then merged. An OWL-based reasoner (Racer) was then used to provide a sophisticated query language (nRQL) to perform integrated queries across the two databases based on the merged ontology. This pilot project is one step toward exploring the use of semantic web technologies in the neurosciences. PMID:17238384

RSAT: regulatory sequence analysis tools.

PubMed

Thomas-Chollier, Morgane; Sand, Olivier; Turatsinze, Jean-Valéry; Janky, Rekin's; Defrance, Matthieu; Vervisch, Eric; Brohée, Sylvain; van Helden, Jacques

2008-07-01

The regulatory sequence analysis tools (RSAT, http://rsat.ulb.ac.be/rsat/) is a software suite that integrates a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. The suite includes programs for sequence retrieval, pattern discovery, phylogenetic footprint detection, pattern matching, genome scanning and feature map drawing. Random controls can be performed with random gene selections or by generating random sequences according to a variety of background models (Bernoulli, Markov). Beyond the original word-based pattern-discovery tools (oligo-analysis and dyad-analysis), we recently added a battery of tools for matrix-based detection of cis-acting elements, with some original features (adaptive background models, Markov-chain estimation of P-values) that do not exist in other matrix-based scanning tools. The web server offers an intuitive interface, where each program can be accessed either separately or connected to the other tools. In addition, the tools are now available as web services, enabling their integration in programmatic workflows. Genomes are regularly updated from various genome repositories (NCBI and EnsEMBL) and 682 organisms are currently supported. Since 1998, the tools have been used by several hundreds of researchers from all over the world. Several predictions made with RSAT were validated experimentally and published.

GDA, a web-based tool for Genomics and Drugs integrated analysis.

PubMed

Caroli, Jimmy; Sorrentino, Giovanni; Forcato, Mattia; Del Sal, Giannino; Bicciato, Silvio

2018-05-25

Several major screenings of genetic profiling and drug testing in cancer cell lines proved that the integration of genomic portraits and compound activities is effective in discovering new genetic markers of drug sensitivity and clinically relevant anticancer compounds. Despite most genetic and drug response data are publicly available, the availability of user-friendly tools for their integrative analysis remains limited, thus hampering an effective exploitation of this information. Here, we present GDA, a web-based tool for Genomics and Drugs integrated Analysis that combines drug response data for >50 800 compounds with mutations and gene expression profiles across 73 cancer cell lines. Genomic and pharmacological data are integrated through a modular architecture that allows users to identify compounds active towards cancer cell lines bearing a specific genomic background and, conversely, the mutational or transcriptional status of cells responding or not-responding to a specific compound. Results are presented through intuitive graphical representations and supplemented with information obtained from public repositories. As both personalized targeted therapies and drug-repurposing are gaining increasing attention, GDA represents a resource to formulate hypotheses on the interplay between genomic traits and drug response in cancer. GDA is freely available at http://gda.unimore.it/.

HCLS 2.0/3.0: health care and life sciences data mashup using Web 2.0/3.0.

PubMed

Cheung, Kei-Hoi; Yip, Kevin Y; Townsend, Jeffrey P; Scotch, Matthew

2008-10-01

We describe the potential of current Web 2.0 technologies to achieve data mashup in the health care and life sciences (HCLS) domains, and compare that potential to the nascent trend of performing semantic mashup. After providing an overview of Web 2.0, we demonstrate two scenarios of data mashup, facilitated by the following Web 2.0 tools and sites: Yahoo! Pipes, Dapper, Google Maps and GeoCommons. In the first scenario, we exploited Dapper and Yahoo! Pipes to implement a challenging data integration task in the context of DNA microarray research. In the second scenario, we exploited Yahoo! Pipes, Google Maps, and GeoCommons to create a geographic information system (GIS) interface that allows visualization and integration of diverse categories of public health data, including cancer incidence and pollution prevalence data. Based on these two scenarios, we discuss the strengths and weaknesses of these Web 2.0 mashup technologies. We then describe Semantic Web, the mainstream Web 3.0 technology that enables more powerful data integration over the Web. We discuss the areas of intersection of Web 2.0 and Semantic Web, and describe the potential benefits that can be brought to HCLS research by combining these two sets of technologies.

HCLS 2.0/3.0: Health Care and Life Sciences Data Mashup Using Web 2.0/3.0

PubMed Central

Cheung, Kei-Hoi; Yip, Kevin Y.; Townsend, Jeffrey P.; Scotch, Matthew

2010-01-01

We describe the potential of current Web 2.0 technologies to achieve data mashup in the health care and life sciences (HCLS) domains, and compare that potential to the nascent trend of performing semantic mashup. After providing an overview of Web 2.0, we demonstrate two scenarios of data mashup, facilitated by the following Web 2.0 tools and sites: Yahoo! Pipes, Dapper, Google Maps and GeoCommons. In the first scenario, we exploited Dapper and Yahoo! Pipes to implement a challenging data integration task in the context of DNA microarray research. In the second scenario, we exploited Yahoo! Pipes, Google Maps, and GeoCommons to create a geographic information system (GIS) interface that allows visualization and integration of diverse categories of public health data, including cancer incidence and pollution prevalence data. Based on these two scenarios, we discuss the strengths and weaknesses of these Web 2.0 mashup technologies. We then describe Semantic Web, the mainstream Web 3.0 technology that enables more powerful data integration over the Web. We discuss the areas of intersection of Web 2.0 and Semantic Web, and describe the potential benefits that can be brought to HCLS research by combining these two sets of technologies. PMID:18487092

A UIMA wrapper for the NCBO annotator.

PubMed

Roeder, Christophe; Jonquet, Clement; Shah, Nigam H; Baumgartner, William A; Verspoor, Karin; Hunter, Lawrence

2010-07-15

The Unstructured Information Management Architecture (UIMA) framework and web services are emerging as useful tools for integrating biomedical text mining tools. This note describes our work, which wraps the National Center for Biomedical Ontology (NCBO) Annotator-an ontology-based annotation service-to make it available as a component in UIMA workflows. This wrapper is freely available on the web at http://bionlp-uima.sourceforge.net/ as part of the UIMA tools distribution from the Center for Computational Pharmacology (CCP) at the University of Colorado School of Medicine. It has been implemented in Java for support on Mac OS X, Linux and MS Windows.

POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations

PubMed Central

Porollo, Aleksey; Meller, Jaroslaw

2010-01-01

Molecular simulations offer important mechanistic and functional clues in studies of proteins and other macromolecules. However, interpreting the results of such simulations increasingly requires tools that can combine information from multiple structural databases and other web resources, and provide highly integrated and versatile analysis tools. Here, we present a new web server that integrates high-quality animation of molecular motion (MM) with structural and functional analysis of macromolecules. The new tool, dubbed POLYVIEW-MM, enables animation of trajectories generated by molecular dynamics and related simulation techniques, as well as visualization of alternative conformers, e.g. obtained as a result of protein structure prediction methods or small molecule docking. To facilitate structural analysis, POLYVIEW-MM combines interactive view and analysis of conformational changes using Jmol and its tailored extensions, publication quality animation using PyMol, and customizable 2D summary plots that provide an overview of MM, e.g. in terms of changes in secondary structure states and relative solvent accessibility of individual residues in proteins. Furthermore, POLYVIEW-MM integrates visualization with various structural annotations, including automated mapping of known inter-action sites from structural homologs, mapping of cavities and ligand binding sites, transmembrane regions and protein domains. URL: http://polyview.cchmc.org/conform.html. PMID:20504857

GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data

PubMed Central

Jung, Sook; Staton, Margaret; Lee, Taein; Blenda, Anna; Svancara, Randall; Abbott, Albert; Main, Dorrie

2008-01-01

The Genome Database for Rosaceae (GDR) is a central repository of curated and integrated genetics and genomics data of Rosaceae, an economically important family which includes apple, cherry, peach, pear, raspberry, rose and strawberry. GDR contains annotated databases of all publicly available Rosaceae ESTs, the genetically anchored peach physical map, Rosaceae genetic maps and comprehensively annotated markers and traits. The ESTs are assembled to produce unigene sets of each genus and the entire Rosaceae. Other annotations include putative function, microsatellites, open reading frames, single nucleotide polymorphisms, gene ontology terms and anchored map position where applicable. Most of the published Rosaceae genetic maps can be viewed and compared through CMap, the comparative map viewer. The peach physical map can be viewed using WebFPC/WebChrom, and also through our integrated GDR map viewer, which serves as a portal to the combined genetic, transcriptome and physical mapping information. ESTs, BACs, markers and traits can be queried by various categories and the search result sites are linked to the mapping visualization tools. GDR also provides online analysis tools such as a batch BLAST/FASTA server for the GDR datasets, a sequence assembly server and microsatellite and primer detection tools. GDR is available at http://www.rosaceae.org. PMID:17932055

Managing and monitoring tuberculosis using web-based tools in combination with traditional approaches

PubMed Central

Chapman, Ann LN; Darton, Thomas C; Foster, Rachel A

2013-01-01

Tuberculosis (TB) remains a global health emergency. Ongoing challenges include the coordination of national and international control programs, high levels of drug resistance in many parts of the world, and availability of accurate and rapid diagnostic tests. The increasing availability and reliability of Internet access throughout both affluent and resource-limited countries brings new opportunities to improve TB management and control through the integration of web-based technologies with traditional approaches. In this review, we explore current and potential future use of web-based tools in the areas of TB diagnosis, treatment, epidemiology, service monitoring, and teaching and training. PMID:24294008

MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.

PubMed

Hospital, Adam; Andrio, Pau; Fenollosa, Carles; Cicin-Sain, Damjan; Orozco, Modesto; Gelpí, Josep Lluís

2012-05-01

MDWeb and MDMoby constitute a web-based platform to help access to molecular dynamics (MD) in the standard and high-throughput regime. The platform provides tools to prepare systems from PDB structures mimicking the procedures followed by human experts. It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs). Tools for analysis of trajectories, either provided by the user or retrieved from our MoDEL database (http://mmb.pcb.ub.es/MoDEL) are also incorporated. The platform has two ways of access, a set of web-services based on the BioMoby framework (MDMoby), programmatically accessible and a web portal (MDWeb). http://mmb.irbbarcelona.org/MDWeb; additional information and methodology details can be found at the web site ( http://mmb.irbbarcelona.org/MDWeb/help.php)

Understanding Kidney Disease: Toward the Integration of Regulatory Networks Across Species

PubMed Central

Ju, Wenjun; Brosius, Frank C.

2010-01-01

Animal models have long been useful in investigating both normal and abnormal human physiology. Systems biology provides a relatively new set of approaches to identify similarities and differences between animal models and humans that may lead to a more comprehensive understanding of human kidney pathophysiology. In this review, we briefly describe how genome-wide analyses of mouse models have helped elucidate features of human kidney diseases, discuss strategies to achieve effective network integration, and summarize currently available web-based tools that may facilitate integration of data across species. The rapid progress in systems biology and orthology, as well as the advent of web-based tools to facilitate these processes, now make it possible to take advantage of knowledge from distant animal species in targeted identification of regulatory networks that may have clinical relevance for human kidney diseases. PMID:21044762

The Quest for Deeper Learning: An Investigation into the Impact of a Knowledge-Pooling WebQuest in Primary Initial Teacher Training

ERIC Educational Resources Information Center

Allan, Jo; Street, Mark

2007-01-01

This paper explores the impact on learning in higher education of the integration of a knowledge-pooling stage into a WebQuest. We explain the concept of WebQuests, consider recent literature regarding the effects and difficulties of this approach to learning, and examine students' perceptions of the impact of this tool on high-order learning. The…

GMODWeb: a web framework for the generic model organism database

PubMed Central

O'Connor, Brian D; Day, Allen; Cain, Scott; Arnaiz, Olivier; Sperling, Linda; Stein, Lincoln D

2008-01-01

The Generic Model Organism Database (GMOD) initiative provides species-agnostic data models and software tools for representing curated model organism data. Here we describe GMODWeb, a GMOD project designed to speed the development of model organism database (MOD) websites. Sites created with GMODWeb provide integration with other GMOD tools and allow users to browse and search through a variety of data types. GMODWeb was built using the open source Turnkey web framework and is available from . PMID:18570664

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.

Facilitating quality control for spectra assignments of small organic molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS for academic service laboratories.

PubMed

Kuhn, Stefan; Schlörer, Nils E

2015-08-01

nmrshiftdb2 supports with its laboratory information management system the integration of an electronic lab administration and management into academic NMR facilities. Also, it offers the setup of a local database, while full access to nmrshiftdb2's World Wide Web database is granted. This freely available system allows on the one hand the submission of orders for measurement, transfers recorded data automatically or manually, and enables download of spectra via web interface, as well as the integrated access to prediction, search, and assignment tools of the NMR database for lab users. On the other hand, for the staff and lab administration, flow of all orders can be supervised; administrative tools also include user and hardware management, a statistic functionality for accounting purposes, and a 'QuickCheck' function for assignment control, to facilitate quality control of assignments submitted to the (local) database. Laboratory information management system and database are based on a web interface as front end and are therefore independent of the operating system in use. Copyright © 2015 John Wiley & Sons, Ltd.

Using ChEMBL web services for building applications and data processing workflows relevant to drug discovery.

PubMed

Nowotka, Michał M; Gaulton, Anna; Mendez, David; Bento, A Patricia; Hersey, Anne; Leach, Andrew

2017-08-01

ChEMBL is a manually curated database of bioactivity data on small drug-like molecules, used by drug discovery scientists. Among many access methods, a REST API provides programmatic access, allowing the remote retrieval of ChEMBL data and its integration into other applications. This approach allows scientists to move from a world where they go to the ChEMBL web site to search for relevant data, to one where ChEMBL data can be simply integrated into their everyday tools and work environment. Areas covered: This review highlights some of the audiences who may benefit from using the ChEMBL API, and the goals they can address, through the description of several use cases. The examples cover a team communication tool (Slack), a data analytics platform (KNIME), batch job management software (Luigi) and Rich Internet Applications. Expert opinion: The advent of web technologies, cloud computing and micro services oriented architectures have made REST APIs an essential ingredient of modern software development models. The widespread availability of tools consuming RESTful resources have made them useful for many groups of users. The ChEMBL API is a valuable resource of drug discovery bioactivity data for professional chemists, chemistry students, data scientists, scientific and web developers.

AnnoLnc: a web server for systematically annotating novel human lncRNAs.

PubMed

Hou, Mei; Tang, Xing; Tian, Feng; Shi, Fangyuan; Liu, Fenglin; Gao, Ge

2016-11-16

Long noncoding RNAs (lncRNAs) have been shown to play essential roles in almost every important biological process through multiple mechanisms. Although the repertoire of human lncRNAs has rapidly expanded, their biological function and regulation remain largely elusive, calling for a systematic and integrative annotation tool. Here we present AnnoLnc ( http://annolnc.cbi.pku.edu.cn ), a one-stop portal for systematically annotating novel human lncRNAs. Based on more than 700 data sources and various tool chains, AnnoLnc enables a systematic annotation covering genomic location, secondary structure, expression patterns, transcriptional regulation, miRNA interaction, protein interaction, genetic association and evolution. An intuitive web interface is available for interactive analysis through both desktops and mobile devices, and programmers can further integrate AnnoLnc into their pipeline through standard JSON-based Web Service APIs. To the best of our knowledge, AnnoLnc is the only web server to provide on-the-fly and systematic annotation for newly identified human lncRNAs. Compared with similar tools, the annotation generated by AnnoLnc covers a much wider spectrum with intuitive visualization. Case studies demonstrate the power of AnnoLnc in not only rediscovering known functions of human lncRNAs but also inspiring novel hypotheses.

InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology.

PubMed

Peng, Jiajie; Li, Hongxiang; Liu, Yongzhuang; Juan, Liran; Jiang, Qinghua; Wang, Yadong; Chen, Jin

2016-08-31

The Gene Ontology (GO) has been used in high-throughput omics research as a major bioinformatics resource. The hierarchical structure of GO provides users a convenient platform for biological information abstraction and hypothesis testing. Computational methods have been developed to identify functionally similar genes. However, none of the existing measurements take into account all the rich information in GO. Similarly, using these existing methods, web-based applications have been constructed to compute gene functional similarities, and to provide pure text-based outputs. Without a graphical visualization interface, it is difficult for result interpretation. We present InteGO2, a web tool that allows researchers to calculate the GO-based gene semantic similarities using seven widely used GO-based similarity measurements. Also, we provide an integrative measurement that synergistically integrates all the individual measurements to improve the overall performance. Using HTML5 and cytoscape.js, we provide a graphical interface in InteGO2 to visualize the resulting gene functional association networks. InteGO2 is an easy-to-use HTML5 based web tool. With it, researchers can measure gene or gene product functional similarity conveniently, and visualize the network of functional interactions in a graphical interface. InteGO2 can be accessed via http://mlg.hit.edu.cn:8089/ .

Mergeomics: a web server for identifying pathological pathways, networks, and key regulators via multidimensional data integration.

PubMed

Arneson, Douglas; Bhattacharya, Anindya; Shu, Le; Mäkinen, Ville-Petteri; Yang, Xia

2016-09-09

Human diseases are commonly the result of multidimensional changes at molecular, cellular, and systemic levels. Recent advances in genomic technologies have enabled an outpour of omics datasets that capture these changes. However, separate analyses of these various data only provide fragmented understanding and do not capture the holistic view of disease mechanisms. To meet the urgent needs for tools that effectively integrate multiple types of omics data to derive biological insights, we have developed Mergeomics, a computational pipeline that integrates multidimensional disease association data with functional genomics and molecular networks to retrieve biological pathways, gene networks, and central regulators critical for disease development. To make the Mergeomics pipeline available to a wider research community, we have implemented an online, user-friendly web server ( http://mergeomics. idre.ucla.edu/ ). The web server features a modular implementation of the Mergeomics pipeline with detailed tutorials. Additionally, it provides curated genomic resources including tissue-specific expression quantitative trait loci, ENCODE functional annotations, biological pathways, and molecular networks, and offers interactive visualization of analytical results. Multiple computational tools including Marker Dependency Filtering (MDF), Marker Set Enrichment Analysis (MSEA), Meta-MSEA, and Weighted Key Driver Analysis (wKDA) can be used separately or in flexible combinations. User-defined summary-level genomic association datasets (e.g., genetic, transcriptomic, epigenomic) related to a particular disease or phenotype can be uploaded and computed real-time to yield biologically interpretable results, which can be viewed online and downloaded for later use. Our Mergeomics web server offers researchers flexible and user-friendly tools to facilitate integration of multidimensional data into holistic views of disease mechanisms in the form of tissue-specific key regulators, biological pathways, and gene networks.

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

PubMed Central

Waagmeester, Andra; Pico, Alexander R.

2016-01-01

The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web. PMID:27336457

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources.

PubMed

Waagmeester, Andra; Kutmon, Martina; Riutta, Anders; Miller, Ryan; Willighagen, Egon L; Evelo, Chris T; Pico, Alexander R

2016-06-01

The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web.

An object-oriented programming system for the integration of internet-based bioinformatics resources.

PubMed

Beveridge, Allan

2006-01-01

The Internet consists of a vast inhomogeneous reservoir of data. Developing software that can integrate a wide variety of different data sources is a major challenge that must be addressed for the realisation of the full potential of the Internet as a scientific research tool. This article presents a semi-automated object-oriented programming system for integrating web-based resources. We demonstrate that the current Internet standards (HTML, CGI [common gateway interface], Java, etc.) can be exploited to develop a data retrieval system that scans existing web interfaces and then uses a set of rules to generate new Java code that can automatically retrieve data from the Web. The validity of the software has been demonstrated by testing it on several biological databases. We also examine the current limitations of the Internet and discuss the need for the development of universal standards for web-based data.

Semantic Web Applications and Tools for the Life Sciences: SWAT4LS 2010

PubMed Central

2012-01-01

As Semantic Web technologies mature and new releases of key elements, such as SPARQL 1.1 and OWL 2.0, become available, the Life Sciences continue to push the boundaries of these technologies with ever more sophisticated tools and applications. Unsurprisingly, therefore, interest in the SWAT4LS (Semantic Web Applications and Tools for the Life Sciences) activities have remained high, as was evident during the third international SWAT4LS workshop held in Berlin in December 2010. Contributors to this workshop were invited to submit extended versions of their papers, the best of which are now made available in the special supplement of BMC Bioinformatics. The papers reflect the wide range of work in this area, covering the storage and querying of Life Sciences data in RDF triple stores, tools for the development of biomedical ontologies and the semantics-based integration of Life Sciences as well as clinicial data. PMID:22373274

Semantic Web applications and tools for the life sciences: SWAT4LS 2010.

PubMed

Burger, Albert; Paschke, Adrian; Romano, Paolo; Marshall, M Scott; Splendiani, Andrea

2012-01-25

As Semantic Web technologies mature and new releases of key elements, such as SPARQL 1.1 and OWL 2.0, become available, the Life Sciences continue to push the boundaries of these technologies with ever more sophisticated tools and applications. Unsurprisingly, therefore, interest in the SWAT4LS (Semantic Web Applications and Tools for the Life Sciences) activities have remained high, as was evident during the third international SWAT4LS workshop held in Berlin in December 2010. Contributors to this workshop were invited to submit extended versions of their papers, the best of which are now made available in the special supplement of BMC Bioinformatics. The papers reflect the wide range of work in this area, covering the storage and querying of Life Sciences data in RDF triple stores, tools for the development of biomedical ontologies and the semantics-based integration of Life Sciences as well as clinicial data.

Smartphones Give You Wings: Pedagogical Affordances of Mobile Web 2.0

ERIC Educational Resources Information Center

Cochrane, Thomas; Bateman, Roger

2010-01-01

Built on the foundation of four years of research and implementation of mobile learning projects (m-learning), this paper provides an overview of the potential of the integration of mobile Web 2.0 tools (based around smartphones) to facilitate social constructivist pedagogies and engage students in tertiary education. Pedagogical affordances of…

Towards Web Service-Based Educational Systems

ERIC Educational Resources Information Center

Sampson, Demetrios G.

2005-01-01

The need for designing the next generation of web service-based educational systems with the ability of integrating components from different tools and platforms is now recognised as the major challenge in advanced learning technologies. In this paper, we discuss this issue and we present the conceptual design of such environment, referred to as…

Course Management Systems: Time for Users to Get What They Need

ERIC Educational Resources Information Center

Ioannou, Andri; Hannafin, Robert D.

2008-01-01

Course management systems (CMSs) are software systems designed to manage course content and course activities. These tools integrate technological and pedagogical features into a web-based system that allows instructors, even those who are unfamiliar with web-based technologies, to design, deliver, and manage an online course. However, CMSs have…

The Study on Integrating WebQuest with Mobile Learning for Environmental Education

ERIC Educational Resources Information Center

Chang, Cheng-Sian; Chen, Tzung-Shi; Hsu, Wei-Hsiang

2011-01-01

This study is to demonstrate the impact of different teaching strategies on the learning performance of environmental education using quantitative methods. Students learned about resource recycling and classification through an instructional website based on the teaching tool of WebQuest. There were 103 sixth-grade students participating in this…

Effects of Group Reflection Variations in Project-Based Learning Integrated in a Web 2.0 Learning Space

ERIC Educational Resources Information Center

Kim, Paul; Hong, Ji-Seong; Bonk, Curtis; Lim, Gloria

2011-01-01

A Web 2.0 environment that is coupled with emerging multimodal interaction tools can have considerable influence on team learning outcomes. Today, technologies supporting social networking, collective intelligence, emotional interaction, and virtual communication are introducing new forms of collaboration that are profoundly impacting education.…

The PartnerWeb Project: a component-based approach to enterprise-wide information integration and dissemination.

PubMed Central

Karson, T. H.; Perkins, C.; Dixon, C.; Ehresman, J. P.; Mammone, G. L.; Sato, L.; Schaffer, J. L.; Greenes, R. A.

1997-01-01

A component-based health information resource, delivered on an intranet and the Internet, utilizing World Wide Web (WWW) technology, has been built to meet the needs of a large integrated delivery network (IDN). Called PartnerWeb, this resource is intended to provide a variety of health care and reference information to both practitioners and consumers/patients. The initial target audience has been providers. Content management for the numerous departments, divisions, and other organizational entities within the IDN is accomplished by a distributed authoring and editing environment. Structured entry using a set of form tools into databases facilitates consistency of information presentation, while empowering designated authors and editors in the various entities to be responsible for their own materials, but not requiring them to be technically skilled. Each form tool manages an encapsulated component. The output of each component can be a dynamically generated display on WWW platforms, or an appropriate interface to other presentation environments. The PartnerWeb project lays the foundation for both an internal and external communication infrastructure for the enterprise that can facilitate information dissemination. PMID:9357648

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).

Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format.

PubMed

Webb, Ryan L; Ma'ayan, Avi

2011-03-21

The World Wide Web plays a critical role in enabling molecular, cell, systems and computational biologists to exchange, search, visualize, integrate, and analyze experimental data. Such efforts can be further enhanced through the development of semantic web concepts. The semantic web idea is to enable machines to understand data through the development of protocol free data exchange formats such as Resource Description Framework (RDF) and the Web Ontology Language (OWL). These standards provide formal descriptors of objects, object properties and their relationships within a specific knowledge domain. However, the overhead of converting datasets typically stored in data tables such as Excel, text or PDF into RDF or OWL formats is not trivial for non-specialists and as such produces a barrier to seamless data exchange between researchers, databases and analysis tools. This problem is particularly of importance in the field of network systems biology where biochemical interactions between genes and their protein products are abstracted to networks. For the purpose of converting biochemical interactions into the BioPAX format, which is the leading standard developed by the computational systems biology community, we developed an open-source command line tool that takes as input tabular data describing different types of molecular biochemical interactions. The tool converts such interactions into the BioPAX level 3 OWL format. We used the tool to convert several existing and new mammalian networks of protein interactions, signalling pathways, and transcriptional regulatory networks into BioPAX. Some of these networks were deposited into PathwayCommons, a repository for consolidating and organizing biochemical networks. The software tool Sig2BioPAX is a resource that enables experimental and computational systems biologists to contribute their identified networks and pathways of molecular interactions for integration and reuse with the rest of the research community.

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.

The CatchMod toolbox: easy and guided access to ICT tools for Water Framework Directive implementation.

PubMed

van Griensven, A; Vanrolleghem, P A

2006-01-01

Web-based toolboxes are handy tools to inform experienced users of existing software in their disciplines. However, for the implementation of the Water Framework Directive, a much more diverse public (water managers, consultancy firms, scientists, etc.) will ask for a very wide diversity of Information and Communication Technology (ICT) tools. It is obvious that the users of a web-based ICT-toolbox providing all this will not be experts in all of the disciplines and that a toolbox for ICT tools for Water Framework Directive implementation should thus go beyond just making interesting web-links. To deal with this issue, expert knowledge is brought to the users through the incorporation of visitor-geared guidance (materials) in the Harmoni-CA toolbox. Small workshops of expert teams were organized to deliver documents explaining why the tools are important, when they are required and what activity they support/perform, as well as a categorization of the multitude of available tools. An integration of this information in the web-based toolbox helps the users to browse through a toolbox containing tools, reports, guidance documents and interesting links. The Harmoni-CA toolbox thus provides not only a virtual toolbox, but incorporates a virtual expert as well.

Examining Literacy Teachers' Perceptions of the Use of VoiceThread in an Elementary, Middle School, and a High School Classroom for Enhancing Instructional Goals

ERIC Educational Resources Information Center

Stover, Katie; Kissel, Brian; Wood, Karen; Putman, Michael

2015-01-01

In today's digital age, Web 2.0 tools such as VoiceThread allow users to integrate images, voices, and responses within one digital platform, providing students with the opportunity to add another layer of meaning to their texts. We conducted this research to expand our understanding of the processes necessary for integrating digital tools into…

[Web-based electronic patient record as an instrument for quality assurance within an integrated care concept].

PubMed

Händel, A; Jünemann, A G M; Prokosch, H-U; Beyer, A; Ganslandt, T; Grolik, R; Klein, A; Mrosek, A; Michelson, G; Kruse, F E

2009-03-01

A prerequisite for integrated care programmes is the implementation of a communication network meeting quality assurance standards. Against this background the main objective of the integrated care project between the University Eye Hospital Erlangen and the health insurance company AOK Bayern was to evaluate the potential and the acceptance of a web-based electronic patient record in the context of cataract and retinal surgery. Standardised modules for capturing pre-, intra- and post-operative data on the basis of clinical pathway guidelines for cataract- and retinal surgery have been developed. There are 6 data sets recorded per patient (1 pre-operative, 1 operative, 4-6 post-operative). For data collection, a web-based communication system (Soarian Integrated Care) has been chosen which meets the high requirements in data security, as well as being easy to handle. This teleconsultation system and the embedded electronic patient record are independent of the software used by respective offices and hospitals. Data transmission and storage were carried out in real-time. At present, 101 private ophthalmologists are taking part in the IGV contract with the University Eye Hospital Erlangen. This corresponds to 52% of all private ophthalmologists in the region. During the period from January 1st 2006 to December 31st 2006, 1844 patients were entered. Complete documentation was achieved in 1390 (75%) of all surgical procedures. For evaluation of this data, a multidimensional report and analysis tool (Cognos) was used. The deviation from target refraction as one quality indicator was in the mean 0.09 diopter. The web-based patient record used in this project was highly accepted by the private ophthalmologists. However there are still general concerns against the exchange of medical data via the internet. Nevertheless, the web-based patient record is an essential tool for a functional integration between the ambulatory and stationary health-care units. In addition to the telemedicine functions of the system, we achieved the export of the data to a data warehouse system in order to provide a flexible and powerful tool for quality assurance analysis and reporting.

Sharing knowledge of Planetary Datasets through the Web-Based PRoGIS

NASA Astrophysics Data System (ADS)

Giordano, M. G.; Morley, J. M.; Muller, J. P. M.; Barnes, R. B.; Tao, Y. T.

2015-10-01

The large amount of raw and derived data available from various planetary surface missions (e.g. Mars and Moon in our case) has been integrated withco-registered and geocoded orbital image data to provide rover traverses and camera site locations in universal global co-ordinates [1]. This then allows an integrated GIS to use these geocoded products for scientific applications: we aim to create a web interface, PRoGIS, with minimal controls focusing on the usability and visualisation of the data, to allow planetary geologists to share annotated surface observations. These observations in a common context are shared between different tools and software (PRoGIS, Pro3D, 3D point cloud viewer). Our aim is to use only Open Source components that integrate Open Web Services for planetary data to make available an universal platform with a WebGIS interface, as well as a 3D point cloud and a Panorama viewer to explore derived data. On top of these tools we are building capabilities to make and share annotations amongst users. We use Python and Django for the server-side framework and Open Layers 3 for the WebGIS client. For good performance previewing 3D data (point clouds, pictures on the surface and panoramas) we employ ThreeJS, a WebGL Javascript library. Additionally, user and group controls allow scientists to store and share their observations. PRoGIS not only displays data but also launches sophisticated 3D vision reprocessing (PRoVIP) and an immersive 3D analysis environment (PRo3D).

iTools: a framework for classification, categorization and integration of computational biology resources.

PubMed

Dinov, Ivo D; Rubin, Daniel; Lorensen, William; Dugan, Jonathan; Ma, Jeff; Murphy, Shawn; Kirschner, Beth; Bug, William; Sherman, Michael; Floratos, Aris; Kennedy, David; Jagadish, H V; Schmidt, Jeanette; Athey, Brian; Califano, Andrea; Musen, Mark; Altman, Russ; Kikinis, Ron; Kohane, Isaac; Delp, Scott; Parker, D Stott; Toga, Arthur W

2008-05-28

The advancement of the computational biology field hinges on progress in three fundamental directions--the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources--data, software tools and web-services. The iTools design, implementation and resource meta-data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource management. We demonstrate several applications of iTools as a framework for integrated bioinformatics. iTools and the complete details about its specifications, usage and interfaces are available at the iTools web page http://iTools.ccb.ucla.edu.

iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources

PubMed Central

Dinov, Ivo D.; Rubin, Daniel; Lorensen, William; Dugan, Jonathan; Ma, Jeff; Murphy, Shawn; Kirschner, Beth; Bug, William; Sherman, Michael; Floratos, Aris; Kennedy, David; Jagadish, H. V.; Schmidt, Jeanette; Athey, Brian; Califano, Andrea; Musen, Mark; Altman, Russ; Kikinis, Ron; Kohane, Isaac; Delp, Scott; Parker, D. Stott; Toga, Arthur W.

2008-01-01

The advancement of the computational biology field hinges on progress in three fundamental directions – the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources–data, software tools and web-services. The iTools design, implementation and resource meta - data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource management. We demonstrate several applications of iTools as a framework for integrated bioinformatics. iTools and the complete details about its specifications, usage and interfaces are available at the iTools web page http://iTools.ccb.ucla.edu. PMID:18509477

shinyGISPA: A web application for characterizing phenotype by gene sets using multiple omics data combinations.

PubMed

Dwivedi, Bhakti; Kowalski, Jeanne

2018-01-01

While many methods exist for integrating multi-omics data or defining gene sets, there is no one single tool that defines gene sets based on merging of multiple omics data sets. We present shinyGISPA, an open-source application with a user-friendly web-based interface to define genes according to their similarity in several molecular changes that are driving a disease phenotype. This tool was developed to help facilitate the usability of a previously published method, Gene Integrated Set Profile Analysis (GISPA), among researchers with limited computer-programming skills. The GISPA method allows the identification of multiple gene sets that may play a role in the characterization, clinical application, or functional relevance of a disease phenotype. The tool provides an automated workflow that is highly scalable and adaptable to applications that go beyond genomic data merging analysis. It is available at http://shinygispa.winship.emory.edu/shinyGISPA/.

shinyGISPA: A web application for characterizing phenotype by gene sets using multiple omics data combinations

PubMed Central

Dwivedi, Bhakti

2018-01-01

While many methods exist for integrating multi-omics data or defining gene sets, there is no one single tool that defines gene sets based on merging of multiple omics data sets. We present shinyGISPA, an open-source application with a user-friendly web-based interface to define genes according to their similarity in several molecular changes that are driving a disease phenotype. This tool was developed to help facilitate the usability of a previously published method, Gene Integrated Set Profile Analysis (GISPA), among researchers with limited computer-programming skills. The GISPA method allows the identification of multiple gene sets that may play a role in the characterization, clinical application, or functional relevance of a disease phenotype. The tool provides an automated workflow that is highly scalable and adaptable to applications that go beyond genomic data merging analysis. It is available at http://shinygispa.winship.emory.edu/shinyGISPA/. PMID:29415010

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.

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.

PubMed

Katayama, Toshiaki; Wilkinson, Mark D; Micklem, Gos; Kawashima, Shuichi; Yamaguchi, Atsuko; Nakao, Mitsuteru; Yamamoto, Yasunori; Okamoto, Shinobu; Oouchida, Kenta; Chun, Hong-Woo; Aerts, Jan; Afzal, Hammad; Antezana, Erick; Arakawa, Kazuharu; Aranda, Bruno; Belleau, Francois; Bolleman, Jerven; Bonnal, Raoul Jp; Chapman, Brad; Cock, Peter Ja; Eriksson, Tore; Gordon, Paul Mk; Goto, Naohisa; Hayashi, Kazuhiro; Horn, Heiko; Ishiwata, Ryosuke; Kaminuma, Eli; Kasprzyk, Arek; Kawaji, Hideya; Kido, Nobuhiro; Kim, Young Joo; Kinjo, Akira R; Konishi, Fumikazu; Kwon, Kyung-Hoon; Labarga, Alberto; Lamprecht, Anna-Lena; Lin, Yu; Lindenbaum, Pierre; McCarthy, Luke; Morita, Hideyuki; Murakami, Katsuhiko; Nagao, Koji; Nishida, Kozo; Nishimura, Kunihiro; Nishizawa, Tatsuya; Ogishima, Soichi; Ono, Keiichiro; Oshita, Kazuki; Park, Keun-Joon; Prins, Pjotr; Saito, Taro L; Samwald, Matthias; Satagopam, Venkata P; Shigemoto, Yasumasa; Smith, Richard; Splendiani, Andrea; Sugawara, Hideaki; Taylor, James; Vos, Rutger A; Withers, David; Yamasaki, Chisato; Zmasek, Christian M; Kawamoto, Shoko; Okubo, Kosaku; Asai, Kiyoshi; Takagi, Toshihisa

2013-02-11

BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

PubMed Central

2013-01-01

Background BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. Results The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. Conclusion We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer. PMID:23398680

RSAT 2018: regulatory sequence analysis tools 20th anniversary.

PubMed

Nguyen, Nga Thi Thuy; Contreras-Moreira, Bruno; Castro-Mondragon, Jaime A; Santana-Garcia, Walter; Ossio, Raul; Robles-Espinoza, Carla Daniela; Bahin, Mathieu; Collombet, Samuel; Vincens, Pierre; Thieffry, Denis; van Helden, Jacques; Medina-Rivera, Alejandra; Thomas-Chollier, Morgane

2018-05-02

RSAT (Regulatory Sequence Analysis Tools) is a suite of modular tools for the detection and the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, including from genome-wide datasets like ChIP-seq/ATAC-seq, (ii) motif scanning, (iii) motif analysis (quality assessment, comparisons and clustering), (iv) analysis of regulatory variations, (v) comparative genomics. Six public servers jointly support 10 000 genomes from all kingdoms. Six novel or refactored programs have been added since the 2015 NAR Web Software Issue, including updated programs to analyse regulatory variants (retrieve-variation-seq, variation-scan, convert-variations), along with tools to extract sequences from a list of coordinates (retrieve-seq-bed), to select motifs from motif collections (retrieve-matrix), and to extract orthologs based on Ensembl Compara (get-orthologs-compara). Three use cases illustrate the integration of new and refactored tools to the suite. This Anniversary update gives a 20-year perspective on the software suite. RSAT is well-documented and available through Web sites, SOAP/WSDL (Simple Object Access Protocol/Web Services Description Language) web services, virtual machines and stand-alone programs at http://www.rsat.eu/.

An integrated web system to support veterinary activities in Italy for the management of information in epidemic emergencies.

PubMed

Iannetti, S; Savini, L; Palma, D; Calistri, P; Natale, F; Di Lorenzo, A; Cerella, A; Giovannini, A

2014-03-01

The management of public health emergencies is improved by quick, exhaustive and standardized flow of data on disease outbreaks, by using specific tools for data collection, registration and analysis. In this context, the National Information System for the Notification of Outbreaks of Animal Diseases (SIMAN) has been developed in Italy to collect and share data on the notifications of outbreaks of animal diseases. SIMAN is connected through web services to the national database of animals and holdings (BDN) and has been integrated with tools for the management of epidemic emergencies. The website has been updated with a section dedicated to the contingency planning in case of epidemic emergency. EpiTrace is one such useful tool also integrated in the BDN and based on the Social Network Analysis (SNA) and on network epidemiological models. This tool gives the possibility of assessing the risk associated to holdings and animals on the basis of their trade, in order to support the veterinary services in tracing back and forward the animals in case of outbreaks of infectious diseases. Copyright © 2014 Elsevier B.V. All rights reserved.

Integration of Problem-Based Learning and Web-Based Multimedia to Enhance Soil Management Course

NASA Astrophysics Data System (ADS)

Strivelli, R.; Krzic, M.; Crowley, C.; Dyanatkar, S.; Bomke, A.; Simard, S.; Grand, S.

2012-04-01

In an attempt to address declining enrolment in soil science programs and the changing learning needs of 21st century students, several universities in North America and around the world have re-organized their soil science curriculum and adopted innovative educational approaches and web-based teaching resources. At the University of British Columbia, Canada, an interdisciplinary team set out to integrate teaching approaches to address this trend. The objective of this project was to develop an interactive web-based teaching resource, which combined a face-to-face problem-based learning (PBL) case study with multimedia to illustrate the impacts of three land-uses on soil transformation and quality. The Land Use Impacts (LUI) tool (http://soilweb.landfood.ubc.ca/luitool/) was a collaborative and concentrated effort to maximize the advantages of two educational approaches: (1) the web's interactivity, flexibility, adaptability and accessibility, and (2) PBL's ability to foster an authentic learning environment, encourage group work and promote the application of core concepts. The design of the LUI case study was guided by Herrington's development principles for web-based authentic learning. The LUI tool presented students with rich multimedia (streaming videos, text, data, photographs, maps, and weblinks) and real world tasks (site assessment and soil analysis) to encourage students to utilize knowledge of soil science in collaborative problem-solving. Preliminary student feedback indicated that the LUI tool effectively conveyed case study objectives and was appealing to students. The resource is intended primarily for students enrolled in an upper level undergraduate/graduate university course titled Sustainable Soil Management but it is flexible enough to be adapted to other natural resource courses. Project planning and an interactive overview of the tool will be given during the presentation.

ballaxy: web services for structural bioinformatics.

PubMed

Hildebrandt, Anna Katharina; Stöckel, Daniel; Fischer, Nina M; de la Garza, Luis; Krüger, Jens; Nickels, Stefan; Röttig, Marc; Schärfe, Charlotta; Schumann, Marcel; Thiel, Philipp; Lenhof, Hans-Peter; Kohlbacher, Oliver; Hildebrandt, Andreas

2015-01-01

Web-based workflow systems have gained considerable momentum in sequence-oriented bioinformatics. In structural bioinformatics, however, such systems are still relatively rare; while commercial stand-alone workflow applications are common in the pharmaceutical industry, academic researchers often still rely on command-line scripting to glue individual tools together. In this work, we address the problem of building a web-based system for workflows in structural bioinformatics. For the underlying molecular modelling engine, we opted for the BALL framework because of its extensive and well-tested functionality in the field of structural bioinformatics. The large number of molecular data structures and algorithms implemented in BALL allows for elegant and sophisticated development of new approaches in the field. We hence connected the versatile BALL library and its visualization and editing front end BALLView with the Galaxy workflow framework. The result, which we call ballaxy, enables the user to simply and intuitively create sophisticated pipelines for applications in structure-based computational biology, integrated into a standard tool for molecular modelling.  ballaxy consists of three parts: some minor modifications to the Galaxy system, a collection of tools and an integration into the BALL framework and the BALLView application for molecular modelling. Modifications to Galaxy will be submitted to the Galaxy project, and the BALL and BALLView integrations will be integrated in the next major BALL release. After acceptance of the modifications into the Galaxy project, we will publish all ballaxy tools via the Galaxy toolshed. In the meantime, all three components are available from http://www.ball-project.org/ballaxy. Also, docker images for ballaxy are available at https://registry.hub.docker.com/u/anhi/ballaxy/dockerfile/. ballaxy is licensed under the terms of the GPL. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

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

BASTet is an advanced software library written in Python. BASTet serves as the analysis and storage library for the OpenMSI project. BASTet is an integrate framework for: i) storage of spectral imaging data, ii) storage of derived analysis data, iii) provenance of analyses, iv) integration and execution of analyses via complex workflows. BASTet implements the API for the HDF5 storage format used by OpenMSI. Analyses that are developed using BASTet benefit from direct integration with storage format, automatic tracking of provenance, and direct integration with command-line and workflow execution tools. BASTet also defines interfaces to enable developers to directly integratemore » their analysis with OpenMSI's web-based viewing infrastruture without having to know OpenMSI. BASTet also provides numerous helper classes and tools to assist with the conversion of data files, ease parallel implementation of analysis algorithms, ease interaction with web-based functions, description methods for data reduction. BASTet also includes detailed developer documentation, user tutorials, iPython notebooks, and other supporting documents.« less

Implementation of a Reverse Colocation Model: Lessons from Two Community Behavioral Health Agencies in Rural Pennsylvania.

PubMed

Gerolamo, Angela M; Kim, Jung Y; Brown, Jonathan D; Schuster, James; Kogan, Jane

2016-07-01

This qualitative study examined the implementation of a reverse colocation pilot program that sought to integrate medical care in two community behavioral health agencies. To accomplish this, each agency hired a registered nurse, provided training for its staff to function as wellness coaches, and implemented a web-based tool for tracking consumer outcomes. The findings from two rounds of stakeholder discussions and consumer focus groups suggested that agencies successfully trained their staffs in wellness coaching, integrated nurses into agency functions, developed integrated care planning processes, and increased awareness of wellness among staff and consumers. Similar to other complex interventions, the agencies experienced challenges including difficulty establishing new procedures and communication protocols, discomfort among staff in addressing physical health concerns, difficulty building collaborative relationships with primary care providers, and modest uptake of the web-based tool. The study offers insights into the practical aspects of integrating care and makes recommendations for future efforts.

