SMARTe: A FREE Web-Based Tool To Help Communities Overcome Revitalization Obstacles

EPA Science Inventory

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

The charged particle accelerators subsystems modeling

NASA Astrophysics Data System (ADS)

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

2017-01-01

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

The Virtual Learning Commons (VLC): Enabling Co-Innovation Across Disciplines

NASA Astrophysics Data System (ADS)

Pennington, D. D.; Gandara, A.; Del Rio, N.

2014-12-01

A key challenge for scientists addressing grand-challenge problems is identifying, understanding, and integrating potentially relevant methods, models and tools that that are rapidly evolving in the informatics community. Such tools are essential for effectively integrating data and models in complex research projects, yet it is often difficult to know what tools are available and it is not easy to understand or evaluate how they might be used in a given research context. The goal of the National Science Foundation-funded Virtual Learning Commons (VLC) is to improve awareness and understanding of emerging methodologies and technologies, facilitate individual and group evaluation of these, and trace the impact of innovations within and across teams, disciplines, and communities. The VLC is a Web-based social bookmarking site designed specifically to support knowledge exchange in research communities. It is founded on well-developed models of technology adoption, diffusion of innovation, and experiential learning. The VLC makes use of Web 2.0 (Social Web) and Web 3.0 (Semantic Web) approaches. Semantic Web approaches enable discovery of potentially relevant methods, models, and tools, while Social Web approaches enable collaborative learning about their function. The VLC is under development and the first release is expected Fall 2014.

The Internet as a research site: establishment of a web-based longitudinal study of the nursing and midwifery workforce in three countries.

PubMed

Huntington, Annette; Gilmour, Jean; Schluter, Philip; Tuckett, Anthony; Bogossian, Fiona; Turner, Catherine

2009-06-01

The aim of this paper is to describe the development of a web-based longitudinal research project, The Nurses and Midwives e-cohort Study. The Internet has only recently been used for health research. However, web-based methodologies are increasingly discussed as significant and inevitable developments in research as Internet access and use rapidly increases worldwide. In 2006, a longitudinal web-based study of nurses and midwives workforce participation patterns, health and wellbeing, and lifestyle choices was established. Participating countries are Australia, New Zealand and the United Kingdom. Data collection is handled through a dedicated website using a range of standardized tools combined into one comprehensive questionnaire. Internet-specific data collection and a range of recruitment and retention strategies have been developed for this study. Internet-based technology can support the maintenance of cohorts across multiple countries and jurisdictions to explore factors influencing workforce participation. However, barriers to widespread adoption of web-based approaches include website development costs, the need for fast broadband connection for large data collection instruments, and varying degrees of Internet and computer literacy in the nursing and midwifery workforce. Many of the issues reported in this paper are transitional in nature at a time of rapid technological development. The development of on-line methods and tools is a major and exciting development in the world of research. Research via the world-wide web can support international collaborations across borders and cultures.

Exploring JavaScript and ROOT technologies to create Web-based ATLAS analysis and monitoring tools

NASA Astrophysics Data System (ADS)

Sánchez Pineda, A.

2015-12-01

We explore the potential of current web applications to create online interfaces that allow the visualization, interaction and real cut-based physics analysis and monitoring of processes through a web browser. The project consists in the initial development of web- based and cloud computing services to allow students and researchers to perform fast and very useful cut-based analysis on a browser, reading and using real data and official Monte- Carlo simulations stored in ATLAS computing facilities. Several tools are considered: ROOT, JavaScript and HTML. Our study case is the current cut-based H → ZZ → llqq analysis of the ATLAS experiment. Preliminary but satisfactory results have been obtained online.

Webquest 2.0: An Instructional Model for Digital Learners

ERIC Educational Resources Information Center

Dell, Diana F. Abernathy

2012-01-01

Teaching and learning tools such as Moodle and Web 2.0 tools are appearing in K-12 classrooms; however, there is a lack of scholarly research to guide the implementation of these tools. The WebQuest model, a widely adopted inquiry-based model for online instruction, has instructional inadequacies and does not make the most of emerging…

Research Techniques Made Simple: Web-Based Survey Research in Dermatology: Conduct and Applications.