A UIMA wrapper for the NCBO annotator

PubMed Central

Roeder, Christophe; Jonquet, Clement; Shah, Nigam H.; Baumgartner, William A.; Verspoor, Karin; Hunter, Lawrence

2010-01-01

Summary: The Unstructured Information Management Architecture (UIMA) framework and web services are emerging as useful tools for integrating biomedical text mining tools. This note describes our work, which wraps the National Center for Biomedical Ontology (NCBO) Annotator—an ontology-based annotation service—to make it available as a component in UIMA workflows. Availability: This wrapper is freely available on the web at http://bionlp-uima.sourceforge.net/ as part of the UIMA tools distribution from the Center for Computational Pharmacology (CCP) at the University of Colorado School of Medicine. It has been implemented in Java for support on Mac OS X, Linux and MS Windows. Contact: chris.roeder@ucdenver.edu PMID:20505005

Revelations from the Literature: How Web-Scale Discovery Has Already Changed Us

ERIC Educational Resources Information Center

Richardson, Hillary A. H.

2013-01-01

For nearly a decade now, librarians have discussed and deliberated ways, for the sake of convenience, to integrate internet-like searching into their own catalogs to mimic what academic library patrons have been using outside the library. Discovery tools and web-scale discovery services (WSDS) attempt to provide users with a similar one-stop shop…

User Identification and Tracking in an Educational Web Environment.

ERIC Educational Resources Information Center

Marzo-Lazaro, J. L.; Verdu-Carbo, T.; Fabregat-Gesa, R.

This paper describes a solution to the user identification and tracking problem within an educational World Wide Web environment. The paper begins with an overview of the Teaching Support System project at the University of Girona (Spain); the main objective of the project is to create an integrated set of tools for teachers to use to create and…

REopt Lite Web Tool

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

NREL developed a free, publicly available web version of the REopt (TM) renewable energy integration and optimization platform called REopt Lite. REopt Lite recommends the optimal size and dispatch strategy for grid-connected photovoltaics (PV) and battery storage at a site. It also allows users to explore how PV and storage can increase a site's resiliency during a grid outage.

Learner Self-Regulation and Web 2.0 Tools Management in Personal Learning Environment

ERIC Educational Resources Information Center

Yen, Cherng-Jyh; Tu, Chih-Hsiung; Sujo-Montes, Laura E.; Armfield, Shadow W. J.; Chan, Junn-Yih

2013-01-01

Web 2.0 technology integration requires a higher level of self-regulated learning skills to create a Personal Learning Environment (PLE). This study examined each of the four aspects of learner self-regulation in online learning (i.e., environment structuring, goal setting, time management, & task strategies) as the predictor for level of…

Competencies in Organizational E-Learning: Concepts and Tools

ERIC Educational Resources Information Center

Sicilia, Miguel-Angel, Ed.

2007-01-01

"Competencies in Organizational E-Learning: Concepts and Tools" provides a comprehensive view of the way competencies can be used to drive organizational e-learning, including the main conceptual elements, competency gap analysis, advanced related computing topics, the application of semantic Web technologies, and the integration of competencies…

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases.

PubMed

Kobayashi, Norio; Ishii, Manabu; Takahashi, Satoshi; Mochizuki, Yoshiki; Matsushima, Akihiro; Toyoda, Tetsuro

2011-07-01

Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross-integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 8.2 million data records, integrated as Linked Open or Private Data (LOD/LPD) using SciNetS.org, the Scientists' Networking System. The huge quantity of linked data this database integration framework covers is based on the Semantic Web, where researchers collaborate by managing metadata across public and private databases in a secured data space. This outstripped the data query capacity of existing interface tools like SPARQL. Actual research also requires specialized tools for data analysis using raw original data. To solve these challenges, in December 2009 we developed the lightweight Semantic-JSON interface to access each fragment of linked and raw life sciences data securely under the control of programming languages popularly used by bioinformaticians such as Perl and Ruby. Researchers successfully used the interface across 28 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers. Semantic-JSON services of SciNetS.org are provided at http://semanticjson.org.

Web-based hybrid-dimensional Visualization and Exploration of Cytological Localization Scenarios.

PubMed

Kovanci, Gökhan; Ghaffar, Mehmood; Sommer, Björn

2016-12-21

The CELLmicrocosmos 4.2 PathwayIntegration (CmPI) is a tool which provides hybrid-dimensional visualization and analysis of intracellular protein and gene localizations in the context of a virtual 3D environment. This tool is developed based on Java/Java3D/JOGL and provides a standalone application compatible to all relevant operating systems. However, it requires Java and the local installation of the software. Here we present the prototype of an alternative web-based visualization approach, using Three.js and D3.js. In this way it is possible to visualize and explore CmPI-generated localization scenarios including networks mapped to 3D cell components by just providing a URL to a collaboration partner. This publication describes the integration of the different technologies – Three.js, D3.js and PHP – as well as an application case: a localization scenario of the citrate cycle. The CmPI web viewer is available at: http://CmPIweb.CELLmicrocosmos.org.

Web-based hybrid-dimensional Visualization and Exploration of Cytological Localization Scenarios.

PubMed

Kovanci, Gökhan; Ghaffar, Mehmood; Sommer, Björn

2016-10-01

The CELLmicrocosmos 4.2 PathwayIntegration (CmPI) is a tool which provides hybriddimensional visualization and analysis of intracellular protein and gene localizations in the context of a virtual 3D environment. This tool is developed based on Java/Java3D/JOGL and provides a standalone application compatible to all relevant operating systems. However, it requires Java and the local installation of the software. Here we present the prototype of an alternative web-based visualization approach, using Three.js and D3.js. In this way it is possible to visualize and explore CmPI-generated localization scenarios including networks mapped to 3D cell components by just providing a URL to a collaboration partner. This publication describes the integration of the different technologies - Three.js, D3.js and PHP - as well as an application case: a localization scenario of the citrate cycle. The CmPI web viewer is available at: http://CmPIweb.CELLmicrocosmos.org.

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

Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence-Function Space and Genome Context to Discover Novel Functions.

PubMed

Gerlt, John A

2017-08-22

The exponentially increasing number of protein and nucleic acid sequences provides opportunities to discover novel enzymes, metabolic pathways, and metabolites/natural products, thereby adding to our knowledge of biochemistry and biology. The challenge has evolved from generating sequence information to mining the databases to integrating and leveraging the available information, i.e., the availability of "genomic enzymology" web tools. Web tools that allow identification of biosynthetic gene clusters are widely used by the natural products/synthetic biology community, thereby facilitating the discovery of novel natural products and the enzymes responsible for their biosynthesis. However, many novel enzymes with interesting mechanisms participate in uncharacterized small-molecule metabolic pathways; their discovery and functional characterization also can be accomplished by leveraging information in protein and nucleic acid databases. This Perspective focuses on two genomic enzymology web tools that assist the discovery novel metabolic pathways: (1) Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST) for generating sequence similarity networks to visualize and analyze sequence-function space in protein families and (2) Enzyme Function Initiative-Genome Neighborhood Tool (EFI-GNT) for generating genome neighborhood networks to visualize and analyze the genome context in microbial and fungal genomes. Both tools have been adapted to other applications to facilitate target selection for enzyme discovery and functional characterization. As the natural products community has demonstrated, the enzymology community needs to embrace the essential role of web tools that allow the protein and genome sequence databases to be leveraged for novel insights into enzymological problems.

Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence–Function Space and Genome Context to Discover Novel Functions

PubMed Central

2017-01-01

The exponentially increasing number of protein and nucleic acid sequences provides opportunities to discover novel enzymes, metabolic pathways, and metabolites/natural products, thereby adding to our knowledge of biochemistry and biology. The challenge has evolved from generating sequence information to mining the databases to integrating and leveraging the available information, i.e., the availability of “genomic enzymology” web tools. Web tools that allow identification of biosynthetic gene clusters are widely used by the natural products/synthetic biology community, thereby facilitating the discovery of novel natural products and the enzymes responsible for their biosynthesis. However, many novel enzymes with interesting mechanisms participate in uncharacterized small-molecule metabolic pathways; their discovery and functional characterization also can be accomplished by leveraging information in protein and nucleic acid databases. This Perspective focuses on two genomic enzymology web tools that assist the discovery novel metabolic pathways: (1) Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST) for generating sequence similarity networks to visualize and analyze sequence–function space in protein families and (2) Enzyme Function Initiative-Genome Neighborhood Tool (EFI-GNT) for generating genome neighborhood networks to visualize and analyze the genome context in microbial and fungal genomes. Both tools have been adapted to other applications to facilitate target selection for enzyme discovery and functional characterization. As the natural products community has demonstrated, the enzymology community needs to embrace the essential role of web tools that allow the protein and genome sequence databases to be leveraged for novel insights into enzymological problems. PMID:28826221

KDE Bioscience: platform for bioinformatics analysis workflows.

PubMed

Lu, Qiang; Hao, Pei; Curcin, Vasa; He, Weizhong; Li, Yuan-Yuan; Luo, Qing-Ming; Guo, Yi-Ke; Li, Yi-Xue

2006-08-01

Bioinformatics is a dynamic research area in which a large number of algorithms and programs have been developed rapidly and independently without much consideration so far of the need for standardization. The lack of such common standards combined with unfriendly interfaces make it difficult for biologists to learn how to use these tools and to translate the data formats from one to another. Consequently, the construction of an integrative bioinformatics platform to facilitate biologists' research is an urgent and challenging task. KDE Bioscience is a java-based software platform that collects a variety of bioinformatics tools and provides a workflow mechanism to integrate them. Nucleotide and protein sequences from local flat files, web sites, and relational databases can be entered, annotated, and aligned. Several home-made or 3rd-party viewers are built-in to provide visualization of annotations or alignments. KDE Bioscience can also be deployed in client-server mode where simultaneous execution of the same workflow is supported for multiple users. Moreover, workflows can be published as web pages that can be executed from a web browser. The power of KDE Bioscience comes from the integrated algorithms and data sources. With its generic workflow mechanism other novel calculations and simulations can be integrated to augment the current sequence analysis functions. Because of this flexible and extensible architecture, KDE Bioscience makes an ideal integrated informatics environment for future bioinformatics or systems biology research.

Integration of modern statistical tools for the analysis of climate extremes into the web-GIS “CLIMATE”

NASA Astrophysics Data System (ADS)

Ryazanova, A. A.; Okladnikov, I. G.; Gordov, E. P.

2017-11-01

The frequency of occurrence and magnitude of precipitation and temperature extreme events show positive trends in several geographical regions. These events must be analyzed and studied in order to better understand their impact on the environment, predict their occurrences, and mitigate their effects. For this purpose, we augmented web-GIS called “CLIMATE” to include a dedicated statistical package developed in the R language. The web-GIS “CLIMATE” is a software platform for cloud storage processing and visualization of distributed archives of spatial datasets. It is based on a combined use of web and GIS technologies with reliable procedures for searching, extracting, processing, and visualizing the spatial data archives. The system provides a set of thematic online tools for the complex analysis of current and future climate changes and their effects on the environment. The package includes new powerful methods of time-dependent statistics of extremes, quantile regression and copula approach for the detailed analysis of various climate extreme events. Specifically, the very promising copula approach allows obtaining the structural connections between the extremes and the various environmental characteristics. The new statistical methods integrated into the web-GIS “CLIMATE” can significantly facilitate and accelerate the complex analysis of climate extremes using only a desktop PC connected to the Internet.

DyNAVacS: an integrative tool for optimized DNA vaccine design.

PubMed

Harish, Nagarajan; Gupta, Rekha; Agarwal, Parul; Scaria, Vinod; Pillai, Beena

2006-07-01

DNA vaccines have slowly emerged as keystones in preventive immunology due to their versatility in inducing both cell-mediated as well as humoral immune responses. The design of an efficient DNA vaccine, involves choice of a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses and providing additional sequence signals for efficient translation. DyNAVacS is a web-based tool created for rapid and easy design of DNA vaccines. It follows a step-wise design flow, which guides the user through the various sequential steps in the design of the vaccine. Further, it allows restriction enzyme mapping, design of primers spanning user specified sequences and provides information regarding the vectors currently used for generation of DNA vaccines. The web version uses Apache HTTP server. The interface was written in HTML and utilizes the Common Gateway Interface scripts written in PERL for functionality. DyNAVacS is an integrated tool consisting of user-friendly programs, which require minimal information from the user. The software is available free of cost, as a web based application at URL: http://miracle.igib.res.in/dynavac/.

A Set of Web-based Tools for Integrating Scientific Research and Decision-Making through Systems Thinking

EPA Science Inventory

Currently, many policy and management decisions are made without considering the goods and services humans derive from ecosystems and the costs associated with protecting them. This approach is unlikely to be sustainable. Conceptual frameworks provide a tool for capturing, visual...

PDB-Metrics: a web tool for exploring the PDB contents.

PubMed

Fileto, Renato; Kuser, Paula R; Yamagishi, Michel E B; Ribeiro, André A; Quinalia, Thiago G; Franco, Eduardo H; Mancini, Adauto L; Higa, Roberto H; Oliveira, Stanley R M; Santos, Edgard H; Vieira, Fabio D; Mazoni, Ivan; Cruz, Sergio A B; Neshich, Goran

2006-06-30

PDB-Metrics (http://sms.cbi.cnptia.embrapa.br/SMS/pdb_metrics/index.html) is a component of the Diamond STING suite of programs for the analysis of protein sequence, structure and function. It summarizes the characteristics of the collection of protein structure descriptions deposited in the Protein Data Bank (PDB) and provides a Web interface to search and browse the PDB, using a variety of alternative criteria. PDB-Metrics is a powerful tool for bioinformaticians to examine the data span in the PDB from several perspectives. Although other Web sites offer some similar resources to explore the PDB contents, PDB-Metrics is among those with the most complete set of such facilities, integrated into a single Web site. This program has been developed using SQLite, a C library that provides all the query facilities of a database management system.

The ontology life cycle: Integrated tools for editing, publishing, peer review, and evolution of ontologies

PubMed Central

Noy, Natalya; Tudorache, Tania; Nyulas, Csongor; Musen, Mark

2010-01-01

Ontologies have become a critical component of many applications in biomedical informatics. However, the landscape of the ontology tools today is largely fragmented, with independent tools for ontology editing, publishing, and peer review: users develop an ontology in an ontology editor, such as Protégé; and publish it on a Web server or in an ontology library, such as BioPortal, in order to share it with the community; they use the tools provided by the library or mailing lists and bug trackers to collect feedback from users. In this paper, we present a set of tools that bring the ontology editing and publishing closer together, in an integrated platform for the entire ontology lifecycle. This integration streamlines the workflow for collaborative development and increases integration between the ontologies themselves through the reuse of terms. PMID:21347039

ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis

PubMed Central

Römer, Michael; Eichner, Johannes; Dräger, Andreas; Wrzodek, Clemens; Wrzodek, Finja; Zell, Andreas

2016-01-01

Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT) Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/. PMID:26882475

In the Driver's Seat: Learning and Library 2.0 Tools

ERIC Educational Resources Information Center

Fredrick, Kathy

2010-01-01

It is important for educators to find the appropriate tool to unlock learning possibilities for students. A first step toward using the appropriate tool is for school librarians to review the course of study. They need to look at the units and projects taught in the past. They then need to think about how to integrate Web 2.0 applications to…

Effect of an Interactive Web-Based Instruction in the Performance of Undergraduate Anatomy and Physiology Lab Students

ERIC Educational Resources Information Center

Gopal, Tamilselvi; Herron, Sherry S.; Mohn, Richard S.; Hartsell, Taralynn; Jawor, Jodie M.; Blickenstaff, Jacob C.

2010-01-01

This study provides an understanding of how different interactive technology tools that are integrated into a Website can be used for teaching undergraduate human anatomy and physiology laboratory students. Technology tools refer to a Website that the authors created to teach the Cardiovascular System that includes dynamic tools such as the…

Web-Enhanced Instruction and Learning: Findings of a Short- and Long-Term Impact Study and Teacher Use of NASA Web Resources

NASA Technical Reports Server (NTRS)

McCarthy, Marianne C.; Grabowski, Barbara L.; Koszalka, Tiffany

2003-01-01

Over a three-year period, researchers and educators from the Pennsylvania State University (PSU), University Park, Pennsylvania, and the NASA Dryden Flight Research Center (DFRC), Edwards, California, worked together to analyze, develop, implement and evaluate materials and tools that enable teachers to use NASA Web resources effectively for teaching science, mathematics, technology and geography. Two conference publications and one technical paper have already been published as part of this educational research series on Web-based instruction and learning. This technical paper, Web-Enhanced Instruction and Learning: Findings of a Short- and Long-Term Impact Study, is the culminating report in this educational research series and is based on the final report submitted to NASA. This report describes the broad spectrum of data gathered from teachers about their experiences using NASA Web resources in the classroom. It also describes participating teachers responses and feedback about the use of the NASA Web-Enhanced Learning Environment Strategies reflection tool on their teaching practices. The reflection tool was designed to help teachers merge the vast array of NASA resources with the best teaching methods, taking into consideration grade levels, subject areas and teaching preferences. The teachers described their attitudes toward technology and innovation in the classroom and their experiences and perceptions as they attempted to integrate Web resources into science, mathematics, technology and geography instruction.

WebCT: integrating computer-mediated communication and resource delivery into a new problem-based curriculum.

PubMed

McLean, Michelle; Murrell, Kathy

2002-03-01

WebCT, front-end software for Internet-delivered material, became an integral part of a problem-based learning, student-centred curriculum introduced in January 2001 at the Nelson R. Mandela School of Medicine (South Africa). A template for six curriculum and two supplementary modules was developed. Organiser and Tool pages were added and files uploaded as each module progressed. This study provides feedback from students with regard to the value of WebCT in their curriculum, as well as discussing the value of WebCT for the delivery of digitized material (e.g., images, videos, PowerPoint presentations). In an anonymous survey following the completion of the first module, students, apparently irrespective of their level of computer literacy, responded positively to the communication facility between staff and students and amongst students, the resources and the URLs. Based on these preliminary responses, WebCT courses for all six modules were developed during 2001. With Faculty support, WebCT will probably be integrated into the rest of the MBChB programme. It will be particularly useful when students are off campus, undertaking electives and community service in the later years.

Multi-Element Integrated Project Planning at Kennedy Space Center

NASA Technical Reports Server (NTRS)

Mullon, Robert

2008-01-01

This presentation demonstrates how the ASRC Scheduling team developed working practices to support multiple NASA and ASRC Project Managers using the enterprise capabilities of Primavera P6 and P6 Web Access. This work has proceeded as part of Kennedy Ground Systems' preparation for its transition from the Shuttle Program to the Constellation Program. The presenters will cover Primavera's enterprise-class capabilities for schedule development, integrated critical path analysis, and reporting, as well as advanced Primavera P6 Web Access tools and techniques for communicating project status.

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.

I Help, Therefore, I Learn: Service Learning on Web 2.0 in an EFL Speaking Class

ERIC Educational Resources Information Center

Sun, Yu-Chih; Yang, Fang-Ying

2015-01-01

The present study integrates service learning into English as a Foreign Language (EFL) speaking class using Web 2.0 tools--YouTube and Facebook--as platforms. Fourteen undergraduate students participated in the study. The purpose of the service-learning project was to link service learning with oral communication training in an EFL speaking class…

The Unseen Digital Divide: Urban, Suburban, and Rural Teacher Use and Perceptions of Web-Based Classroom Technologies

ERIC Educational Resources Information Center

Kormos, Erik M.

2018-01-01

This quantitative study investigated the differences in perceptions and attitudes toward technology integration of K-12 public school teachers in rural, suburban, and urban environments. The purpose was to examine the relationship between frequency of use and perception of effectiveness of web-based learning tools based upon the type of school…

BEAT: A Web-Based Boolean Expression Fault-Based Test Case Generation Tool

ERIC Educational Resources Information Center

Chen, T. Y.; Grant, D. D.; Lau, M. F.; Ng, S. P.; Vasa, V. R.

2006-01-01

BEAT is a Web-based system that generates fault-based test cases from Boolean expressions. It is based on the integration of our several fault-based test case selection strategies. The generated test cases are considered to be fault-based, because they are aiming at the detection of particular faults. For example, when the Boolean expression is in…

Technology in ELT: English Teachers Investigate Animoto and Fotobabble

ERIC Educational Resources Information Center

Coskun, Abdullah; Marlowe, Zoe

2015-01-01

Because of being socially interactive, portable and multimodal, the Internet has had an impact on the field of foreign language education (Warschauer, 2001), and Web 2.0 tools have become integral parts of our everyday teaching. Thus, the aims of this study are twofold: On the one hand, it aims to introduce Animoto and Fotobabble as free Web 2.0…

Toward a Model of Sources of Influence in Online Education: Cognitive Learning and the Effects of Web 2.0

ERIC Educational Resources Information Center

Carr, Caleb T.; Zube, Paul; Dickens, Eric; Hayter, Carolyn A.; Barterian, Justin A.

2013-01-01

To explore the integration of education processes into social media, we tested an initial model of student learning via interactive web tools and theorized three sources of influence: interpersonal, intrapersonal, and masspersonal. Three-hundred thirty-seven students observed an online lecture and then completed a series of scales. Structural…

Beyond accuracy: creating interoperable and scalable text-mining web services.

PubMed

Wei, Chih-Hsuan; Leaman, Robert; Lu, Zhiyong

2016-06-15

The biomedical literature is a knowledge-rich resource and an important foundation for future research. With over 24 million articles in PubMed and an increasing growth rate, research in automated text processing is becoming increasingly important. We report here our recently developed web-based text mining services for biomedical concept recognition and normalization. Unlike most text-mining software tools, our web services integrate several state-of-the-art entity tagging systems (DNorm, GNormPlus, SR4GN, tmChem and tmVar) and offer a batch-processing mode able to process arbitrary text input (e.g. scholarly publications, patents and medical records) in multiple formats (e.g. BioC). We support multiple standards to make our service interoperable and allow simpler integration with other text-processing pipelines. To maximize scalability, we have preprocessed all PubMed articles, and use a computer cluster for processing large requests of arbitrary text. Our text-mining web service is freely available at http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/tmTools/#curl : Zhiyong.Lu@nih.gov. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the US.

Casimage project: a digital teaching files authoring environment.

PubMed

Rosset, Antoine; Muller, Henning; Martins, Martina; Dfouni, Natalia; Vallée, Jean-Paul; Ratib, Osman

2004-04-01

The goal of the Casimage project is to offer an authoring and editing environment integrated with the Picture Archiving and Communication Systems (PACS) for creating image-based electronic teaching files. This software is based on a client/server architecture allowing remote access of users to a central database. This authoring environment allows radiologists to create reference databases and collection of digital images for teaching and research directly from clinical cases being reviewed on PACS diagnostic workstations. The environment includes all tools to create teaching files, including textual description, annotations, and image manipulation. The software also allows users to generate stand-alone CD-ROMs and web-based teaching files to easily share their collections. The system includes a web server compatible with the Medical Imaging Resource Center standard (MIRC, http://mirc.rsna.org) to easily integrate collections in the RSNA web network dedicated to teaching files. This software could be installed on any PACS workstation to allow users to add new cases at any time and anywhere during clinical operations. Several images collections were created with this tool, including thoracic imaging that was subsequently made available on a CD-Rom and on our web site and through the MIRC network for public access.

IRIS Earthquake Browser with Integration to the GEON IDV for 3-D Visualization of Hypocenters.

NASA Astrophysics Data System (ADS)

Weertman, B. R.

2007-12-01

We present a new generation of web based earthquake query tool - the IRIS Earthquake Browser (IEB). The IEB combines the DMC's large set of earthquake catalogs (provided by USGS/NEIC, ISC and the ANF) with the popular Google Maps web interface. With the IEB you can quickly and easily find earthquakes in any region of the globe. Using Google's detailed satellite images, earthquakes can be easily co-located with natural geographic features such as volcanoes as well as man made features such as commercial mines. A set of controls allow earthquakes to be filtered by time, magnitude, and depth range as well as catalog name, contributor name and magnitude type. Displayed events can be easily exported in NetCDF format into the GEON Integrated Data Viewer (IDV) where hypocenters may be visualized in three dimensions. Looking "under the hood", the IEB is based on AJAX technology and utilizes REST style web services hosted at the IRIS DMC. The IEB is part of a broader effort at the DMC aimed at making our data holdings available via web services. The IEB is useful both educationally and as a research tool.

COMAN: a web server for comprehensive metatranscriptomics analysis.

PubMed

Ni, Yueqiong; Li, Jun; Panagiotou, Gianni

2016-08-11

Microbiota-oriented studies based on metagenomic or metatranscriptomic sequencing have revolutionised our understanding on microbial ecology and the roles of both clinical and environmental microbes. The analysis of massive metatranscriptomic data requires extensive computational resources, a collection of bioinformatics tools and expertise in programming. We developed COMAN (Comprehensive Metatranscriptomics Analysis), a web-based tool dedicated to automatically and comprehensively analysing metatranscriptomic data. COMAN pipeline includes quality control of raw reads, removal of reads derived from non-coding RNA, followed by functional annotation, comparative statistical analysis, pathway enrichment analysis, co-expression network analysis and high-quality visualisation. The essential data generated by COMAN are also provided in tabular format for additional analysis and integration with other software. The web server has an easy-to-use interface and detailed instructions, and is freely available at http://sbb.hku.hk/COMAN/ CONCLUSIONS: COMAN is an integrated web server dedicated to comprehensive functional analysis of metatranscriptomic data, translating massive amount of reads to data tables and high-standard figures. It is expected to facilitate the researchers with less expertise in bioinformatics in answering microbiota-related biological questions and to increase the accessibility and interpretation of microbiota RNA-Seq data.

Hosted Services for Advanced V and V Technologies: An Approach to Achieving Adoption without the Woes of Usage

NASA Technical Reports Server (NTRS)

Koga, Dennis (Technical Monitor); Penix, John; Markosian, Lawrence Z.; OMalley, Owen; Brew, William A.

2003-01-01

Attempts to achieve widespread use of software verification tools have been notably unsuccessful. Even 'straightforward', classic, and potentially effective verification tools such as lint-like tools face limits on their acceptance. These limits are imposed by the expertise required applying the tools and interpreting the results, the high false positive rate of many verification tools, and the need to integrate the tools into development environments. The barriers are even greater for more complex advanced technologies such as model checking. Web-hosted services for advanced verification technologies may mitigate these problems by centralizing tool expertise. The possible benefits of this approach include eliminating the need for software developer expertise in tool application and results filtering, and improving integration with other development tools.

JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing.

PubMed

Brown, David K; Penkler, David L; Musyoka, Thommas M; Bishop, Özlem Tastan

2015-01-01

Complex computational pipelines are becoming a staple of modern scientific research. Often these pipelines are resource intensive and require days of computing time. In such cases, it makes sense to run them over high performance computing (HPC) clusters where they can take advantage of the aggregated resources of many powerful computers. In addition to this, researchers often want to integrate their workflows into their own web servers. In these cases, software is needed to manage the submission of jobs from the web interface to the cluster and then return the results once the job has finished executing. We have developed the Job Management System (JMS), a workflow management system and web interface for high performance computing (HPC). JMS provides users with a user-friendly web interface for creating complex workflows with multiple stages. It integrates this workflow functionality with the resource manager, a tool that is used to control and manage batch jobs on HPC clusters. As such, JMS combines workflow management functionality with cluster administration functionality. In addition, JMS provides developer tools including a code editor and the ability to version tools and scripts. JMS can be used by researchers from any field to build and run complex computational pipelines and provides functionality to include these pipelines in external interfaces. JMS is currently being used to house a number of bioinformatics pipelines at the Research Unit in Bioinformatics (RUBi) at Rhodes University. JMS is an open-source project and is freely available at https://github.com/RUBi-ZA/JMS.

JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing

PubMed Central

Brown, David K.; Penkler, David L.; Musyoka, Thommas M.; Bishop, Özlem Tastan

2015-01-01

Complex computational pipelines are becoming a staple of modern scientific research. Often these pipelines are resource intensive and require days of computing time. In such cases, it makes sense to run them over high performance computing (HPC) clusters where they can take advantage of the aggregated resources of many powerful computers. In addition to this, researchers often want to integrate their workflows into their own web servers. In these cases, software is needed to manage the submission of jobs from the web interface to the cluster and then return the results once the job has finished executing. We have developed the Job Management System (JMS), a workflow management system and web interface for high performance computing (HPC). JMS provides users with a user-friendly web interface for creating complex workflows with multiple stages. It integrates this workflow functionality with the resource manager, a tool that is used to control and manage batch jobs on HPC clusters. As such, JMS combines workflow management functionality with cluster administration functionality. In addition, JMS provides developer tools including a code editor and the ability to version tools and scripts. JMS can be used by researchers from any field to build and run complex computational pipelines and provides functionality to include these pipelines in external interfaces. JMS is currently being used to house a number of bioinformatics pipelines at the Research Unit in Bioinformatics (RUBi) at Rhodes University. JMS is an open-source project and is freely available at https://github.com/RUBi-ZA/JMS. PMID:26280450

Web-based platform for collaborative medical imaging research

NASA Astrophysics Data System (ADS)

Rittner, Leticia; Bento, Mariana P.; Costa, André L.; Souza, Roberto M.; Machado, Rubens C.; Lotufo, Roberto A.

2015-03-01

Medical imaging research depends basically on the availability of large image collections, image processing and analysis algorithms, hardware and a multidisciplinary research team. It has to be reproducible, free of errors, fast, accessible through a large variety of devices spread around research centers and conducted simultaneously by a multidisciplinary team. Therefore, we propose a collaborative research environment, named Adessowiki, where tools and datasets are integrated and readily available in the Internet through a web browser. Moreover, processing history and all intermediate results are stored and displayed in automatic generated web pages for each object in the research project or clinical study. It requires no installation or configuration from the client side and offers centralized tools and specialized hardware resources, since processing takes place in the cloud.

Web-Based Architecture to Enable Compute-Intensive CAD Tools and Multi-user Synchronization in Teleradiology

NASA Astrophysics Data System (ADS)

Mehta, Neville; Kompalli, Suryaprakash; Chaudhary, Vipin

Teleradiology is the electronic transmission of radiological patient images, such as x-rays, CT, or MR across multiple locations. The goal could be interpretation, consultation, or medical records keeping. Information technology solutions have enabled electronic records and their associated benefits are evident in health care today. However, salient aspects of collaborative interfaces, and computer assisted diagnostic (CAD) tools are yet to be integrated into workflow designs. The Computer Assisted Diagnostics and Interventions (CADI) group at the University at Buffalo has developed an architecture that facilitates web-enabled use of CAD tools, along with the novel concept of synchronized collaboration. The architecture can support multiple teleradiology applications and case studies are presented here.

Evaluation of a web based informatics system with data mining tools for predicting outcomes with quantitative imaging features in stroke rehabilitation clinical trials

NASA Astrophysics Data System (ADS)

Wang, Ximing; Kim, Bokkyu; Park, Ji Hoon; Wang, Erik; Forsyth, Sydney; Lim, Cody; Ravi, Ragini; Karibyan, Sarkis; Sanchez, Alexander; Liu, Brent

2017-03-01

Quantitative imaging biomarkers are used widely in clinical trials for tracking and evaluation of medical interventions. Previously, we have presented a web based informatics system utilizing quantitative imaging features for predicting outcomes in stroke rehabilitation clinical trials. The system integrates imaging features extraction tools and a web-based statistical analysis tool. The tools include a generalized linear mixed model(GLMM) that can investigate potential significance and correlation based on features extracted from clinical data and quantitative biomarkers. The imaging features extraction tools allow the user to collect imaging features and the GLMM module allows the user to select clinical data and imaging features such as stroke lesion characteristics from the database as regressors and regressands. This paper discusses the application scenario and evaluation results of the system in a stroke rehabilitation clinical trial. The system was utilized to manage clinical data and extract imaging biomarkers including stroke lesion volume, location and ventricle/brain ratio. The GLMM module was validated and the efficiency of data analysis was also evaluated.

Science Initiatives of the US Virtual Astronomical Observatory

NASA Astrophysics Data System (ADS)

Hanisch, R. J.

2012-09-01

The United States Virtual Astronomical Observatory program is the operational facility successor to the National Virtual Observatory development project. The primary goal of the US VAO is to build on the standards, protocols, and associated infrastructure developed by NVO and the International Virtual Observatory Alliance partners and to bring to fruition a suite of applications and web-based tools that greatly enhance the research productivity of professional astronomers. To this end, and guided by the advice of our Science Council (Fabbiano et al. 2011), we have focused on five science initiatives in the first two years of VAO operations: 1) scalable cross-comparisons between astronomical source catalogs, 2) dynamic spectral energy distribution construction, visualization, and model fitting, 3) integration and periodogram analysis of time series data from the Harvard Time Series Center and NASA Star and Exoplanet Database, 4) integration of VO data discovery and access tools into the IRAF data analysis environment, and 5) a web-based portal to VO data discovery, access, and display tools. We are also developing tools for data linking and semantic discovery, and have a plan for providing data mining and advanced statistical analysis resources for VAO users. Initial versions of these applications and web-based services are being released over the course of the summer and fall of 2011, with further updates and enhancements planned for throughout 2012 and beyond.

Rtools: a web server for various secondary structural analyses on single RNA sequences.

PubMed

Hamada, Michiaki; Ono, Yukiteru; Kiryu, Hisanori; Sato, Kengo; Kato, Yuki; Fukunaga, Tsukasa; Mori, Ryota; Asai, Kiyoshi

2016-07-08

The secondary structures, as well as the nucleotide sequences, are the important features of RNA molecules to characterize their functions. According to the thermodynamic model, however, the probability of any secondary structure is very small. As a consequence, any tool to predict the secondary structures of RNAs has limited accuracy. On the other hand, there are a few tools to compensate the imperfect predictions by calculating and visualizing the secondary structural information from RNA sequences. It is desirable to obtain the rich information from those tools through a friendly interface. We implemented a web server of the tools to predict secondary structures and to calculate various structural features based on the energy models of secondary structures. By just giving an RNA sequence to the web server, the user can get the different types of solutions of the secondary structures, the marginal probabilities such as base-paring probabilities, loop probabilities and accessibilities of the local bases, the energy changes by arbitrary base mutations as well as the measures for validations of the predicted secondary structures. The web server is available at http://rtools.cbrc.jp, which integrates software tools, CentroidFold, CentroidHomfold, IPKnot, CapR, Raccess, Rchange and RintD. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Using Web-Based Collaborative Forecasting to Enhance Information Literacy and Disciplinary Knowledge

ERIC Educational Resources Information Center

Buckley, Patrick; Doyle, Elaine

2016-01-01

This paper outlines how an existing collaborative forecasting tool called a prediction market (PM) can be integrated into an educational context to enhance information literacy skills and cognitive disciplinary knowledge. The paper makes a number of original contributions. First, it describes how this tool can be packaged as a pedagogical…

Leading Pedagogical Change with Innovative Web Tools and Social Media

ERIC Educational Resources Information Center

McLoughlin, Catherine

2011-01-01

Today, in a globalised, digital world, leadership challenges in the adoption and integration of emerging social software tools to support learning abound. Today's students, who have grown up in technology saturated environments, have never known a world without the internet, mobile phones, video on demand and personal computers. Leaders and…

RacerGISOnline: Enhancing Learning in Marketing Classes with Web-Based Business GIS

ERIC Educational Resources Information Center

Miller, Fred L.; Mangold, W. Glynn; Roach, Joy; Brockway, Gary; Johnston, Timothy; Linnhoff, Stefan; McNeely, Sam; Smith, Kathy; Holmes, Terence

2014-01-01

Geographic Information Systems (GIS) offer geospatial analytical tools with great potential for applications in marketing decision making. However, for various reasons, the rate of adoption of these tools in academic marketing programs has lagged behind that of marketing practitioners. RacerGISOnline is an innovative approach to integrating these…

Fuels planning: science synthesis and integration; environmental consequences fact sheet 13: Root Disease Analyzer-Armillaria Response Tool (ART)

Treesearch

Geral I. McDonald; Philip D. Tanimoto; Thomas M. Rice; David E. Hall; Jane E. Stewart; Paul J. Zambino; Jonalea R. Tonn; Ned B. Klopfenstein; Mee-Sook Kim

2005-01-01

The Root Disease Analyzer-Armillaria Response Tool (ART) is a Web-based tool that estimates Armillaria root disease risk in dry forests of the Western United States. This fact sheet identifies the intended users and uses, required inputs, what the model does and does not do, and tells the user how to obtain the model.

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

PubMed

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

2016-12-01

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

VIPER: a web application for rapid expert review of variant calls.

PubMed

Wöste, Marius; Dugas, Martin

2018-06-01

With the rapid development in next-generation sequencing, cost and time requirements for genomic sequencing are decreasing, enabling applications in many areas such as cancer research. Many tools have been developed to analyze genomic variation ranging from single nucleotide variants to whole chromosomal aberrations. As sequencing throughput increases, the number of variants called by such tools also grows. Often employed manual inspection of such calls is thus becoming a time-consuming procedure. We developed the Variant InsPector and Expert Rating tool (VIPER) to speed up this process by integrating the Integrative Genomics Viewer into a web application. Analysts can then quickly iterate through variants, apply filters and make decisions based on the generated images and variant metadata. VIPER was successfully employed in analyses with manual inspection of more than 10 000 calls. VIPER is implemented in Java and Javascript and is freely available at https://github.com/MarWoes/viper. marius.woeste@uni-muenster.de. Supplementary data are available at Bioinformatics online.

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

Geothopica and the interactive analysis and visualization of the updated Italian National Geothermal Database

NASA Astrophysics Data System (ADS)

Trumpy, Eugenio; Manzella, Adele

2017-02-01

The Italian National Geothermal Database (BDNG), is the largest collection of Italian Geothermal data and was set up in the 1980s. It has since been updated both in terms of content and management tools: information on deep wells and thermal springs (with temperature > 30 °C) are currently organized and stored in a PostgreSQL relational database management system, which guarantees high performance, data security and easy access through different client applications. The BDNG is the core of the Geothopica web site, whose webGIS tool allows different types of user to access geothermal data, to visualize multiple types of datasets, and to perform integrated analyses. The webGIS tool has been recently improved by two specially designed, programmed and implemented visualization tools to display data on well lithology and underground temperatures. This paper describes the contents of the database and its software and data update, as well as the webGIS tool including the new tools for data lithology and temperature visualization. The geoinformation organized in the database and accessible through Geothopica is of use not only for geothermal purposes, but also for any kind of georesource and CO2 storage project requiring the organization of, and access to, deep underground data. Geothopica also supports project developers, researchers, and decision makers in the assessment, management and sustainable deployment of georesources.

Information and Communication Technologies in Enhancing Learning Ability in Secondary Schools in Edo State, Nigeria

ERIC Educational Resources Information Center

Osagie, Roseline O.

2012-01-01

The dismal results of 2011, 2010, 2009, and previous years WAEC and NECO Senior School Certificate Examinations (SSCE) show the pitiable state of education in secondary schools in Nigeria. The youths of today live in a digital age. Web technologies and sites have become an integral part of the youth culture. Today's youths use the web tools to…

Hermes, the Information Messenger, Integrating Information Services and Delivering Them to the End User.

ERIC Educational Resources Information Center

Coello-Coutino, Gerardo; Ainsworth, Shirley; Escalante-Gonzalbo, Ana Marie

2002-01-01

Describes Hermes, a research tool that uses specially designed acquisition, parsing and presentation methods to integrate information resources on the Internet, from searching in disparate bibliographic databases, to accessing full text articles online, and developing a web of information associated with each reference via one common interface.…

An Integrated Pest Management Tool for Evaluating Schools

ERIC Educational Resources Information Center

Bennett, Blake; Hurley, Janet; Merchant, Mike

2016-01-01

Having the ability to assess pest problems in schools is essential for a successful integrated pest management (IPM) program. However, such expertise can be costly and is not available to all school districts across the United States. The web-based IPM Calculator was developed to address this problem. By answering questions about the condition of…

Generic Service Integration in Adaptive Learning Experiences Using IMS Learning Design

ERIC Educational Resources Information Center

de-la-Fuente-Valentin, Luis; Pardo, Abelardo; Kloos, Carlos Delgado

2011-01-01

IMS Learning Design is a specification to capture the orchestration taking place in a learning scenario. This paper presents an extension called Generic Service Integration. This paradigm allows a bidirectional communication between the course engine in charge of the orchestration and conventional Web 2.0 tools. This communication allows the…

Integration of e-Management, e-Development and e-Learning Technologies for Blended Course Delivery

ERIC Educational Resources Information Center

Johnson, Lynn E.; Tang, Michael

2005-01-01

This paper describes and assesses a pre-engineering curriculum development project called Foundations of Engineering, Science and Technology (FEST). FEST integrates web-based technologies into an inter-connected system to enable delivery of a blended program at multiple institutions. Tools and systems described include 1) technologies to deliver…

Technology Integration by General Education Teachers of English Language Learners

ERIC Educational Resources Information Center

Anglin, Marie Simone

2017-01-01

There is a growing population of English language learners (ELLs) in elementary schools across the United States, and a current academic achievement gap between ELLs and non-ELLs. Researchers have found that integration of Web 2.0 tools has benefitted ELLs in language learning settings, outside of the general classroom. The research problem…

Matching Alternative Addresses: a Semantic Web Approach

NASA Astrophysics Data System (ADS)

Ariannamazi, S.; Karimipour, F.; Hakimpour, F.

2015-12-01

Rapid development of crowd-sourcing or volunteered geographic information (VGI) provides opportunities for authoritatives that deal with geospatial information. Heterogeneity of multiple data sources and inconsistency of data types is a key characteristics of VGI datasets. The expansion of cities resulted in the growing number of POIs in the OpenStreetMap, a well-known VGI source, which causes the datasets to outdate in short periods of time. These changes made to spatial and aspatial attributes of features such as names and addresses might cause confusion or ambiguity in the processes that require feature's literal information like addressing and geocoding. VGI sources neither will conform specific vocabularies nor will remain in a specific schema for a long period of time. As a result, the integration of VGI sources is crucial and inevitable in order to avoid duplication and the waste of resources. Information integration can be used to match features and qualify different annotation alternatives for disambiguation. This study enhances the search capabilities of geospatial tools with applications able to understand user terminology to pursuit an efficient way for finding desired results. Semantic web is a capable tool for developing technologies that deal with lexical and numerical calculations and estimations. There are a vast amount of literal-spatial data representing the capability of linguistic information in knowledge modeling, but these resources need to be harmonized based on Semantic Web standards. The process of making addresses homogenous generates a helpful tool based on spatial data integration and lexical annotation matching and disambiguating.

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases

PubMed Central

Kobayashi, Norio; Ishii, Manabu; Takahashi, Satoshi; Mochizuki, Yoshiki; Matsushima, Akihiro; Toyoda, Tetsuro

2011-01-01

Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross-integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 8.2 million data records, integrated as Linked Open or Private Data (LOD/LPD) using SciNetS.org, the Scientists' Networking System. The huge quantity of linked data this database integration framework covers is based on the Semantic Web, where researchers collaborate by managing metadata across public and private databases in a secured data space. This outstripped the data query capacity of existing interface tools like SPARQL. Actual research also requires specialized tools for data analysis using raw original data. To solve these challenges, in December 2009 we developed the lightweight Semantic-JSON interface to access each fragment of linked and raw life sciences data securely under the control of programming languages popularly used by bioinformaticians such as Perl and Ruby. Researchers successfully used the interface across 28 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers. Semantic-JSON services of SciNetS.org are provided at http://semanticjson.org. PMID:21632604

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.

Improving Adherence to Smoking Cessation Treatment: Intervention Effects in a Web-Based Randomized Trial.

PubMed

Graham, Amanda L; Papandonatos, George D; Cha, Sarah; Erar, Bahar; Amato, Michael S; Cobb, Nathan K; Niaura, Raymond S; Abrams, David B

2017-03-01

Web-based smoking cessation interventions can deliver evidence-based treatments to a wide swath of the population, but effectiveness is often limited by insufficient adherence to proven treatment components. This study evaluated the impact of a social network (SN) intervention and free nicotine replacement therapy (NRT) on adherence to evidence-based components of smoking cessation treatment in the context of a Web-based intervention. A sample of adult U.S. smokers (N = 5290) was recruited via BecomeAnEX.org, a free smoking cessation Web site. Smokers were randomized to one of four arms: (1) an interactive, evidence-based smoking cessation Web site (WEB) alone; (2) WEB in conjunction with an SN intervention designed to integrate participants into the online community (WEB+SN); (3) WEB plus free NRT (WEB+NRT); and (4) the combination of all treatments (WEB+SN+NRT). Adherence outcomes assessed at 3-month follow-up were as follows: Web site utilization metrics, use of skills training components, intratreatment social support, and pharmacotherapy use. WEB+SN+NRT outperformed all others on Web site utilization metrics, use of practical counseling tools, intratreatment social support, and NRT use. It was the only intervention to promote the sending of private messages and the viewing of community pages over WEB alone. Both social network arms outperformed WEB on most metrics of online community engagement. Both NRT arms showed higher medication use compared to WEB alone. This study demonstrated the effectiveness of two approaches for improving adherence to evidence-based components of smoking cessation treatment. Integrated approaches to medication provision and social network engagement can enhance adherence to components known to improve cessation. This study demonstrated that an integrated approach to medication provision and social network integration, when delivered through an online program, can enhance adherence across all three recommended components of an evidence-based smoking cessation program (skills training, social support, and pharmacotherapy use). Nicotine replacement therapy-when provided as part of an integrated program-increases adherence to other program elements, which in turn augment its own therapeutic effects. An explicit focus on approaches to improve treatment adherence is an important first step to identifying leverage points for optimizing intervention effectiveness. © The Author 2016. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Extraction, integration and analysis of alternative splicing and protein structure distributed information

PubMed Central

D'Antonio, Matteo; Masseroli, Marco

2009-01-01

Background Alternative splicing has been demonstrated to affect most of human genes; different isoforms from the same gene encode for proteins which differ for a limited number of residues, thus yielding similar structures. This suggests possible correlations between alternative splicing and protein structure. In order to support the investigation of such relationships, we have developed the Alternative Splicing and Protein Structure Scrutinizer (PASS), a Web application to automatically extract, integrate and analyze human alternative splicing and protein structure data sparsely available in the Alternative Splicing Database, Ensembl databank and Protein Data Bank. Primary data from these databases have been integrated and analyzed using the Protein Identifier Cross-Reference, BLAST, CLUSTALW and FeatureMap3D software tools. Results A database has been developed to store the considered primary data and the results from their analysis; a system of Perl scripts has been implemented to automatically create and update the database and analyze the integrated data; a Web interface has been implemented to make the analyses easily accessible; a database has been created to manage user accesses to the PASS Web application and store user's data and searches. Conclusion PASS automatically integrates data from the Alternative Splicing Database with protein structure data from the Protein Data Bank. Additionally, it comprehensively analyzes the integrated data with publicly available well-known bioinformatics tools in order to generate structural information of isoform pairs. Further analysis of such valuable information might reveal interesting relationships between alternative splicing and protein structure differences, which may be significantly associated with different functions. PMID:19828075

Web tools for effective retrieval, visualization, and evaluation of cardiology medical images and records

NASA Astrophysics Data System (ADS)

Masseroli, Marco; Pinciroli, Francesco

2000-12-01

To provide easy retrieval, integration and evaluation of multimodal cardiology images and data in a web browser environment, distributed application technologies and java programming were used to implement a client-server architecture based on software agents. The server side manages secure connections and queries to heterogeneous remote databases and file systems containing patient personal and clinical data. The client side is a Java applet running in a web browser and providing a friendly medical user interface to perform queries on patient and medical test dat and integrate and visualize properly the various query results. A set of tools based on Java Advanced Imaging API enables to process and analyze the retrieved cardiology images, and quantify their features in different regions of interest. The platform-independence Java technology makes the developed prototype easy to be managed in a centralized form and provided in each site where an intranet or internet connection can be located. Giving the healthcare providers effective tools for querying, visualizing and evaluating comprehensively cardiology medical images and records in all locations where they can need them- i.e. emergency, operating theaters, ward, or even outpatient clinics- the developed prototype represents an important aid in providing more efficient diagnoses and medical treatments.

Diy Geospatial Web Service Chains: Geochaining Make it Easy

NASA Astrophysics Data System (ADS)

Wu, H.; You, L.; Gui, Z.

2011-08-01

It is a great challenge for beginners to create, deploy and utilize a Geospatial Web Service Chain (GWSC). People in Computer Science are usually not familiar with geospatial domain knowledge. Geospatial practitioners may lack the knowledge about web services and service chains. The end users may lack both. However, integrated visual editing interfaces, validation tools, and oneclick deployment wizards may help to lower the learning curve and improve modelling skills so beginners will have a better experience. GeoChaining is a GWSC modelling tool designed and developed based on these ideas. GeoChaining integrates visual editing, validation, deployment, execution etc. into a unified platform. By employing a Virtual Globe, users can intuitively visualize raw data and results produced by GeoChaining. All of these features allow users to easily start using GWSC, regardless of their professional background and computer skills. Further, GeoChaining supports GWSC model reuse, meaning that an entire GWSC model created or even a specific part can be directly reused in a new model. This greatly improves the efficiency of creating a new GWSC, and also contributes to the sharing and interoperability of GWSC.

A web-enabled system for integrated assessment of watershed development

USGS Publications Warehouse

Dymond, R.; Lohani, V.; Regmi, B.; Dietz, R.

2004-01-01

Researchers at Virginia Tech have put together the primary structure of a web enabled integrated modeling system that has potential to be a planning tool to help decision makers and stakeholders in making appropriate watershed management decisions. This paper describes the integrated system, including data sources, collection, analysis methods, system software and design, and issues of integrating the various component models. The integrated system has three modeling components, namely hydrology, economics, and fish health, and is accompanied by descriptive 'help files.' Since all three components have a related spatial aspect, GIS technology provides the integration platform. When completed, a user will access the integrated system over the web to choose pre-selected land development patterns to create a 'what if' scenario using an easy-to-follow interface. The hydrologic model simulates effects of the scenario on annual runoff volume, flood peaks of various return periods, and ground water recharge. The economics model evaluates tax revenue and fiscal costs as a result of a new land development scenario. The fish health model evaluates effects of new land uses in zones of influence to the health of fish populations in those areas. Copyright ASCE 2004.

SEPHYDRO: An Integrated Multi-Filter Web-Based Tool for Baseflow Separation

NASA Astrophysics Data System (ADS)

Serban, D.; MacQuarrie, K. T. B.; Popa, A.

2017-12-01

Knowledge of baseflow contributions to streamflow is important for understanding watershed scale hydrology, including groundwater-surface water interactions, impact of geology and landforms on baseflow, estimation of groundwater recharge rates, etc. Baseflow (or hydrograph) separation methods can be used as supporting tools in many areas of environmental research, such as the assessment of the impact of agricultural practices, urbanization and climate change on surface water and groundwater. Over the past few decades various digital filtering and graphically-based methods have been developed in an attempt to improve the assessment of the dynamics of the various sources of streamflow (e.g. groundwater, surface runoff, subsurface flow); however, these methods are not available under an integrated platform and, individually, often require significant effort for implementation. Here we introduce SEPHYDRO, an open access, customizable web-based tool, which integrates 11 algorithms allowing for separation of streamflow hydrographs. The streamlined interface incorporates a reference guide as well as additional information that allows users to import their own data, customize the algorithms, and compare, visualise and export results. The tool includes one-, two- and three-parameter digital filters as well as graphical separation methods and has been successfully applied in Atlantic Canada, in studies dealing with nutrient loading to fresh water and coastal water ecosystems. Future developments include integration of additional separation algorithms as well as incorporation of geochemical separation methods. SEPHYDRO has been developed through a collaborative research effort between the Canadian Rivers Institute, University of New Brunswick (Fredericton, New Brunswick, Canada), Agriculture and Agri-Food Canada and Environment and Climate Change Canada and is currently available at http://canadianriversinstitute.com/tool/

Leveraging Learning Technologies for Collaborative Writing in an Online Pharmacotherapy Course

ERIC Educational Resources Information Center

Pittenger, Amy L.; Olson-Kellogg, Becky

2012-01-01

The purpose of this project was to evaluate the development and delivery of a hypertext case scenario document to be used as the capstone assessment tool for doctoral-level physical therapy students. The integration of Web-based collaborative tools (PBworks[TM] and Google Sites[TM]) allowed students in this all-online course to apply their…

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

PubMed

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

2017-05-01

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

GeneFisher-P: variations of GeneFisher as processes in Bio-jETI

PubMed Central

Lamprecht, Anna-Lena; Margaria, Tiziana; Steffen, Bernhard; Sczyrba, Alexander; Hartmeier, Sven; Giegerich, Robert

2008-01-01

Background PCR primer design is an everyday, but not trivial task requiring state-of-the-art software. We describe the popular tool GeneFisher and explain its recent restructuring using workflow techniques. We apply a service-oriented approach to model and implement GeneFisher-P, a process-based version of the GeneFisher web application, as a part of the Bio-jETI platform for service modeling and execution. We show how to introduce a flexible process layer to meet the growing demand for improved user-friendliness and flexibility. Results Within Bio-jETI, we model the process using the jABC framework, a mature model-driven, service-oriented process definition platform. We encapsulate remote legacy tools and integrate web services using jETI, an extension of the jABC for seamless integration of remote resources as basic services, ready to be used in the process. Some of the basic services used by GeneFisher are in fact already provided as individual web services at BiBiServ and can be directly accessed. Others are legacy programs, and are made available to Bio-jETI via the jETI technology. The full power of service-based process orientation is required when more bioinformatics tools, available as web services or via jETI, lead to easy extensions or variations of the basic process. This concerns for instance variations of data retrieval or alignment tools as provided by the European Bioinformatics Institute (EBI). Conclusions The resulting service- and process-oriented GeneFisher-P demonstrates how basic services from heterogeneous sources can be easily orchestrated in the Bio-jETI platform and lead to a flexible family of specialized processes tailored to specific tasks. PMID:18460174

Environmental impact assessment of rail infrastructure.

DOT National Transportation Integrated Search

2016-01-29

This project resulted in three products: a comprehensive "Sustainable Rail Checklist," a rail planning GIS database, and a web GIS tool that integrates sustainability metrics and facilitates a rapid assessment before a formal NEPA process is implemen...

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.

The Integrated Waste Tracking System - A Flexible Waste Management Tool

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

Anderson, Robert Stephen

2001-02-01

The US Department of Energy (DOE) Idaho National Engineering and Environmental Laboratory (INEEL) has fully embraced a flexible, computer-based tool to help increase waste management efficiency and integrate multiple operational functions from waste generation through waste disposition while reducing cost. The Integrated Waste Tracking System (IWTS)provides comprehensive information management for containerized waste during generation,storage, treatment, transport, and disposal. The IWTS provides all information necessary for facilities to properly manage and demonstrate regulatory compliance. As a platformindependent, client-server and Web-based inventory and compliance system, the IWTS has proven to be a successful tracking, characterization, compliance, and reporting tool that meets themore » needs of both operations and management while providing a high level of management flexibility.« less

Web Based GIS System For Monitoring the Implementation of County Integrated Development Plan a Case Study of Nandi County, Kenya.

NASA Astrophysics Data System (ADS)

Kurui, P. K.; Mutua, F.

2016-12-01

The paper seek to propose a conceptual framework of a way of monitoring and evaluating the implementation of the projects listed in the county integrated development plan by applying the use of the geospatial technologies with the focus being developing a web based GIS system in which the public can be able to track and monitor the progress of implementation of the projects in various parts of the county , although the guidelines developed by the ministry of devolution provides for the inclusion of the implementation monitoring and evaluation framework specifying projects to be implemented during the plan period and specification of veriable indicators it does not provide mechanisms for public participation during implementation and monitoring stage. This calls for a system that the public can interact with. The web based GIS system has been developed using the free open source softwares. Development projects have been categorized into; ongoing, completed and planned It can also be shown that a web based GIS system can be used as an important tool for monitoring the implementation of the CIDP due to its easy to use nature and supported by the fact that internet is easily accessed by the majority of the public making it a powerful tool for public participation.

InteGO2: A web tool for measuring and visualizing gene semantic similarities using Gene Ontology

DOE PAGES

Peng, Jiajie; Li, Hongxiang; Liu, Yongzhuang; ...

2016-08-31

Here, the Gene Ontology (GO) has been used in high-throughput omics research as a major bioinformatics resource. The hierarchical structure of GO provides users a convenient platform for biological information abstraction and hypothesis testing. Computational methods have been developed to identify functionally similar genes. However, none of the existing measurements take into account all the rich information in GO. Similarly, using these existing methods, web-based applications have been constructed to compute gene functional similarities, and to provide pure text-based outputs. Without a graphical visualization interface, it is difficult for result interpretation. As a result, we present InteGO2, a web toolmore » that allows researchers to calculate the GO-based gene semantic similarities using seven widely used GO-based similarity measurements. Also, we provide an integrative measurement that synergistically integrates all the individual measurements to improve the overall performance. Using HTML5 and cytoscape.js, we provide a graphical interface in InteGO2 to visualize the resulting gene functional association networks. In conclusion, InteGO2 is an easy-to-use HTML5 based web tool. With it, researchers can measure gene or gene product functional similarity conveniently, and visualize the network of functional interactions in a graphical interface.« less

InteGO2: A web tool for measuring and visualizing gene semantic similarities using Gene Ontology

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

Peng, Jiajie; Li, Hongxiang; Liu, Yongzhuang

Here, the Gene Ontology (GO) has been used in high-throughput omics research as a major bioinformatics resource. The hierarchical structure of GO provides users a convenient platform for biological information abstraction and hypothesis testing. Computational methods have been developed to identify functionally similar genes. However, none of the existing measurements take into account all the rich information in GO. Similarly, using these existing methods, web-based applications have been constructed to compute gene functional similarities, and to provide pure text-based outputs. Without a graphical visualization interface, it is difficult for result interpretation. As a result, we present InteGO2, a web toolmore » that allows researchers to calculate the GO-based gene semantic similarities using seven widely used GO-based similarity measurements. Also, we provide an integrative measurement that synergistically integrates all the individual measurements to improve the overall performance. Using HTML5 and cytoscape.js, we provide a graphical interface in InteGO2 to visualize the resulting gene functional association networks. In conclusion, InteGO2 is an easy-to-use HTML5 based web tool. With it, researchers can measure gene or gene product functional similarity conveniently, and visualize the network of functional interactions in a graphical interface.« less

GREAT: a web portal for Genome Regulatory Architecture Tools

PubMed Central

Bouyioukos, Costas; Bucchini, François; Elati, Mohamed; Képès, François

2016-01-01

GREAT (Genome REgulatory Architecture Tools) is a novel web portal for tools designed to generate user-friendly and biologically useful analysis of genome architecture and regulation. The online tools of GREAT are freely accessible and compatible with essentially any operating system which runs a modern browser. GREAT is based on the analysis of genome layout -defined as the respective positioning of co-functional genes- and its relation with chromosome architecture and gene expression. GREAT tools allow users to systematically detect regular patterns along co-functional genomic features in an automatic way consisting of three individual steps and respective interactive visualizations. In addition to the complete analysis of regularities, GREAT tools enable the use of periodicity and position information for improving the prediction of transcription factor binding sites using a multi-view machine learning approach. The outcome of this integrative approach features a multivariate analysis of the interplay between the location of a gene and its regulatory sequence. GREAT results are plotted in web interactive graphs and are available for download either as individual plots, self-contained interactive pages or as machine readable tables for downstream analysis. The GREAT portal can be reached at the following URL https://absynth.issb.genopole.fr/GREAT and each individual GREAT tool is available for downloading. PMID:27151196

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

NASA Astrophysics Data System (ADS)

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

2009-12-01

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

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.

Expert system for web based collaborative CAE

NASA Astrophysics Data System (ADS)

Hou, Liang; Lin, Zusheng

2006-11-01

An expert system for web based collaborative CAE was developed based on knowledge engineering, relational database and commercial FEA (Finite element analysis) software. The architecture of the system was illustrated. In this system, the experts' experiences, theories and typical examples and other related knowledge, which will be used in the stage of pre-process in FEA, were categorized into analysis process and object knowledge. Then, the integrated knowledge model based on object-oriented method and rule based method was described. The integrated reasoning process based on CBR (case based reasoning) and rule based reasoning was presented. Finally, the analysis process of this expert system in web based CAE application was illustrated, and an analysis example of a machine tool's column was illustrated to prove the validity of the system.

A Smart Curriculum for Middle-School Science Instruction: A Web-Based Curriculum Integrating Assessment and Instruction.

ERIC Educational Resources Information Center

1996

This paper discusses a model of integrated instruction and assessment called SMART (Special Multimedia Arenas for Refining Thinking). SMART involves interactive use of the Internet and multimedia software. The Internet serves three important functions: it acts as a formative assessment tool by providing individualized feedback to students, creates…

A Web Geographic Information System to share data and explorative analysis tools: The application to West Nile disease in the Mediterranean basin.

PubMed

Savini, Lara; Tora, Susanna; Di Lorenzo, Alessio; Cioci, Daniela; Monaco, Federica; Polci, Andrea; Orsini, Massimiliano; Calistri, Paolo; Conte, Annamaria

2018-01-01

In the last decades an increasing number of West Nile Disease cases was observed in equines and humans in the Mediterranean basin and surveillance systems are set up in numerous countries to manage and control the disease. The collection, storage and distribution of information on the spread of the disease becomes important for a shared intervention and control strategy. To this end, a Web Geographic Information System has been developed and disease data, climatic and environmental remote sensed data, full genome sequences of selected isolated strains are made available. This paper describes the Disease Monitoring Dashboard (DMD) web system application, the tools available for the preliminary analysis on climatic and environmental factors and the other interactive tools for epidemiological analysis. WNV occurrence data are collected from multiple official and unofficial sources. Whole genome sequences and metadata of WNV strains are retrieved from public databases or generated in the framework of the Italian surveillance activities. Climatic and environmental data are provided by NASA website. The Geographical Information System is composed by Oracle 10g Database and ESRI ArcGIS Server 10.03; the web mapping client application is developed with the ArcGIS API for Javascript and Phylocanvas library to facilitate and optimize the mash-up approach. ESRI ArcSDE 10.1 has been used to store spatial data. The DMD application is accessible through a generic web browser at https://netmed.izs.it/networkMediterraneo/. The system collects data through on-line forms and automated procedures and visualizes data as interactive graphs, maps and tables. The spatial and temporal dynamic visualization of disease events is managed by a time slider that returns results on both map and epidemiological curve. Climatic and environmental data can be associated to cases through python procedures and downloaded as Excel files. The system compiles multiple datasets through user-friendly web tools; it integrates entomological, veterinary and human surveillance, molecular information on pathogens and environmental and climatic data. The principal result of the DMD development is the transfer and dissemination of knowledge and technologies to develop strategies for integrated prevention and control measures of animal and human diseases.

The BiSciCol Triplifier: bringing biodiversity data to the Semantic Web.

PubMed

Stucky, Brian J; Deck, John; Conlin, Tom; Ziemba, Lukasz; Cellinese, Nico; Guralnick, Robert

2014-07-29

Recent years have brought great progress in efforts to digitize the world's biodiversity data, but integrating data from many different providers, and across research domains, remains challenging. Semantic Web technologies have been widely recognized by biodiversity scientists for their potential to help solve this problem, yet these technologies have so far seen little use for biodiversity data. Such slow uptake has been due, in part, to the relative complexity of Semantic Web technologies along with a lack of domain-specific software tools to help non-experts publish their data to the Semantic Web. The BiSciCol Triplifier is new software that greatly simplifies the process of converting biodiversity data in standard, tabular formats, such as Darwin Core-Archives, into Semantic Web-ready Resource Description Framework (RDF) representations. The Triplifier uses a vocabulary based on the popular Darwin Core standard, includes both Web-based and command-line interfaces, and is fully open-source software. Unlike most other RDF conversion tools, the Triplifier does not require detailed familiarity with core Semantic Web technologies, and it is tailored to a widely popular biodiversity data format and vocabulary standard. As a result, the Triplifier can often fully automate the conversion of biodiversity data to RDF, thereby making the Semantic Web much more accessible to biodiversity scientists who might otherwise have relatively little knowledge of Semantic Web technologies. Easy availability of biodiversity data as RDF will allow researchers to combine data from disparate sources and analyze them with powerful linked data querying tools. However, before software like the Triplifier, and Semantic Web technologies in general, can reach their full potential for biodiversity science, the biodiversity informatics community must address several critical challenges, such as the widespread failure to use robust, globally unique identifiers for biodiversity data.

Demonstration of New OLAF Capabilities and Technologies

NASA Astrophysics Data System (ADS)

Kingston, C.; Palmer, E.; Stone, J.; Neese, C.; Mueller, B.

2017-06-01

Upgrades to the On-Line Archiving Facility (OLAF) PDS tool are leading to improved usability and additional functionality by integration of JavaScript web app frameworks. Also included is the capability to upload tabular data as CSV files.

WISE Design for Knowledge Integration.

ERIC Educational Resources Information Center

Linn, Marcia C.; Clark, Douglas; Slotta, James D.

2003-01-01

Examines the implementation of Web-based Inquiry Science Environment (WISE), which can incorporate modeling tools and hand-held devices. Describes WISE design team practices, features of the WISE learning environment, and patterns of feature use in WISE library projects. (SOE)

Protein Sequence Annotation Tool (PSAT): A centralized web-based meta-server for high-throughput sequence annotations

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

Leung, Elo; Huang, Amy; Cadag, Eithon

In this study, we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics tools, (2) enable functional annotations and enzyme predictions over large input protein fasta data sets, and (3) provide a web interface for convenient execution of the tools. In this paper, we demonstrate the utility of PSAT by annotating the predicted peptide gene products of Herbaspirillum sp. strain RV1423, importing the results of PSAT into EC2KEGG, and using the resultingmore » functional comparisons to identify a putative catabolic pathway, thereby distinguishing RV1423 from a well annotated Herbaspirillum species. This analysis demonstrates that high-throughput enzyme predictions, provided by PSAT processing, can be used to identify metabolic potential in an otherwise poorly annotated genome. Lastly, PSAT is a meta server that combines the results from several sequence-based annotation and function prediction codes, and is available at http://psat.llnl.gov/psat/. PSAT stands apart from other sequencebased genome annotation systems in providing a high-throughput platform for rapid de novo enzyme predictions and sequence annotations over large input protein sequence data sets in FASTA. PSAT is most appropriately applied in annotation of large protein FASTA sets that may or may not be associated with a single genome.« less

Protein Sequence Annotation Tool (PSAT): A centralized web-based meta-server for high-throughput sequence annotations

DOE PAGES

Leung, Elo; Huang, Amy; Cadag, Eithon; ...

2016-01-20

In this study, we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics tools, (2) enable functional annotations and enzyme predictions over large input protein fasta data sets, and (3) provide a web interface for convenient execution of the tools. In this paper, we demonstrate the utility of PSAT by annotating the predicted peptide gene products of Herbaspirillum sp. strain RV1423, importing the results of PSAT into EC2KEGG, and using the resultingmore » functional comparisons to identify a putative catabolic pathway, thereby distinguishing RV1423 from a well annotated Herbaspirillum species. This analysis demonstrates that high-throughput enzyme predictions, provided by PSAT processing, can be used to identify metabolic potential in an otherwise poorly annotated genome. Lastly, PSAT is a meta server that combines the results from several sequence-based annotation and function prediction codes, and is available at http://psat.llnl.gov/psat/. PSAT stands apart from other sequencebased genome annotation systems in providing a high-throughput platform for rapid de novo enzyme predictions and sequence annotations over large input protein sequence data sets in FASTA. PSAT is most appropriately applied in annotation of large protein FASTA sets that may or may not be associated with a single genome.« less

Wikis, blogs and podcasts: a new generation of Web-based tools for virtual collaborative clinical practice and education.

PubMed

Boulos, Maged N Kamel; Maramba, Inocencio; Wheeler, Steve

2006-08-15

We have witnessed a rapid increase in the use of Web-based 'collaborationware' in recent years. These Web 2.0 applications, particularly wikis, blogs and podcasts, have been increasingly adopted by many online health-related professional and educational services. Because of their ease of use and rapidity of deployment, they offer the opportunity for powerful information sharing and ease of collaboration. Wikis are Web sites that can be edited by anyone who has access to them. The word 'blog' is a contraction of 'Web Log' - an online Web journal that can offer a resource rich multimedia environment. Podcasts are repositories of audio and video materials that can be "pushed" to subscribers, even without user intervention. These audio and video files can be downloaded to portable media players that can be taken anywhere, providing the potential for "anytime, anywhere" learning experiences (mobile learning). Wikis, blogs and podcasts are all relatively easy to use, which partly accounts for their proliferation. The fact that there are many free and Open Source versions of these tools may also be responsible for their explosive growth. Thus it would be relatively easy to implement any or all within a Health Professions' Educational Environment. Paradoxically, some of their disadvantages also relate to their openness and ease of use. With virtually anybody able to alter, edit or otherwise contribute to the collaborative Web pages, it can be problematic to gauge the reliability and accuracy of such resources. While arguably, the very process of collaboration leads to a Darwinian type 'survival of the fittest' content within a Web page, the veracity of these resources can be assured through careful monitoring, moderation, and operation of the collaborationware in a closed and secure digital environment. Empirical research is still needed to build our pedagogic evidence base about the different aspects of these tools in the context of medical/health education. If effectively deployed, wikis, blogs and podcasts could offer a way to enhance students', clinicians' and patients' learning experiences, and deepen levels of learners' engagement and collaboration within digital learning environments. Therefore, research should be conducted to determine the best ways to integrate these tools into existing e-Learning programmes for students, health professionals and patients, taking into account the different, but also overlapping, needs of these three audience classes and the opportunities of virtual collaboration between them. Of particular importance is research into novel integrative applications, to serve as the "glue" to bind the different forms of Web-based collaborationware synergistically in order to provide a coherent wholesome learning experience.

WebBioBank: a new platform for integrating clinical forms and shared neurosignal analyses to support multi-centre studies in Parkinson's Disease.

PubMed

Rossi, Elena; Rosa, Manuela; Rossi, Lorenzo; Priori, Alberto; Marceglia, Sara

2014-12-01

The web-based systems available for multi-centre clinical trials do not combine clinical data collection (Electronic Health Records, EHRs) with signal processing storage and analysis tools. However, in pathophysiological research, the correlation between clinical data and signals is crucial for uncovering the underlying neurophysiological mechanisms. A specific example is the investigation of the mechanisms of action for Deep Brain Stimulation (DBS) used for Parkinson's Disease (PD); the neurosignals recorded from the DBS target structure and clinical data must be investigated. The aim of this study is the development and testing of a new system dedicated to a multi-centre study of Parkinson's Disease that integrates biosignal analysis tools and data collection in a shared and secure environment. We designed a web-based platform (WebBioBank) for managing the clinical data and biosignals of PD patients treated with DBS in different clinical research centres. Homogeneous data collection was ensured in the different centres (Operative Units, OUs). The anonymity of the data was preserved using unique identifiers associated with patients (ID BAC). The patients' personal details and their equivalent ID BACs were archived inside the corresponding OU and were not uploaded on the web-based platform; data sharing occurred using the ID BACs. The system allowed researchers to upload different signal processing functions (in a .dll extension) onto the web-based platform and to combine them to define dedicated algorithms. Four clinical research centres used WebBioBank for 1year. The clinical data from 58 patients treated using DBS were managed, and 186 biosignals were uploaded and classified into 4 categories based on the treatment (pharmacological and/or electrical). The user's satisfaction mean score exceeded the satisfaction threshold. WebBioBank enabled anonymous data sharing for a clinical study conducted at multiple centres and demonstrated the capabilities of the signal processing chain configuration as well as its effectiveness and efficiency for integrating the neurophysiological results with clinical data in multi-centre studies, which will allow the future collection of homogeneous data in large cohorts of patients. Copyright © 2014 Elsevier Inc. All rights reserved.

OmicsNet: a web-based tool for creation and visual analysis of biological networks in 3D space.

PubMed

Zhou, Guangyan; Xia, Jianguo

2018-06-07

Biological networks play increasingly important roles in omics data integration and systems biology. Over the past decade, many excellent tools have been developed to support creation, analysis and visualization of biological networks. However, important limitations remain: most tools are standalone programs, the majority of them focus on protein-protein interaction (PPI) or metabolic networks, and visualizations often suffer from 'hairball' effects when networks become large. To help address these limitations, we developed OmicsNet - a novel web-based tool that allows users to easily create different types of molecular interaction networks and visually explore them in a three-dimensional (3D) space. Users can upload one or multiple lists of molecules of interest (genes/proteins, microRNAs, transcription factors or metabolites) to create and merge different types of biological networks. The 3D network visualization system was implemented using the powerful Web Graphics Library (WebGL) technology that works natively in most major browsers. OmicsNet supports force-directed layout, multi-layered perspective layout, as well as spherical layout to help visualize and navigate complex networks. A rich set of functions have been implemented to allow users to perform coloring, shading, topology analysis, and enrichment analysis. OmicsNet is freely available at http://www.omicsnet.ca.

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

PubMed

Kurt, Serhat

2017-12-08

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

Spatial Data Uncertainty in a Webgis Tool Supporting Sediments Management in Wallonia

NASA Astrophysics Data System (ADS)

Stéphenne, N. R.; Beaumont, B.; Veschkens, M.; Palm, S.; Charlemagne, C.

2015-08-01

This paper describes a WebGIS prototype developed for the Walloon administration to improve the communication and the management of sediments dredging actions carried out in rivers and lakes. In Wallonia, levelling dredged sediments on banks requires an official authorization from the administration. This request refers to geospatial datasets such as the official land use map, the cadastral map or the distance to potential pollution sources. Centralising geodatabases within a web interface facilitate the management of these authorizations for the managers and the central administration. The proposed system integrates various data from disparate sources. Some issues in map scale, spatial search quality and cartographic visualisation are discussed in this paper with the solutions provided. The prototype web application is currently discussed with some potential users in order to understand in which way this tool facilitate the communication, the management and the quality of the authorisation process. The structure of the paper states the why, what, who and how of this communication tool with a special focus on errors and uncertainties.

ICM: a web server for integrated clustering of multi-dimensional biomedical data.

PubMed

He, Song; He, Haochen; Xu, Wenjian; Huang, Xin; Jiang, Shuai; Li, Fei; He, Fuchu; Bo, Xiaochen

2016-07-08

Large-scale efforts for parallel acquisition of multi-omics profiling continue to generate extensive amounts of multi-dimensional biomedical data. Thus, integrated clustering of multiple types of omics data is essential for developing individual-based treatments and precision medicine. However, while rapid progress has been made, methods for integrated clustering are lacking an intuitive web interface that facilitates the biomedical researchers without sufficient programming skills. Here, we present a web tool, named Integrated Clustering of Multi-dimensional biomedical data (ICM), that provides an interface from which to fuse, cluster and visualize multi-dimensional biomedical data and knowledge. With ICM, users can explore the heterogeneity of a disease or a biological process by identifying subgroups of patients. The results obtained can then be interactively modified by using an intuitive user interface. Researchers can also exchange the results from ICM with collaborators via a web link containing a Project ID number that will directly pull up the analysis results being shared. ICM also support incremental clustering that allows users to add new sample data into the data of a previous study to obtain a clustering result. Currently, the ICM web server is available with no login requirement and at no cost at http://biotech.bmi.ac.cn/icm/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Characterizing stroke lesions using digital templates and lesion quantification tools in a web-based imaging informatics system for a large-scale stroke rehabilitation clinical trial

NASA Astrophysics Data System (ADS)

Wang, Ximing; Edwardson, Matthew; Dromerick, Alexander; Winstein, Carolee; Wang, Jing; Liu, Brent

2015-03-01

Previously, we presented an Interdisciplinary Comprehensive Arm Rehabilitation Evaluation (ICARE) imaging informatics system that supports a large-scale phase III stroke rehabilitation trial. The ePR system is capable of displaying anonymized patient imaging studies and reports, and the system is accessible to multiple clinical trial sites and users across the United States via the web. However, the prior multicenter stroke rehabilitation trials lack any significant neuroimaging analysis infrastructure. In stroke related clinical trials, identification of the stroke lesion characteristics can be meaningful as recent research shows that lesion characteristics are related to stroke scale and functional recovery after stroke. To facilitate the stroke clinical trials, we hope to gain insight into specific lesion characteristics, such as vascular territory, for patients enrolled into large stroke rehabilitation trials. To enhance the system's capability for data analysis and data reporting, we have integrated new features with the system: a digital brain template display, a lesion quantification tool and a digital case report form. The digital brain templates are compiled from published vascular territory templates at each of 5 angles of incidence. These templates were updated to include territories in the brainstem using a vascular territory atlas and the Medical Image Processing, Analysis and Visualization (MIPAV) tool. The digital templates are displayed for side-by-side comparisons and transparent template overlay onto patients' images in the image viewer. The lesion quantification tool quantifies planimetric lesion area from user-defined contour. The digital case report form stores user input into a database, then displays contents in the interface to allow for reviewing, editing, and new inputs. In sum, the newly integrated system features provide the user with readily-accessible web-based tools to identify the vascular territory involved, estimate lesion area, and store these results in a web-based digital format.

Improving adherence to web-based cessation programs: a randomized controlled trial study protocol

PubMed Central

2013-01-01

Background Reducing smoking prevalence is a public health priority that can save more lives and money than almost any other known preventive intervention. Internet interventions have the potential for enormous public health impact given their broad reach and effectiveness. However, most users engage only minimally with even the best designed websites, diminishing their impact due to an insufficient ‘dose’. Two approaches to improve adherence to Internet cessation programs are integrating smokers into an online social network and providing free nicotine replacement therapy (NRT). Active participation in online communities is associated with higher rates of cessation. Integrating smokers into an online social network can increase support and may also increase utilization of cessation tools and NRT. Removing barriers to NRT may increase uptake and adherence, and may also increase use of online cessation tools as smokers look for information and support while quitting. The combination of both strategies may exert the most powerful effects on adherence compared to either strategy alone. Methods/Design This study compares the efficacy of a smoking cessation website (WEB) alone and in conjunction with free NRT and a social network (SN) protocol designed to integrate participants into the online community. Using a 2 (SN, no SN) x 2 (NRT, no NRT) randomized, controlled factorial design with repeated measures at baseline, 3 months, and 9 months, this study will recruit N = 4,000 new members of an internet cessation program and randomize them to: 1) WEB, 2) WEB + SN, 3) WEB + NRT, or 4) WEB + SN + NRT. Hypotheses are that all interventions will outperform WEB and that WEB + SN + NRT will outperform WEB + NRT and WEB + SN on 30-day point prevalence abstinence at 9 months. Exploratory analyses will examine theory-driven hypotheses about the mediators and moderators of outcome. Discussion Addressing adherence in internet cessation programs is critical and timely to leverage their potential public health impact. This study is innovative in its use of a social network approach to improve behavioral and pharmacological treatment utilization to improve cessation. This approach is significant for reducing tobacco’s devastating disease burden and for optimizing behavior change in other arenas where adherence is just as critical. Trial registration ISRCTN:ISRCTN45127327 PMID:23414086

Allocation of DSST in the New implementation of Tastrodyweb Tools Web-site

NASA Astrophysics Data System (ADS)

San Juan, J. F.; Lara, M.; López, R.; López, L. M.; Weeden, B.; Cefola, P. J.

2012-09-01

The Draper Semianalytic Satellite Theory (DSST) is a semianalytic orbit propagator, which was carried out on Fortran to run from a command line interface. The construction of DSST began at the Computer Sciences Corporation and continued at the Draper Laboratory in the late 1970's and early 1980's. There are two versions of this application. One of them can be found as an option within the Goddard Trajectory Determination System (GTDS), whereas the other is available as a Standalone Orbit Propagator Package. Both versions are constantly evolving and updating. This constant evolution and updating allows DSST to take into account a wide variety of perturbation forces, which can be selected by means of a non-trivial options system at run time, and makes DSST a useful tool for performing short-term high accuracy orbit determination as well as long-term evolution. DSST has been included as part of an open source project for Space Situational Awareness and space object catalog work. On the last IAC 2011 a first step was taken in this sense and DSST was included on the tastrody Web-Site prototype [3, 4], which provided DSST with a friendly web interface, thus simplifying its use for both expert and non-expert users. However, this prototype has evolved into a stable platform based on the Drupal open source content management system (http://drupal.org Drupal), which simplifies the integration of our own application server. Drupal is supported by a large group of developers and users. Furthermore, a significant number of web-sites have been created using Drupal. In this work we present the integration of DSST in the new web-site, the new facilities provide by this platform to create the research community based on DSST and the comparison tests between the GTDS DSST, DSST Standalone and DSST Web version. These tests will be available in order to facilitate the user with better understanding of DSST. REFERENCES [1] J. G. Neelon, P. J. Cefola, and R. J. Proulx, Current Development of the Draper Semianalytical Satellite Theory Standalone Orbit Propagator Package", AAS Pre-print 97-731, presented at the AAS/AIAA Astrodynamics Conference, Sun Valley, ID, August 1997. [2] P. J. Cefola, D. Phillion, and K. S. Kim, Improving Access to the Semi-Analytical Satellite Theory, AAS 09-341, presented at the AAS/AIAA Astrodynamic Specialist Conference, Pittsburgh, PA, August 2009. [3] P. J. Cefola, B. Weeden and C. Levit, Open Source Software Suite for Space Situational Awareness and Space Object Catalog Work, 4th International Conference on Astrodynamics Tools Techniques, Madrid, Spain, 3-6 May 2010. [4] J. F. San Juan, R. López and I. Pérez, Nonlinear Dynamics Web Tools, 4th International Conference on Astrodynamics Tools Techniques, Madrid, Spain, 3-6 May 2010. [5] J. F. San Juan, M. Lara, R. López. L. M. López, B. Weeden and P. J. Cefola, Using the DSST Semi-Analytical Orbit. Propagator Package via the NondyWebTools/. AstrodyWebTools. Proceedings of 62nd International Astronautical Congress, Cape Town, SA., 2011.

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

ERIC Educational Resources Information Center

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

2016-01-01

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

Integrating Popular Web Applications in Classroom Learning Environments and Its Effects on Teaching, Student Learning Motivation and Performance

ERIC Educational Resources Information Center

Lin, Yen-Ting; Jou, Min

2013-01-01

Advancements in information and communication technology (ICT) allowed several tools and systems to be proposed for improving classroom experiences to both instructors and students. However, most of these tools were brand-new and stand-alone programs that require users to invest additional time and effort to become familiar with their use. This…

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.

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

NASA Astrophysics Data System (ADS)

Fatkhutdinov, Aybulat; Stefan, Catalin; Junghanns, Ralf

2016-04-01

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

Immersive Environments - A Connectivist Approach

NASA Astrophysics Data System (ADS)

Loureiro, Ana; Bettencourt, Teresa

We are conducting a research project with the aim of achieving better and more efficient ways to facilitate teaching and learning in Higher Level Education. We have chosen virtual environments, with particular emphasis to Second Life® platform augmented by web 2.0 tools, to develop the study. The Second Life® environment has some interesting characteristics that captured our attention, it is immersive; it is a real world simulator; it is a social network; it allows real time communication, cooperation, collaboration and interaction; it is a safe and controlled environment. We specifically chose tools from web 2.0 that enable sharing and collaborative way of learning. Through understanding the characteristics of this learning environment, we believe that immersive learning along with other virtual tools can be integrated in today's pedagogical practices.

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

NASA Astrophysics Data System (ADS)

Knörchen, Achim; Ketzler, Gunnar; Schneider, Christoph

2015-01-01

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

MyWEST: my Web Extraction Software Tool for effective mining of annotations from web-based databanks.

PubMed

Masseroli, Marco; Stella, Andrea; Meani, Natalia; Alcalay, Myriam; Pinciroli, Francesco

2004-12-12

High-throughput technologies create the necessity to mine large amounts of gene annotations from diverse databanks, and to integrate the resulting data. Most databanks can be interrogated only via Web, for a single gene at a time, and query results are generally available only in the HTML format. Although some databanks provide batch retrieval of data via FTP, this requires expertise and resources for locally reimplementing the databank. We developed MyWEST, a tool aimed at researchers without extensive informatics skills or resources, which exploits user-defined templates to easily mine selected annotations from different Web-interfaced databanks, and aggregates and structures results in an automatically updated database. Using microarray results from a model system of retinoic acid-induced differentiation, MyWEST effectively gathered relevant annotations from various biomolecular databanks, highlighted significant biological characteristics and supported a global approach to the understanding of complex cellular mechanisms. MyWEST is freely available for non-profit use at http://www.medinfopoli.polimi.it/MyWEST/

Web accessibility and open source software.

PubMed

Obrenović, Zeljko

2009-07-01

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

VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites.

PubMed

Spinozzi, Giulio; Calabria, Andrea; Brasca, Stefano; Beretta, Stefano; Merelli, Ivan; Milanesi, Luciano; Montini, Eugenio

2017-11-25

Bioinformatics tools designed to identify lentiviral or retroviral vector insertion sites in the genome of host cells are used to address the safety and long-term efficacy of hematopoietic stem cell gene therapy applications and to study the clonal dynamics of hematopoietic reconstitution. The increasing number of gene therapy clinical trials combined with the increasing amount of Next Generation Sequencing data, aimed at identifying integration sites, require both highly accurate and efficient computational software able to correctly process "big data" in a reasonable computational time. Here we present VISPA2 (Vector Integration Site Parallel Analysis, version 2), the latest optimized computational pipeline for integration site identification and analysis with the following features: (1) the sequence analysis for the integration site processing is fully compliant with paired-end reads and includes a sequence quality filter before and after the alignment on the target genome; (2) an heuristic algorithm to reduce false positive integration sites at nucleotide level to reduce the impact of Polymerase Chain Reaction or trimming/alignment artifacts; (3) a classification and annotation module for integration sites; (4) a user friendly web interface as researcher front-end to perform integration site analyses without computational skills; (5) the time speedup of all steps through parallelization (Hadoop free). We tested VISPA2 performances using simulated and real datasets of lentiviral vector integration sites, previously obtained from patients enrolled in a hematopoietic stem cell gene therapy clinical trial and compared the results with other preexisting tools for integration site analysis. On the computational side, VISPA2 showed a > 6-fold speedup and improved precision and recall metrics (1 and 0.97 respectively) compared to previously developed computational pipelines. These performances indicate that VISPA2 is a fast, reliable and user-friendly tool for integration site analysis, which allows gene therapy integration data to be handled in a cost and time effective fashion. Moreover, the web access of VISPA2 ( http://openserver.itb.cnr.it/vispa/ ) ensures accessibility and ease of usage to researches of a complex analytical tool. We released the source code of VISPA2 in a public repository ( https://bitbucket.org/andreacalabria/vispa2 ).

Head in the clouds: Re-imagining the experimental laboratory record for the web-based networked world

PubMed Central

2009-01-01

The means we use to record the process of carrying out research remains tied to the concept of a paginated paper notebook despite the advances over the past decade in web based communication and publication tools. The development of these tools offers an opportunity to re-imagine what the laboratory record would look like if it were re-built in a web-native form. In this paper I describe a distributed approach to the laboratory record based which uses the most appropriate tool available to house and publish each specific object created during the research process, whether they be a physical sample, a digital data object, or the record of how one was created from another. I propose that the web-native laboratory record would act as a feed of relationships between these items. This approach can be seen as complementary to, rather than competitive with, integrative approaches that aim to aggregate relevant objects together to describe knowledge. The potential for the recent announcement of the Google Wave protocol to have a significant impact on realizing this vision is discussed along with the issues of security and provenance that are raised by such an approach. PMID:20098590

RE Data Explorer: Informing Variable Renewable Energy Grid Integration for Low Emission Development

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

Cox, Sarah L

The RE Data Explorer, developed by the National Renewable Energy Laboratory, is an innovative web-based analysis tool that utilizes geospatial and spatiotemporal renewable energy data to visualize, execute, and support analysis of renewable energy potential under various user-defined scenarios. This analysis can inform high-level prospecting, integrated planning, and policy making to enable low emission development.

In-Service Teachers' Self-Efficacy, Professional Development, and Web 2.0 Tools for Integration

ERIC Educational Resources Information Center

Pan, Shu Chien; Franklin, Teresa

2011-01-01

Background: The implementation and integration of computer technologies in K-12 education has seen nearly constant growth since the early 1980s (Culp, Honey, Mandinach & Bailey, 2003), in part because this trend has become synonymous with skills that students will need as participants in a competitive global economy (Culp et al., 2003). It has…

Virus-Clip: a fast and memory-efficient viral integration site detection tool at single-base resolution with annotation capability.

PubMed

Ho, Daniel W H; Sze, Karen M F; Ng, Irene O L

2015-08-28

Viral integration into the human genome upon infection is an important risk factor for various human malignancies. We developed viral integration site detection tool called Virus-Clip, which makes use of information extracted from soft-clipped sequencing reads to identify exact positions of human and virus breakpoints of integration events. With initial read alignment to virus reference genome and streamlined procedures, Virus-Clip delivers a simple, fast and memory-efficient solution to viral integration site detection. Moreover, it can also automatically annotate the integration events with the corresponding affected human genes. Virus-Clip has been verified using whole-transcriptome sequencing data and its detection was validated to have satisfactory sensitivity and specificity. Marked advancement in performance was detected, compared to existing tools. It is applicable to versatile types of data including whole-genome sequencing, whole-transcriptome sequencing, and targeted sequencing. Virus-Clip is available at http://web.hku.hk/~dwhho/Virus-Clip.zip.

Web-Based Geographic Information System Tool for Accessing Hanford Site Environmental Data

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

Triplett, Mark B.; Seiple, Timothy E.; Watson, David J.

Data volume, complexity, and access issues pose severe challenges for analysts, regulators and stakeholders attempting to efficiently use legacy data to support decision making at the U.S. Department of Energy’s (DOE) Hanford Site. DOE has partnered with the Pacific Northwest National Laboratory (PNNL) on the PHOENIX (PNNL-Hanford Online Environmental Information System) project, which seeks to address data access, transparency, and integration challenges at Hanford to provide effective decision support. PHOENIX is a family of spatially-enabled web applications providing quick access to decades of valuable scientific data and insight through intuitive query, visualization, and analysis tools. PHOENIX realizes broad, public accessibilitymore » by relying only on ubiquitous web-browsers, eliminating the need for specialized software. It accommodates a wide range of users with intuitive user interfaces that require little or no training to quickly obtain and visualize data. Currently, PHOENIX is actively hosting three applications focused on groundwater monitoring, groundwater clean-up performance reporting, and in-tank monitoring. PHOENIX-based applications are being used to streamline investigative and analytical processes at Hanford, saving time and money. But more importantly, by integrating previously isolated datasets and developing relevant visualization and analysis tools, PHOENIX applications are enabling DOE to discover new correlations hidden in legacy data, allowing them to more effectively address complex issues at Hanford.« less

Life Sciences and the web: a new era for collaboration.

PubMed

Sagotsky, Jonathan A; Zhang, Le; Wang, Zhihui; Martin, Sean; Deisboeck, Thomas S

2008-01-01

The World Wide Web has revolutionized how researchers from various disciplines collaborate over long distances. This is nowhere more important than in the Life Sciences, where interdisciplinary approaches are becoming increasingly powerful as a driver of both integration and discovery. Data access, data quality, identity, and provenance are all critical ingredients to facilitate and accelerate these collaborative enterprises and it is here where Semantic Web technologies promise to have a profound impact. This paper reviews the need for, and explores advantages of as well as challenges with these novel Internet information tools as illustrated with examples from the biomedical community.

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.

U.S. Geological Survey Community for Data Integration-NWIS Web Services Snapshot Tool for ArcGIS

USGS Publications Warehouse

Holl, Sally

2011-01-01

U.S. Geological Survey (USGS) data resources are so vast that many scientists are unaware of data holdings that may be directly relevant to their research. Data are also difficult to access and large corporate databases, such as the National Water Information System (NWIS) that houses hydrologic data for the Nation, are challenging to use without considerable expertise and investment of time. The USGS Community for Data Integration (CDI) was established in 2009 to address data and information management issues affecting the proficiency of earth science research. A CDI workshop convened in 2009 identified common data integration needs of USGS scientists and targeted high value opportunities that might address these needs by leveraging existing projects in USGS science centers, in-kind contributions, and supplemental funding. To implement this strategy, CDI sponsored a software development project in 2010 to facilitate access and use of NWIS data with ArcGIS, a widely used Geographic Information System. The resulting software product, the NWIS Web Services Snapshot Tool for ArcGIS, is presented here.

Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform.

PubMed

List, Markus

2017-06-10

Docker virtualization allows for software tools to be executed in an isolated and controlled environment referred to as a container. In Docker containers, dependencies are provided exactly as intended by the developer and, consequently, they simplify the distribution of scientific software and foster reproducible research. The Docker paradigm is that each container encapsulates one particular software tool. However, to analyze complex biomedical data sets, it is often necessary to combine several software tools into elaborate workflows. To address this challenge, several Docker containers need to be instantiated and properly integrated, which complicates the software deployment process unnecessarily. Here, we demonstrate how an extension to Docker, Docker compose, can be used to mitigate these problems by providing a unified setup routine that deploys several tools in an integrated fashion. We demonstrate the power of this approach by example of a Docker compose setup for a drug target screening platform consisting of five integrated web applications and shared infrastructure, deployable in just two lines of codes.

SOCRAT Platform Design: A Web Architecture for Interactive Visual Analytics Applications

PubMed Central

Kalinin, Alexandr A.; Palanimalai, Selvam; Dinov, Ivo D.

2018-01-01

The modern web is a successful platform for large scale interactive web applications, including visualizations. However, there are no established design principles for building complex visual analytics (VA) web applications that could efficiently integrate visualizations with data management, computational transformation, hypothesis testing, and knowledge discovery. This imposes a time-consuming design and development process on many researchers and developers. To address these challenges, we consider the design requirements for the development of a module-based VA system architecture, adopting existing practices of large scale web application development. We present the preliminary design and implementation of an open-source platform for Statistics Online Computational Resource Analytical Toolbox (SOCRAT). This platform defines: (1) a specification for an architecture for building VA applications with multi-level modularity, and (2) methods for optimizing module interaction, re-usage, and extension. To demonstrate how this platform can be used to integrate a number of data management, interactive visualization, and analysis tools, we implement an example application for simple VA tasks including raw data input and representation, interactive visualization and analysis. PMID:29630069

SOCRAT Platform Design: A Web Architecture for Interactive Visual Analytics Applications.

PubMed

Kalinin, Alexandr A; Palanimalai, Selvam; Dinov, Ivo D

2017-04-01

The modern web is a successful platform for large scale interactive web applications, including visualizations. However, there are no established design principles for building complex visual analytics (VA) web applications that could efficiently integrate visualizations with data management, computational transformation, hypothesis testing, and knowledge discovery. This imposes a time-consuming design and development process on many researchers and developers. To address these challenges, we consider the design requirements for the development of a module-based VA system architecture, adopting existing practices of large scale web application development. We present the preliminary design and implementation of an open-source platform for Statistics Online Computational Resource Analytical Toolbox (SOCRAT). This platform defines: (1) a specification for an architecture for building VA applications with multi-level modularity, and (2) methods for optimizing module interaction, re-usage, and extension. To demonstrate how this platform can be used to integrate a number of data management, interactive visualization, and analysis tools, we implement an example application for simple VA tasks including raw data input and representation, interactive visualization and analysis.

search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information

PubMed Central

2013-01-01

Background Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one place by third-party software developers without significant investment in hardware and software infrastructure, its maintenance and administration. Web services allow development of software applications that integrate in one place the functionality and processing logic of distributed software components, without integrating the components themselves and without integrating the resources to which they have access. This is achieved by appropriate orchestration or choreography of available Web services and their shared functions. After the successful application of Web services in the business sector, this technology can now be used to build composite software tools that are oriented towards biomedical data processing. Results We have developed a new tool for efficient and dynamic data exploration in GenBank and other NCBI databases. A dedicated search GenBank system makes use of NCBI Web services and a package of Entrez Programming Utilities (eUtils) in order to provide extended searching capabilities in NCBI data repositories. In search GenBank users can use one of the three exploration paths: simple data searching based on the specified user’s query, advanced data searching based on the specified user’s query, and advanced data exploration with the use of macros. search GenBank orchestrates calls of particular tools available through the NCBI Web service providing requested functionality, while users interactively browse selected records in search GenBank and traverse between NCBI databases using available links. On the other hand, by building macros in the advanced data exploration mode, users create choreographies of eUtils calls, which can lead to the automatic discovery of related data in the specified databases. Conclusions search GenBank extends standard capabilities of the NCBI Entrez search engine in querying biomedical databases. The possibility of creating and saving macros in the search GenBank is a unique feature and has a great potential. The potential will further grow in the future with the increasing density of networks of relationships between data stored in particular databases. search GenBank is available for public use at http://sgb.biotools.pl/. PMID:23452691

search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information.

PubMed

Mrozek, Dariusz; Małysiak-Mrozek, Bożena; Siążnik, Artur

2013-03-01

Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one place by third-party software developers without significant investment in hardware and software infrastructure, its maintenance and administration. Web services allow development of software applications that integrate in one place the functionality and processing logic of distributed software components, without integrating the components themselves and without integrating the resources to which they have access. This is achieved by appropriate orchestration or choreography of available Web services and their shared functions. After the successful application of Web services in the business sector, this technology can now be used to build composite software tools that are oriented towards biomedical data processing. We have developed a new tool for efficient and dynamic data exploration in GenBank and other NCBI databases. A dedicated search GenBank system makes use of NCBI Web services and a package of Entrez Programming Utilities (eUtils) in order to provide extended searching capabilities in NCBI data repositories. In search GenBank users can use one of the three exploration paths: simple data searching based on the specified user's query, advanced data searching based on the specified user's query, and advanced data exploration with the use of macros. search GenBank orchestrates calls of particular tools available through the NCBI Web service providing requested functionality, while users interactively browse selected records in search GenBank and traverse between NCBI databases using available links. On the other hand, by building macros in the advanced data exploration mode, users create choreographies of eUtils calls, which can lead to the automatic discovery of related data in the specified databases. search GenBank extends standard capabilities of the NCBI Entrez search engine in querying biomedical databases. The possibility of creating and saving macros in the search GenBank is a unique feature and has a great potential. The potential will further grow in the future with the increasing density of networks of relationships between data stored in particular databases. search GenBank is available for public use at http://sgb.biotools.pl/.

SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases.

PubMed

Schweiger, Dominik; Trajanoski, Zlatko; Pabinger, Stephan

2014-08-15

Semantic Web has established itself as a framework for using and sharing data across applications and database boundaries. Here, we present a web-based platform for querying biological Semantic Web databases in a graphical way. SPARQLGraph offers an intuitive drag & drop query builder, which converts the visual graph into a query and executes it on a public endpoint. The tool integrates several publicly available Semantic Web databases, including the databases of the just recently released EBI RDF platform. Furthermore, it provides several predefined template queries for answering biological questions. Users can easily create and save new query graphs, which can also be shared with other researchers. This new graphical way of creating queries for biological Semantic Web databases considerably facilitates usability as it removes the requirement of knowing specific query languages and database structures. The system is freely available at http://sparqlgraph.i-med.ac.at.

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

PubMed Central

Kuzniar, Arnold; Kanaar, Roland

2014-01-01

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

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

PubMed

Kuzniar, Arnold; Kanaar, Roland

2014-07-01

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

Research, Collaboration, and Open Science Using Web 2.0

PubMed Central

Shee, Kevin; Strong, Michael; Guido, Nicholas J.; Lue, Robert A.; Church, George M.; Viel, Alain

2010-01-01

There is little doubt that the Internet has transformed the world in which we live. Information that was once archived in bricks and mortar libraries is now only a click away, and people across the globe have become connected in a manner inconceivable only 20 years ago. Although many scientists and educators have embraced the Internet as an invaluable tool for research, education and data sharing, some have been somewhat slower to take full advantage of emerging Web 2.0 technologies. Here we discuss the benefits and challenges of integrating Web 2.0 applications into undergraduate research and education programs, based on our experience utilizing these technologies in a summer undergraduate research program in synthetic biology at Harvard University. We discuss the use of applications including wiki-based documentation, digital brainstorming, and open data sharing via the Web, to facilitate the educational aspects and collaborative progress of undergraduate research projects. We hope to inspire others to integrate these technologies into their own coursework or research projects. PMID:23653712

CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization.

PubMed

Frias, Silvia; Bryan, Kenneth; Brinkman, Fiona S L; Lynn, David J

2015-01-01

CerebralWeb is a light-weight JavaScript plug-in that extends Cytoscape.js to enable fast and interactive visualization of molecular interaction networks stratified based on subcellular localization or other user-supplied annotation. The application is designed to be easily integrated into any website and is configurable to support customized network visualization. CerebralWeb also supports the automatic retrieval of Cerebral-compatible localizations for human, mouse and bovine genes via a web service and enables the automated parsing of Cytoscape compatible XGMML network files. CerebralWeb currently supports embedded network visualization on the InnateDB (www.innatedb.com) and Allergy and Asthma Portal (allergen.innatedb.com) database and analysis resources. Database tool URL: http://www.innatedb.com/CerebralWeb © The Author(s) 2015. Published by Oxford University Press.

GREAT: a web portal for Genome Regulatory Architecture Tools.

PubMed

Bouyioukos, Costas; Bucchini, François; Elati, Mohamed; Képès, François

2016-07-08

GREAT (Genome REgulatory Architecture Tools) is a novel web portal for tools designed to generate user-friendly and biologically useful analysis of genome architecture and regulation. The online tools of GREAT are freely accessible and compatible with essentially any operating system which runs a modern browser. GREAT is based on the analysis of genome layout -defined as the respective positioning of co-functional genes- and its relation with chromosome architecture and gene expression. GREAT tools allow users to systematically detect regular patterns along co-functional genomic features in an automatic way consisting of three individual steps and respective interactive visualizations. In addition to the complete analysis of regularities, GREAT tools enable the use of periodicity and position information for improving the prediction of transcription factor binding sites using a multi-view machine learning approach. The outcome of this integrative approach features a multivariate analysis of the interplay between the location of a gene and its regulatory sequence. GREAT results are plotted in web interactive graphs and are available for download either as individual plots, self-contained interactive pages or as machine readable tables for downstream analysis. The GREAT portal can be reached at the following URL https://absynth.issb.genopole.fr/GREAT and each individual GREAT tool is available for downloading. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Blogging within a Social Networking Site as a Form of Literature Response in a Teacher Education Course

ERIC Educational Resources Information Center

Hutchison, Amy; Wang, Wei

2012-01-01

The purpose of this qualitative study was to document how pre-service teachers in a children's literature course experienced blogging on a social networking site as a form of literature response. Understanding how pre-service teachers experience these tools can inform the ways we instruct them to integrate Web 2.0 tools into their teaching.…

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.

EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management

PubMed Central

Barton, G; Abbott, J; Chiba, N; Huang, DW; Huang, Y; Krznaric, M; Mack-Smith, J; Saleem, A; Sherman, BT; Tiwari, B; Tomlinson, C; Aitman, T; Darlington, J; Game, L; Sternberg, MJE; Butcher, SA

2008-01-01

Background Microarray experimentation requires the application of complex analysis methods as well as the use of non-trivial computer technologies to manage the resultant large data sets. This, together with the proliferation of tools and techniques for microarray data analysis, makes it very challenging for a laboratory scientist to keep up-to-date with the latest developments in this field. Our aim was to develop a distributed e-support system for microarray data analysis and management. Results EMAAS (Extensible MicroArray Analysis System) is a multi-user rich internet application (RIA) providing simple, robust access to up-to-date resources for microarray data storage and analysis, combined with integrated tools to optimise real time user support and training. The system leverages the power of distributed computing to perform microarray analyses, and provides seamless access to resources located at various remote facilities. The EMAAS framework allows users to import microarray data from several sources to an underlying database, to pre-process, quality assess and analyse the data, to perform functional analyses, and to track data analysis steps, all through a single easy to use web portal. This interface offers distance support to users both in the form of video tutorials and via live screen feeds using the web conferencing tool EVO. A number of analysis packages, including R-Bioconductor and Affymetrix Power Tools have been integrated on the server side and are available programmatically through the Postgres-PLR library or on grid compute clusters. Integrated distributed resources include the functional annotation tool DAVID, GeneCards and the microarray data repositories GEO, CELSIUS and MiMiR. EMAAS currently supports analysis of Affymetrix 3' and Exon expression arrays, and the system is extensible to cater for other microarray and transcriptomic platforms. Conclusion EMAAS enables users to track and perform microarray data management and analysis tasks through a single easy-to-use web application. The system architecture is flexible and scalable to allow new array types, analysis algorithms and tools to be added with relative ease and to cope with large increases in data volume. PMID:19032776

Construction of a Distributed-network Digital Watershed Management System with B/S Techniques

NASA Astrophysics Data System (ADS)

Zhang, W. C.; Liu, Y. M.; Fang, J.

2017-07-01

Integrated watershed assessment tools for supporting land management and hydrologic research are becoming established tools in both basic and applied research. The core of these tools are mainly spatially distributed hydrologic models as they can provide a mechanism for investigating interactions among climate, topography, vegetation, and soil. However, the extensive data requirements and the difficult task of building input parameter files for driving these distributed models, have long been an obstacle to the timely and cost-effective use of such complex models by watershed managers and policy-makers. Recently, a web based geographic information system (GIS) tool to facilitate this process has been developed for a large watersheds of Jinghe and Weihe catchments located in the loess plateau of the Huanghe River basin in north-western China. A web-based GIS provides the framework within which spatially distributed data are collected and used to prepare model input files of these two watersheds and evaluate model results as well as to provide the various clients for watershed information inquiring, visualizing and assessment analysis. This Web-based Automated Geospatial Watershed Assessment GIS (WAGWA-GIS) tool uses widely available standardized spatial datasets that can be obtained via the internet oracle databank designed with association of Map Guide platform to develop input parameter files for online simulation at different spatial and temporal scales with Xing’anjiang and TOPMODEL that integrated with web-based digital watershed. WAGWA-GIS automates the process of transforming both digital data including remote sensing data, DEM, Land use/cover, soil digital maps and meteorological and hydrological station geo-location digital maps and text files containing meteorological and hydrological data obtained from stations of the watershed into hydrological models for online simulation and geo-spatial analysis and provides a visualization tool to help the user interpret results. The utility of WAGWA-GIS in jointing hydrologic and ecological investigations has been demonstrated on such diverse landscapes as Jinhe and Weihe watersheds, and will be extended to be utilized in the other watersheds in China step by step in coming years

A journey to Semantic Web query federation in the life sciences.

PubMed

Cheung, Kei-Hoi; Frost, H Robert; Marshall, M Scott; Prud'hommeaux, Eric; Samwald, Matthias; Zhao, Jun; Paschke, Adrian

2009-10-01

As interest in adopting the Semantic Web in the biomedical domain continues to grow, Semantic Web technology has been evolving and maturing. A variety of technological approaches including triplestore technologies, SPARQL endpoints, Linked Data, and Vocabulary of Interlinked Datasets have emerged in recent years. In addition to the data warehouse construction, these technological approaches can be used to support dynamic query federation. As a community effort, the BioRDF task force, within the Semantic Web for Health Care and Life Sciences Interest Group, is exploring how these emerging approaches can be utilized to execute distributed queries across different neuroscience data sources. We have created two health care and life science knowledge bases. We have explored a variety of Semantic Web approaches to describe, map, and dynamically query multiple datasets. We have demonstrated several federation approaches that integrate diverse types of information about neurons and receptors that play an important role in basic, clinical, and translational neuroscience research. Particularly, we have created a prototype receptor explorer which uses OWL mappings to provide an integrated list of receptors and executes individual queries against different SPARQL endpoints. We have also employed the AIDA Toolkit, which is directed at groups of knowledge workers who cooperatively search, annotate, interpret, and enrich large collections of heterogeneous documents from diverse locations. We have explored a tool called "FeDeRate", which enables a global SPARQL query to be decomposed into subqueries against the remote databases offering either SPARQL or SQL query interfaces. Finally, we have explored how to use the vocabulary of interlinked Datasets (voiD) to create metadata for describing datasets exposed as Linked Data URIs or SPARQL endpoints. We have demonstrated the use of a set of novel and state-of-the-art Semantic Web technologies in support of a neuroscience query federation scenario. We have identified both the strengths and weaknesses of these technologies. While Semantic Web offers a global data model including the use of Uniform Resource Identifiers (URI's), the proliferation of semantically-equivalent URI's hinders large scale data integration. Our work helps direct research and tool development, which will be of benefit to this community.

A journey to Semantic Web query federation in the life sciences

PubMed Central

Cheung, Kei-Hoi; Frost, H Robert; Marshall, M Scott; Prud'hommeaux, Eric; Samwald, Matthias; Zhao, Jun; Paschke, Adrian

2009-01-01

Background As interest in adopting the Semantic Web in the biomedical domain continues to grow, Semantic Web technology has been evolving and maturing. A variety of technological approaches including triplestore technologies, SPARQL endpoints, Linked Data, and Vocabulary of Interlinked Datasets have emerged in recent years. In addition to the data warehouse construction, these technological approaches can be used to support dynamic query federation. As a community effort, the BioRDF task force, within the Semantic Web for Health Care and Life Sciences Interest Group, is exploring how these emerging approaches can be utilized to execute distributed queries across different neuroscience data sources. Methods and results We have created two health care and life science knowledge bases. We have explored a variety of Semantic Web approaches to describe, map, and dynamically query multiple datasets. We have demonstrated several federation approaches that integrate diverse types of information about neurons and receptors that play an important role in basic, clinical, and translational neuroscience research. Particularly, we have created a prototype receptor explorer which uses OWL mappings to provide an integrated list of receptors and executes individual queries against different SPARQL endpoints. We have also employed the AIDA Toolkit, which is directed at groups of knowledge workers who cooperatively search, annotate, interpret, and enrich large collections of heterogeneous documents from diverse locations. We have explored a tool called "FeDeRate", which enables a global SPARQL query to be decomposed into subqueries against the remote databases offering either SPARQL or SQL query interfaces. Finally, we have explored how to use the vocabulary of interlinked Datasets (voiD) to create metadata for describing datasets exposed as Linked Data URIs or SPARQL endpoints. Conclusion We have demonstrated the use of a set of novel and state-of-the-art Semantic Web technologies in support of a neuroscience query federation scenario. We have identified both the strengths and weaknesses of these technologies. While Semantic Web offers a global data model including the use of Uniform Resource Identifiers (URI's), the proliferation of semantically-equivalent URI's hinders large scale data integration. Our work helps direct research and tool development, which will be of benefit to this community. PMID:19796394

Data management integration for biomedical core facilities

NASA Astrophysics Data System (ADS)

Zhang, Guo-Qiang; Szymanski, Jacek; Wilson, David

2007-03-01

We present the design, development, and pilot-deployment experiences of MIMI, a web-based, Multi-modality Multi-Resource Information Integration environment for biomedical core facilities. This is an easily customizable, web-based software tool that integrates scientific and administrative support for a biomedical core facility involving a common set of entities: researchers; projects; equipments and devices; support staff; services; samples and materials; experimental workflow; large and complex data. With this software, one can: register users; manage projects; schedule resources; bill services; perform site-wide search; archive, back-up, and share data. With its customizable, expandable, and scalable characteristics, MIMI not only provides a cost-effective solution to the overarching data management problem of biomedical core facilities unavailable in the market place, but also lays a foundation for data federation to facilitate and support discovery-driven research.

ResearchEHR: use of semantic web technologies and archetypes for the description of EHRs.

PubMed

Robles, Montserrat; Fernández-Breis, Jesualdo Tomás; Maldonado, Jose A; Moner, David; Martínez-Costa, Catalina; Bosca, Diego; Menárguez-Tortosa, Marcos

2010-01-01

In this paper, we present the ResearchEHR project. It focuses on the usability of Electronic Health Record (EHR) sources and EHR standards for building advanced clinical systems. The aim is to support healthcare professional, institutions and authorities by providing a set of generic methods and tools for the capture, standardization, integration, description and dissemination of health related information. ResearchEHR combines several tools to manage EHR at two different levels. The internal level that deals with the normalization and semantic upgrading of exiting EHR by using archetypes and the external level that uses Semantic Web technologies to specify clinical archetypes for advanced EHR architectures and systems.

Workflow and web application for annotating NCBI BioProject transcriptome data

PubMed Central

Vera Alvarez, Roberto; Medeiros Vidal, Newton; Garzón-Martínez, Gina A.; Barrero, Luz S.; Landsman, David

2017-01-01

Abstract The volume of transcriptome data is growing exponentially due to rapid improvement of experimental technologies. In response, large central resources such as those of the National Center for Biotechnology Information (NCBI) are continually adapting their computational infrastructure to accommodate this large influx of data. New and specialized databases, such as Transcriptome Shotgun Assembly Sequence Database (TSA) and Sequence Read Archive (SRA), have been created to aid the development and expansion of centralized repositories. Although the central resource databases are under continual development, they do not include automatic pipelines to increase annotation of newly deposited data. Therefore, third-party applications are required to achieve that aim. Here, we present an automatic workflow and web application for the annotation of transcriptome data. The workflow creates secondary data such as sequencing reads and BLAST alignments, which are available through the web application. They are based on freely available bioinformatics tools and scripts developed in-house. The interactive web application provides a search engine and several browser utilities. Graphical views of transcript alignments are available through SeqViewer, an embedded tool developed by NCBI for viewing biological sequence data. The web application is tightly integrated with other NCBI web applications and tools to extend the functionality of data processing and interconnectivity. We present a case study for the species Physalis peruviana with data generated from BioProject ID 67621. Database URL: http://www.ncbi.nlm.nih.gov/projects/physalis/ PMID:28605765

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.

Automated Comparative Metabolite Profiling of Large LC-ESIMS Data Sets in an ACD/MS Workbook Suite Add-in, and Data Clustering on a New Open-Source Web Platform FreeClust.

PubMed

Božičević, Alen; Dobrzyński, Maciej; De Bie, Hans; Gafner, Frank; Garo, Eliane; Hamburger, Matthias

2017-12-05

The technological development of LC-MS instrumentation has led to significant improvements of performance and sensitivity, enabling high-throughput analysis of complex samples, such as plant extracts. Most software suites allow preprocessing of LC-MS chromatograms to obtain comprehensive information on single constituents. However, more advanced processing needs, such as the systematic and unbiased comparative metabolite profiling of large numbers of complex LC-MS chromatograms remains a challenge. Currently, users have to rely on different tools to perform such data analyses. We developed a two-step protocol comprising a comparative metabolite profiling tool integrated in ACD/MS Workbook Suite, and a web platform developed in R language designed for clustering and visualization of chromatographic data. Initially, all relevant chromatographic and spectroscopic data (retention time, molecular ions with the respective ion abundance, and sample names) are automatically extracted and assembled in an Excel spreadsheet. The file is then loaded into an online web application that includes various statistical algorithms and provides the user with tools to compare and visualize the results in intuitive 2D heatmaps. We applied this workflow to LC-ESIMS profiles obtained from 69 honey samples. Within few hours of calculation with a standard PC, honey samples were preprocessed and organized in clusters based on their metabolite profile similarities, thereby highlighting the common metabolite patterns and distributions among samples. Implementation in the ACD/Laboratories software package enables ulterior integration of other analytical data, and in silico prediction tools for modern drug discovery.

Watershed Management Optimization Support Tool (WMOST) ...

EPA Pesticide Factsheets

EPA's Watershed Management Optimization Support Tool (WMOST) version 2 is a decision support tool designed to facilitate integrated water management by communities at the small watershed scale. WMOST allows users to look across management options in stormwater (including green infrastructure), wastewater, drinking water, and land conservation programs to find the least cost solutions. The pdf version of these presentations accompany the recorded webinar with closed captions to be posted on the WMOST web page. The webinar was recorded at the time a training workshop took place for EPA's Watershed Management Optimization Support Tool (WMOST, v2).

Software ``Best'' Practices: Agile Deconstructed

NASA Astrophysics Data System (ADS)

Fraser, Steven

Software “best” practices depend entirely on context - in terms of the problem domain, the system constructed, the software designers, and the “customers” ultimately deriving value from the system. Agile practices no longer have the luxury of “choosing” small non-mission critical projects with co-located teams. Project stakeholders are selecting and adapting practices based on a combina tion of interest, need and staffing. For example, growing product portfolios through a merger or the acquisition of a company exposes legacy systems to new staff, new software integration challenges, and new ideas. Innovation in communications (tools and processes) to span the growth and contraction of both information and organizations, while managing the adoption of changing software practices, is imperative for success. Traditional web-based tools such as web pages, document libraries, and forums are not suf ficient. A blend of tweeting, blogs, wikis, instant messaging, web-based confer encing, and telepresence creates a new dimension of communication “best” practices.

Overview of codes and tools for nuclear engineering education

NASA Astrophysics Data System (ADS)

Yakovlev, D.; Pryakhin, A.; Medvedeva, L.

2017-01-01

The recent world trends in nuclear education have been developed in the direction of social education, networking, virtual tools and codes. MEPhI as a global leader on the world education market implements new advanced technologies for the distance and online learning and for student research work. MEPhI produced special codes, tools and web resources based on the internet platform to support education in the field of nuclear technology. At the same time, MEPhI actively uses codes and tools from the third parties. Several types of the tools are considered: calculation codes, nuclear data visualization tools, virtual labs, PC-based educational simulators for nuclear power plants (NPP), CLP4NET, education web-platforms, distance courses (MOOCs and controlled and managed content systems). The university pays special attention to integrated products such as CLP4NET, which is not a learning course, but serves to automate the process of learning through distance technologies. CLP4NET organizes all tools in the same information space. Up to now, MEPhI has achieved significant results in the field of distance education and online system implementation.

The Advent of Portals.

ERIC Educational Resources Information Center

Jackson, Mary E.

2002-01-01

Explains portals as tools that gather a variety of electronic information resources, including local library resources, into a single Web page. Highlights include cross-database searching; integration with university portals and course management software; the ARL (Association of Research Libraries) Scholars Portal Initiative; and selected vendors…

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.

Silicon photonics cloud (SiCloud)

NASA Astrophysics Data System (ADS)

DeVore, Peter T. S.; Jiang, Yunshan; Lynch, Michael; Miyatake, Taira; Carmona, Christopher; Chan, Andrew C.; Muniam, Kuhan; Jalali, Bahram

2015-02-01

We present SiCloud (Silicon Photonics Cloud), the first free, instructional web-based research and education tool for silicon photonics. SiCloud's vision is to provide a host of instructional and research web-based tools. Such interactive learning tools enhance traditional teaching methods by extending access to a very large audience, resulting in very high impact. Interactive tools engage the brain in a way different from merely reading, and so enhance and reinforce the learning experience. Understanding silicon photonics is challenging as the topic involves a wide range of disciplines, including material science, semiconductor physics, electronics and waveguide optics. This web-based calculator is an interactive analysis tool for optical properties of silicon and related material (SiO2, Si3N4, Al2O3, etc.). It is designed to be a one stop resource for students, researchers and design engineers. The first and most basic aspect of Silicon Photonics is the Material Parameters, which provides the foundation for the Device, Sub-System and System levels. SiCloud includes the common dielectrics and semiconductors for waveguide core, cladding, and photodetection, as well as metals for electrical contacts. SiCloud is a work in progress and its capability is being expanded. SiCloud is being developed at UCLA with funding from the National Science Foundation's Center for Integrated Access Networks (CIAN) Engineering Research Center.

Integration of Dynamic Models in Range Operations

NASA Technical Reports Server (NTRS)

Bardina, Jorge; Thirumalainambi, Rajkumar

2004-01-01

This work addresses the various model interactions in real-time to make an efficient internet based decision making tool for Shuttle launch. The decision making tool depends on the launch commit criteria coupled with physical models. Dynamic interaction between a wide variety of simulation applications and techniques, embedded algorithms, and data visualizations are needed to exploit the full potential of modeling and simulation. This paper also discusses in depth details of web based 3-D graphics and applications to range safety. The advantages of this dynamic model integration are secure accessibility and distribution of real time information to other NASA centers.

The Visual Geophysical Exploration Environment: A Multi-dimensional Scientific Visualization

NASA Astrophysics Data System (ADS)

Pandya, R. E.; Domenico, B.; Murray, D.; Marlino, M. R.

2003-12-01

The Visual Geophysical Exploration Environment (VGEE) is an online learning environment designed to help undergraduate students understand fundamental Earth system science concepts. The guiding principle of the VGEE is the importance of hands-on interaction with scientific visualization and data. The VGEE consists of four elements: 1) an online, inquiry-based curriculum for guiding student exploration; 2) a suite of El Nino-related data sets adapted for student use; 3) a learner-centered interface to a scientific visualization tool; and 4) a set of concept models (interactive tools that help students understand fundamental scientific concepts). There are two key innovations featured in this interactive poster session. One is the integration of concept models and the visualization tool. Concept models are simple, interactive, Java-based illustrations of fundamental physical principles. We developed eight concept models and integrated them into the visualization tool to enable students to probe data. The ability to probe data using a concept model addresses the common problem of transfer: the difficulty students have in applying theoretical knowledge to everyday phenomenon. The other innovation is a visualization environment and data that are discoverable in digital libraries, and installed, configured, and used for investigations over the web. By collaborating with the Integrated Data Viewer developers, we were able to embed a web-launchable visualization tool and access to distributed data sets into the online curricula. The Thematic Real-time Environmental Data Distributed Services (THREDDS) project is working to provide catalogs of datasets that can be used in new VGEE curricula under development. By cataloging this curricula in the Digital Library for Earth System Education (DLESE), learners and educators can discover the data and visualization tool within a framework that guides their use.

Integrated web visualizations for protein-protein interaction databases.

PubMed

Jeanquartier, Fleur; Jean-Quartier, Claire; Holzinger, Andreas

2015-06-16

Understanding living systems is crucial for curing diseases. To achieve this task we have to understand biological networks based on protein-protein interactions. Bioinformatics has come up with a great amount of databases and tools that support analysts in exploring protein-protein interactions on an integrated level for knowledge discovery. They provide predictions and correlations, indicate possibilities for future experimental research and fill the gaps to complete the picture of biochemical processes. There are numerous and huge databases of protein-protein interactions used to gain insights into answering some of the many questions of systems biology. Many computational resources integrate interaction data with additional information on molecular background. However, the vast number of diverse Bioinformatics resources poses an obstacle to the goal of understanding. We present a survey of databases that enable the visual analysis of protein networks. We selected M=10 out of N=53 resources supporting visualization, and we tested against the following set of criteria: interoperability, data integration, quantity of possible interactions, data visualization quality and data coverage. The study reveals differences in usability, visualization features and quality as well as the quantity of interactions. StringDB is the recommended first choice. CPDB presents a comprehensive dataset and IntAct lets the user change the network layout. A comprehensive comparison table is available via web. The supplementary table can be accessed on http://tinyurl.com/PPI-DB-Comparison-2015. Only some web resources featuring graph visualization can be successfully applied to interactive visual analysis of protein-protein interaction. Study results underline the necessity for further enhancements of visualization integration in biochemical analysis tools. Identified challenges are data comprehensiveness, confidence, interactive feature and visualization maturing.

Wikis, blogs and podcasts: a new generation of Web-based tools for virtual collaborative clinical practice and education

PubMed Central

Boulos, Maged N Kamel; Maramba, Inocencio; Wheeler, Steve

2006-01-01

Background We have witnessed a rapid increase in the use of Web-based 'collaborationware' in recent years. These Web 2.0 applications, particularly wikis, blogs and podcasts, have been increasingly adopted by many online health-related professional and educational services. Because of their ease of use and rapidity of deployment, they offer the opportunity for powerful information sharing and ease of collaboration. Wikis are Web sites that can be edited by anyone who has access to them. The word 'blog' is a contraction of 'Web Log' – an online Web journal that can offer a resource rich multimedia environment. Podcasts are repositories of audio and video materials that can be "pushed" to subscribers, even without user intervention. These audio and video files can be downloaded to portable media players that can be taken anywhere, providing the potential for "anytime, anywhere" learning experiences (mobile learning). Discussion Wikis, blogs and podcasts are all relatively easy to use, which partly accounts for their proliferation. The fact that there are many free and Open Source versions of these tools may also be responsible for their explosive growth. Thus it would be relatively easy to implement any or all within a Health Professions' Educational Environment. Paradoxically, some of their disadvantages also relate to their openness and ease of use. With virtually anybody able to alter, edit or otherwise contribute to the collaborative Web pages, it can be problematic to gauge the reliability and accuracy of such resources. While arguably, the very process of collaboration leads to a Darwinian type 'survival of the fittest' content within a Web page, the veracity of these resources can be assured through careful monitoring, moderation, and operation of the collaborationware in a closed and secure digital environment. Empirical research is still needed to build our pedagogic evidence base about the different aspects of these tools in the context of medical/health education. Summary and conclusion If effectively deployed, wikis, blogs and podcasts could offer a way to enhance students', clinicians' and patients' learning experiences, and deepen levels of learners' engagement and collaboration within digital learning environments. Therefore, research should be conducted to determine the best ways to integrate these tools into existing e-Learning programmes for students, health professionals and patients, taking into account the different, but also overlapping, needs of these three audience classes and the opportunities of virtual collaboration between them. Of particular importance is research into novel integrative applications, to serve as the "glue" to bind the different forms of Web-based collaborationware synergistically in order to provide a coherent wholesome learning experience. PMID:16911779

visPIG--a web tool for producing multi-region, multi-track, multi-scale plots of genetic data.

PubMed

Scales, Matthew; Jäger, Roland; Migliorini, Gabriele; Houlston, Richard S; Henrion, Marc Y R

2014-01-01

We present VISual Plotting Interface for Genetics (visPIG; http://vispig.icr.ac.uk), a web application to produce multi-track, multi-scale, multi-region plots of genetic data. visPIG has been designed to allow users not well versed with mathematical software packages and/or programming languages such as R, Matlab®, Python, etc., to integrate data from multiple sources for interpretation and to easily create publication-ready figures. While web tools such as the UCSC Genome Browser or the WashU Epigenome Browser allow custom data uploads, such tools are primarily designed for data exploration. This is also true for the desktop-run Integrative Genomics Viewer (IGV). Other locally run data visualisation software such as Circos require significant computer skills of the user. The visPIG web application is a menu-based interface that allows users to upload custom data tracks and set track-specific parameters. Figures can be downloaded as PDF or PNG files. For sensitive data, the underlying R code can also be downloaded and run locally. visPIG is multi-track: it can display many different data types (e.g association, functional annotation, intensity, interaction, heat map data,…). It also allows annotation of genes and other custom features in the plotted region(s). Data tracks can be plotted individually or on a single figure. visPIG is multi-region: it supports plotting multiple regions, be they kilo- or megabases apart or even on different chromosomes. Finally, visPIG is multi-scale: a sub-region of particular interest can be 'zoomed' in. We describe the various features of visPIG and illustrate its utility with examples. visPIG is freely available through http://vispig.icr.ac.uk under a GNU General Public License (GPLv3).

Web-Based Geospatial Visualization of GPM Data with CesiumJS

NASA Technical Reports Server (NTRS)

Lammers, Matt

2018-01-01

Advancements in the capabilities of JavaScript frameworks and web browsing technology have made online visualization of large geospatial datasets such as those coming from precipitation satellites viable. These data benefit from being visualized on and above a three-dimensional surface. The open-source JavaScript framework CesiumJS (http://cesiumjs.org), developed by Analytical Graphics, Inc., leverages the WebGL protocol to do just that. This presentation will describe how CesiumJS has been used in three-dimensional visualization products developed as part of the NASA Precipitation Processing System (PPS) STORM data-order website. Existing methods of interacting with Global Precipitation Measurement (GPM) Mission data primarily focus on two-dimensional static images, whether displaying vertical slices or horizontal surface/height-level maps. These methods limit interactivity with the robust three-dimensional data coming from the GPM core satellite. Integrating the data with CesiumJS in a web-based user interface has allowed us to create the following products. We have linked with the data-order interface an on-the-fly visualization tool for any GPM/partner satellite orbit. A version of this tool also focuses on high-impact weather events. It enables viewing of combined radar and microwave-derived precipitation data on mobile devices and in a way that can be embedded into other websites. We also have used CesiumJS to visualize a method of integrating gridded precipitation data with modeled wind speeds that animates over time. Emphasis in the presentation will be placed on how a variety of technical methods were used to create these tools, and how the flexibility of the CesiumJS framework facilitates creative approaches to interact with the data.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

COEUS: “semantic web in a box” for biomedical applications

PubMed Central

2012-01-01

Background As the “omics” revolution unfolds, the growth in data quantity and diversity is bringing about the need for pioneering bioinformatics software, capable of significantly improving the research workflow. To cope with these computer science demands, biomedical software engineers are adopting emerging semantic web technologies that better suit the life sciences domain. The latter’s complex relationships are easily mapped into semantic web graphs, enabling a superior understanding of collected knowledge. Despite increased awareness of semantic web technologies in bioinformatics, their use is still limited. Results COEUS is a new semantic web framework, aiming at a streamlined application development cycle and following a “semantic web in a box” approach. The framework provides a single package including advanced data integration and triplification tools, base ontologies, a web-oriented engine and a flexible exploration API. Resources can be integrated from heterogeneous sources, including CSV and XML files or SQL and SPARQL query results, and mapped directly to one or more ontologies. Advanced interoperability features include REST services, a SPARQL endpoint and LinkedData publication. These enable the creation of multiple applications for web, desktop or mobile environments, and empower a new knowledge federation layer. Conclusions The platform, targeted at biomedical application developers, provides a complete skeleton ready for rapid application deployment, enhancing the creation of new semantic information systems. COEUS is available as open source at http://bioinformatics.ua.pt/coeus/. PMID:23244467

COEUS: "semantic web in a box" for biomedical applications.

PubMed

Lopes, Pedro; Oliveira, José Luís

2012-12-17

As the "omics" revolution unfolds, the growth in data quantity and diversity is bringing about the need for pioneering bioinformatics software, capable of significantly improving the research workflow. To cope with these computer science demands, biomedical software engineers are adopting emerging semantic web technologies that better suit the life sciences domain. The latter's complex relationships are easily mapped into semantic web graphs, enabling a superior understanding of collected knowledge. Despite increased awareness of semantic web technologies in bioinformatics, their use is still limited. COEUS is a new semantic web framework, aiming at a streamlined application development cycle and following a "semantic web in a box" approach. The framework provides a single package including advanced data integration and triplification tools, base ontologies, a web-oriented engine and a flexible exploration API. Resources can be integrated from heterogeneous sources, including CSV and XML files or SQL and SPARQL query results, and mapped directly to one or more ontologies. Advanced interoperability features include REST services, a SPARQL endpoint and LinkedData publication. These enable the creation of multiple applications for web, desktop or mobile environments, and empower a new knowledge federation layer. The platform, targeted at biomedical application developers, provides a complete skeleton ready for rapid application deployment, enhancing the creation of new semantic information systems. COEUS is available as open source at http://bioinformatics.ua.pt/coeus/.

SpirPro: A Spirulina proteome database and web-based tools for the analysis of protein-protein interactions at the metabolic level in Spirulina (Arthrospira) platensis C1.

PubMed

Senachak, Jittisak; Cheevadhanarak, Supapon; Hongsthong, Apiradee

2015-07-29

Spirulina (Arthrospira) platensis is the only cyanobacterium that in addition to being studied at the molecular level and subjected to gene manipulation, can also be mass cultivated in outdoor ponds for commercial use as a food supplement. Thus, encountering environmental changes, including temperature stresses, is common during the mass production of Spirulina. The use of cyanobacteria as an experimental platform, especially for photosynthetic gene manipulation in plants and bacteria, is becoming increasingly important. Understanding the mechanisms and protein-protein interaction networks that underlie low- and high-temperature responses is relevant to Spirulina mass production. To accomplish this goal, high-throughput techniques such as OMICs analyses are used. Thus, large datasets must be collected, managed and subjected to information extraction. Therefore, databases including (i) proteomic analysis and protein-protein interaction (PPI) data and (ii) domain/motif visualization tools are required for potential use in temperature response models for plant chloroplasts and photosynthetic bacteria. A web-based repository was developed including an embedded database, SpirPro, and tools for network visualization. Proteome data were analyzed integrated with protein-protein interactions and/or metabolic pathways from KEGG. The repository provides various information, ranging from raw data (2D-gel images) to associated results, such as data from interaction and/or pathway analyses. This integration allows in silico analyses of protein-protein interactions affected at the metabolic level and, particularly, analyses of interactions between and within the affected metabolic pathways under temperature stresses for comparative proteomic analysis. The developed tool, which is coded in HTML with CSS/JavaScript and depicted in Scalable Vector Graphics (SVG), is designed for interactive analysis and exploration of the constructed network. SpirPro is publicly available on the web at http://spirpro.sbi.kmutt.ac.th . SpirPro is an analysis platform containing an integrated proteome and PPI database that provides the most comprehensive data on this cyanobacterium at the systematic level. As an integrated database, SpirPro can be applied in various analyses, such as temperature stress response networking analysis in cyanobacterial models and interacting domain-domain analysis between proteins of interest.

Formalization of treatment guidelines using Fuzzy Cognitive Maps and semantic web tools.

PubMed

Papageorgiou, Elpiniki I; Roo, Jos De; Huszka, Csaba; Colaert, Dirk

2012-02-01

Therapy decision making and support in medicine deals with uncertainty and needs to take into account the patient's clinical parameters, the context of illness and the medical knowledge of the physician and guidelines to recommend a treatment therapy. This research study is focused on the formalization of medical knowledge using a cognitive process, called Fuzzy Cognitive Maps (FCMs) and semantic web approach. The FCM technique is capable of dealing with situations including uncertain descriptions using similar procedure such as human reasoning does. Thus, it was selected for the case of modeling and knowledge integration of clinical practice guidelines. The semantic web tools were established to implement the FCM approach. The knowledge base was constructed from the clinical guidelines as the form of if-then fuzzy rules. These fuzzy rules were transferred to FCM modeling technique and, through the semantic web tools, the whole formalization was accomplished. The problem of urinary tract infection (UTI) in adult community was examined for the proposed approach. Forty-seven clinical concepts and eight therapy concepts were identified for the antibiotic treatment therapy problem of UTIs. A preliminary pilot-evaluation study with 55 patient cases showed interesting findings; 91% of the antibiotic treatments proposed by the implemented approach were in fully agreement with the guidelines and physicians' opinions. The results have shown that the suggested approach formalizes medical knowledge efficiently and gives a front-end decision on antibiotics' suggestion for cystitis. Concluding, modeling medical knowledge/therapeutic guidelines using cognitive methods and web semantic tools is both reliable and useful. Copyright © 2011 Elsevier Inc. All rights reserved.

Leveraging the Affordances of YouTube: The Role of Pedagogical Knowledge and Mental Models of Technology Functions for Lesson Planning with Technology

ERIC Educational Resources Information Center

Krauskopf, Karsten; Zahn, Carmen; Hesse, Friedrich W.

2012-01-01

Web-based digital video tools enable learners to access video sources in constructive ways. To leverage these affordances teachers need to integrate their knowledge of a technology with their professional knowledge about teaching. We suggest that this is a cognitive process, which is strongly connected to a teacher's mental model of the tool's…

BingEO: Enable Distributed Earth Observation Data for Environmental Research

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

TryTransDB: A web-based resource for transport proteins in Trypanosomatidae.

PubMed

Sonar, Krushna; Kabra, Ritika; Singh, Shailza

2018-03-12

TryTransDB is a web-based resource that stores transport protein data which can be retrieved using a standalone BLAST tool. We have attempted to create an integrated database that can be a one-stop shop for the researchers working with transport proteins of Trypanosomatidae family. TryTransDB (Trypanosomatidae Transport Protein Database) is a web based comprehensive resource that can fire a BLAST search against most of the transport protein sequences (protein and nucleotide) from Trypanosomatidae family organisms. This web resource further allows to compute a phylogenetic tree by performing multiple sequence alignment (MSA) using CLUSTALW suite embedded in it. Also, cross-linking to other databases helps in gathering more information for a certain transport protein in a single website.

IntegromeDB: an integrated system and biological search engine.

PubMed

Baitaluk, Michael; Kozhenkov, Sergey; Dubinina, Yulia; Ponomarenko, Julia

2012-01-19

With the growth of biological data in volume and heterogeneity, web search engines become key tools for researchers. However, general-purpose search engines are not specialized for the search of biological data. Here, we present an approach at developing a biological web search engine based on the Semantic Web technologies and demonstrate its implementation for retrieving gene- and protein-centered knowledge. The engine is available at http://www.integromedb.org. The IntegromeDB search engine allows scanning data on gene regulation, gene expression, protein-protein interactions, pathways, metagenomics, mutations, diseases, and other gene- and protein-related data that are automatically retrieved from publicly available databases and web pages using biological ontologies. To perfect the resource design and usability, we welcome and encourage community feedback.

Biological data integration: wrapping data and tools.

PubMed

Lacroix, Zoé

2002-06-01

Nowadays scientific data is inevitably digital and stored in a wide variety of formats in heterogeneous systems. Scientists need to access an integrated view of remote or local heterogeneous data sources with advanced data accessing, analyzing, and visualization tools. Building a digital library for scientific data requires accessing and manipulating data extracted from flat files or databases, documents retrieved from the Web as well as data generated by software. We present an approach to wrapping web data sources, databases, flat files, or data generated by tools through a database view mechanism. Generally, a wrapper has two tasks: it first sends a query to the source to retrieve data and, second builds the expected output with respect to the virtual structure. Our wrappers are composed of a retrieval component based on an intermediate object view mechanism called search views mapping the source capabilities to attributes, and an eXtensible Markup Language (XML) engine, respectively, to perform these two tasks. The originality of the approach consists of: 1) a generic view mechanism to access seamlessly data sources with limited capabilities and 2) the ability to wrap data sources as well as the useful specific tools they may provide. Our approach has been developed and demonstrated as part of the multidatabase system supporting queries via uniform object protocol model (OPM) interfaces.

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

Flexible querying of Web data to simulate bacterial growth in food.

PubMed

Buche, Patrice; Couvert, Olivier; Dibie-Barthélemy, Juliette; Hignette, Gaëlle; Mettler, Eric; Soler, Lydie

2011-06-01

A preliminary step in microbial risk assessment in foods is the gathering of experimental data. In the framework of the Sym'Previus project, we have designed a complete data integration system opened on the Web which allows a local database to be complemented by data extracted from the Web and annotated using a domain ontology. We focus on the Web data tables as they contain, in general, a synthesis of data published in the documents. We propose in this paper a flexible querying system using the domain ontology to scan simultaneously local and Web data, this in order to feed the predictive modeling tools available on the Sym'Previus platform. Special attention is paid on the way fuzzy annotations associated with Web data are taken into account in the querying process, which is an important and original contribution of the proposed system. Copyright © 2010 Elsevier Ltd. All rights reserved.

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.

Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms.

PubMed

Bianco, Luca; Riccadonna, Samantha; Lavezzo, Enrico; Falda, Marco; Formentin, Elide; Cavalieri, Duccio; Toppo, Stefano; Fontana, Paolo

2017-02-01

Pathway Inspector is an easy-to-use web application helping researchers to find patterns of expression in complex RNAseq experiments. The tool combines two standard approaches for RNAseq analysis: the identification of differentially expressed genes and a topology-based analysis of enriched pathways. Pathway Inspector is equipped with ad hoc interactive graphical interfaces simplifying the discovery of modulated pathways and the integration of the differentially expressed genes in the corresponding pathway topology. Pathway Inspector is available at the website http://admiral.fmach.it/PI and has been developed in Python, making use of the Django Web Framework. Contact:paolo.fontana@fmach.it

Web-based interactive visualization in a Grid-enabled neuroimaging application using HTML5.

PubMed

Siewert, René; Specovius, Svenja; Wu, Jie; Krefting, Dagmar

2012-01-01

Interactive visualization and correction of intermediate results are required in many medical image analysis pipelines. To allow certain interaction in the remote execution of compute- and data-intensive applications, new features of HTML5 are used. They allow for transparent integration of user interaction into Grid- or Cloud-enabled scientific workflows. Both 2D and 3D visualization and data manipulation can be performed through a scientific gateway without the need to install specific software or web browser plugins. The possibilities of web-based visualization are presented along the FreeSurfer-pipeline, a popular compute- and data-intensive software tool for quantitative neuroimaging.

A Hybrid Evaluation System Framework (Shell & Web) with Standardized Access to Climate Model Data and Verification Tools for a Clear Climate Science Infrastructure on Big Data High Performance Computers

NASA Astrophysics Data System (ADS)

Kadow, C.; Illing, S.; Kunst, O.; Cubasch, U.

2014-12-01

The project 'Integrated Data and Evaluation System for Decadal Scale Prediction' (INTEGRATION) as part of the German decadal prediction project MiKlip develops a central evaluation system. The fully operational hybrid features a HPC shell access and an user friendly web-interface. It employs one common system with a variety of verification tools and validation data from different projects in- and outside of MiKlip. The evaluation system is located at the German Climate Computing Centre (DKRZ) and has direct access to the bulk of its ESGF node including millions of climate model data sets, e.g. from CMIP5 and CORDEX. The database is organized by the international CMOR standard using the meta information of the self-describing model, reanalysis and observational data sets. Apache Solr is used for indexing the different data projects into one common search environment. This implemented meta data system with its advanced but easy to handle search tool supports users, developers and their tools to retrieve the required information. A generic application programming interface (API) allows scientific developers to connect their analysis tools with the evaluation system independently of the programming language used. Users of the evaluation techniques benefit from the common interface of the evaluation system without any need to understand the different scripting languages. Facilitating the provision and usage of tools and climate data increases automatically the number of scientists working with the data sets and identify discrepancies. Additionally, the history and configuration sub-system stores every analysis performed with the evaluation system in a MySQL database. Configurations and results of the tools can be shared among scientists via shell or web-system. Therefore, plugged-in tools gain automatically from transparency and reproducibility. Furthermore, when configurations match while starting a evaluation tool, the system suggests to use results already produced by other users-saving CPU time, I/O and disk space. This study presents the different techniques and advantages of such a hybrid evaluation system making use of a Big Data HPC in climate science. website: www-miklip.dkrz.de visitor-login: guest password: miklip

A Hybrid Evaluation System Framework (Shell & Web) with Standardized Access to Climate Model Data and Verification Tools for a Clear Climate Science Infrastructure on Big Data High Performance Computers

NASA Astrophysics Data System (ADS)

Kadow, Christopher; Illing, Sebastian; Kunst, Oliver; Ulbrich, Uwe; Cubasch, Ulrich

2015-04-01

The project 'Integrated Data and Evaluation System for Decadal Scale Prediction' (INTEGRATION) as part of the German decadal prediction project MiKlip develops a central evaluation system. The fully operational hybrid features a HPC shell access and an user friendly web-interface. It employs one common system with a variety of verification tools and validation data from different projects in- and outside of MiKlip. The evaluation system is located at the German Climate Computing Centre (DKRZ) and has direct access to the bulk of its ESGF node including millions of climate model data sets, e.g. from CMIP5 and CORDEX. The database is organized by the international CMOR standard using the meta information of the self-describing model, reanalysis and observational data sets. Apache Solr is used for indexing the different data projects into one common search environment. This implemented meta data system with its advanced but easy to handle search tool supports users, developers and their tools to retrieve the required information. A generic application programming interface (API) allows scientific developers to connect their analysis tools with the evaluation system independently of the programming language used. Users of the evaluation techniques benefit from the common interface of the evaluation system without any need to understand the different scripting languages. Facilitating the provision and usage of tools and climate data increases automatically the number of scientists working with the data sets and identify discrepancies. Additionally, the history and configuration sub-system stores every analysis performed with the evaluation system in a MySQL database. Configurations and results of the tools can be shared among scientists via shell or web-system. Therefore, plugged-in tools gain automatically from transparency and reproducibility. Furthermore, when configurations match while starting a evaluation tool, the system suggests to use results already produced by other users-saving CPU time, I/O and disk space. This study presents the different techniques and advantages of such a hybrid evaluation system making use of a Big Data HPC in climate science. website: www-miklip.dkrz.de visitor-login: click on "Guest"

Web services-based text-mining demonstrates broad impacts for interoperability and process simplification.

PubMed

Wiegers, Thomas C; Davis, Allan Peter; Mattingly, Carolyn J

2014-01-01

The Critical Assessment of Information Extraction systems in Biology (BioCreAtIvE) challenge evaluation tasks collectively represent a community-wide effort to evaluate a variety of text-mining and information extraction systems applied to the biological domain. The BioCreative IV Workshop included five independent subject areas, including Track 3, which focused on named-entity recognition (NER) for the Comparative Toxicogenomics Database (CTD; http://ctdbase.org). Previously, CTD had organized document ranking and NER-related tasks for the BioCreative Workshop 2012; a key finding of that effort was that interoperability and integration complexity were major impediments to the direct application of the systems to CTD's text-mining pipeline. This underscored a prevailing problem with software integration efforts. Major interoperability-related issues included lack of process modularity, operating system incompatibility, tool configuration complexity and lack of standardization of high-level inter-process communications. One approach to potentially mitigate interoperability and general integration issues is the use of Web services to abstract implementation details; rather than integrating NER tools directly, HTTP-based calls from CTD's asynchronous, batch-oriented text-mining pipeline could be made to remote NER Web services for recognition of specific biological terms using BioC (an emerging family of XML formats) for inter-process communications. To test this concept, participating groups developed Representational State Transfer /BioC-compliant Web services tailored to CTD's NER requirements. Participants were provided with a comprehensive set of training materials. CTD evaluated results obtained from the remote Web service-based URLs against a test data set of 510 manually curated scientific articles. Twelve groups participated in the challenge. Recall, precision, balanced F-scores and response times were calculated. Top balanced F-scores for gene, chemical and disease NER were 61, 74 and 51%, respectively. Response times ranged from fractions-of-a-second to over a minute per article. We present a description of the challenge and summary of results, demonstrating how curation groups can effectively use interoperable NER technologies to simplify text-mining pipeline implementation. Database URL: http://ctdbase.org/ © The Author(s) 2014. Published by Oxford University Press.

Web services-based text-mining demonstrates broad impacts for interoperability and process simplification

PubMed Central

Wiegers, Thomas C.; Davis, Allan Peter; Mattingly, Carolyn J.

2014-01-01

The Critical Assessment of Information Extraction systems in Biology (BioCreAtIvE) challenge evaluation tasks collectively represent a community-wide effort to evaluate a variety of text-mining and information extraction systems applied to the biological domain. The BioCreative IV Workshop included five independent subject areas, including Track 3, which focused on named-entity recognition (NER) for the Comparative Toxicogenomics Database (CTD; http://ctdbase.org). Previously, CTD had organized document ranking and NER-related tasks for the BioCreative Workshop 2012; a key finding of that effort was that interoperability and integration complexity were major impediments to the direct application of the systems to CTD's text-mining pipeline. This underscored a prevailing problem with software integration efforts. Major interoperability-related issues included lack of process modularity, operating system incompatibility, tool configuration complexity and lack of standardization of high-level inter-process communications. One approach to potentially mitigate interoperability and general integration issues is the use of Web services to abstract implementation details; rather than integrating NER tools directly, HTTP-based calls from CTD's asynchronous, batch-oriented text-mining pipeline could be made to remote NER Web services for recognition of specific biological terms using BioC (an emerging family of XML formats) for inter-process communications. To test this concept, participating groups developed Representational State Transfer /BioC-compliant Web services tailored to CTD's NER requirements. Participants were provided with a comprehensive set of training materials. CTD evaluated results obtained from the remote Web service-based URLs against a test data set of 510 manually curated scientific articles. Twelve groups participated in the challenge. Recall, precision, balanced F-scores and response times were calculated. Top balanced F-scores for gene, chemical and disease NER were 61, 74 and 51%, respectively. Response times ranged from fractions-of-a-second to over a minute per article. We present a description of the challenge and summary of results, demonstrating how curation groups can effectively use interoperable NER technologies to simplify text-mining pipeline implementation. Database URL: http://ctdbase.org/ PMID:24919658

KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems

PubMed Central

2014-01-01

Background The kinetic modeling of biological systems is mainly composed of three steps that proceed iteratively: model building, simulation and analysis. In the first step, it is usually required to set initial metabolite concentrations, and to assign kinetic rate laws, along with estimating parameter values using kinetic data through optimization when these are not known. Although the rapid development of high-throughput methods has generated much omics data, experimentalists present only a summary of obtained results for publication, the experimental data files are not usually submitted to any public repository, or simply not available at all. In order to automatize as much as possible the steps of building kinetic models, there is a growing requirement in the systems biology community for easily exchanging data in combination with models, which represents the main motivation of KiMoSys development. Description KiMoSys is a user-friendly platform that includes a public data repository of published experimental data, containing concentration data of metabolites and enzymes and flux data. It was designed to ensure data management, storage and sharing for a wider systems biology community. This community repository offers a web-based interface and upload facility to turn available data into publicly accessible, centralized and structured-format data files. Moreover, it compiles and integrates available kinetic models associated with the data. KiMoSys also integrates some tools to facilitate the kinetic model construction process of large-scale metabolic networks, especially when the systems biologists perform computational research. Conclusions KiMoSys is a web-based system that integrates a public data and associated model(s) repository with computational tools, providing the systems biology community with a novel application facilitating data storage and sharing, thus supporting construction of ODE-based kinetic models and collaborative research projects. The web application implemented using Ruby on Rails framework is freely available for web access at http://kimosys.org, along with its full documentation. PMID:25115331

HyQue: evaluating hypotheses using Semantic Web technologies.

PubMed

Callahan, Alison; Dumontier, Michel; Shah, Nigam H

2011-05-17

Key to the success of e-Science is the ability to computationally evaluate expert-composed hypotheses for validity against experimental data. Researchers face the challenge of collecting, evaluating and integrating large amounts of diverse information to compose and evaluate a hypothesis. Confronted with rapidly accumulating data, researchers currently do not have the software tools to undertake the required information integration tasks. We present HyQue, a Semantic Web tool for querying scientific knowledge bases with the purpose of evaluating user submitted hypotheses. HyQue features a knowledge model to accommodate diverse hypotheses structured as events and represented using Semantic Web languages (RDF/OWL). Hypothesis validity is evaluated against experimental and literature-sourced evidence through a combination of SPARQL queries and evaluation rules. Inference over OWL ontologies (for type specifications, subclass assertions and parthood relations) and retrieval of facts stored as Bio2RDF linked data provide support for a given hypothesis. We evaluate hypotheses of varying levels of detail about the genetic network controlling galactose metabolism in Saccharomyces cerevisiae to demonstrate the feasibility of deploying such semantic computing tools over a growing body of structured knowledge in Bio2RDF. HyQue is a query-based hypothesis evaluation system that can currently evaluate hypotheses about the galactose metabolism in S. cerevisiae. Hypotheses as well as the supporting or refuting data are represented in RDF and directly linked to one another allowing scientists to browse from data to hypothesis and vice versa. HyQue hypotheses and data are available at http://semanticscience.org/projects/hyque.

The climate4impact platform: Providing, tailoring and facilitating climate model data access

NASA Astrophysics Data System (ADS)

Pagé, Christian; Pagani, Andrea; Plieger, Maarten; Som de Cerff, Wim; Mihajlovski, Andrej; de Vreede, Ernst; Spinuso, Alessandro; Hutjes, Ronald; de Jong, Fokke; Bärring, Lars; Vega, Manuel; Cofiño, Antonio; d'Anca, Alessandro; Fiore, Sandro; Kolax, Michael

2017-04-01

One of the main objectives of climate4impact is to provide standardized web services and tools that are reusable in other portals. These services include web processing services, web coverage services and web mapping services (WPS, WCS and WMS). Tailored portals can be targeted to specific communities and/or countries/regions while making use of those services. Easier access to climate data is very important for the climate change impact communities. To fulfill this objective, the climate4impact (http://climate4impact.eu/) web portal and services has been developed, targeting climate change impact modellers, impact and adaptation consultants, as well as other experts using climate change data. It provides to users harmonized access to climate model data through tailored services. It features static and dynamic documentation, Use Cases and best practice examples, an advanced search interface, an integrated authentication and authorization system with the Earth System Grid Federation (ESGF), a visualization interface with ADAGUC web mapping tools. In the latest version, statistical downscaling services, provided by the Santander Meteorology Group Downscaling Portal, were integrated. An innovative interface to integrate statistical downscaling services will be released in the upcoming version. The latter will be a big step in bridging the gap between climate scientists and the climate change impact communities. The climate4impact portal builds on the infrastructure of an international distributed database that has been set to disseminate the results from the global climate model results of the Coupled Model Intercomparison project Phase 5 (CMIP5). This database, the ESGF, is an international collaboration that develops, deploys and maintains software infrastructure for the management, dissemination, and analysis of climate model data. The European FP7 project IS-ENES, Infrastructure for the European Network for Earth System modelling, supports the European contribution to ESGF and contributes to the ESGF open source effort, notably through the development of search, monitoring, quality control, and metadata services. In its second phase, IS-ENES2 supports the implementation of regional climate model results from the international Coordinated Regional Downscaling Experiments (CORDEX). These services were extended within the European FP7 Climate Information Portal for Copernicus (CLIPC) project, and some could be later integrated into the European Copernicus platform.

Challenges in integrative approaches to modelling the marine ecosystems of the North Atlantic: Physics to fish and coasts to ocean

NASA Astrophysics Data System (ADS)

Holt, Jason; Icarus Allen, J.; Anderson, Thomas R.; Brewin, Robert; Butenschön, Momme; Harle, James; Huse, Geir; Lehodey, Patrick; Lindemann, Christian; Memery, Laurent; Salihoglu, Baris; Senina, Inna; Yool, Andrew

2014-12-01

It has long been recognised that there are strong interactions and feedbacks between climate, upper ocean biogeochemistry and marine food webs, and also that food web structure and phytoplankton community distribution are important determinants of variability in carbon production and export from the euphotic zone. Numerical models provide a vital tool to explore these interactions, given their capability to investigate multiple connected components of the system and the sensitivity to multiple drivers, including potential future conditions. A major driver for ecosystem model development is the demand for quantitative tools to support ecosystem-based management initiatives. The purpose of this paper is to review approaches to the modelling of marine ecosystems with a focus on the North Atlantic Ocean and its adjacent shelf seas, and to highlight the challenges they face and suggest ways forward. We consider the state of the art in simulating oceans and shelf sea physics, planktonic and higher trophic level ecosystems, and look towards building an integrative approach with these existing tools. We note how the different approaches have evolved historically and that many of the previous obstacles to harmonisation may no longer be present. We illustrate this with examples from the on-going and planned modelling effort in the Integrative Modelling Work Package of the EURO-BASIN programme.

Web-based interactive 2D/3D medical image processing and visualization software.

PubMed

Mahmoudi, Seyyed Ehsan; Akhondi-Asl, Alireza; Rahmani, Roohollah; Faghih-Roohi, Shahrooz; Taimouri, Vahid; Sabouri, Ahmad; Soltanian-Zadeh, Hamid

2010-05-01

There are many medical image processing software tools available for research and diagnosis purposes. However, most of these tools are available only as local applications. This limits the accessibility of the software to a specific machine, and thus the data and processing power of that application are not available to other workstations. Further, there are operating system and processing power limitations which prevent such applications from running on every type of workstation. By developing web-based tools, it is possible for users to access the medical image processing functionalities wherever the internet is available. In this paper, we introduce a pure web-based, interactive, extendable, 2D and 3D medical image processing and visualization application that requires no client installation. Our software uses a four-layered design consisting of an algorithm layer, web-user-interface layer, server communication layer, and wrapper layer. To compete with extendibility of the current local medical image processing software, each layer is highly independent of other layers. A wide range of medical image preprocessing, registration, and segmentation methods are implemented using open source libraries. Desktop-like user interaction is provided by using AJAX technology in the web-user-interface. For the visualization functionality of the software, the VRML standard is used to provide 3D features over the web. Integration of these technologies has allowed implementation of our purely web-based software with high functionality without requiring powerful computational resources in the client side. The user-interface is designed such that the users can select appropriate parameters for practical research and clinical studies. Copyright (c) 2009 Elsevier Ireland Ltd. All rights reserved.

Interactive and Approachable Web-Based Tools for Exploring Global Geophysical Data Records

NASA Astrophysics Data System (ADS)

Croteau, M. J.; Nerem, R. S.; Merrifield, M. A.; Thompson, P. R.; Loomis, B. D.; Wiese, D. N.; Zlotnicki, V.; Larson, J.; Talpe, M.; Hardy, R. A.

2017-12-01

Making global and regional data accessible and understandable for non-experts can be both challenging and hazardous. While data products are often developed with end users in mind, the ease of use of these data can vary greatly. Scientists must take care to provide detailed guides for how to use data products to ensure users are not incorrectly applying data to their problem. For example, terrestrial water storage data from the Gravity Recovery and Climate Experiment (GRACE) satellite mission is notoriously difficult for non-experts to access and correctly use. However, allowing these data to be easily accessible to scientists outside the GRACE community is desirable because this would allow that data to see much wider-spread use. We have developed a web-based interactive mapping and plotting tool that provides easy access to geophysical data. This work presents an intuitive method for making such data widely accessible to experts and non-experts alike, making the data approachable and ensuring proper use of the data. This tool has proven helpful to experts by providing fast and detailed access to the data. Simultaneously, the tool allows non-experts to gain familiarity with the information contained in the data and access to that information for both scientific studies and public use. In this presentation, we discuss the development of this tool and application to both GRACE and ocean altimetry satellite missions, and demonstrate the capabilities of the tool. Focusing on the data visualization aspects of the tool, we showcase our integrations of the Mapbox API and the D3.js data-driven web document framework. We then explore the potential of these tools in other web-based visualization projects, and how incorporation of such tools into science can improve the presentation of research results. We demonstrate how the development of an interactive and exploratory resource can enable further layers of exploratory and scientific discovery.

Strategic Integration of Multiple Bioinformatics Resources for System Level Analysis of Biological Networks.

PubMed

D'Souza, Mark; Sulakhe, Dinanath; Wang, Sheng; Xie, Bing; Hashemifar, Somaye; Taylor, Andrew; Dubchak, Inna; Conrad Gilliam, T; Maltsev, Natalia

2017-01-01

Recent technological advances in genomics allow the production of biological data at unprecedented tera- and petabyte scales. Efficient mining of these vast and complex datasets for the needs of biomedical research critically depends on a seamless integration of the clinical, genomic, and experimental information with prior knowledge about genotype-phenotype relationships. Such experimental data accumulated in publicly available databases should be accessible to a variety of algorithms and analytical pipelines that drive computational analysis and data mining.We present an integrated computational platform Lynx (Sulakhe et al., Nucleic Acids Res 44:D882-D887, 2016) ( http://lynx.cri.uchicago.edu ), a web-based database and knowledge extraction engine. It provides advanced search capabilities and a variety of algorithms for enrichment analysis and network-based gene prioritization. It gives public access to the Lynx integrated knowledge base (LynxKB) and its analytical tools via user-friendly web services and interfaces. The Lynx service-oriented architecture supports annotation and analysis of high-throughput experimental data. Lynx tools assist the user in extracting meaningful knowledge from LynxKB and experimental data, and in the generation of weighted hypotheses regarding the genes and molecular mechanisms contributing to human phenotypes or conditions of interest. The goal of this integrated platform is to support the end-to-end analytical needs of various translational projects.

Can You See Me Now?

ERIC Educational Resources Information Center

Raths, David

2013-01-01

Ten years ago, integrating videoconferencing into a college course required considerable effort on the part of the instructor and IT support staff. Today, video- and web-conferencing tools are more sophisticated. Distance education has morphed from audio- and videocassettes featuring talking heads to a more interactive experience with greater…

Looking for Collection 2.0

ERIC Educational Resources Information Center

Buczynski, James A.

2008-01-01

Libraries are integrating Web 2.0 services into work practices, positioning themselves in online social environments, and deploying enhanced search and discovery tools. Collections conversely are not progressing to the same degree. Like many public services today, library budgets are stained. User-pay options are appearing in library systems,…

Managing Mission-Critical Infrastructure

ERIC Educational Resources Information Center

Breeding, Marshall

2012-01-01

In the library context, they depend on sophisticated business applications specifically designed to support their work. This infrastructure consists of such components as integrated library systems, their associated online catalogs or discovery services, and self-check equipment, as well as a Web site and the various online tools and services…

Visual Communication: Integrating Visual Instruction into Business Communication Courses

ERIC Educational Resources Information Center

Baker, William H.

2006-01-01

Business communication courses are ideal for teaching visual communication principles and techniques. Many assignments lend themselves to graphic enrichment, such as flyers, handouts, slide shows, Web sites, and newsletters. Microsoft Publisher and Microsoft PowerPoint are excellent tools for these assignments, with Publisher being best for…

A Case Study of Technology-Enhanced Historical Inquiry

ERIC Educational Resources Information Center

Yang, Shu Ching

2009-01-01

The paper describes the integration of web resources and technology as instructional and learning tools in oral history projects. The computer-mediated oral history project centred around interviews with community elders combined with new technologies to engage students in authentic historical inquiry. The study examined learners' affective…

SCALEUS: Semantic Web Services Integration for Biomedical Applications.

PubMed

Sernadela, Pedro; González-Castro, Lorena; Oliveira, José Luís

2017-04-01

In recent years, we have witnessed an explosion of biological data resulting largely from the demands of life science research. The vast majority of these data are freely available via diverse bioinformatics platforms, including relational databases and conventional keyword search applications. This type of approach has achieved great results in the last few years, but proved to be unfeasible when information needs to be combined or shared among different and scattered sources. During recent years, many of these data distribution challenges have been solved with the adoption of semantic web. Despite the evident benefits of this technology, its adoption introduced new challenges related with the migration process, from existent systems to the semantic level. To facilitate this transition, we have developed Scaleus, a semantic web migration tool that can be deployed on top of traditional systems in order to bring knowledge, inference rules, and query federation to the existent data. Targeted at the biomedical domain, this web-based platform offers, in a single package, straightforward data integration and semantic web services that help developers and researchers in the creation process of new semantically enhanced information systems. SCALEUS is available as open source at http://bioinformatics-ua.github.io/scaleus/ .

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

PubMed

Weirick, Tyler; John, David; Uchida, Shizuka

2017-03-01

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

Evaluation of flood hazard maps in print and web mapping services as information tools in flood risk communication

NASA Astrophysics Data System (ADS)

Hagemeier-Klose, M.; Wagner, K.

2009-04-01

Flood risk communication with the general public and the population at risk is getting increasingly important for flood risk management, especially as a precautionary measure. This is also underlined by the EU Flood Directive. The flood related authorities therefore have to develop adjusted information tools which meet the demands of different user groups. This article presents the formative evaluation of flood hazard maps and web mapping services according to the specific requirements and needs of the general public using the dynamic-transactional approach as a theoretical framework. The evaluation was done by a mixture of different methods; an analysis of existing tools, a creative workshop with experts and laymen and an online survey. The currently existing flood hazard maps or web mapping services or web GIS still lack a good balance between simplicity and complexity with adequate readability and usability for the public. Well designed and associative maps (e.g. using blue colours for water depths) which can be compared with past local flood events and which can create empathy in viewers, can help to raise awareness, to heighten the activity and knowledge level or can lead to further information seeking. Concerning web mapping services, a linkage between general flood information like flood extents of different scenarios and corresponding water depths and real time information like gauge levels is an important demand by users. Gauge levels of these scenarios are easier to understand than the scientifically correct return periods or annualities. The recently developed Bavarian web mapping service tries to integrate these requirements.

Workflow and web application for annotating NCBI BioProject transcriptome data.

PubMed

Vera Alvarez, Roberto; Medeiros Vidal, Newton; Garzón-Martínez, Gina A; Barrero, Luz S; Landsman, David; Mariño-Ramírez, Leonardo

2017-01-01

The volume of transcriptome data is growing exponentially due to rapid improvement of experimental technologies. In response, large central resources such as those of the National Center for Biotechnology Information (NCBI) are continually adapting their computational infrastructure to accommodate this large influx of data. New and specialized databases, such as Transcriptome Shotgun Assembly Sequence Database (TSA) and Sequence Read Archive (SRA), have been created to aid the development and expansion of centralized repositories. Although the central resource databases are under continual development, they do not include automatic pipelines to increase annotation of newly deposited data. Therefore, third-party applications are required to achieve that aim. Here, we present an automatic workflow and web application for the annotation of transcriptome data. The workflow creates secondary data such as sequencing reads and BLAST alignments, which are available through the web application. They are based on freely available bioinformatics tools and scripts developed in-house. The interactive web application provides a search engine and several browser utilities. Graphical views of transcript alignments are available through SeqViewer, an embedded tool developed by NCBI for viewing biological sequence data. The web application is tightly integrated with other NCBI web applications and tools to extend the functionality of data processing and interconnectivity. We present a case study for the species Physalis peruviana with data generated from BioProject ID 67621. URL: http://www.ncbi.nlm.nih.gov/projects/physalis/. Published by Oxford University Press 2017. This work is written by US Government employees and is in the public domain in the US.

Integration of a Zero-footprint Cloud-based Picture Archiving and Communication System with Customizable Forms for Radiology Research and Education.

PubMed

Hostetter, Jason; Khanna, Nishanth; Mandell, Jacob C

2018-06-01

The purpose of this study was to integrate web-based forms with a zero-footprint cloud-based Picture Archiving and Communication Systems (PACS) to create a tool of potential benefit to radiology research and education. Web-based forms were created with a front-end and back-end architecture utilizing common programming languages including Vue.js, Node.js and MongoDB, and integrated into an existing zero-footprint cloud-based PACS. The web-based forms application can be accessed in any modern internet browser on desktop or mobile devices and allows the creation of customizable forms consisting of a variety of questions types. Each form can be linked to an individual DICOM examination or a collection of DICOM examinations. Several uses are demonstrated through a series of case studies, including implementation of a research platform for multi-reader multi-case (MRMC) studies and other imaging research, and creation of an online Objective Structure Clinical Examination (OSCE) and an educational case file. Copyright © 2018 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

NCBI BLAST+ integrated into Galaxy.

PubMed

Cock, Peter J A; Chilton, John M; Grüning, Björn; Johnson, James E; Soranzo, Nicola

2015-01-01

The NCBI BLAST suite has become ubiquitous in modern molecular biology and is used for small tasks such as checking capillary sequencing results of single PCR products, genome annotation or even larger scale pan-genome analyses. For early adopters of the Galaxy web-based biomedical data analysis platform, integrating BLAST into Galaxy was a natural step for sequence comparison workflows. The command line NCBI BLAST+ tool suite was wrapped for use within Galaxy. Appropriate datatypes were defined as needed. The integration of the BLAST+ tool suite into Galaxy has the goal of making common BLAST tasks easy and advanced tasks possible. This project is an informal international collaborative effort, and is deployed and used on Galaxy servers worldwide. Several examples of applications are described here.

ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells.

PubMed

Xu, Huilei; Baroukh, Caroline; Dannenfelser, Ruth; Chen, Edward Y; Tan, Christopher M; Kou, Yan; Kim, Yujin E; Lemischka, Ihor R; Ma'ayan, Avi

2013-01-01

High content studies that profile mouse and human embryonic stem cells (m/hESCs) using various genome-wide technologies such as transcriptomics and proteomics are constantly being published. However, efforts to integrate such data to obtain a global view of the molecular circuitry in m/hESCs are lagging behind. Here, we present an m/hESC-centered database called Embryonic Stem Cell Atlas from Pluripotency Evidence integrating data from many recent diverse high-throughput studies including chromatin immunoprecipitation followed by deep sequencing, genome-wide inhibitory RNA screens, gene expression microarrays or RNA-seq after knockdown (KD) or overexpression of critical factors, immunoprecipitation followed by mass spectrometry proteomics and phosphoproteomics. The database provides web-based interactive search and visualization tools that can be used to build subnetworks and to identify known and novel regulatory interactions across various regulatory layers. The web-interface also includes tools to predict the effects of combinatorial KDs by additive effects controlled by sliders, or through simulation software implemented in MATLAB. Overall, the Embryonic Stem Cell Atlas from Pluripotency Evidence database is a comprehensive resource for the stem cell systems biology community. Database URL: http://www.maayanlab.net/ESCAPE

JNSViewer—A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures

PubMed Central

Dong, Min; Graham, Mitchell; Yadav, Nehul

2017-01-01

Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome) were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html. PMID:28582416

Radio and Optical Telescopes for School Students and Professional Astronomers

NASA Astrophysics Data System (ADS)

Hosmer, Laura; Langston, G.; Heatherly, S.; Towner, A. P.; Ford, J.; Simon, R. S.; White, S.; O'Neil, K. L.; Haipslip, J.; Reichart, D.

2013-01-01

The NRAO 20m telescope is now on-line as a part of UNC's Skynet worldwide telescope network. The NRAO is completing integration of radio astronomy tools with the Skynet web interface. We present the web interface and astronomy projects that allow students and astronomers from all over the country to become Radio Astronomers. The 20 meter radio telescope at NRAO in Green Bank, WV is dedicated to public education and also is part of an experiment in public funding for astronomy. The telescope has a fantastic new web-based interface, with priority queuing, accommodating priority for paying customers and enabling free use of otherwise unused time. This revival included many software and hardware improvements including automatic calibration and improved time integration resulting in improved data processing, and a new ultra high resolution spectrometer. This new spectrometer is optimized for very narrow spectral lines, which will allow astronomers to study complex molecules and very cold regions of space in remarkable detail. In accordance with focusing on broader impacts, many public outreach and high school education activities have been completed with many confirmed future activities. The 20 meter is now a fully automated, powerful tool capable of professional grade results available to anyone in the world. Drop by our poster and try out real-time telescope control!

Earth Observation oriented teaching materials development based on OGC Web services and Bashyt generated reports

NASA Astrophysics Data System (ADS)

Stefanut, T.; Gorgan, D.; Giuliani, G.; Cau, P.

2012-04-01

Creating e-Learning materials in the Earth Observation domain is a difficult task especially for non-technical specialists who have to deal with distributed repositories, large amounts of information and intensive processing requirements. Furthermore, due to the lack of specialized applications for developing teaching resources, technical knowledge is required also for defining data presentation structures or in the development and customization of user interaction techniques for better teaching results. As a response to these issues during the GiSHEO FP7 project [1] and later in the EnviroGRIDS FP7 [2] project, we have developed the eGLE e-Learning Platform [3], a tool based application that provides dedicated functionalities to the Earth Observation specialists for developing teaching materials. The proposed architecture is built around a client-server design that provides the core functionalities (e.g. user management, tools integration, teaching materials settings, etc.) and has been extended with a distributed component implemented through the tools that are integrated into the platform, as described further. Our approach in dealing with multiple transfer protocol types, heterogeneous data formats or various user interaction techniques involve the development and integration of very specialized elements (tools) that can be customized by the trainers in a visual manner through simple user interfaces. In our concept each tool is dedicated to a specific data type, implementing optimized mechanisms for searching, retrieving, visualizing and interacting with it. At the same time, in each learning resource can be integrated any number of tools, through drag-and-drop interaction, allowing the teacher to retrieve pieces of data of various types (e.g. images, charts, tables, text, videos etc.) from different sources (e.g. OGC web services, charts created through Bashyt application, etc.) through different protocols (ex. WMS, BASHYT API, FTP, HTTP etc.) and to display them all together in a unitary manner using the same visual structure [4]. Addressing the High Power Computation requirements that are met while processing environmental data, our platform can be easily extended through tools that connect to GRID infrastructures, WCS web services, Bashyt API (for creating specialized hydrological reports) or any other specialized services (ex. graphics cluster visualization) that can be reached over the Internet. At run time, on the trainee's computer each tool is launched in an asynchronous running mode and connects to the data source that has been established by the teacher, retrieving and displaying the information to the user. The data transfer is accomplished directly between the trainee's computer and the corresponding services (e.g. OGC, Bashyt API, etc.) without passing through the core server platform. In this manner, the eGLE application can provide better and more responsive connections to a large number of users.

Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis.

PubMed

Weber, Nick; Liou, David; Dommer, Jennifer; MacMenamin, Philip; Quiñones, Mariam; Misner, Ian; Oler, Andrew J; Wan, Joe; Kim, Lewis; Coakley McCarthy, Meghan; Ezeji, Samuel; Noble, Karlynn; Hurt, Darrell E

2018-04-15

Widespread interest in the study of the microbiome has resulted in data proliferation and the development of powerful computational tools. However, many scientific researchers lack the time, training, or infrastructure to work with large datasets or to install and use command line tools. The National Institute of Allergy and Infectious Diseases (NIAID) has created Nephele, a cloud-based microbiome data analysis platform with standardized pipelines and a simple web interface for transforming raw data into biological insights. Nephele integrates common microbiome analysis tools as well as valuable reference datasets like the healthy human subjects cohort of the Human Microbiome Project (HMP). Nephele is built on the Amazon Web Services cloud, which provides centralized and automated storage and compute capacity, thereby reducing the burden on researchers and their institutions. https://nephele.niaid.nih.gov and https://github.com/niaid/Nephele. darrell.hurt@nih.gov.

Effects of weld damage on the dynamics of energy-absorbing lanyards.

PubMed

Katona, David N; Bennett, Charlie R; McKoryk, Michael; Brisson, Andre L; Sparrey, Carolyn J

2017-12-01

Manufacturers recommend removing fall protection system components from service for any indication of weld spatter or tool damage; however, little is known about the specific effects of lanyard damage on fall arrest dynamics. Thirty-two energy-absorbing lanyards were drop tested after being damaged with weld spatter, plasma torches and cutting tools and compared with new, undamaged lanyards. Two lanyards damaged with a plasma torch failed completely without deploying the energy absorber while weld spatter damage and tool cuts, up to two-thirds through the width of the webbing, had no effect on fall arrest dynamics. The results highlight the catastrophic implications of high-temperature damage to lanyard webbing resulting from plasma torches - which require immediate removal from service. In addition, the integrated energy absorber design in bungee-style lanyards makes them more susceptible to damage anywhere along the length. We therefore recommended against bungee lanyards for ironworkers and welders.

Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis

PubMed Central

Weber, Nick; Liou, David; Dommer, Jennifer; MacMenamin, Philip; Quiñones, Mariam; Misner, Ian; Oler, Andrew J; Wan, Joe; Kim, Lewis; Coakley McCarthy, Meghan; Ezeji, Samuel; Noble, Karlynn; Hurt, Darrell E

2018-01-01

Abstract Motivation Widespread interest in the study of the microbiome has resulted in data proliferation and the development of powerful computational tools. However, many scientific researchers lack the time, training, or infrastructure to work with large datasets or to install and use command line tools. Results The National Institute of Allergy and Infectious Diseases (NIAID) has created Nephele, a cloud-based microbiome data analysis platform with standardized pipelines and a simple web interface for transforming raw data into biological insights. Nephele integrates common microbiome analysis tools as well as valuable reference datasets like the healthy human subjects cohort of the Human Microbiome Project (HMP). Nephele is built on the Amazon Web Services cloud, which provides centralized and automated storage and compute capacity, thereby reducing the burden on researchers and their institutions. Availability and implementation https://nephele.niaid.nih.gov and https://github.com/niaid/Nephele Contact darrell.hurt@nih.gov PMID:29028892

SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery

PubMed Central

Jewell, Erica; Robinson, Andrew; Savage, David; Erwin, Tim; Love, Christopher G.; Lim, Geraldine A. C.; Li, Xi; Batley, Jacqueline; Spangenberg, German C.; Edwards, David

2006-01-01

Simple sequence repeat (SSR) molecular genetic markers have become important tools for a broad range of applications such as genome mapping and genetic diversity studies. SSRs are readily identified within DNA sequence data and PCR primers can be designed for their amplification. These PCR primers frequently cross amplify within related species. We report a web-based tool, SSR Primer, that integrates SPUTNIK, an SSR repeat finder, with Primer3, a primer design program, within one pipeline. On submission of multiple FASTA formatted sequences, the script screens each sequence for SSRs using SPUTNIK. Results are then parsed to Primer3 for locus specific primer design. We have applied this tool for the discovery of SSRs within the complete GenBank database, and have designed PCR amplification primers for over 13 million SSRs. The SSR Taxonomy Tree server provides web-based searching and browsing of species and taxa for the visualisation and download of these SSR amplification primers. These tools are available at . PMID:16845092

SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery.

PubMed

Jewell, Erica; Robinson, Andrew; Savage, David; Erwin, Tim; Love, Christopher G; Lim, Geraldine A C; Li, Xi; Batley, Jacqueline; Spangenberg, German C; Edwards, David

2006-07-01

Simple sequence repeat (SSR) molecular genetic markers have become important tools for a broad range of applications such as genome mapping and genetic diversity studies. SSRs are readily identified within DNA sequence data and PCR primers can be designed for their amplification. These PCR primers frequently cross amplify within related species. We report a web-based tool, SSR Primer, that integrates SPUTNIK, an SSR repeat finder, with Primer3, a primer design program, within one pipeline. On submission of multiple FASTA formatted sequences, the script screens each sequence for SSRs using SPUTNIK. Results are then parsed to Primer3 for locus specific primer design. We have applied this tool for the discovery of SSRs within the complete GenBank database, and have designed PCR amplification primers for over 13 million SSRs. The SSR Taxonomy Tree server provides web-based searching and browsing of species and taxa for the visualisation and download of these SSR amplification primers. These tools are available at http://bioinformatics.pbcbasc.latrobe.edu.au/ssrdiscovery.html.

Listeriomics: an Interactive Web Platform for Systems Biology of Listeria

PubMed Central

Koutero, Mikael; Tchitchek, Nicolas; Cerutti, Franck; Lechat, Pierre; Maillet, Nicolas; Hoede, Claire; Chiapello, Hélène; Gaspin, Christine

2017-01-01

ABSTRACT As for many model organisms, the amount of Listeria omics data produced has recently increased exponentially. There are now >80 published complete Listeria genomes, around 350 different transcriptomic data sets, and 25 proteomic data sets available. The analysis of these data sets through a systems biology approach and the generation of tools for biologists to browse these various data are a challenge for bioinformaticians. We have developed a web-based platform, named Listeriomics, that integrates different tools for omics data analyses, i.e., (i) an interactive genome viewer to display gene expression arrays, tiling arrays, and sequencing data sets along with proteomics and genomics data sets; (ii) an expression and protein atlas that connects every gene, small RNA, antisense RNA, or protein with the most relevant omics data; (iii) a specific tool for exploring protein conservation through the Listeria phylogenomic tree; and (iv) a coexpression network tool for the discovery of potential new regulations. Our platform integrates all the complete Listeria species genomes, transcriptomes, and proteomes published to date. This website allows navigation among all these data sets with enriched metadata in a user-friendly format and can be used as a central database for systems biology analysis. IMPORTANCE In the last decades, Listeria has become a key model organism for the study of host-pathogen interactions, noncoding RNA regulation, and bacterial adaptation to stress. To study these mechanisms, several genomics, transcriptomics, and proteomics data sets have been produced. We have developed Listeriomics, an interactive web platform to browse and correlate these heterogeneous sources of information. Our website will allow listeriologists and microbiologists to decipher key regulation mechanism by using a systems biology approach. PMID:28317029

Attitudes and awareness of web-based self-care resources in the military: a preliminary survey study.

PubMed

Luxton, David D; Armstrong, Christina M; Fantelli, Emily E; Thomas, Elissa K

2011-09-01

Web-based self-care resources have a number of potential benefits for military service members (SMs) and their families such as convenience, anonymity, and immediate 24/7 access to useful information. There is limited data available, however, regarding SM and military healthcare provider use of online self-care resources. Our goal with this study was to conduct a preliminary survey assessment of self-care Web site awareness, general attitudes about use, and usage behaviors of Web-based self-care resources among SMs and military healthcare providers. Results show that the majority of SMs and providers use the Internet often, use Internet self-care resources, and are willing to use additional Web-based resources and capabilities. SMs and providers also indicated a preference for Web-based self-care resources as adjunct tools to face-to-face/in-person care. Data from this preliminary study are useful for informing additional research and best practices for integrating Web-based self-care for the military community.

WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations

PubMed Central

Wangkumhang, Pongsakorn; Chaichoompu, Kridsadakorn; Ngamphiw, Chumpol; Ruangrit, Uttapong; Chanprasert, Juntima; Assawamakin, Anunchai; Tongsima, Sissades

2007-01-01

Background Allele-specific (AS) Polymerase Chain Reaction is a convenient and inexpensive method for genotyping Single Nucleotide Polymorphisms (SNPs) and mutations. It is applied in many recent studies including population genetics, molecular genetics and pharmacogenomics. Using known AS primer design tools to create primers leads to cumbersome process to inexperience users since information about SNP/mutation must be acquired from public databases prior to the design. Furthermore, most of these tools do not offer the mismatch enhancement to designed primers. The available web applications do not provide user-friendly graphical input interface and intuitive visualization of their primer results. Results This work presents a web-based AS primer design application called WASP. This tool can efficiently design AS primers for human SNPs as well as mutations. To assist scientists with collecting necessary information about target polymorphisms, this tool provides a local SNP database containing over 10 million SNPs of various populations from public domain databases, namely NCBI dbSNP, HapMap and JSNP respectively. This database is tightly integrated with the tool so that users can perform the design for existing SNPs without going off the site. To guarantee specificity of AS primers, the proposed system incorporates a primer specificity enhancement technique widely used in experiment protocol. In particular, WASP makes use of different destabilizing effects by introducing one deliberate 'mismatch' at the penultimate (second to last of the 3'-end) base of AS primers to improve the resulting AS primers. Furthermore, WASP offers graphical user interface through scalable vector graphic (SVG) draw that allow users to select SNPs and graphically visualize designed primers and their conditions. Conclusion WASP offers a tool for designing AS primers for both SNPs and mutations. By integrating the database for known SNPs (using gene ID or rs number), this tool facilitates the awkward process of getting flanking sequences and other related information from public SNP databases. It takes into account the underlying destabilizing effect to ensure the effectiveness of designed primers. With user-friendly SVG interface, WASP intuitively presents resulting designed primers, which assist users to export or to make further adjustment to the design. This software can be freely accessed at . PMID:17697334

Instant Gratification: Striking a Balance Between Rich Interactive Visualization and Ease of Use for Casual Web Surfers

NASA Astrophysics Data System (ADS)

Russell, R. M.; Johnson, R. M.; Gardiner, E. S.; Bergman, J. J.; Genyuk, J.; Henderson, S.

2004-12-01

Interactive visualizations can be powerful tools for helping students, teachers, and the general public comprehend significant features in rich datasets and complex systems. Successful use of such visualizations requires viewers to have, or to acquire, adequate expertise in use of the relevant visualization tools. In many cases, the learning curve associated with competent use of such tools is too steep for casual users, such as members of the lay public browsing science outreach web sites or K-12 students and teachers trying to integrate such tools into their learning about geosciences. "Windows to the Universe" (http://www.windows.ucar.edu) is a large (roughly 6,000 web pages), well-established (first posted online in 1995), and popular (over 5 million visitor sessions and 40 million pages viewed per year) science education web site that covers a very broad range of Earth science and space science topics. The primary audience of the site consists of K-12 students and teachers and the general public. We have developed several interactive visualizations for use on the site in conjunction with text and still image reference materials. One major emphasis in the design of these interactives has been to ensure that casual users can quickly learn how to use the interactive features without becoming frustrated and departing before they were able to appreciate the visualizations displayed. We will demonstrate several of these "user-friendly" interactive visualizations and comment on the design philosophy we have employed in developing them.

Lynx: a database and knowledge extraction engine for integrative medicine.

PubMed

Sulakhe, Dinanath; Balasubramanian, Sandhya; Xie, Bingqing; Feng, Bo; Taylor, Andrew; Wang, Sheng; Berrocal, Eduardo; Dave, Utpal; Xu, Jinbo; Börnigen, Daniela; Gilliam, T Conrad; Maltsev, Natalia

2014-01-01

We have developed Lynx (http://lynx.ci.uchicago.edu)--a web-based database and a knowledge extraction engine, supporting annotation and analysis of experimental data and generation of weighted hypotheses on molecular mechanisms contributing to human phenotypes and disorders of interest. Its underlying knowledge base (LynxKB) integrates various classes of information from >35 public databases and private collections, as well as manually curated data from our group and collaborators. Lynx provides advanced search capabilities and a variety of algorithms for enrichment analysis and network-based gene prioritization to assist the user in extracting meaningful knowledge from LynxKB and experimental data, whereas its service-oriented architecture provides public access to LynxKB and its analytical tools via user-friendly web services and interfaces.

SNPit: a federated data integration system for the purpose of functional SNP annotation.

PubMed

Shen, Terry H; Carlson, Christopher S; Tarczy-Hornoch, Peter

2009-08-01

Genome wide association studies can potentially identify the genetic causes behind the majority of human diseases. With the advent of more advanced genotyping techniques, there is now an explosion of data gathered on single nucleotide polymorphisms (SNPs). The need exists for an integrated system that can provide up-to-date functional annotation information on SNPs. We have developed the SNP Integration Tool (SNPit) system to address this need. Built upon a federated data integration system, SNPit provides current information on a comprehensive list of SNP data sources. Additional logical inference analysis was included through an inference engine plug in. The SNPit web servlet is available online for use. SNPit allows users to go to one source for up-to-date information on the functional annotation of SNPs. A tool that can help to integrate and analyze the potential functional significance of SNPs is important for understanding the results from genome wide association studies.

WebGIVI: a web-based gene enrichment analysis and visualization tool.

PubMed

Sun, Liang; Zhu, Yongnan; Mahmood, A S M Ashique; Tudor, Catalina O; Ren, Jia; Vijay-Shanker, K; Chen, Jian; Schmidt, Carl J

2017-05-04

A major challenge of high throughput transcriptome studies is presenting the data to researchers in an interpretable format. In many cases, the outputs of such studies are gene lists which are then examined for enriched biological concepts. One approach to help the researcher interpret large gene datasets is to associate genes and informative terms (iTerm) that are obtained from the biomedical literature using the eGIFT text-mining system. However, examining large lists of iTerm and gene pairs is a daunting task. We have developed WebGIVI, an interactive web-based visualization tool ( http://raven.anr.udel.edu/webgivi/ ) to explore gene:iTerm pairs. WebGIVI was built via Cytoscape and Data Driven Document JavaScript libraries and can be used to relate genes to iTerms and then visualize gene and iTerm pairs. WebGIVI can accept a gene list that is used to retrieve the gene symbols and corresponding iTerm list. This list can be submitted to visualize the gene iTerm pairs using two distinct methods: a Concept Map or a Cytoscape Network Map. In addition, WebGIVI also supports uploading and visualization of any two-column tab separated data. WebGIVI provides an interactive and integrated network graph of gene and iTerms that allows filtering, sorting, and grouping, which can aid biologists in developing hypothesis based on the input gene lists. In addition, WebGIVI can visualize hundreds of nodes and generate a high-resolution image that is important for most of research publications. The source code can be freely downloaded at https://github.com/sunliang3361/WebGIVI . The WebGIVI tutorial is available at http://raven.anr.udel.edu/webgivi/tutorial.php .

CottonGen: a genomics, genetics and breeding database for cotton research

USDA-ARS?s Scientific Manuscript database

CottonGen (http://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, vis...

A Study of the Predictive Relationship between Online Social Presence and ONLE Interaction

ERIC Educational Resources Information Center

Tu, Chih-Hsiung; Yen, Cherng-Jyh; Blocher, J. Michael; Chan, Junn-Yih

2012-01-01

Open Network Learning Environments (ONLE) are online networks that afford learners the opportunity to participate in creative content endeavors, personalized identity projections, networked mechanism management, and effective collaborative community integration by applying Web 2.0 tools in open environments. It supports social interaction by…

Kidspiration[R] for Inquiry-Centered Activities

ERIC Educational Resources Information Center

Shaw, Edward L., Jr.; Baggett, Paige V.; Salyer, Barbara

2004-01-01

Computer technology can be integrated into science inquiry activities to increase student motivation and enhance and expand scientific thinking. Fifth-grade students used the visual thinking tools in the Kidspiration[R] software program to generate and represent a web of hypotheses around the question, "What affects the distance a marble rolls?"…

Exploring the Decision Landscape using System Sketch: Integration and Display of Ecosystem Services & Indicators Using the DPSIR Framework and Dynamic Web Application

EPA Science Inventory

Stakeholders can use the tool to accomplish their sustainability goals by: Understanding interactions and feedback loops within human-environmental systems; Identifying areas of the system not previously considered and avoiding unintended consequences; Identifying metrics, indica...

Exploring the Decision Landscape: Integration of Human and Natural Systems Using the Driver-Pressure-State-Impact-Response Framework and Dynamic Web Application

EPA Science Inventory

Making decisions to increase community or regional sustainability requires a comprehensive understanding of the linkages between environmental, social, and economic systems. We present a visualization tool that can improve decision processes and improve interdisciplinary research...

Artificial intelligence, neural network, and Internet tool integration in a pathology workstation to improve information access

NASA Astrophysics Data System (ADS)

Sargis, J. C.; Gray, W. A.

1999-03-01

The APWS allows user friendly access to several legacy systems which would normally each demand domain expertise for proper utilization. The generalized model, including objects, classes, strategies and patterns is presented. The core components of the APWS are the Microsoft Windows 95 Operating System, Oracle, Oracle Power Objects, Artificial Intelligence tools, a medical hyperlibrary and a web site. The paper includes a discussion of how could be automated by taking advantage of the expert system, object oriented programming and intelligent relational database tools within the APWS.

IntegromeDB: an integrated system and biological search engine

PubMed Central

2012-01-01

Background With the growth of biological data in volume and heterogeneity, web search engines become key tools for researchers. However, general-purpose search engines are not specialized for the search of biological data. Description Here, we present an approach at developing a biological web search engine based on the Semantic Web technologies and demonstrate its implementation for retrieving gene- and protein-centered knowledge. The engine is available at http://www.integromedb.org. Conclusions The IntegromeDB search engine allows scanning data on gene regulation, gene expression, protein-protein interactions, pathways, metagenomics, mutations, diseases, and other gene- and protein-related data that are automatically retrieved from publicly available databases and web pages using biological ontologies. To perfect the resource design and usability, we welcome and encourage community feedback. PMID:22260095

Individualized Communications

NASA Technical Reports Server (NTRS)

1997-01-01

IntelliWeb and IntelliPrint, products from MicroMass Communications, utilize C Language Integrated Production System (CLIPS), a development and delivery expert systems tool developed at Johnson Space Center. IntelliWeb delivers personalized messages by dynamically creating single web pages or entire web sites based on information provided by each website visitor. IntelliPrint is a product designed to create tailored, individualized messages via printed media. The software uses proprietary technology to generate printed messages that are personally relevant and tailored to meet each individual's needs. Intelliprint is in use in many operations including Brystol-Myers Squibb's personalized newsletter, "Living at Your Best," geared to each recipient based on a health and lifestyle survey taken earlier; and SmithKline Beecham's "Nicorette Committed Quitters Program," in which customized motivational materials support participants in their attempt to quit smoking.

QuakeSim 2.0

NASA Technical Reports Server (NTRS)

Donnellan, Andrea; Parker, Jay W.; Lyzenga, Gregory A.; Granat, Robert A.; Norton, Charles D.; Rundle, John B.; Pierce, Marlon E.; Fox, Geoffrey C.; McLeod, Dennis; Ludwig, Lisa Grant

2012-01-01

QuakeSim 2.0 improves understanding of earthquake processes by providing modeling tools and integrating model applications and various heterogeneous data sources within a Web services environment. QuakeSim is a multisource, synergistic, data-intensive environment for modeling the behavior of earthquake faults individually, and as part of complex interacting systems. Remotely sensed geodetic data products may be explored, compared with faults and landscape features, mined by pattern analysis applications, and integrated with models and pattern analysis applications in a rich Web-based and visualization environment. Integration of heterogeneous data products with pattern informatics tools enables efficient development of models. Federated database components and visualization tools allow rapid exploration of large datasets, while pattern informatics enables identification of subtle, but important, features in large data sets. QuakeSim is valuable for earthquake investigations and modeling in its current state, and also serves as a prototype and nucleus for broader systems under development. The framework provides access to physics-based simulation tools that model the earthquake cycle and related crustal deformation. Spaceborne GPS and Inter ferometric Synthetic Aperture (InSAR) data provide information on near-term crustal deformation, while paleoseismic geologic data provide longerterm information on earthquake fault processes. These data sources are integrated into QuakeSim's QuakeTables database system, and are accessible by users or various model applications. UAVSAR repeat pass interferometry data products are added to the QuakeTables database, and are available through a browseable map interface or Representational State Transfer (REST) interfaces. Model applications can retrieve data from Quake Tables, or from third-party GPS velocity data services; alternatively, users can manually input parameters into the models. Pattern analysis of GPS and seismicity data has proved useful for mid-term forecasting of earthquakes, and for detecting subtle changes in crustal deformation. The GPS time series analysis has also proved useful as a data-quality tool, enabling the discovery of station anomalies and data processing and distribution errors. Improved visualization tools enable more efficient data exploration and understanding. Tools provide flexibility to science users for exploring data in new ways through download links, but also facilitate standard, intuitive, and routine uses for science users and end users such as emergency responders.

NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways.

PubMed

Brohée, Sylvain; Faust, Karoline; Lima-Mendez, Gipsi; Sand, Olivier; Janky, Rekin's; Vanderstocken, Gilles; Deville, Yves; van Helden, Jacques

2008-07-01

The network analysis tools (NeAT) (http://rsat.ulb.ac.be/neat/) provide a user-friendly web access to a collection of modular tools for the analysis of networks (graphs) and clusters (e.g. microarray clusters, functional classes, etc.). A first set of tools supports basic operations on graphs (comparison between two graphs, neighborhood of a set of input nodes, path finding and graph randomization). Another set of programs makes the connection between networks and clusters (graph-based clustering, cliques discovery and mapping of clusters onto a network). The toolbox also includes programs for detecting significant intersections between clusters/classes (e.g. clusters of co-expression versus functional classes of genes). NeAT are designed to cope with large datasets and provide a flexible toolbox for analyzing biological networks stored in various databases (protein interactions, regulation and metabolism) or obtained from high-throughput experiments (two-hybrid, mass-spectrometry and microarrays). The web interface interconnects the programs in predefined analysis flows, enabling to address a series of questions about networks of interest. Each tool can also be used separately by entering custom data for a specific analysis. NeAT can also be used as web services (SOAP/WSDL interface), in order to design programmatic workflows and integrate them with other available resources.

Web-based tool for visualization of electric field distribution in deep-seated body structures and planning of electroporation-based treatments.

PubMed

Marčan, Marija; Pavliha, Denis; Kos, Bor; Forjanič, Tadeja; Miklavčič, Damijan

2015-01-01

Treatments based on electroporation are a new and promising approach to treating tumors, especially non-resectable ones. The success of the treatment is, however, heavily dependent on coverage of the entire tumor volume with a sufficiently high electric field. Ensuring complete coverage in the case of deep-seated tumors is not trivial and can in best way be ensured by patient-specific treatment planning. The basis of the treatment planning process consists of two complex tasks: medical image segmentation, and numerical modeling and optimization. In addition to previously developed segmentation algorithms for several tissues (human liver, hepatic vessels, bone tissue and canine brain) and the algorithms for numerical modeling and optimization of treatment parameters, we developed a web-based tool to facilitate the translation of the algorithms and their application in the clinic. The developed web-based tool automatically builds a 3D model of the target tissue from the medical images uploaded by the user and then uses this 3D model to optimize treatment parameters. The tool enables the user to validate the results of the automatic segmentation and make corrections if necessary before delivering the final treatment plan. Evaluation of the tool was performed by five independent experts from four different institutions. During the evaluation, we gathered data concerning user experience and measured performance times for different components of the tool. Both user reports and performance times show significant reduction in treatment-planning complexity and time-consumption from 1-2 days to a few hours. The presented web-based tool is intended to facilitate the treatment planning process and reduce the time needed for it. It is crucial for facilitating expansion of electroporation-based treatments in the clinic and ensuring reliable treatment for the patients. The additional value of the tool is the possibility of easy upgrade and integration of modules with new functionalities as they are developed.

Web-based tool for visualization of electric field distribution in deep-seated body structures and planning of electroporation-based treatments

PubMed Central

2015-01-01

Background Treatments based on electroporation are a new and promising approach to treating tumors, especially non-resectable ones. The success of the treatment is, however, heavily dependent on coverage of the entire tumor volume with a sufficiently high electric field. Ensuring complete coverage in the case of deep-seated tumors is not trivial and can in best way be ensured by patient-specific treatment planning. The basis of the treatment planning process consists of two complex tasks: medical image segmentation, and numerical modeling and optimization. Methods In addition to previously developed segmentation algorithms for several tissues (human liver, hepatic vessels, bone tissue and canine brain) and the algorithms for numerical modeling and optimization of treatment parameters, we developed a web-based tool to facilitate the translation of the algorithms and their application in the clinic. The developed web-based tool automatically builds a 3D model of the target tissue from the medical images uploaded by the user and then uses this 3D model to optimize treatment parameters. The tool enables the user to validate the results of the automatic segmentation and make corrections if necessary before delivering the final treatment plan. Results Evaluation of the tool was performed by five independent experts from four different institutions. During the evaluation, we gathered data concerning user experience and measured performance times for different components of the tool. Both user reports and performance times show significant reduction in treatment-planning complexity and time-consumption from 1-2 days to a few hours. Conclusions The presented web-based tool is intended to facilitate the treatment planning process and reduce the time needed for it. It is crucial for facilitating expansion of electroporation-based treatments in the clinic and ensuring reliable treatment for the patients. The additional value of the tool is the possibility of easy upgrade and integration of modules with new functionalities as they are developed. PMID:26356007

Tools for Data Analysis in the Middle School Classroom: A Teacher Professional Development Program

NASA Astrophysics Data System (ADS)

Ledley, T. S.; Haddad, N.; McAuliffe, C.; Dahlman, L.

2006-12-01

In order for students to learn how to engage with scientific data to answer questions about the real world, it is imperative that their teachers are 1) comfortable with the data and the tools used to analyze it, and 2) feel prepared to support their students in this complex endeavor. TERC's Tools for Data Analysis in the Middle School Classroom (DataTools) professional development program, funded by NSF's ITEST program, prepares middle school teachers to integrate Web-based scientific data and analysis tools into their existing curricula. This 13-month program supports teachers in using a set of freely or commonly available tools with a wide range of data. It also gives them an opportunity to practice teaching these skills to students before teaching in their own classrooms. The ultimate goal of the program is to increase the number of middle school students who work directly with scientific data, who use the tools of technology to import, manipulate, visualize and analyze the data, who come to understand the power of data-based arguments, and who will consider pursuing a career in technical and scientific fields. In this session, we will describe the elements of the DataTools program and the Earth Exploration Toolbook (EET, http://serc.carleton.edu/eet), a Web-based resource that supports Earth system education for teachers and students in grades 6 through 16. The EET provides essential support to DataTools teachers as they use it to learn to locate and download Web-based data and use data analysis tools. We will also share what we have learned during the first year of this three-year program.

Improving Conceptual Design for Launch Vehicles

NASA Technical Reports Server (NTRS)

Olds, John R.

1998-01-01

This report summarizes activities performed during the second year of a three year cooperative agreement between NASA - Langley Research Center and Georgia Tech. Year 1 of the project resulted in the creation of a new Cost and Business Assessment Model (CABAM) for estimating the economic performance of advanced reusable launch vehicles including non-recurring costs, recurring costs, and revenue. The current year (second year) activities were focused on the evaluation of automated, collaborative design frameworks (computation architectures or computational frameworks) for automating the design process in advanced space vehicle design. Consistent with NASA's new thrust area in developing and understanding Intelligent Synthesis Environments (ISE), the goals of this year's research efforts were to develop and apply computer integration techniques and near-term computational frameworks for conducting advanced space vehicle design. NASA - Langley (VAB) has taken a lead role in developing a web-based computing architectures within which the designer can interact with disciplinary analysis tools through a flexible web interface. The advantages of this approach are, 1) flexible access to the designer interface through a simple web browser (e.g. Netscape Navigator), 2) ability to include existing 'legacy' codes, and 3) ability to include distributed analysis tools running on remote computers. To date, VAB's internal emphasis has been on developing this test system for the planetary entry mission under the joint Integrated Design System (IDS) program with NASA - Ames and JPL. Georgia Tech's complementary goals this year were to: 1) Examine an alternate 'custom' computational architecture for the three-discipline IDS planetary entry problem to assess the advantages and disadvantages relative to the web-based approach.and 2) Develop and examine a web-based interface and framework for a typical launch vehicle design problem.

Managing and Integrating Open Environmental Data - Technological Requirements and Challenges

NASA Astrophysics Data System (ADS)

Devaraju, Anusuriya; Kunkel, Ralf; Jirka, Simon

2014-05-01

Understanding environment conditions and trends requires information. This information is usually generated from sensor observations. Today, several infrastructures (e.g., GEOSS, EarthScope, NEON, NETLAKE, OOI, TERENO, WASCAL, and PEER-EurAqua) have been deployed to promote full and open exchange of environmental data. Standards for interfaces as well as data models/formats (OGC, CUAHSI, INSPIRE, SEE Grid, ISO) and open source tools have been developed to support seamless data exchange between various domains and organizations. In spite of this growing interest, it remains a challenge to manage and integrate open environmental data on the fly due to the distributed and heterogeneous nature of the data. Intuitive tools and standardized interfaces are vital to hide the technical complexity of underlying data management infrastructures. Meaningful descriptions of raw sensor data are necessary to achieve interoperability among different sources. As raw sensor data sets usually goes through several layers of summarization and aggregation, metadata and quality measures associated with these should be captured. Further processing of sensor data sets requires that they should be made compatible with existing environmental models. We need data policies and management plans on how to handle and publish open sensor data coming from different institutions. Clearly, a better management and usability of open environmental data is crucial, not only to gather large amounts of data, but also to cater various aspects such as data integration, privacy and trust, uncertainty, quality control, visualization, and data management policies. The proposed talk presents several key findings in terms of requirements, ongoing developments and technical challenges concerning these aspects from our recent work. This includes two workshops on open observation data and supporting tools, as well as the long-term environmental monitoring initiatives such as TERENO and TERENO-MED. Workshops Details: Spin the Sensor Web: Sensor Web Workshop 2013, Muenster, 21st-22nd November 2013 (http://52north.org/news/spin-the-sensor-web-sensor-web-workshop-2013) Special Session on Management of Open Environmental Observation Data - MOEOD 2014, Lisbon, 8th January 2014 (http://www.sensornets.org/MOEOD.aspx?y=2014) Monitoring Networks: TERENO : http://teodoor.icg.kfa-juelich.de/ TERENO-MED : http://www.tereno-med.net/

Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms

PubMed Central

Bianco, Luca; Riccadonna, Samantha; Lavezzo, Enrico; Falda, Marco; Formentin, Elide; Cavalieri, Duccio; Toppo, Stefano

2017-01-01

Abstract Summary: Pathway Inspector is an easy-to-use web application helping researchers to find patterns of expression in complex RNAseq experiments. The tool combines two standard approaches for RNAseq analysis: the identification of differentially expressed genes and a topology-based analysis of enriched pathways. Pathway Inspector is equipped with ad hoc interactive graphical interfaces simplifying the discovery of modulated pathways and the integration of the differentially expressed genes in the corresponding pathway topology. Availability and Implementation: Pathway Inspector is available at the website http://admiral.fmach.it/PI and has been developed in Python, making use of the Django Web Framework. Contact: paolo.fontana@fmach.it PMID:28158604

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

PubMed

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

2018-05-21

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

The Plant Genome Integrative Explorer Resource: PlantGenIE.org.

PubMed

Sundell, David; Mannapperuma, Chanaka; Netotea, Sergiu; Delhomme, Nicolas; Lin, Yao-Cheng; Sjödin, Andreas; Van de Peer, Yves; Jansson, Stefan; Hvidsten, Torgeir R; Street, Nathaniel R

2015-12-01

Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

dada - a web-based 2D detector analysis tool

NASA Astrophysics Data System (ADS)

Osterhoff, Markus

2017-06-01

The data daemon, dada, is a server backend for unified access to 2D pixel detector image data stored with different detectors, file formats and saved with varying naming conventions and folder structures across instruments. Furthermore, dada implements basic pre-processing and analysis routines from pixel binning over azimuthal integration to raster scan processing. Common user interactions with dada are by a web frontend, but all parameters for an analysis are encoded into a Uniform Resource Identifier (URI) which can also be written by hand or scripts for batch processing.

ExPASy: SIB bioinformatics resource portal.

PubMed

Artimo, Panu; Jonnalagedda, Manohar; Arnold, Konstantin; Baratin, Delphine; Csardi, Gabor; de Castro, Edouard; Duvaud, Séverine; Flegel, Volker; Fortier, Arnaud; Gasteiger, Elisabeth; Grosdidier, Aurélien; Hernandez, Céline; Ioannidis, Vassilios; Kuznetsov, Dmitry; Liechti, Robin; Moretti, Sébastien; Mostaguir, Khaled; Redaschi, Nicole; Rossier, Grégoire; Xenarios, Ioannis; Stockinger, Heinz

2012-07-01

ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access seamlessly a wide range of resources in many different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. The individual resources (databases, web-based and downloadable software tools) are hosted in a 'decentralized' way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions. Specifically, a single web portal provides a common entry point to a wide range of resources developed and operated by different SIB groups and external institutions. The portal features a search function across 'selected' resources. Additionally, the availability and usage of resources are monitored. The portal is aimed for both expert users and people who are not familiar with a specific domain in life sciences. The new web interface provides, in particular, visual guidance for newcomers to ExPASy.

High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis.

PubMed

Simonyan, Vahan; Mazumder, Raja

2014-09-30

The High-performance Integrated Virtual Environment (HIVE) is a high-throughput cloud-based infrastructure developed for the storage and analysis of genomic and associated biological data. HIVE consists of a web-accessible interface for authorized users to deposit, retrieve, share, annotate, compute and visualize Next-generation Sequencing (NGS) data in a scalable and highly efficient fashion. The platform contains a distributed storage library and a distributed computational powerhouse linked seamlessly. Resources available through the interface include algorithms, tools and applications developed exclusively for the HIVE platform, as well as commonly used external tools adapted to operate within the parallel architecture of the system. HIVE is composed of a flexible infrastructure, which allows for simple implementation of new algorithms and tools. Currently, available HIVE tools include sequence alignment and nucleotide variation profiling tools, metagenomic analyzers, phylogenetic tree-building tools using NGS data, clone discovery algorithms, and recombination analysis algorithms. In addition to tools, HIVE also provides knowledgebases that can be used in conjunction with the tools for NGS sequence and metadata analysis.

High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis

PubMed Central

Simonyan, Vahan; Mazumder, Raja

2014-01-01

The High-performance Integrated Virtual Environment (HIVE) is a high-throughput cloud-based infrastructure developed for the storage and analysis of genomic and associated biological data. HIVE consists of a web-accessible interface for authorized users to deposit, retrieve, share, annotate, compute and visualize Next-generation Sequencing (NGS) data in a scalable and highly efficient fashion. The platform contains a distributed storage library and a distributed computational powerhouse linked seamlessly. Resources available through the interface include algorithms, tools and applications developed exclusively for the HIVE platform, as well as commonly used external tools adapted to operate within the parallel architecture of the system. HIVE is composed of a flexible infrastructure, which allows for simple implementation of new algorithms and tools. Currently, available HIVE tools include sequence alignment and nucleotide variation profiling tools, metagenomic analyzers, phylogenetic tree-building tools using NGS data, clone discovery algorithms, and recombination analysis algorithms. In addition to tools, HIVE also provides knowledgebases that can be used in conjunction with the tools for NGS sequence and metadata analysis. PMID:25271953

A Tropical Marine Microbial Natural Products Geobibliography as an Example of Desktop Exploration of Current Research Using Web Visualisation Tools

PubMed Central

Mukherjee, Joydeep; Llewellyn, Lyndon E; Evans-Illidge, Elizabeth A

2008-01-01

Microbial marine biodiscovery is a recent scientific endeavour developing at a time when information and other technologies are also undergoing great technical strides. Global visualisation of datasets is now becoming available to the world through powerful and readily available software such as Worldwind™, ArcGIS Explorer™ and Google Earth™. Overlaying custom information upon these tools is within the hands of every scientist and more and more scientific organisations are making data available that can also be integrated into these global visualisation tools. The integrated global view that these tools enable provides a powerful desktop exploration tool. Here we demonstrate the value of this approach to marine microbial biodiscovery by developing a geobibliography that incorporates citations on tropical and near-tropical marine microbial natural products research with Google Earth™ and additional ancillary global data sets. The tools and software used are all readily available and the reader is able to use and install the material described in this article. PMID:19172194

ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology.

PubMed

Waese, Jamie; Fan, Jim; Pasha, Asher; Yu, Hans; Fucile, Geoffrey; Shi, Ruian; Cumming, Matthew; Kelley, Lawrence A; Sternberg, Michael J; Krishnakumar, Vivek; Ferlanti, Erik; Miller, Jason; Town, Chris; Stuerzlinger, Wolfgang; Provart, Nicholas J

2017-08-01

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. © 2017 American Society of Plant Biologists. All rights reserved.

KAGLVis - On-line 3D Visualisation of Earth-observing-satellite Data

NASA Astrophysics Data System (ADS)

Szuba, Marek; Ameri, Parinaz; Grabowski, Udo; Maatouki, Ahmad; Meyer, Jörg

2015-04-01

One of the goals of the Large-Scale Data Management and Analysis project is to provide a high-performance framework facilitating management of data acquired by Earth-observing satellites such as Envisat. On the client-facing facet of this framework, we strive to provide visualisation and basic analysis tool which could be used by scientists with minimal to no knowledge of the underlying infrastructure. Our tool, KAGLVis, is a JavaScript client-server Web application which leverages modern Web technologies to provide three-dimensional visualisation of satellite observables on a wide range of client systems. It takes advantage of the WebGL API to employ locally available GPU power for 3D rendering; this approach has been demonstrated to perform well even on relatively weak hardware such as integrated graphics chipsets found in modern laptop computers and with some user-interface tuning could even be usable on embedded devices such as smartphones or tablets. Data is fetched from the database back-end using a ReST API and cached locally, both in memory and using HTML5 Web Storage, to minimise network use. Computations, calculation of cloud altitude from cloud-index measurements for instance, can depending on configuration be performed on either the client or the server side. Keywords: satellite data, Envisat, visualisation, 3D graphics, Web application, WebGL, MEAN stack.

Moby and Moby 2: creatures of the deep (web).

PubMed

Vandervalk, Ben P; McCarthy, E Luke; Wilkinson, Mark D

2009-03-01

Facile and meaningful integration of data from disparate resources is the 'holy grail' of bioinformatics. Some resources have begun to address this problem by providing their data using Semantic Web standards, specifically the Resource Description Framework (RDF) and the Web Ontology Language (OWL). Unfortunately, adoption of Semantic Web standards has been slow overall, and even in cases where the standards are being utilized, interconnectivity between resources is rare. In response, we have seen the emergence of centralized 'semantic warehouses' that collect public data from third parties, integrate it, translate it into OWL/RDF and provide it to the community as a unified and queryable resource. One limitation of the warehouse approach is that queries are confined to the resources that have been selected for inclusion. A related problem, perhaps of greater concern, is that the majority of bioinformatics data exists in the 'Deep Web'-that is, the data does not exist until an application or analytical tool is invoked, and therefore does not have a predictable Web address. The inability to utilize Uniform Resource Identifiers (URIs) to address this data is a barrier to its accessibility via URI-centric Semantic Web technologies. Here we examine 'The State of the Union' for the adoption of Semantic Web standards in the health care and life sciences domain by key bioinformatics resources, explore the nature and connectivity of several community-driven semantic warehousing projects, and report on our own progress with the CardioSHARE/Moby-2 project, which aims to make the resources of the Deep Web transparently accessible through SPARQL queries.

PipelineDog: a simple and flexible graphic pipeline construction and maintenance tool.

PubMed

Zhou, Anbo; Zhang, Yeting; Sun, Yazhou; Xing, Jinchuan

2018-05-01

Analysis pipelines are an essential part of bioinformatics research, and ad hoc pipelines are frequently created by researchers for prototyping and proof-of-concept purposes. However, most existing pipeline management system or workflow engines are too complex for rapid prototyping or learning the pipeline concept. A lightweight, user-friendly and flexible solution is thus desirable. In this study, we developed a new pipeline construction and maintenance tool, PipelineDog. This is a web-based integrated development environment with a modern web graphical user interface. It offers cross-platform compatibility, project management capabilities, code formatting and error checking functions and an online repository. It uses an easy-to-read/write script system that encourages code reuse. With the online repository, it also encourages sharing of pipelines, which enhances analysis reproducibility and accountability. For most users, PipelineDog requires no software installation. Overall, this web application provides a way to rapidly create and easily manage pipelines. PipelineDog web app is freely available at http://web.pipeline.dog. The command line version is available at http://www.npmjs.com/package/pipelinedog and online repository at http://repo.pipeline.dog. ysun@kean.edu or xing@biology.rutgers.edu or ysun@diagnoa.com. Supplementary data are available at Bioinformatics online.

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.

TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model.

PubMed

Kawano, Shin; Watanabe, Tsutomu; Mizuguchi, Sohei; Araki, Norie; Katayama, Toshiaki; Yamaguchi, Atsuko

2014-07-01

TogoTable (http://togotable.dbcls.jp/) is a web tool that adds user-specified annotations to a table that a user uploads. Annotations are drawn from several biological databases that use the Resource Description Framework (RDF) data model. TogoTable uses database identifiers (IDs) in the table as a query key for searching. RDF data, which form a network called Linked Open Data (LOD), can be searched from SPARQL endpoints using a SPARQL query language. Because TogoTable uses RDF, it can integrate annotations from not only the reference database to which the IDs originally belong, but also externally linked databases via the LOD network. For example, annotations in the Protein Data Bank can be retrieved using GeneID through links provided by the UniProt RDF. Because RDF has been standardized by the World Wide Web Consortium, any database with annotations based on the RDF data model can be easily incorporated into this tool. We believe that TogoTable is a valuable Web tool, particularly for experimental biologists who need to process huge amounts of data such as high-throughput experimental output. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Interactive text mining with Pipeline Pilot: a bibliographic web-based tool for PubMed.

PubMed

Vellay, S G P; Latimer, N E Miller; Paillard, G

2009-06-01

Text mining has become an integral part of all research in the medical field. Many text analysis software platforms support particular use cases and only those. We show an example of a bibliographic tool that can be used to support virtually any use case in an agile manner. Here we focus on a Pipeline Pilot web-based application that interactively analyzes and reports on PubMed search results. This will be of interest to any scientist to help identify the most relevant papers in a topical area more quickly and to evaluate the results of query refinement. Links with Entrez databases help both the biologist and the chemist alike. We illustrate this application with Leishmaniasis, a neglected tropical disease, as a case study.

Generation of open biomedical datasets through ontology-driven transformation and integration processes.

PubMed

Carmen Legaz-García, María Del; Miñarro-Giménez, José Antonio; Menárguez-Tortosa, Marcos; Fernández-Breis, Jesualdo Tomás

2016-06-03

Biomedical research usually requires combining large volumes of data from multiple heterogeneous sources, which makes difficult the integrated exploitation of such data. The Semantic Web paradigm offers a natural technological space for data integration and exploitation by generating content readable by machines. Linked Open Data is a Semantic Web initiative that promotes the publication and sharing of data in machine readable semantic formats. We present an approach for the transformation and integration of heterogeneous biomedical data with the objective of generating open biomedical datasets in Semantic Web formats. The transformation of the data is based on the mappings between the entities of the data schema and the ontological infrastructure that provides the meaning to the content. Our approach permits different types of mappings and includes the possibility of defining complex transformation patterns. Once the mappings are defined, they can be automatically applied to datasets to generate logically consistent content and the mappings can be reused in further transformation processes. The results of our research are (1) a common transformation and integration process for heterogeneous biomedical data; (2) the application of Linked Open Data principles to generate interoperable, open, biomedical datasets; (3) a software tool, called SWIT, that implements the approach. In this paper we also describe how we have applied SWIT in different biomedical scenarios and some lessons learned. We have presented an approach that is able to generate open biomedical repositories in Semantic Web formats. SWIT is able to apply the Linked Open Data principles in the generation of the datasets, so allowing for linking their content to external repositories and creating linked open datasets. SWIT datasets may contain data from multiple sources and schemas, thus becoming integrated datasets.

Technology and tuberculosis control: the OUT-TB Web experience.

PubMed

Guthrie, Jennifer L; Alexander, David C; Marchand-Austin, Alex; Lam, Karen; Whelan, Michael; Lee, Brenda; Furness, Colin; Rea, Elizabeth; Stuart, Rebecca; Lechner, Julia; Varia, Monali; McLean, Jennifer; Jamieson, Frances B

2017-04-01

Develop a tool to disseminate integrated laboratory, clinical, and demographic case data necessary for improved contact tracing and outbreak detection of tuberculosis (TB). In 2007, the Public Health Ontario Laboratories implemented a universal genotyping program to monitor the spread of TB strains within Ontario. Ontario Universal Typing of TB (OUT-TB) Web utilizes geographic information system (GIS) technology with a relational database platform, allowing TB control staff to visualize genotyping matches and microbiological data within the context of relevant epidemiological and demographic data. OUT-TB Web is currently available to the 8 health units responsible for >85% of Ontario's TB cases and is a valuable tool for TB case investigation. Users identified key features to implement for application enhancements, including an e-mail alert function, customizable heat maps for visualizing TB and drug-resistant cases, socioeconomic map layers, a dashboard providing TB surveillance metrics, and a feature for animating the geographic spread of strains over time. OUT-TB Web has proven to be an award-winning application and a useful tool. Developed and enhanced using regular user feedback, future versions will include additional data sources, enhanced map and line-list filter capabilities, and development of a mobile app. © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

HyQue: evaluating hypotheses using Semantic Web technologies

PubMed Central

2011-01-01

Background Key to the success of e-Science is the ability to computationally evaluate expert-composed hypotheses for validity against experimental data. Researchers face the challenge of collecting, evaluating and integrating large amounts of diverse information to compose and evaluate a hypothesis. Confronted with rapidly accumulating data, researchers currently do not have the software tools to undertake the required information integration tasks. Results We present HyQue, a Semantic Web tool for querying scientific knowledge bases with the purpose of evaluating user submitted hypotheses. HyQue features a knowledge model to accommodate diverse hypotheses structured as events and represented using Semantic Web languages (RDF/OWL). Hypothesis validity is evaluated against experimental and literature-sourced evidence through a combination of SPARQL queries and evaluation rules. Inference over OWL ontologies (for type specifications, subclass assertions and parthood relations) and retrieval of facts stored as Bio2RDF linked data provide support for a given hypothesis. We evaluate hypotheses of varying levels of detail about the genetic network controlling galactose metabolism in Saccharomyces cerevisiae to demonstrate the feasibility of deploying such semantic computing tools over a growing body of structured knowledge in Bio2RDF. Conclusions HyQue is a query-based hypothesis evaluation system that can currently evaluate hypotheses about the galactose metabolism in S. cerevisiae. Hypotheses as well as the supporting or refuting data are represented in RDF and directly linked to one another allowing scientists to browse from data to hypothesis and vice versa. HyQue hypotheses and data are available at http://semanticscience.org/projects/hyque. PMID:21624158

The Papillomavirus Episteme: a central resource for papillomavirus sequence data and analysis.

PubMed

Van Doorslaer, Koenraad; Tan, Qina; Xirasagar, Sandhya; Bandaru, Sandya; Gopalan, Vivek; Mohamoud, Yasmin; Huyen, Yentram; McBride, Alison A

2013-01-01

The goal of the Papillomavirus Episteme (PaVE) is to provide an integrated resource for the analysis of papillomavirus (PV) genome sequences and related information. The PaVE is a freely accessible, web-based tool (http://pave.niaid.nih.gov) created around a relational database, which enables storage, analysis and exchange of sequence information. From a design perspective, the PaVE adopts an Open Source software approach and stresses the integration and reuse of existing tools. Reference PV genome sequences have been extracted from publicly available databases and reannotated using a custom-created tool. To date, the PaVE contains 241 annotated PV genomes, 2245 genes and regions, 2004 protein sequences and 47 protein structures, which users can explore, analyze or download. The PaVE provides scientists with the data and tools needed to accelerate scientific progress for the study and treatment of diseases caused by PVs.

The MetabolomeExpress Project: enabling web-based processing, analysis and transparent dissemination of GC/MS metabolomics datasets.

PubMed

Carroll, Adam J; Badger, Murray R; Harvey Millar, A

2010-07-14

Standardization of analytical approaches and reporting methods via community-wide collaboration can work synergistically with web-tool development to result in rapid community-driven expansion of online data repositories suitable for data mining and meta-analysis. In metabolomics, the inter-laboratory reproducibility of gas-chromatography/mass-spectrometry (GC/MS) makes it an obvious target for such development. While a number of web-tools offer access to datasets and/or tools for raw data processing and statistical analysis, none of these systems are currently set up to act as a public repository by easily accepting, processing and presenting publicly submitted GC/MS metabolomics datasets for public re-analysis. Here, we present MetabolomeExpress, a new File Transfer Protocol (FTP) server and web-tool for the online storage, processing, visualisation and statistical re-analysis of publicly submitted GC/MS metabolomics datasets. Users may search a quality-controlled database of metabolite response statistics from publicly submitted datasets by a number of parameters (eg. metabolite, species, organ/biofluid etc.). Users may also perform meta-analysis comparisons of multiple independent experiments or re-analyse public primary datasets via user-friendly tools for t-test, principal components analysis, hierarchical cluster analysis and correlation analysis. They may interact with chromatograms, mass spectra and peak detection results via an integrated raw data viewer. Researchers who register for a free account may upload (via FTP) their own data to the server for online processing via a novel raw data processing pipeline. MetabolomeExpress https://www.metabolome-express.org provides a new opportunity for the general metabolomics community to transparently present online the raw and processed GC/MS data underlying their metabolomics publications. Transparent sharing of these data will allow researchers to assess data quality and draw their own insights from published metabolomics datasets.

From PACS to Web-based ePR system with image distribution for enterprise-level filmless healthcare delivery.

PubMed

Huang, H K

2011-07-01

The concept of PACS (picture archiving and communication system) was initiated in 1982 during the SPIE medical imaging conference in New Port Beach, CA. Since then PACS has been matured to become an everyday clinical tool for image archiving, communication, display, and review. This paper follows the continuous development of PACS technology including Web-based PACS, PACS and ePR (electronic patient record), enterprise PACS to ePR with image distribution (ID). The concept of large-scale Web-based enterprise PACS and ePR with image distribution is presented along with its implementation, clinical deployment, and operation. The Hong Kong Hospital Authority's (HKHA) integration of its home-grown clinical management system (CMS) with PACS and ePR with image distribution is used as a case study. The current concept and design criteria of the HKHA enterprise integration of the CMS, PACS, and ePR-ID for filmless healthcare delivery are discussed, followed by its work-in-progress and current status.

Integrating service user and practitioner expertise within a web-based system for collaborative mental-health risk and safety management.

PubMed

Buckingham, Christopher D; Adams, Ann; Vail, Laura; Kumar, Ashish; Ahmed, Abu; Whelan, Annie; Karasouli, Eleni

2015-10-01

To develop a decision support system (DSS), myGRaCE, that integrates service user (SU) and practitioner expertise about mental health and associated risks of suicide, self-harm, harm to others, self-neglect, and vulnerability. The intention is to help SUs assess and manage their own mental health collaboratively with practitioners. An iterative process involving interviews, focus groups, and agile software development with 115 SUs, to elicit and implement myGRaCE requirements. Findings highlight shared understanding of mental health risk between SUs and practitioners that can be integrated within a single model. However, important differences were revealed in SUs' preferred process of assessing risks and safety, which are reflected in the distinctive interface, navigation, tool functionality and language developed for myGRaCE. A challenge was how to provide flexible access without overwhelming and confusing users. The methods show that practitioner expertise can be reformulated in a format that simultaneously captures SU expertise, to provide a tool highly valued by SUs. A stepped process adds necessary structure to the assessment, each step with its own feedback and guidance. The GRiST web-based DSS (www.egrist.org) links and integrates myGRaCE self-assessments with GRiST practitioner assessments for supporting collaborative and self-managed healthcare. Copyright © 2015. Published by Elsevier Ireland Ltd.

AEGIS: a wildfire prevention and management information system

Treesearch

Kostas Kalabokidis; Alan Ager; Mark Finney; Nikos Athanasis; Palaiologos Palaiologou; Christos Vasilakos

2016-01-01

We describe a Web-GIS wildfire prevention and management platform (AEGIS) developed as an integrated and easy-to-use decision support tool to manage wildland fire hazards in Greece (http://aegis.aegean.gr). The AEGIS platform assists with early fire warning, fire planning, fire control and coordination of firefighting forces by providing online access to...

WWW Entrez: A Hypertext Retrieval Tool for Molecular Biology.

ERIC Educational Resources Information Center

Epstein, Jonathan A.; Kans, Jonathan A.; Schuler, Gregory D.

This article describes the World Wide Web (WWW) Entrez server which is based upon the National Center for Biotechnology Information's (NCBI) Entrez retrieval database and software. Entrez is a molecular sequence retrieval system that contains an integrated view of portions of Medline and all publicly available nucleotide and protein databases,…

LOL Teacher! Using Humor to Enhance Student Learning

ERIC Educational Resources Information Center

Terrell, Shelly

2015-01-01

Laughing with students can help them connect on a deeper level with the teacher and the learning. This article offers the following four strategies to incorporate humor into teaching: (1) Integrate humorous bits to boost engagement; (2) Choose humorous materials; (3) Create interest with humorous web tools and apps; and (4) Teach with silly…

Autonomous Learning through Task-Based Instruction in Fully Online Language Courses

ERIC Educational Resources Information Center

Lee, Lina

2016-01-01

This study investigated the affordances for autonomous learning in a fully online learning environment involving the implementation of task-based instruction in conjunction with Web 2.0 technologies. To that end, four-skill-integrated tasks and digital tools were incorporated into the coursework. Data were collected using midterm reflections,…

Exploring the Decision Landscape: Integration and Display of Ecosystem Services & Indicators Using the Driver-Pressure-State-Impact-Response Framework and Dynamic Web Application

EPA Science Inventory

Making decisions to increase community or regional sustainability requires a comprehensive understanding of the linkages between environmental, social, and economic systems. We present a visualization tool that can improve decision processes by enhancing understanding of system c...

The Use of "Socrative" in ESL Classrooms: Towards Active Learning

ERIC Educational Resources Information Center

El Shaban, Abir

2017-01-01

The online student response system (SRS) is a technological tool that can be effectively implemented in English language classroom contexts and be used to promote students' active learning. In this qualitative study, "Socrative", a Web 2.0 software, was integrated with active learning activities and used as an SRS to explore English…

Fuels planning: science synthesis and integration; environmental consequences fact sheet 15: The Wildlife Habitat Response Model

Treesearch

David Pilliod

2005-01-01

The Wildlife Habitat Response Model (WHRM) is a Web-based computer tool for evaluating the potential effects of fuel-reduction projects on terrestrial wildlife habitats. It uses species-habitat associations in ponderosa pine (Pinus ponderosa), dry-type Douglas-fir (Pseudotsuga menziesii), lodgepole pine (Pinus...

Music Teacher Perceptions of a Model of Technology Training and Support in Virginia

ERIC Educational Resources Information Center

Welch, Lee Arthur

2013-01-01

A plethora of technology resources currently exists for the music classroom of the twenty-first century, including digital audio and video, music software, electronic instruments, Web 2.0 tools and more. Research shows a strong need for professional development for teachers to properly implement and integrate instructional technology resources…

Student Interaction and Community Building: An Evaluation of Social Networking in Online Learning Environments

ERIC Educational Resources Information Center

Cardona-Divale, Maria Victoria

2012-01-01

Learners often report difficulty maintaining social connectivity in online courses. Technology is quickly changing how people communicate, collaborate and learn using online social networking sites (SNSs). These sites have transformed education in a way that provides new learning opportunities when integrated with web 2.0 tools. Little research is…

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform

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

Li, Po-E; Lo, Chien -Chi; Anderson, Joseph J.

Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the easemore » of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. As a result, this bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research.« less

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform

PubMed Central

Li, Po-E; Lo, Chien-Chi; Anderson, Joseph J.; Davenport, Karen W.; Bishop-Lilly, Kimberly A.; Xu, Yan; Ahmed, Sanaa; Feng, Shihai; Mokashi, Vishwesh P.; Chain, Patrick S.G.

2017-01-01

Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the ease of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. This bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research. PMID:27899609

Cryosphere Science Outreach using the NASA/JPL Virtual Earth System Laboratory

NASA Astrophysics Data System (ADS)

Larour, E. Y.; Cheng, D. L. C.; Quinn, J.; Halkides, D. J.; Perez, G. L.

2016-12-01

Understanding the role of Cryosphere Science within the larger context of Sea Level Rise is both a technical and educational challenge that needs to be addressed if the public at large is to truly understand the implications and consequences of Climate Change. Within this context, we propose a new approach in which scientific tools are used directly inside a mobile/website platform geared towards Education/Outreach. Here, we apply this approach by using the Ice Sheet System Model, a state of the art Cryosphere model developed at NASA, and integrated within a Virtual Earth System Laboratory, with the goal to outreach Cryosphere science to K-12 and College level students. The approach mixes laboratory experiments, interactive classes/lessons on a website, and a simplified interface to a full-fledged instance of ISSM to validate the classes/lessons. This novel approach leverages new insights from the Outreach/Educational community and the interest of new generations in web based technologies and simulation tools, all of it delivered in a seamlessly integrated web platform, relying on a state of the art climate model and live simulations.

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform

DOE PAGES

Li, Po-E; Lo, Chien -Chi; Anderson, Joseph J.; ...

2016-11-24

Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the easemore » of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. As a result, this bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research.« less

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

PubMed

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

2017-10-30

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

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

DOE PAGES

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

2017-10-30

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

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

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

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

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

XML-Based Visual Specification of Multidisciplinary Applications

NASA Technical Reports Server (NTRS)

Al-Theneyan, Ahmed; Jakatdar, Amol; Mehrotra, Piyush; Zubair, Mohammad

2001-01-01

The advancements in the Internet and Web technologies have fueled a growing interest in developing a web-based distributed computing environment. We have designed and developed Arcade, a web-based environment for designing, executing, monitoring, and controlling distributed heterogeneous applications, which is easy to use and access, portable, and provides support through all phases of the application development and execution. A major focus of the environment is the specification of heterogeneous, multidisciplinary applications. In this paper we focus on the visual and script-based specification interface of Arcade. The web/browser-based visual interface is designed to be intuitive to use and can also be used for visual monitoring during execution. The script specification is based on XML to: (1) make it portable across different frameworks, and (2) make the development of our tools easier by using the existing freely available XML parsers and editors. There is a one-to-one correspondence between the visual and script-based interfaces allowing users to go back and forth between the two. To support this we have developed translators that translate a script-based specification to a visual-based specification, and vice-versa. These translators are integrated with our tools and are transparent to users.

Lynx: a database and knowledge extraction engine for integrative medicine

PubMed Central

Sulakhe, Dinanath; Balasubramanian, Sandhya; Xie, Bingqing; Feng, Bo; Taylor, Andrew; Wang, Sheng; Berrocal, Eduardo; Dave, Utpal; Xu, Jinbo; Börnigen, Daniela; Gilliam, T. Conrad; Maltsev, Natalia

2014-01-01

We have developed Lynx (http://lynx.ci.uchicago.edu)—a web-based database and a knowledge extraction engine, supporting annotation and analysis of experimental data and generation of weighted hypotheses on molecular mechanisms contributing to human phenotypes and disorders of interest. Its underlying knowledge base (LynxKB) integrates various classes of information from >35 public databases and private collections, as well as manually curated data from our group and collaborators. Lynx provides advanced search capabilities and a variety of algorithms for enrichment analysis and network-based gene prioritization to assist the user in extracting meaningful knowledge from LynxKB and experimental data, whereas its service-oriented architecture provides public access to LynxKB and its analytical tools via user-friendly web services and interfaces. PMID:24270788

Optimizing Libraries’ Content Findability Using Simple Object Access Protocol (SOAP) With Multi-Tier Architecture

NASA Astrophysics Data System (ADS)

Lahinta, A.; Haris, I.; Abdillah, T.

2017-03-01

The aim of this paper is to describe a developed application of Simple Object Access Protocol (SOAP) as a model for improving libraries’ digital content findability on the library web. The study applies XML text-based protocol tools in the collection of data about libraries’ visibility performance in the search results of the book. Model from the integrated Web Service Document Language (WSDL) and Universal Description, Discovery and Integration (UDDI) are applied to analyse SOAP as element within the system. The results showed that the developed application of SOAP with multi-tier architecture can help people simply access the website in the library server Gorontalo Province and support access to digital collections, subscription databases, and library catalogs in each library in Regency or City in Gorontalo Province.

Computational framework to support integration of biomolecular and clinical data within a translational approach.

PubMed

Miyoshi, Newton Shydeo Brandão; Pinheiro, Daniel Guariz; Silva, Wilson Araújo; Felipe, Joaquim Cezar

2013-06-06

The use of the knowledge produced by sciences to promote human health is the main goal of translational medicine. To make it feasible we need computational methods to handle the large amount of information that arises from bench to bedside and to deal with its heterogeneity. A computational challenge that must be faced is to promote the integration of clinical, socio-demographic and biological data. In this effort, ontologies play an essential role as a powerful artifact for knowledge representation. Chado is a modular ontology-oriented database model that gained popularity due to its robustness and flexibility as a generic platform to store biological data; however it lacks supporting representation of clinical and socio-demographic information. We have implemented an extension of Chado - the Clinical Module - to allow the representation of this kind of information. Our approach consists of a framework for data integration through the use of a common reference ontology. The design of this framework has four levels: data level, to store the data; semantic level, to integrate and standardize the data by the use of ontologies; application level, to manage clinical databases, ontologies and data integration process; and web interface level, to allow interaction between the user and the system. The clinical module was built based on the Entity-Attribute-Value (EAV) model. We also proposed a methodology to migrate data from legacy clinical databases to the integrative framework. A Chado instance was initialized using a relational database management system. The Clinical Module was implemented and the framework was loaded using data from a factual clinical research database. Clinical and demographic data as well as biomaterial data were obtained from patients with tumors of head and neck. We implemented the IPTrans tool that is a complete environment for data migration, which comprises: the construction of a model to describe the legacy clinical data, based on an ontology; the Extraction, Transformation and Load (ETL) process to extract the data from the source clinical database and load it in the Clinical Module of Chado; the development of a web tool and a Bridge Layer to adapt the web tool to Chado, as well as other applications. Open-source computational solutions currently available for translational science does not have a model to represent biomolecular information and also are not integrated with the existing bioinformatics tools. On the other hand, existing genomic data models do not represent clinical patient data. A framework was developed to support translational research by integrating biomolecular information coming from different "omics" technologies with patient's clinical and socio-demographic data. This framework should present some features: flexibility, compression and robustness. The experiments accomplished from a use case demonstrated that the proposed system meets requirements of flexibility and robustness, leading to the desired integration. The Clinical Module can be accessed in http://dcm.ffclrp.usp.br/caib/pg=iptrans.

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

PubMed

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

2010-10-01

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

Integration of cardiac proteome biology and medicine by a specialized knowledgebase.

PubMed

Zong, Nobel C; Li, Haomin; Li, Hua; Lam, Maggie P Y; Jimenez, Rafael C; Kim, Christina S; Deng, Ning; Kim, Allen K; Choi, Jeong Ho; Zelaya, Ivette; Liem, David; Meyer, David; Odeberg, Jacob; Fang, Caiyun; Lu, Hao-Jie; Xu, Tao; Weiss, James; Duan, Huilong; Uhlen, Mathias; Yates, John R; Apweiler, Rolf; Ge, Junbo; Hermjakob, Henning; Ping, Peipei

2013-10-12

Omics sciences enable a systems-level perspective in characterizing cardiovascular biology. Integration of diverse proteomics data via a computational strategy will catalyze the assembly of contextualized knowledge, foster discoveries through multidisciplinary investigations, and minimize unnecessary redundancy in research efforts. The goal of this project is to develop a consolidated cardiac proteome knowledgebase with novel bioinformatics pipeline and Web portals, thereby serving as a new resource to advance cardiovascular biology and medicine. We created Cardiac Organellar Protein Atlas Knowledgebase (COPaKB; www.HeartProteome.org), a centralized platform of high-quality cardiac proteomic data, bioinformatics tools, and relevant cardiovascular phenotypes. Currently, COPaKB features 8 organellar modules, comprising 4203 LC-MS/MS experiments from human, mouse, drosophila, and Caenorhabditis elegans, as well as expression images of 10,924 proteins in human myocardium. In addition, the Java-coded bioinformatics tools provided by COPaKB enable cardiovascular investigators in all disciplines to retrieve and analyze pertinent organellar protein properties of interest. COPaKB provides an innovative and interactive resource that connects research interests with the new biological discoveries in protein sciences. With an array of intuitive tools in this unified Web server, nonproteomics investigators can conveniently collaborate with proteomics specialists to dissect the molecular signatures of cardiovascular phenotypes.

Outreach for Outreach: Targeting social media audiences to promote a NASA kids’ web site

NASA Astrophysics Data System (ADS)

Pham, C. C.

2009-12-01

The Space Place is a successful NASA web site that benefits upper elementary school students and educators by providing games, activities, and resources to stimulate interest in science, technology, engineering, and mathematics, as well as to inform the audience of NASA’s contributions. As online social networking grows to be a central component of modern communication, The Space Place has explored the benefits of integrating social networks with the web site to increase awareness of materials the web site offers. This study analyzes the capabilities of social networks, and specifically the demographics of Twitter and Facebook. It then compares these results with the content, audience, and perceived demographics of The Space Place web site. Based upon the demographic results, we identified a target constituency that would benefit from the integration of social networks into The Space Place web site. As a result of this study, a Twitter feed has been established that releases a daily tweet from The Space Place. In addition, a Facebook page has been created to showcase new content and prompt interaction among fans of The Space Place. Currently, plans are under way to populate the Space Place Facebook page. Each social network has been utilized in an effort to spark excitement about the content on The Space Place, as well as to attract followers to the main NASA Space Place web site. To pursue this idea further, a plan has been developed to promote NASA Space Place’s social media tools among the target audience.

MycoCosm, an Integrated Fungal Genomics Resource

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

Shabalov, Igor; Grigoriev, Igor

2012-03-16

MycoCosm is a web-based interactive fungal genomics resource, which was first released in March 2010, in response to an urgent call from the fungal community for integration of all fungal genomes and analytical tools in one place (Pan-fungal data resources meeting, Feb 21-22, 2010, Alexandria, VA). MycoCosm integrates genomics data and analysis tools to navigate through over 100 fungal genomes sequenced at JGI and elsewhere. This resource allows users to explore fungal genomes in the context of both genome-centric analysis and comparative genomics, and promotes user community participation in data submission, annotation and analysis. MycoCosm has over 4500 unique visitors/monthmore » or 35000+ visitors/year as well as hundreds of registered users contributing their data and expertise to this resource. Its scalable architecture allows significant expansion of the data expected from JGI Fungal Genomics Program, its users, and integration with external resources used by fungal community.« less

The UAH GeoIntegrator: A Web Mapping System for On-site Data Insertion and Viewing

NASA Astrophysics Data System (ADS)

He, M.; Hardin, D.; Sever, T.; Irwin, D.

2005-12-01

There is a growing need in the scientific community to combine data colleted in the field with maps, imagery and other layered sources. For example, a biologist, who has collected pollination data during a field study, may want to see his data presented on a regional map. There are many commercial web mapping tools available, but they are expensive, and may require advanced computer knowledge to operate. Researchers from the Information Technology and Systems Center at the University of Alabama in Huntsville are developing a web mapping system that will allow scientists to map their data in an easy way. This system is called the UAH GeoIntegrator. The UAH GeoIntegrator is built on top of three open-source components: the Apache web server, MapServer, and the Chameleon viewer. Chameleon allows developers to customize its map viewer interface by adding widgets. These widgets provide unique functionality focused to the specific needs of the researcher. The UAH GeoIntegrator utilizes a suite of widgets that bring new functionality focused on specific needs, to a typical web map viewer. Specifically, a common input text file format was defined and widgets developed to convert user's field collections into web map layers. These layers can then laid on top of other map layers to produce data products that are versatile, informative and easy to distribute via web services. The UAH GeoIntegrator is being developed as part of the SERVIR project. SERVIR (a Spanish acronym meaning to serve) is part of an international effort to preserve the remaining forested regions of Mesoamerica and to help establish sustainable development in the region. The National Aeronautics and Space Administration along with the World Bank, the United States Agency for International Development and the Central American Commission for Environment and Development are cooperating in this effort. The UAH GeoIntegrator is part of an advanced decision support system that will provide scientists, educators, and policy makers the capabilities needed to monitor and forecast ecological changes, respond to natural disasters, and better understand both natural and human induced effects in Mesoamerica. In this paper, the architecture of the system, data input format, and details of the suite of will be presented.

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications

PubMed Central

2011-01-01

Background The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009. Results Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system for analysis of the transcription factor binding sites (TFBSs) enriched based on differential gene expression data obtained from a microarray experiment; iii) a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv) a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs. Conclusions Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i) the absence of several useful data or analysis functions in the Web service "space"; ii) the lack of documentation of methods; iii) lack of compliance with the SOAP/WSDL specification among and between various programming-language libraries; and iv) incompatibility between various bioinformatics data formats. Although it was still difficult to solve real world problems posed to the developers by the biological researchers in attendance because of these problems, we note the promise of addressing these issues within a semantic framework. PMID:21806842

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.

PubMed

Katayama, Toshiaki; Wilkinson, Mark D; Vos, Rutger; Kawashima, Takeshi; Kawashima, Shuichi; Nakao, Mitsuteru; Yamamoto, Yasunori; Chun, Hong-Woo; Yamaguchi, Atsuko; Kawano, Shin; Aerts, Jan; Aoki-Kinoshita, Kiyoko F; Arakawa, Kazuharu; Aranda, Bruno; Bonnal, Raoul Jp; Fernández, José M; Fujisawa, Takatomo; Gordon, Paul Mk; Goto, Naohisa; Haider, Syed; Harris, Todd; Hatakeyama, Takashi; Ho, Isaac; Itoh, Masumi; Kasprzyk, Arek; Kido, Nobuhiro; Kim, Young-Joo; Kinjo, Akira R; Konishi, Fumikazu; Kovarskaya, Yulia; von Kuster, Greg; Labarga, Alberto; Limviphuvadh, Vachiranee; McCarthy, Luke; Nakamura, Yasukazu; Nam, Yunsun; Nishida, Kozo; Nishimura, Kunihiro; Nishizawa, Tatsuya; Ogishima, Soichi; Oinn, Tom; Okamoto, Shinobu; Okuda, Shujiro; Ono, Keiichiro; Oshita, Kazuki; Park, Keun-Joon; Putnam, Nicholas; Senger, Martin; Severin, Jessica; Shigemoto, Yasumasa; Sugawara, Hideaki; Taylor, James; Trelles, Oswaldo; Yamasaki, Chisato; Yamashita, Riu; Satoh, Noriyuki; Takagi, Toshihisa

2011-08-02

The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009. Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system for analysis of the transcription factor binding sites (TFBSs) enriched based on differential gene expression data obtained from a microarray experiment; iii) a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv) a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs. Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i) the absence of several useful data or analysis functions in the Web service "space"; ii) the lack of documentation of methods; iii) lack of compliance with the SOAP/WSDL specification among and between various programming-language libraries; and iv) incompatibility between various bioinformatics data formats. Although it was still difficult to solve real world problems posed to the developers by the biological researchers in attendance because of these problems, we note the promise of addressing these issues within a semantic framework.

Tool independence for the Web Accessibility Quantitative Metric.

PubMed

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

2009-07-01

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

AstrodyToolsWeb an e-Science project in Astrodynamics and Celestial Mechanics fields

NASA Astrophysics Data System (ADS)

López, R.; San-Juan, J. F.

2013-05-01

Astrodynamics Web Tools, AstrodyToolsWeb (http://tastrody.unirioja.es), is an ongoing collaborative Web Tools computing infrastructure project which has been specially designed to support scientific computation. AstrodyToolsWeb provides project collaborators with all the technical and human facilities in order to wrap, manage, and use specialized noncommercial software tools in Astrodynamics and Celestial Mechanics fields, with the aim of optimizing the use of resources, both human and material. However, this project is open to collaboration from the whole scientific community in order to create a library of useful tools and their corresponding theoretical backgrounds. AstrodyToolsWeb offers a user-friendly web interface in order to choose applications, introduce data, and select appropriate constraints in an intuitive and easy way for the user. After that, the application is executed in real time, whenever possible; then the critical information about program behavior (errors and logs) and output, including the postprocessing and interpretation of its results (graphical representation of data, statistical analysis or whatever manipulation therein), are shown via the same web interface or can be downloaded to the user's computer.

Use of XML and Java for collaborative petroleum reservoir modeling on the Internet

NASA Astrophysics Data System (ADS)

Victorine, John; Watney, W. Lynn; Bhattacharya, Saibal

2005-11-01

The GEMINI (Geo-Engineering Modeling through INternet Informatics) is a public-domain, web-based freeware that is made up of an integrated suite of 14 Java-based software tools to accomplish on-line, real-time geologic and engineering reservoir modeling. GEMINI facilitates distant collaborations for small company and academic clients, negotiating analyses of both single and multiple wells. The system operates on a single server and an enterprise database. External data sets must be uploaded into this database. Feedback from GEMINI users provided the impetus to develop Stand Alone Web Start Applications of GEMINI modules that reside in and operate from the user's PC. In this version, the GEMINI modules run as applets, which may reside in local user PCs, on the server, or Java Web Start. In this enhanced version, XML-based data handling procedures are used to access data from remote and local databases and save results for later access and analyses. The XML data handling process also integrates different stand-alone GEMINI modules enabling the user(s) to access multiple databases. It provides flexibility to the user to customize analytical approach, database location, and level of collaboration. An example integrated field-study using GEMINI modules and Stand Alone Web Start Applications is provided to demonstrate the versatile applicability of this freeware for cost-effective reservoir modeling.

Use of XML and Java for collaborative petroleum reservoir modeling on the Internet

USGS Publications Warehouse

Victorine, J.; Watney, W.L.; Bhattacharya, S.

2005-01-01

The GEMINI (Geo-Engineering Modeling through INternet Informatics) is a public-domain, web-based freeware that is made up of an integrated suite of 14 Java-based software tools to accomplish on-line, real-time geologic and engineering reservoir modeling. GEMINI facilitates distant collaborations for small company and academic clients, negotiating analyses of both single and multiple wells. The system operates on a single server and an enterprise database. External data sets must be uploaded into this database. Feedback from GEMINI users provided the impetus to develop Stand Alone Web Start Applications of GEMINI modules that reside in and operate from the user's PC. In this version, the GEMINI modules run as applets, which may reside in local user PCs, on the server, or Java Web Start. In this enhanced version, XML-based data handling procedures are used to access data from remote and local databases and save results for later access and analyses. The XML data handling process also integrates different stand-alone GEMINI modules enabling the user(s) to access multiple databases. It provides flexibility to the user to customize analytical approach, database location, and level of collaboration. An example integrated field-study using GEMINI modules and Stand Alone Web Start Applications is provided to demonstrate the versatile applicability of this freeware for cost-effective reservoir modeling. ?? 2005 Elsevier Ltd. All rights reserved.

Parmodel: a web server for automated comparative modeling of proteins.

PubMed

Uchôa, Hugo Brandão; Jorge, Guilherme Eberhart; Freitas Da Silveira, Nelson José; Camera, João Carlos; Canduri, Fernanda; De Azevedo, Walter Filgueira

2004-12-24

Parmodel is a web server for automated comparative modeling and evaluation of protein structures. The aim of this tool is to help inexperienced users to perform modeling, assessment, visualization, and optimization of protein models as well as crystallographers to evaluate structures solved experimentally. It is subdivided in four modules: Parmodel Modeling, Parmodel Assessment, Parmodel Visualization, and Parmodel Optimization. The main module is the Parmodel Modeling that allows the building of several models for a same protein in a reduced time, through the distribution of modeling processes on a Beowulf cluster. Parmodel automates and integrates the main softwares used in comparative modeling as MODELLER, Whatcheck, Procheck, Raster3D, Molscript, and Gromacs. This web server is freely accessible at .

Web Time-Management Tool

NASA Technical Reports Server (NTRS)

2000-01-01

Oak Grove Reactor, developed by Oak Grove Systems, is a new software program that allows users to integrate workflow processes. It can be used with portable communication devices. The software can join e-mail, calendar/scheduling and legacy applications into one interactive system via the web. Priority tasks and due dates are organized and highlighted to keep the user up to date with developments. Reactor works with existing software and few new skills are needed to use it. Using a web browser, a user can can work on something while other users can work on the same procedure or view its status while it is being worked on at another site. The software was developed by the Jet Propulsion Lab and originally put to use at Johnson Space Center.

Semantic Integration for Marine Science Interoperability Using Web Technologies

NASA Astrophysics Data System (ADS)

Rueda, C.; Bermudez, L.; Graybeal, J.; Isenor, A. W.

2008-12-01

The Marine Metadata Interoperability Project, MMI (http://marinemetadata.org) promotes the exchange, integration, and use of marine data through enhanced data publishing, discovery, documentation, and accessibility. A key effort is the definition of an Architectural Framework and Operational Concept for Semantic Interoperability (http://marinemetadata.org/sfc), which is complemented with the development of tools that realize critical use cases in semantic interoperability. In this presentation, we describe a set of such Semantic Web tools that allow performing important interoperability tasks, ranging from the creation of controlled vocabularies and the mapping of terms across multiple ontologies, to the online registration, storage, and search services needed to work with the ontologies (http://mmisw.org). This set of services uses Web standards and technologies, including Resource Description Framework (RDF), Web Ontology language (OWL), Web services, and toolkits for Rich Internet Application development. We will describe the following components: MMI Ontology Registry: The MMI Ontology Registry and Repository provides registry and storage services for ontologies. Entries in the registry are associated with projects defined by the registered users. Also, sophisticated search functions, for example according to metadata items and vocabulary terms, are provided. Client applications can submit search requests using the WC3 SPARQL Query Language for RDF. Voc2RDF: This component converts an ASCII comma-delimited set of terms and definitions into an RDF file. Voc2RDF facilitates the creation of controlled vocabularies by using a simple form-based user interface. Created vocabularies and their descriptive metadata can be submitted to the MMI Ontology Registry for versioning and community access. VINE: The Vocabulary Integration Environment component allows the user to map vocabulary terms across multiple ontologies. Various relationships can be established, for example exactMatch, narrowerThan, and subClassOf. VINE can compute inferred mappings based on the given associations. Attributes about each mapping, like comments and a confidence level, can also be included. VINE also supports registering and storing resulting mapping files in the Ontology Registry. The presentation will describe the application of semantic technologies in general, and our planned applications in particular, to solve data management problems in the marine and environmental sciences.

cGRNB: a web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets.

PubMed

Xu, Huayong; Yu, Hui; Tu, Kang; Shi, Qianqian; Wei, Chaochun; Li, Yuan-Yuan; Li, Yi-Xue

2013-01-01

We are witnessing rapid progress in the development of methodologies for building the combinatorial gene regulatory networks involving both TFs (Transcription Factors) and miRNAs (microRNAs). There are a few tools available to do these jobs but most of them are not easy to use and not accessible online. A web server is especially needed in order to allow users to upload experimental expression datasets and build combinatorial regulatory networks corresponding to their particular contexts. In this work, we compiled putative TF-gene, miRNA-gene and TF-miRNA regulatory relationships from forward-engineering pipelines and curated them as built-in data libraries. We streamlined the R codes of our two separate forward-and-reverse engineering algorithms for combinatorial gene regulatory network construction and formalized them as two major functional modules. As a result, we released the cGRNB (combinatorial Gene Regulatory Networks Builder): a web server for constructing combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets. The cGRNB enables two major network-building modules, one for MPGE (miRNA-perturbed gene expression) datasets and the other for parallel miRNA/mRNA expression datasets. A miRNA-centered two-layer combinatorial regulatory cascade is the output of the first module and a comprehensive genome-wide network involving all three types of combinatorial regulations (TF-gene, TF-miRNA, and miRNA-gene) are the output of the second module. In this article we propose cGRNB, a web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets. Since parallel miRNA/mRNA expression datasets are rapidly accumulated by the advance of next-generation sequencing techniques, cGRNB will be very useful tool for researchers to build combinatorial gene regulatory networks based on expression datasets. The cGRNB web-server is free and available online at http://www.scbit.org/cgrnb.

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

NASA Technical Reports Server (NTRS)

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

1998-01-01

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

Software Tools Streamline Project Management

NASA Technical Reports Server (NTRS)

2009-01-01

Three innovative software inventions from Ames Research Center (NETMARK, Program Management Tool, and Query-Based Document Management) are finding their way into NASA missions as well as industry applications. The first, NETMARK, is a program that enables integrated searching of data stored in a variety of databases and documents, meaning that users no longer have to look in several places for related information. NETMARK allows users to search and query information across all of these sources in one step. This cross-cutting capability in information analysis has exponentially reduced the amount of time needed to mine data from days or weeks to mere seconds. NETMARK has been used widely throughout NASA, enabling this automatic integration of information across many documents and databases. NASA projects that use NETMARK include the internal reporting system and project performance dashboard, Erasmus, NASA s enterprise management tool, which enhances organizational collaboration and information sharing through document routing and review; the Integrated Financial Management Program; International Space Station Knowledge Management; Mishap and Anomaly Information Reporting System; and management of the Mars Exploration Rovers. Approximately $1 billion worth of NASA s projects are currently managed using Program Management Tool (PMT), which is based on NETMARK. PMT is a comprehensive, Web-enabled application tool used to assist program and project managers within NASA enterprises in monitoring, disseminating, and tracking the progress of program and project milestones and other relevant resources. The PMT consists of an integrated knowledge repository built upon advanced enterprise-wide database integration techniques and the latest Web-enabled technologies. The current system is in a pilot operational mode allowing users to automatically manage, track, define, update, and view customizable milestone objectives and goals. The third software invention, Query-Based Document Management (QBDM) is a tool that enables content or context searches, either simple or hierarchical, across a variety of databases. The system enables users to specify notification subscriptions where they associate "contexts of interest" and "events of interest" to one or more documents or collection(s) of documents. Based on these subscriptions, users receive notification when the events of interest occur within the contexts of interest for associated document or collection(s) of documents. Users can also associate at least one notification time as part of the notification subscription, with at least one option for the time period of notifications.

Freva - Freie Univ Evaluation System Framework for Scientific Infrastructures in Earth System Modeling

NASA Astrophysics Data System (ADS)

Kadow, Christopher; Illing, Sebastian; Kunst, Oliver; Schartner, Thomas; Kirchner, Ingo; Rust, Henning W.; Cubasch, Ulrich; Ulbrich, Uwe

2016-04-01

The Freie Univ Evaluation System Framework (Freva - freva.met.fu-berlin.de) is a software infrastructure for standardized data and tool solutions in Earth system science. Freva runs on high performance computers to handle customizable evaluation systems of research projects, institutes or universities. It combines different software technologies into one common hybrid infrastructure, including all features present in the shell and web environment. The database interface satisfies the international standards provided by the Earth System Grid Federation (ESGF). Freva indexes different data projects into one common search environment by storing the meta data information of the self-describing model, reanalysis and observational data sets in a database. This implemented meta data system with its advanced but easy-to-handle search tool supports users, developers and their plugins to retrieve the required information. A generic application programming interface (API) allows scientific developers to connect their analysis tools with the evaluation system independently of the programming language used. Users of the evaluation techniques benefit from the common interface of the evaluation system without any need to understand the different scripting languages. Facilitation of the provision and usage of tools and climate data automatically increases the number of scientists working with the data sets and identifying discrepancies. The integrated web-shell (shellinabox) adds a degree of freedom in the choice of the working environment and can be used as a gate to the research projects HPC. Plugins are able to integrate their e.g. post-processed results into the database of the user. This allows e.g. post-processing plugins to feed statistical analysis plugins, which fosters an active exchange between plugin developers of a research project. Additionally, the history and configuration sub-system stores every analysis performed with the evaluation system in a database. Configurations and results of the tools can be shared among scientists via shell or web system. Therefore, plugged-in tools benefit from transparency and reproducibility. Furthermore, if configurations match while starting an evaluation plugin, the system suggests to use results already produced by other users - saving CPU/h, I/O, disk space and time. The efficient interaction between different technologies improves the Earth system modeling science framed by Freva.

Final Report on the Creation of the Wind Integration National Dataset (WIND) Toolkit and API: October 1, 2013 - September 30, 2015

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

Hodge, Bri-Mathias

2016-04-08

The primary objective of this work was to create a state-of-the-art national wind resource data set and to provide detailed wind plant output data for specific sites based on that data set. Corresponding retrospective wind forecasts were also included at all selected locations. The combined information from these activities was used to create the Wind Integration National Dataset (WIND), and an extraction tool was developed to allow web-based data access.

A Hyperbolic Ontology Visualization Tool for Model Application Programming Interface Documentation

NASA Technical Reports Server (NTRS)

Hyman, Cody

2011-01-01

Spacecraft modeling, a critically important portion in validating planned spacecraft activities, is currently carried out using a time consuming method of mission to mission model implementations and integration. A current project in early development, Integrated Spacecraft Analysis (ISCA), aims to remedy this hindrance by providing reusable architectures and reducing time spent integrating models with planning and sequencing tools. The principle objective of this internship was to develop a user interface for an experimental ontology-based structure visualization of navigation and attitude control system modeling software. To satisfy this, a number of tree and graph visualization tools were researched and a Java based hyperbolic graph viewer was selected for experimental adaptation. Early results show promise in the ability to organize and display large amounts of spacecraft model documentation efficiently and effectively through a web browser. This viewer serves as a conceptual implementation for future development but trials with both ISCA developers and end users should be performed to truly evaluate the effectiveness of continued development of such visualizations.

TSVdb: a web-tool for TCGA splicing variants analysis.

PubMed

Sun, Wenjie; Duan, Ting; Ye, Panmeng; Chen, Kelie; Zhang, Guanling; Lai, Maode; Zhang, Honghe

2018-05-29

Collaborative projects such as The Cancer Genome Atlas (TCGA) have generated various -omics and clinical data on cancer. Many computational tools have been developed to facilitate the study of the molecular characterization of tumors using data from the TCGA. Alternative splicing of a gene produces splicing variants, and accumulating evidence has revealed its essential role in cancer-related processes, implying the urgent need to discover tumor-specific isoforms and uncover their potential functions in tumorigenesis. We developed TSVdb, a web-based tool, to explore alternative splicing based on TCGA samples with 30 clinical variables from 33 tumors. TSVdb has an integrated and well-proportioned interface for visualization of the clinical data, gene expression, usage of exons/junctions and splicing patterns. Researchers can interpret the isoform expression variations between or across clinical subgroups and estimate the relationships between isoforms and patient prognosis. TSVdb is available at http://www.tsvdb.com , and the source code is available at https://github.com/wenjie1991/TSVdb . TSVdb will inspire oncologists and accelerate isoform-level advances in cancer research.

Integrated Internet based tools for learning and evaluating the International Classification of Nursing Practice.

PubMed

Alecu, C S; Jitaru, E; Moisil, I

2000-01-01

This paper presents some tools designed and implemented for learning-related purposes; these tools can be downloaded or run on the TeleNurse web site. Among other facilities, TeleNurse web site is hosting now the version 1.2 of SysTerN (terminology system for nursing) which can be downloaded on request and also the "Evaluation of Translation" form which has been designed in order to improve the Romanian translation of the ICNP (the International Classification of Nursing Practice). SysTerN has been developed using the framework of the TeleNurse ID--ENTITY Telematics for Health EU project. This version is using the beta version of ICNP containing Phenomena and Actions classification. This classification is intended to facilitate documentation of nursing practice, by providing a terminology or vocabulary for use in the description of the nursing process. The TeleNurse site is bilingual, Romanian-English, in order to enlarge the discussion forum with members from other CEE (or Non-CEE) countries.

MapMyFlu: visualizing spatio-temporal relationships between related influenza sequences

PubMed Central

Nolte, Nicholas; Kurzawa, Nils; Eils, Roland; Herrmann, Carl

2015-01-01

Understanding the molecular dynamics of viral spreading is crucial for anticipating the epidemiological implications of disease outbreaks. In the case of influenza, reassortments or point mutations affect the adaption to new hosts or resistance to anti-viral drugs and can determine whether a new strain will result in a pandemic infection or a less severe progression. To this end, tools integrating molecular information with epidemiological parameters are important to understand how molecular characteristics reflect in the infection dynamics. We present a new web tool, MapMyFlu, which allows to spatially and temporally display influenza viruses related to a query sequence on a Google Map based on BLAST results against the NCBI Influenza Database. Temporal and geographical trends appear clearly and may help in reconstructing the evolutionary history of a particular sequence. The tool is accessible through a web server, hence without the need for local installation. The website has an intuitive design and provides an easy-to-use service, and is available at http://mapmyflu.ipmb.uni-heidelberg.de PMID:25940623

BrainBrowser: distributed, web-based neurological data visualization.

PubMed

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

2014-01-01

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

BrainBrowser: distributed, web-based neurological data visualization

PubMed Central

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

2015-01-01

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

The Earth Observation Monitor - Automated monitoring and alerting for spatial time-series data based on OGC web services

NASA Astrophysics Data System (ADS)

Eberle, J.; Hüttich, C.; Schmullius, C.

2014-12-01

Spatial time series data are freely available around the globe from earth observation satellites and meteorological stations for many years until now. They provide useful and important information to detect ongoing changes of the environment; but for end-users it is often too complex to extract this information out of the original time series datasets. This issue led to the development of the Earth Observation Monitor (EOM), an operational framework and research project to provide simple access, analysis and monitoring tools for global spatial time series data. A multi-source data processing middleware in the backend is linked to MODIS data from Land Processes Distributed Archive Center (LP DAAC) and Google Earth Engine as well as daily climate station data from NOAA National Climatic Data Center. OGC Web Processing Services are used to integrate datasets from linked data providers or external OGC-compliant interfaces to the EOM. Users can either use the web portal (webEOM) or the mobile application (mobileEOM) to execute these processing services and to retrieve the requested data for a given point or polygon in userfriendly file formats (CSV, GeoTiff). Beside providing just data access tools, users can also do further time series analyses like trend calculations, breakpoint detections or the derivation of phenological parameters from vegetation time series data. Furthermore data from climate stations can be aggregated over a given time interval. Calculated results can be visualized in the client and downloaded for offline usage. Automated monitoring and alerting of the time series data integrated by the user is provided by an OGC Sensor Observation Service with a coupled OGC Web Notification Service. Users can decide which datasets and parameters are monitored with a given filter expression (e.g., precipitation value higher than x millimeter per day, occurrence of a MODIS Fire point, detection of a time series anomaly). Datasets integrated in the SOS service are updated in near-realtime based on the linked data providers mentioned above. An alert is automatically pushed to the user if the new data meets the conditions of the registered filter expression. This monitoring service is available on the web portal with alerting by email and within the mobile app with alerting by email and push notification.

Interacting With A Near Real-Time Urban Digital Watershed Using Emerging Geospatial Web Technologies

NASA Astrophysics Data System (ADS)

Liu, Y.; Fazio, D. J.; Abdelzaher, T.; Minsker, B.

2007-12-01

The value of real-time hydrologic data dissemination including river stage, streamflow, and precipitation for operational stormwater management efforts is particularly high for communities where flash flooding is common and costly. Ideally, such data would be presented within a watershed-scale geospatial context to portray a holistic view of the watershed. Local hydrologic sensor networks usually lack comprehensive integration with sensor networks managed by other agencies sharing the same watershed due to administrative, political, but mostly technical barriers. Recent efforts on providing unified access to hydrological data have concentrated on creating new SOAP-based web services and common data format (e.g. WaterML and Observation Data Model) for users to access the data (e.g. HIS and HydroSeek). Geospatial Web technology including OGC sensor web enablement (SWE), GeoRSS, Geo tags, Geospatial browsers such as Google Earth and Microsoft Virtual Earth and other location-based service tools provides possibilities for us to interact with a digital watershed in near-real-time. OGC SWE proposes a revolutionary concept towards a web-connected/controllable sensor networks. However, these efforts have not provided the capability to allow dynamic data integration/fusion among heterogeneous sources, data filtering and support for workflows or domain specific applications where both push and pull mode of retrieving data may be needed. We propose a light weight integration framework by extending SWE with open source Enterprise Service Bus (e.g., mule) as a backbone component to dynamically transform, transport, and integrate both heterogeneous sensor data sources and simulation model outputs. We will report our progress on building such framework where multi-agencies" sensor data and hydro-model outputs (with map layers) will be integrated and disseminated in a geospatial browser (e.g. Microsoft Virtual Earth). This is a collaborative project among NCSA, USGS Illinois Water Science Center, Computer Science Department at UIUC funded by the Adaptive Environmental Infrastructure Sensing and Information Systems initiative at UIUC.

Global search tool for the Advanced Photon Source Integrated Relational Model of Installed Systems (IRMIS) database.

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

Quock, D. E. R.; Cianciarulo, M. B.; APS Engineering Support Division

2007-01-01

The Integrated Relational Model of Installed Systems (IRMIS) is a relational database tool that has been implemented at the Advanced Photon Source to maintain an updated account of approximately 600 control system software applications, 400,000 process variables, and 30,000 control system hardware components. To effectively display this large amount of control system information to operators and engineers, IRMIS was initially built with nine Web-based viewers: Applications Organizing Index, IOC, PLC, Component Type, Installed Components, Network, Controls Spares, Process Variables, and Cables. However, since each viewer is designed to provide details from only one major category of the control system, themore » necessity for a one-stop global search tool for the entire database became apparent. The user requirements for extremely fast database search time and ease of navigation through search results led to the choice of Asynchronous JavaScript and XML (AJAX) technology in the implementation of the IRMIS global search tool. Unique features of the global search tool include a two-tier level of displayed search results, and a database data integrity validation and reporting mechanism.« less

Delivering Electronic Resources with Web OPACs and Other Web-based Tools: Needs of Reference Librarians.

ERIC Educational Resources Information Center

Bordeianu, Sever; Carter, Christina E.; Dennis, Nancy K.

2000-01-01

Describes Web-based online public access catalogs (Web OPACs) and other Web-based tools as gateway methods for providing access to library collections. Addresses solutions for overcoming barriers to information, such as through the implementation of proxy servers and other authentication tools for remote users. (Contains 18 references.)…

GelScape: a web-based server for interactively annotating, manipulating, comparing and archiving 1D and 2D gel images.

PubMed

Young, Nelson; Chang, Zhan; Wishart, David S

2004-04-12

GelScape is a web-based tool that permits facile, interactive annotation, comparison, manipulation and storage of protein gel images. It uses Java applet-servlet technology to allow rapid, remote image handling and image processing in a platform-independent manner. It supports many of the features found in commercial, stand-alone gel analysis software including spot annotation, spot integration, gel warping, image resizing, HTML image mapping, image overlaying as well as the storage of gel image and gel annotation data in compliance with Federated Gel Database requirements.

Freeware eLearning Flash-ECG for learning electrocardiography.

PubMed

Romanov, Kalle; Kuusi, Timo

2009-06-01

Electrocardiographic (ECG) analysis can be taught in eLearning programmes with suitable software that permits the effective use of basic tools such as a ruler and a magnifier, required for measurements. The Flash-ECG (Research & Development Unit for Medical Education, University of Helsinki, Finland) was developed to enable teachers and students to use scanned and archived ECGs on computer screens and classroom projectors. The software requires only a standard web browser with a Flash plug-in and can be integrated with learning environments (Blackboard/WebCT, Moodle). The Flash-ECG is freeware and is available to medical teachers worldwide.

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).

The Electron Microscopy Outreach Program: A Web-based resource for research and education.

PubMed

Sosinsky, G E; Baker, T S; Hand, G; Ellisman, M H

1999-01-01

We have developed a centralized World Wide Web (WWW)-based environment that serves as a resource of software tools and expertise for biological electron microscopy. A major focus is molecular electron microscopy, but the site also includes information and links on structural biology at all levels of resolution. This site serves to help integrate or link structural biology techniques in accordance with user needs. The WWW site, called the Electron Microscopy (EM) Outreach Program (URL: http://emoutreach.sdsc.edu), provides scientists with computational and educational tools for their research and edification. In particular, we have set up a centralized resource containing course notes, references, and links to image analysis and three-dimensional reconstruction software for investigators wanting to learn about EM techniques either within or outside of their fields of expertise. Copyright 1999 Academic Press.

Web-based software tool for constraint-based design specification of synthetic biological systems.

PubMed

Oberortner, Ernst; Densmore, Douglas

2015-06-19

miniEugene provides computational support for solving combinatorial design problems, enabling users to specify and enumerate designs for novel biological systems based on sets of biological constraints. This technical note presents a brief tutorial for biologists and software engineers in the field of synthetic biology on how to use miniEugene. After reading this technical note, users should know which biological constraints are available in miniEugene, understand the syntax and semantics of these constraints, and be able to follow a step-by-step guide to specify the design of a classical synthetic biological system-the genetic toggle switch.1 We also provide links and references to more information on the miniEugene web application and the integration of the miniEugene software library into sophisticated Computer-Aided Design (CAD) tools for synthetic biology ( www.eugenecad.org ).

Development of an integrated e-health tool for people with, or at high risk of, cardiovascular disease: The Consumer Navigation of Electronic Cardiovascular Tools (CONNECT) web application.

PubMed

Neubeck, Lis; Coorey, Genevieve; Peiris, David; Mulley, John; Heeley, Emma; Hersch, Fred; Redfern, Julie

2016-12-01

Cardiovascular disease is the leading killer globally and secondary prevention substantially reduces risk. Uptake of, and adherence to, face-to-face preventive programs is often low. Alternative models of care are exploiting the prominence of technology in daily life to facilitate lifestyle behavior change. To inform the development of a web-based application integrated with the primary care electronic health record, we undertook a collaborative user-centered design process to develop a consumer-focused e-health tool for cardiovascular disease risk reduction. A four-phase iterative process involved ten multidisciplinary clinicians and academics (primary care physician, nurses and allied health professionals), two design consultants, one graphic designer, three software developers and fourteen proposed end-users. This 18-month process involved, (1) defining the target audience and needs, (2) pilot testing and refinement, (3) software development including validation and testing the algorithm, (4) user acceptance testing and beta testing. From this process, researchers were able to better understand end-user needs and preferences, thereby improving and enriching the increasingly detailed system designs and prototypes for a mobile responsive web application. We reviewed 14 relevant applications/websites and sixteen observational and interventional studies to derive a set of core components and ideal features for the system. These included the need for interactivity, visual appeal, credible health information, virtual rewards, and emotional and physical support. The features identified as essential were: (i) both mobile and web-enabled 'apps', (ii) an emphasis on medication management, (iii) a strong psychosocial support component. Subsequent workshops (n=6; 2×1.5h) informed the development of functionality and lo-fidelity sketches of application interfaces. These ideas were next tested in consumer focus groups (n=9; 3×1.5h). Specifications for the application were refined from this feedback and a graphic designer iteratively developed the interface. Concurrently, the electronic health record was linked to the consumer portal. A written description of the final algorithms for all decisions and outputs was provided to software programmers. These algorithmic outputs to the app were first validated against those obtained from an independently programmed version in STATA 11. User acceptance testing (n=5, 2×1.0h) and beta testing revealed technical bugs and interface concerns across commonly-used web browsers and smartphones. These were resolved and re-tested until functionality was optimized. End-users of a cardiovascular disease prevention program have complex needs. A user-centered design approach aided the integration of these needs into the concept, specifications, development and refinement of a responsive web application for risk factor reduction and disease prevention. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Evaluation of the impact of furniture on communications performance for ubiquitous deployment of Wireless Sensor Networks in smart homes.

PubMed

Bleda, Andrés L; Jara, Antonio J; Maestre, Rafael; Santa, Guadalupe; Gómez Skarmeta, Antonio F

2012-01-01

The extensions of the environment with the integration of sensing systems in any space, in conjunction with ubiquitous computing are enabling the so-called Smart Space Sensor Networks. This new generation of networks are offering full connectivity with any object, through the Internet of Things (IoT) and/or the Web, i.e., the Web of Things. These connectivity capabilities are making it feasible to sense the behaviours of people at home and act accordingly. These sensing systems must be integrated within typical elements found at home such as furniture. For that reason, this work considers furniture as an interesting element for the transparent location of sensors. Furniture is a ubiquitous object, i.e., it can be found everywhere at home or the office, and it can integrate and hide the sensors of a network. This work addresses the lack of an exhaustive study of the effect of furniture on signal losses. In addition an easy-to-use tool for estimating the robustness of the communication channel among the sensor nodes and gateways is proposed. Specifically, the losses in a sensor network signal due to the materials found within the communication link are evaluated. Then, this work proposes a software tool that gathers the obtained results and is capable of evaluating the impact of a given set of materials on the communications. This tool also provides a mechanism to optimize the sensor network deployments during the definition of smart spaces. Specifically, it provides information such as: maximum distances between sensor nodes, most suitable type of furniture to integrate sensors, or battery life of sensor nodes. This tool has been validated empirically in the lab, and it is currently being used by several enterprise partners of the Technological Centre of Furniture and Wood in the southeast of Spain.

Evaluation of the Impact of Furniture on Communications Performance for Ubiquitous Deployment of Wireless Sensor Networks in Smart Homes

PubMed Central

Bleda, Andrés L.; Jara, Antonio J.; Maestre, Rafael; Santa, Guadalupe; Gómez Skarmeta, Antonio F.

2012-01-01

The extensions of the environment with the integration of sensing systems in any space, in conjunction with ubiquitous computing are enabling the so-called Smart Space Sensor Networks. This new generation of networks are offering full connectivity with any object, through the Internet of Things (IoT) and/or the Web, i.e., the Web of Things. These connectivity capabilities are making it feasible to sense the behaviours of people at home and act accordingly. These sensing systems must be integrated within typical elements found at home such as furniture. For that reason, this work considers furniture as an interesting element for the transparent location of sensors. Furniture is a ubiquitous object, i.e., it can be found everywhere at home or the office, and it can integrate and hide the sensors of a network. This work addresses the lack of an exhaustive study of the effect of furniture on signal losses. In addition an easy-to-use tool for estimating the robustness of the communication channel among the sensor nodes and gateways is proposed. Specifically, the losses in a sensor network signal due to the materials found within the communication link are evaluated. Then, this work proposes a software tool that gathers the obtained results and is capable of evaluating the impact of a given set of materials on the communications. This tool also provides a mechanism to optimize the sensor network deployments during the definition of smart spaces. Specifically, it provides information such as: maximum distances between sensor nodes, most suitable type of furniture to integrate sensors, or battery life of sensor nodes. This tool has been validated empirically in the lab, and it is currently being used by several enterprise partners of the Technological Centre of Furniture and Wood in the southeast of Spain. PMID:22778653

SNPit: a federated data integration system for the purpose of functional SNP annotation

PubMed Central

Shen, Terry H; Carlson, Christopher S; Tarczy-Hornoch, Peter

2009-01-01

Genome wide association studies can potentially identify the genetic causes behind the majority of human diseases. With the advent of more advanced genotyping techniques, there is now an explosion of data gathered on single nucleotide polymorphisms (SNPs). The need exists for an integrated system that can provide up-to-date functional annotation information on SNPs. We have developed the SNP Integration Tool (SNPit) system to address this need. Built upon a federated data integration system, SNPit provides current information on a comprehensive list of SNP data sources. Additional logical inference analysis was included through an inference engine plug in. The SNPit web servlet is available online for use. SNPit allows users to go to one source for up-to-date information on the functional annotation of SNPs. A tool that can help to integrate and analyze the potential functional significance of SNPs is important for understanding the results from genome wide association studies. PMID:19327864

A Case Study of Integrating Interwise: Interaction, Internet Self-Efficacy, and Satisfaction in Synchronous Online Learning Environments

ERIC Educational Resources Information Center

Kuo, Yu-Chun; Walker, Andrew E.; Belland, Brian R.; Schroder, Kerstin E. E.; Kuo, Yu-Tung

2014-01-01

This paper reports research on the implementation of a web-based videoconferencing tool (Interwise) for synchronous learning sessions on an industrial technology course offered through a university in northern Taiwan. The participants included undergraduate students from the same course offered in two different semesters. We investigated students'…

The Online Writing Lab (OWL) and the Forum: A Tool for Writers in Distance Education Environments.

ERIC Educational Resources Information Center

Terryberry, Karl

2002-01-01

Demonstrates how to integrate static web pages with the dynamic forum for an effective learning experience on the online writing lab (OWL). Explains why asynchronous feedback provides effective, individualized writing instruction to students with various learning styles and how collaborative learning is fostered through threaded discussion groups.…

Blogs as a Learning Space: Creating Text of Talks

ERIC Educational Resources Information Center

Santos, Arnold Nicholas E.

2011-01-01

This paper explored the pedagogical preparations taken by the researcher in integrating blogs to the traditional classroom experience as well as its use in online classes as a tool for students to write about what they have learned in class and relate it to everyday life. The researcher utilized web blog, combined Facebook and Multiply blogsites,…

The Pilot Study of Integrating Spatial Educational Experiences (Isee) in an Undergraduate Crop Production Course

ERIC Educational Resources Information Center

Mitzman, Stephanie; Snyder, Lori Unruh; Schulze, Darrell G.; Owens, Phillip R.; Bracke, Marianne Stowell

2011-01-01

Recent National Research Council reports make compelling arguments for the need to incorporate spatial abilities and use spatial technologies throughout our educational system. We conducted a pilot study to determine the pedagogical effectiveness of teaching with geographic information systems (GIS) by using a web-based GIS tool of Indiana soils.…

Development of a unified web-based national HIV/AIDS information system in China

PubMed Central

Mao, Yurong; Wu, Zunyou; Poundstone, Katharine; Wang, Changhe; Qin, Qianqian; Ma, Ye; Ma, Wei

2010-01-01

Background In the past, many data collection systems were in operation for different HIV/AIDS projects in China. We describe the creation of a unified, web-based national HIV/AIDS information system designed to streamline data collection and facilitate data use. Methods Integration of separate HIV/AIDS data systems was carried out in three phases. Phase 1, from January 2006 to December 2007, involved creating a set of unified data collection forms that took into account existing program needs and the reporting requirements of various international organizations. Phase 2, from January to October 2007, involved creating a web-based platform to host the integrated HIV/AIDS data collection system. Phase 3, from November to December 2007, involved pilot testing the new, integrated system prior to nationwide application. Results Eight web-based data collection subsystems based on one platform began operation on 1 January 2008. These eight subsystems cover: (i) HIV/AIDS case reporting; (ii) HIV testing and counselling; (iii) antiretroviral treatment (ART) for adults; (iv) ART for children; (v) behavioural interventions for high-risk groups; (vi) methadone maintenance treatment; (vii) sentinel and behavioural surveillance; and (viii) local county background information. The system provides real-time data to monitor HIV testing, prevention and treatment programs across the country. Conclusion China’s new unified, web-based HIV/AIDS information system has improved the efficiency of data collection, reporting, analysis and use, as well as data quality and security. It is a powerful tool to support policy making, program evaluation and implementation of the national HIV/AIDS program and, thus, may serve a model for other countries. PMID:21113041

Topographic Science

USGS Publications Warehouse

Poppenga, Sandra K.; Evans, Gayla; Gesch, Dean; Stoker, Jason M.; Queija, Vivian R.; Worstell, Bruce; Tyler, Dean J.; Danielson, Jeff; Bliss, Norman; Greenlee, Susan

2010-01-01

The mission of U.S. Geological Survey (USGS) Earth Resources Observation and Science (EROS) Center Topographic Science is to establish partnerships and conduct research and applications that facilitate the development and use of integrated national and global topographic datasets. Topographic Science includes a wide range of research and applications that result in improved seamless topographic datasets, advanced elevation technology, data integration and terrain visualization, new and improved elevation derivatives, and development of Web-based tools. In cooperation with our partners, Topographic Science is developing integrated-science applications for mapping, national natural resource initiatives, hazards, and global change science. http://topotools.cr.usgs.gov/.

Helioviewer: A Web 2.0 Tool for Visualizing Heterogeneous Heliophysics Data

NASA Astrophysics Data System (ADS)

Hughitt, V. K.; Ireland, J.; Lynch, M. J.; Schmeidel, P.; Dimitoglou, G.; Müeller, D.; Fleck, B.

2008-12-01

Solar physics datasets are becoming larger, richer, more numerous and more distributed. Feature/event catalogs (describing objects of interest in the original data) are becoming important tools in navigating these data. In the wake of this increasing influx of data and catalogs there has been a growing need for highly sophisticated tools for accessing and visualizing this wealth of information. Helioviewer is a novel tool for integrating and visualizing disparate sources of solar and Heliophysics data. Taking advantage of the newly available power of modern web application frameworks, Helioviewer merges image and feature catalog data, and provides for Heliophysics data a familiar interface not unlike Google Maps or MapQuest. In addition to streamlining the process of combining heterogeneous Heliophysics datatypes such as full-disk images and coronagraphs, the inclusion of visual representations of automated and human-annotated features provides the user with an integrated and intuitive view of how different factors may be interacting on the Sun. Currently, Helioviewer offers images from The Extreme ultraviolet Imaging Telescope (EIT), The Large Angle and Spectrometric COronagraph experiment (LASCO) and the Michelson Doppler Imager (MDI) instruments onboard The Solar and Heliospheric Observatory (SOHO), as well as The Transition Region and Coronal Explorer (TRACE). Helioviewer also incorporates feature/event information from the LASCO CME List, NOAA Active Regions, CACTus CME and Type II Radio Bursts feature/event catalogs. The project is undergoing continuous development with many more data sources and additional functionality planned for the near future.

First Operational Experience With a High-Energy Physics Run Control System Based on Web Technologies

NASA Astrophysics Data System (ADS)

Bauer, Gerry; Beccati, Barbara; Behrens, Ulf; Biery, Kurt; Branson, James; Bukowiec, Sebastian; Cano, Eric; Cheung, Harry; Ciganek, Marek; Cittolin, Sergio; Coarasa Perez, Jose Antonio; Deldicque, Christian; Erhan, Samim; Gigi, Dominique; Glege, Frank; Gomez-Reino, Robert; Gulmini, Michele; Hatton, Derek; Hwong, Yi Ling; Loizides, Constantin; Ma, Frank; Masetti, Lorenzo; Meijers, Frans; Meschi, Emilio; Meyer, Andreas; Mommsen, Remigius K.; Moser, Roland; O'Dell, Vivian; Oh, Alexander; Orsini, Luciano; Paus, Christoph; Petrucci, Andrea; Pieri, Marco; Racz, Attila; Raginel, Olivier; Sakulin, Hannes; Sani, Matteo; Schieferdecker, Philipp; Schwick, Christoph; Shpakov, Dennis; Simon, Michal; Sumorok, Konstanty; Yoon, Andre Sungho

2012-08-01

Run control systems of modern high-energy particle physics experiments have requirements similar to those of today's Internet applications. The Compact Muon Solenoid (CMS) collaboration at CERN's Large Hadron Collider (LHC) therefore decided to build the run control system for its detector based on web technologies. The system is composed of Java Web Applications distributed over a set of Apache Tomcat servlet containers that connect to a database back-end. Users interact with the system through a web browser. The present paper reports on the successful scaling of the system from a small test setup to the production data acquisition system that comprises around 10.000 applications running on a cluster of about 1600 hosts. We report on operational aspects during the first phase of operation with colliding beams including performance, stability, integration with the CMS Detector Control System and tools to guide the operator.

FlaME: Flash Molecular Editor - a 2D structure input tool for the web.

PubMed

Dallakian, Pavel; Haider, Norbert

2011-02-01

So far, there have been no Flash-based web tools available for chemical structure input. The authors herein present a feasibility study, aiming at the development of a compact and easy-to-use 2D structure editor, using Adobe's Flash technology and its programming language, ActionScript. As a reference model application from the Java world, we selected the Java Molecular Editor (JME). In this feasibility study, we made an attempt to realize a subset of JME's functionality in the Flash Molecular Editor (FlaME) utility. These basic capabilities are: structure input, editing and depiction of single molecules, data import and export in molfile format. The result of molecular diagram sketching in FlaME is accessible in V2000 molfile format. By integrating the molecular editor into a web page, its communication with the HTML elements on this page is established using the two JavaScript functions, getMol() and setMol(). In addition, structures can be copied to the system clipboard. A first attempt was made to create a compact single-file application for 2D molecular structure input/editing on the web, based on Flash technology. With the application examples presented in this article, it could be demonstrated that the Flash methods are principally well-suited to provide the requisite communication between the Flash object (application) and the HTML elements on a web page, using JavaScript functions.

Teaching Web Security Using Portable Virtual Labs

ERIC Educational Resources Information Center

Chen, Li-Chiou; Tao, Lixin

2012-01-01

We have developed a tool called Secure WEb dEvelopment Teaching (SWEET) to introduce security concepts and practices for web application development. This tool provides introductory tutorials, teaching modules utilizing virtualized hands-on exercises, and project ideas in web application security. In addition, the tool provides pre-configured…

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.

JSME: a free molecule editor in JavaScript.

PubMed

Bienfait, Bruno; Ertl, Peter

2013-01-01

A molecule editor, i.e. a program facilitating graphical input and interactive editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. Today, when a web browser has become the universal scientific user interface, a tool to edit molecules directly within the web browser is essential. One of the most popular tools for molecular structure input on the web is the JME applet. Since its release nearly 15 years ago, however the web environment has changed and Java applets are facing increasing implementation hurdles due to their maintenance and support requirements, as well as security issues. This prompted us to update the JME editor and port it to a modern Internet programming language - JavaScript. The actual molecule editing Java code of the JME editor was translated into JavaScript with help of the Google Web Toolkit compiler and a custom library that emulates a subset of the GUI features of the Java runtime environment. In this process, the editor was enhanced by additional functionalities including a substituent menu, copy/paste, drag and drop and undo/redo capabilities and an integrated help. In addition to desktop computers, the editor supports molecule editing on touch devices, including iPhone, iPad and Android phones and tablets. In analogy to JME the new editor is named JSME. This new molecule editor is compact, easy to use and easy to incorporate into web pages. A free molecule editor written in JavaScript was developed and is released under the terms of permissive BSD license. The editor is compatible with JME, has practically the same user interface as well as the web application programming interface. The JSME editor is available for download from the project web page http://peter-ertl.com/jsme/

Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information

NASA Astrophysics Data System (ADS)

Sushko, Iurii; Novotarskyi, Sergii; Körner, Robert; Pandey, Anil Kumar; Rupp, Matthias; Teetz, Wolfram; Brandmaier, Stefan; Abdelaziz, Ahmed; Prokopenko, Volodymyr V.; Tanchuk, Vsevolod Y.; Todeschini, Roberto; Varnek, Alexandre; Marcou, Gilles; Ertl, Peter; Potemkin, Vladimir; Grishina, Maria; Gasteiger, Johann; Schwab, Christof; Baskin, Igor I.; Palyulin, Vladimir A.; Radchenko, Eugene V.; Welsh, William J.; Kholodovych, Vladyslav; Chekmarev, Dmitriy; Cherkasov, Artem; Aires-de-Sousa, Joao; Zhang, Qing-You; Bender, Andreas; Nigsch, Florian; Patiny, Luc; Williams, Antony; Tkachenko, Valery; Tetko, Igor V.

2011-06-01

The Online Chemical Modeling Environment is a web-based platform that aims to automate and simplify the typical steps required for QSAR modeling. The platform consists of two major subsystems: the database of experimental measurements and the modeling framework. A user-contributed database contains a set of tools for easy input, search and modification of thousands of records. The OCHEM database is based on the wiki principle and focuses primarily on the quality and verifiability of the data. The database is tightly integrated with the modeling framework, which supports all the steps required to create a predictive model: data search, calculation and selection of a vast variety of molecular descriptors, application of machine learning methods, validation, analysis of the model and assessment of the applicability domain. As compared to other similar systems, OCHEM is not intended to re-implement the existing tools or models but rather to invite the original authors to contribute their results, make them publicly available, share them with other users and to become members of the growing research community. Our intention is to make OCHEM a widely used platform to perform the QSPR/QSAR studies online and share it with other users on the Web. The ultimate goal of OCHEM is collecting all possible chemoinformatics tools within one simple, reliable and user-friendly resource. The OCHEM is free for web users and it is available online at http://www.ochem.eu.

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

PubMed Central

Passman, Dina B.

2013-01-01

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

Computational Tools and Facilities for the Next-Generation Analysis and Design Environment

NASA Technical Reports Server (NTRS)

Noor, Ahmed K. (Compiler); Malone, John B. (Compiler)

1997-01-01

This document contains presentations from the joint UVA/NASA Workshop on Computational Tools and Facilities for the Next-Generation Analysis and Design Environment held at the Virginia Consortium of Engineering and Science Universities in Hampton, Virginia on September 17-18, 1996. The presentations focused on the computational tools and facilities for analysis and design of engineering systems, including, real-time simulations, immersive systems, collaborative engineering environment, Web-based tools and interactive media for technical training. Workshop attendees represented NASA, commercial software developers, the aerospace industry, government labs, and academia. The workshop objectives were to assess the level of maturity of a number of computational tools and facilities and their potential for application to the next-generation integrated design environment.

Teaching bioinformatics and neuroinformatics by using free web-based tools.

PubMed

Grisham, William; Schottler, Natalie A; Valli-Marill, Joanne; Beck, Lisa; Beatty, Jackson

2010-01-01

This completely computer-based module's purpose is to introduce students to bioinformatics resources. We present an easy-to-adopt module that weaves together several important bioinformatic tools so students can grasp how these tools are used in answering research questions. Students integrate information gathered from websites dealing with anatomy (Mouse Brain Library), quantitative trait locus analysis (WebQTL from GeneNetwork), bioinformatics and gene expression analyses (University of California, Santa Cruz Genome Browser, National Center for Biotechnology Information's Entrez Gene, and the Allen Brain Atlas), and information resources (PubMed). Instructors can use these various websites in concert to teach genetics from the phenotypic level to the molecular level, aspects of neuroanatomy and histology, statistics, quantitative trait locus analysis, and molecular biology (including in situ hybridization and microarray analysis), and to introduce bioinformatic resources. Students use these resources to discover 1) the region(s) of chromosome(s) influencing the phenotypic trait, 2) a list of candidate genes-narrowed by expression data, 3) the in situ pattern of a given gene in the region of interest, 4) the nucleotide sequence of the candidate gene, and 5) articles describing the gene. Teaching materials such as a detailed student/instructor's manual, PowerPoints, sample exams, and links to free Web resources can be found at http://mdcune.psych.ucla.edu/modules/bioinformatics.

Using Web 2.0 (and Beyond?) in Space Flight Operations Control Centers

NASA Technical Reports Server (NTRS)

Scott, David W.

2010-01-01

Word processing was one of the earliest uses for small workstations, but we quickly learned that desktop computers were far more than e-typewriters. Similarly, "Web 2.0" capabilities, particularly advanced search engines, chats, wikis, blogs, social networking, and the like, offer tools that could significantly improve our efficiency at managing the avalanche of information and decisions needed to operate space vehicles in realtime. However, could does not necessarily equal should. We must wield two-edged swords carefully to avoid stabbing ourselves. This paper examines some Web 2.0 tools, with an emphasis on social media, and suggests which ones might be useful or harmful in real-time space operations co rnotl environments, based on the author s experience as a Payload Crew Communicator (PAYCOM) at Marshall Space Flight Center s (MSFC) Payload Operations Integration Center (POIC) for the International Space Station (ISS) and on discussions with other space flight operations control organizations and centers. There is also some discussion of an offering or two that may come from beyond the current cyber-horizon.

PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data.

PubMed

Hernández-de-Diego, Rafael; Tarazona, Sonia; Martínez-Mira, Carlos; Balzano-Nogueira, Leandro; Furió-Tarí, Pedro; Pappas, Georgios J; Conesa, Ana

2018-05-25

The increasing availability of multi-omic platforms poses new challenges to data analysis. Joint visualization of multi-omics data is instrumental in better understanding interconnections across molecular layers and in fully utilizing the multi-omic resources available to make biological discoveries. We present here PaintOmics 3, a web-based resource for the integrated visualization of multiple omic data types onto KEGG pathway diagrams. PaintOmics 3 combines server-end capabilities for data analysis with the potential of modern web resources for data visualization, providing researchers with a powerful framework for interactive exploration of their multi-omics information. Unlike other visualization tools, PaintOmics 3 covers a comprehensive pathway analysis workflow, including automatic feature name/identifier conversion, multi-layered feature matching, pathway enrichment, network analysis, interactive heatmaps, trend charts, and more. It accepts a wide variety of omic types, including transcriptomics, proteomics and metabolomics, as well as region-based approaches such as ATAC-seq or ChIP-seq data. The tool is freely available at www.paintomics.org.

Setup Instructions for the Applied Anomaly Detection Tool (AADT) Web Server

DTIC Science & Technology

2016-09-01

ARL-TR-7798 ● SEP 2016 US Army Research Laboratory Setup Instructions for the Applied Anomaly Detection Tool (AADT) Web Server...for the Applied Anomaly Detection Tool (AADT) Web Server by Christian D Schlesiger Computational and Information Sciences Directorate, ARL...SUBTITLE Setup Instructions for the Applied Anomaly Detection Tool (AADT) Web Server 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT

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

NASA Astrophysics Data System (ADS)

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

2007-12-01

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

Web-Enabled Mechanistic Case Diagramming: A Novel Tool for Assessing Students' Ability to Integrate Foundational and Clinical Sciences.

PubMed

Ferguson, Kristi J; Kreiter, Clarence D; Haugen, Thomas H; Dee, Fred R

2018-02-20

As medical schools move from discipline-based courses to more integrated approaches, identifying assessment tools that parallel this change is an important goal. The authors describe the use of test item statistics to assess the reliability and validity of web-enabled mechanistic case diagrams (MCDs) as a potential tool to assess students' ability to integrate basic science and clinical information. Students review a narrative clinical case and construct an MCD using items provided by the case author. Students identify the relationships among underlying risk factors, etiology, pathogenesis and pathophysiology, and the patients' signs and symptoms. They receive one point for each correctly-identified link. In 2014-15 and 2015-16, case diagrams were implemented in consecutive classes of 150 medical students. The alpha reliability coefficient for the overall score, constructed using each student's mean proportion correct across all cases, was 0.82. Discrimination indices for each of the case scores with the overall score ranged from 0.23 to 0.51. In a G study using those students with complete data (n = 251) on all 16 cases, 10% of the variance was true score variance, and systematic case variance was large. Using 16 cases generated a G coefficient (relative score reliability) equal to .72 and a Phi equal to .65. The next phase of the project will involve deploying MCDs in higher-stakes settings to determine whether similar results can be achieved. Further analyses will determine whether these assessments correlate with other measures of higher-order thinking skills.

RIMS: An Integrated Mapping and Analysis System with Applications to Earth Sciences and Hydrology

NASA Astrophysics Data System (ADS)

Proussevitch, A. A.; Glidden, S.; Shiklomanov, A. I.; Lammers, R. B.

2011-12-01

A web-based information and computational system for analysis of spatially distributed Earth system, climate, and hydrologic data have been developed. The System allows visualization, data exploration, querying, manipulation and arbitrary calculations with any loaded gridded or vector polygon dataset. The system's acronym, RIMS, stands for its core functionality as a Rapid Integrated Mapping System. The system can be deployed for a Global scale projects as well as for regional hydrology and climatology studies. In particular, the Water Systems Analysis Group of the University of New Hampshire developed the global and regional (Northern Eurasia, pan-Arctic) versions of the system with different map projections and specific data. The system has demonstrated its potential for applications in other fields of Earth sciences and education. The key Web server/client components of the framework include (a) a visualization engine built on Open Source libraries (GDAL, PROJ.4, etc.) that are utilized in a MapServer; (b) multi-level data querying tools built on XML server-client communication protocols that allow downloading map data on-the-fly to a client web browser; and (c) data manipulation and grid cell level calculation tools that mimic desktop GIS software functionality via a web interface. Server side data management of the system is designed around a simple database of dataset metadata facilitating mounting of new data to the system and maintaining existing data in an easy manner. RIMS contains "built-in" river network data that allows for query of upstream areas on-demand which can be used for spatial data aggregation and analysis of sub-basin areas. RIMS is an ongoing effort and currently being used to serve a number of websites hosting a suite of hydrologic, environmental and other GIS data.

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.

A Web Tool for Generating High Quality Machine-readable Biological Pathways.

PubMed

Ramirez-Gaona, Miguel; Marcu, Ana; Pon, Allison; Grant, Jason; Wu, Anthony; Wishart, David S

2017-02-08

PathWhiz is a web server built to facilitate the creation of colorful, interactive, visually pleasing pathway diagrams that are rich in biological information. The pathways generated by this online application are machine-readable and fully compatible with essentially all web-browsers and computer operating systems. It uses a specially developed, web-enabled pathway drawing interface that permits the selection and placement of different combinations of pre-drawn biological or biochemical entities to depict reactions, interactions, transport processes and binding events. This palette of entities consists of chemical compounds, proteins, nucleic acids, cellular membranes, subcellular structures, tissues, and organs. All of the visual elements in it can be interactively adjusted and customized. Furthermore, because this tool is a web server, all pathways and pathway elements are publicly accessible. This kind of pathway "crowd sourcing" means that PathWhiz already contains a large and rapidly growing collection of previously drawn pathways and pathway elements. Here we describe a protocol for the quick and easy creation of new pathways and the alteration of existing pathways. To further facilitate pathway editing and creation, the tool contains replication and propagation functions. The replication function allows existing pathways to be used as templates to create or edit new pathways. The propagation function allows one to take an existing pathway and automatically propagate it across different species. Pathways created with this tool can be "re-styled" into different formats (KEGG-like or text-book like), colored with different backgrounds, exported to BioPAX, SBGN-ML, SBML, or PWML data exchange formats, and downloaded as PNG or SVG images. The pathways can easily be incorporated into online databases, integrated into presentations, posters or publications, or used exclusively for online visualization and exploration. This protocol has been successfully applied to generate over 2,000 pathway diagrams, which are now found in many online databases including HMDB, DrugBank, SMPDB, and ECMDB.

Usage and applications of Semantic Web techniques and technologies to support chemistry research

PubMed Central

2014-01-01

Background The drug discovery process is now highly dependent on the management, curation and integration of large amounts of potentially useful data. Semantics are necessary in order to interpret the information and derive knowledge. Advances in recent years have mitigated concerns that the lack of robust, usable tools has inhibited the adoption of methodologies based on semantics. Results This paper presents three examples of how Semantic Web techniques and technologies can be used in order to support chemistry research: a controlled vocabulary for quantities, units and symbols in physical chemistry; a controlled vocabulary for the classification and labelling of chemical substances and mixtures; and, a database of chemical identifiers. This paper also presents a Web-based service that uses the datasets in order to assist with the completion of risk assessment forms, along with a discussion of the legal implications and value-proposition for the use of such a service. Conclusions We have introduced the Semantic Web concepts, technologies, and methodologies that can be used to support chemistry research, and have demonstrated the application of those techniques in three areas very relevant to modern chemistry research, generating three new datasets that we offer as exemplars of an extensible portfolio of advanced data integration facilities. We have thereby established the importance of Semantic Web techniques and technologies for meeting Wild’s fourth “grand challenge”. PMID:24855494

Usage and applications of Semantic Web techniques and technologies to support chemistry research.

PubMed

Borkum, Mark I; Frey, Jeremy G

2014-01-01

The drug discovery process is now highly dependent on the management, curation and integration of large amounts of potentially useful data. Semantics are necessary in order to interpret the information and derive knowledge. Advances in recent years have mitigated concerns that the lack of robust, usable tools has inhibited the adoption of methodologies based on semantics. THIS PAPER PRESENTS THREE EXAMPLES OF HOW SEMANTIC WEB TECHNIQUES AND TECHNOLOGIES CAN BE USED IN ORDER TO SUPPORT CHEMISTRY RESEARCH: a controlled vocabulary for quantities, units and symbols in physical chemistry; a controlled vocabulary for the classification and labelling of chemical substances and mixtures; and, a database of chemical identifiers. This paper also presents a Web-based service that uses the datasets in order to assist with the completion of risk assessment forms, along with a discussion of the legal implications and value-proposition for the use of such a service. We have introduced the Semantic Web concepts, technologies, and methodologies that can be used to support chemistry research, and have demonstrated the application of those techniques in three areas very relevant to modern chemistry research, generating three new datasets that we offer as exemplars of an extensible portfolio of advanced data integration facilities. We have thereby established the importance of Semantic Web techniques and technologies for meeting Wild's fourth "grand challenge".

Towards the Geospatial Web: Media Platforms for Managing Geotagged Knowledge Repositories

NASA Astrophysics Data System (ADS)

Scharl, Arno

International media have recognized the visual appeal of geo-browsers such as NASA World Wind and Google Earth, for example, when Web and television coverage on Hurricane Katrina used interactive geospatial projections to illustrate its path and the scale of destruction in August 2005. Yet these early applications only hint at the true potential of geospatial technology to build and maintain virtual communities and to revolutionize the production, distribution and consumption of media products. This chapter investigates this potential by reviewing the literature and discussing the integration of geospatial and semantic reference systems, with an emphasis on extracting geospatial context from unstructured text. A content analysis of news coverage based on a suite of text mining tools (webLyzard) sheds light on the popularity and adoption of geospatial platforms.

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.

Web Tools: The Second Generation

ERIC Educational Resources Information Center

Pascopella, Angela

2008-01-01

Web 2.0 tools and technologies, or second generation tools, help districts to save time and money, and eliminate the need to transfer or move files back and forth across computers. Many Web 2.0 tools help students think critically and solve problems, which falls under the 21st-century skills. The second-generation tools are growing in popularity…

The coronary artery disease quality dashboard: a chronic care disease management tool in an electronic health record.

PubMed

Jung, Eunice; Schnipper, Jeffrey L; Li, Qi; Linder, Jeffrey A; Rose, Alan F; Li, Ruzhuo; Eskin, Michael S; Housman, Dan; Middleton, Blackford; Einbinder, Jonathan S

2007-10-11

Quality reporting tools, integrated with ambulatory electronic health records (EHRs), may help clinicians understand performance, manage populations, and improve quality. The Coronary Artery Disease Quality Dash board (CAD QD) is a secure web report for performance measurement of a chronic care condition delivered through a central data warehouse and custom-built reporting tool. Pilot evaluation of the CAD Quality Dash board indicates that clinicians prefer a quality report that combines not only structured data from EHRs but one that facilitates actions to be taken on individual patients or on a population, i.e., for case management.

STAR: an integrated solution to management and visualization of sequencing data.

PubMed

Wang, Tao; Liu, Jie; Shen, Li; Tonti-Filippini, Julian; Zhu, Yun; Jia, Haiyang; Lister, Ryan; Whitaker, John W; Ecker, Joseph R; Millar, A Harvey; Ren, Bing; Wang, Wei

2013-12-15

Easily visualization of complex data features is a necessary step to conduct studies on next-generation sequencing (NGS) data. We developed STAR, an integrated web application that enables online management, visualization and track-based analysis of NGS data. STAR is a multilayer web service system. On the client side, STAR leverages JavaScript, HTML5 Canvas and asynchronous communications to deliver a smoothly scrolling desktop-like graphical user interface with a suite of in-browser analysis tools that range from providing simple track configuration controls to sophisticated feature detection within datasets. On the server side, STAR supports private session state retention via an account management system and provides data management modules that enable collection, visualization and analysis of third-party sequencing data from the public domain with over thousands of tracks hosted to date. Overall, STAR represents a next-generation data exploration solution to match the requirements of NGS data, enabling both intuitive visualization and dynamic analysis of data. STAR browser system is freely available on the web at http://wanglab.ucsd.edu/star/browser and https://github.com/angell1117/STAR-genome-browser.

MetaSEEk: a content-based metasearch engine for images

NASA Astrophysics Data System (ADS)

Beigi, Mandis; Benitez, Ana B.; Chang, Shih-Fu

1997-12-01

Search engines are the most powerful resources for finding information on the rapidly expanding World Wide Web (WWW). Finding the desired search engines and learning how to use them, however, can be very time consuming. The integration of such search tools enables the users to access information across the world in a transparent and efficient manner. These systems are called meta-search engines. The recent emergence of visual information retrieval (VIR) search engines on the web is leading to the same efficiency problem. This paper describes and evaluates MetaSEEk, a content-based meta-search engine used for finding images on the Web based on their visual information. MetaSEEk is designed to intelligently select and interface with multiple on-line image search engines by ranking their performance for different classes of user queries. User feedback is also integrated in the ranking refinement. We compare MetaSEEk with a base line version of meta-search engine, which does not use the past performance of the different search engines in recommending target search engines for future queries.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

A document centric metadata registration tool constructing earth environmental data infrastructure

NASA Astrophysics Data System (ADS)

Ichino, M.; Kinutani, H.; Ono, M.; Shimizu, T.; Yoshikawa, M.; Masuda, K.; Fukuda, K.; Kawamoto, H.

2009-12-01

DIAS (Data Integration and Analysis System) is one of GEOSS activities in Japan. It is also a leading part of the GEOSS task with the same name defined in GEOSS Ten Year Implementation Plan. The main mission of DIAS is to construct data infrastructure that can effectively integrate earth environmental data such as observation data, numerical model outputs, and socio-economic data provided from the fields of climate, water cycle, ecosystem, ocean, biodiversity and agriculture. Some of DIAS's data products are available at the following web site of http://www.jamstec.go.jp/e/medid/dias. Most of earth environmental data commonly have spatial and temporal attributes such as the covering geographic scope or the created date. The metadata standards including these common attributes are published by the geographic information technical committee (TC211) in ISO (the International Organization for Standardization) as specifications of ISO 19115:2003 and 19139:2007. Accordingly, DIAS metadata is developed with basing on ISO/TC211 metadata standards. From the viewpoint of data users, metadata is useful not only for data retrieval and analysis but also for interoperability and information sharing among experts, beginners and nonprofessionals. On the other hand, from the viewpoint of data providers, two problems were pointed out after discussions. One is that data providers prefer to minimize another tasks and spending time for creating metadata. Another is that data providers want to manage and publish documents to explain their data sets more comprehensively. Because of solving these problems, we have been developing a document centric metadata registration tool. The features of our tool are that the generated documents are available instantly and there is no extra cost for data providers to generate metadata. Also, this tool is developed as a Web application. So, this tool does not demand any software for data providers if they have a web-browser. The interface of the tool provides the section titles of the documents and by filling out the content of each section, the documents for the data sets are automatically published in PDF and HTML format. Furthermore, the metadata XML file which is compliant with ISO19115 and ISO19139 is created at the same moment. The generated metadata are managed in the metadata database of the DIAS project, and will be used in various ISO19139 compliant metadata management tools, such as GeoNetwork.

The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability.

PubMed

He, Yongqun; Xiang, Zuoshuang; Zheng, Jie; Lin, Yu; Overton, James A; Ong, Edison

2018-01-12

Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interoperability and the usage of interoperable ontologies for standardized data representation and integration. The suite of web-based Ontoanimal tools (e.g., Ontofox, Ontorat, and Ontobee) support different aspects of extensible ontology development. By summarizing the common features of Ontoanimal and other similar tools, we identified and proposed an "eXtensible Ontology Development" (XOD) strategy and its associated four principles. These XOD principles reuse existing terms and semantic relations from reliable ontologies, develop and apply well-established ontology design patterns (ODPs), and involve community efforts to support new ontology development, promoting standardized and interoperable data and knowledge representation and integration. The adoption of the XOD strategy, together with robust XOD tool development, will greatly support ontology interoperability and robust ontology applications to support data to be Findable, Accessible, Interoperable and Reusable (i.e., FAIR).