PubMed

Maymone, Mayra B C; Venkatesh, Samantha; Secemsky, Eric; Reddy, Kavitha; Vashi, Neelam A

2018-07-01

Web-based surveys, or e-surveys, are surveys designed and delivered using the internet. The use of these survey tools is becoming increasingly common in medical research. Their advantages are appealing to surveyors because they allow for rapid development and administration of surveys, fast data collection and analysis, low cost, and fewer errors due to manual data entry than telephone or mailed questionnaires. Internet surveys may be used in clinical and academic research settings with improved speed and efficacy of data collection compared with paper or verbal survey modalities. However, limitations such as potentially low response rates, demographic biases, and variations in computer literacy and internet access remain areas of concern. We aim to briefly describe some of the currently available Web-based survey tools, focusing on advantages and limitations to help guide their use and application in dermatologic research. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

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…

SMARTe: A FREE Web-Based Tool To Help Communities Overcome Revitalization Obstacles - Detroit, MI, May 6, 2008

EPA Science Inventory

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

Collaborative Writing among Second Language Learners in Academic Web-Based Projects

ERIC Educational Resources Information Center

Kessler, Greg; Bikowski, Dawn; Boggs, Jordan

2012-01-01

This study investigates Web-based, project oriented, many-to-many collaborative writing for academic purposes. Thirty-eight Fulbright scholars in an orientation program at a large Midwestern university used a Web-based word processing tool to collaboratively plan and report on a research project. The purpose of this study is to explore and…

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

Proposition and Organization of an Adaptive Learning Domain Based on Fusion from the Web

ERIC Educational Resources Information Center

Chaoui, Mohammed; Laskri, Mohamed Tayeb

2013-01-01

The Web allows self-navigated education through interaction with large amounts of Web resources. While enjoying the flexibility of Web tools, authors may suffer from research and filtering Web resources, when they face various resources formats and complex structures. An adaptation of extracted Web resources must be assured by authors, to give…

The use of advanced web-based survey design in Delphi research.

PubMed

Helms, Christopher; Gardner, Anne; McInnes, Elizabeth

2017-12-01

A discussion of the application of metadata, paradata and embedded data in web-based survey research, using two completed Delphi surveys as examples. Metadata, paradata and embedded data use in web-based Delphi surveys has not been described in the literature. The rapid evolution and widespread use of online survey methods imply that paper-based Delphi methods will likely become obsolete. Commercially available web-based survey tools offer a convenient and affordable means of conducting Delphi research. Researchers and ethics committees may be unaware of the benefits and risks of using metadata in web-based surveys. Discussion paper. Two web-based, three-round Delphi surveys were conducted sequentially between August 2014 - January 2015 and April - May 2016. Their aims were to validate the Australian nurse practitioner metaspecialties and their respective clinical practice standards. Our discussion paper is supported by researcher experience and data obtained from conducting both web-based Delphi surveys. Researchers and ethics committees should consider the benefits and risks of metadata use in web-based survey methods. Web-based Delphi research using paradata and embedded data may introduce efficiencies that improve individual participant survey experiences and reduce attrition across iterations. Use of embedded data allows the efficient conduct of multiple simultaneous Delphi surveys across a shorter timeframe than traditional survey methods. The use of metadata, paradata and embedded data appears to improve response rates, identify bias and give possible explanation for apparent outlier responses, providing an efficient method of conducting web-based Delphi surveys. © 2017 John Wiley & Sons Ltd.

Investigating Pedagogical Value of Wiki Technology

ERIC Educational Resources Information Center

Hazari, Sunil; North, Alexa; Moreland, Deborah

2009-01-01

This exploratory study investigates the potential of Wiki technology as a tool for teaching and learning. Wikis are a component of Web 2.0 technology tools that provide collaborative features and active learning opportunities in a web-based environment. This research study sought to empirically determine the pedagogical value of using Wiki…

Reliability, Compliance, and Security in Web-Based Course Assessments

ERIC Educational Resources Information Center

Bonham, Scott

2008-01-01

Pre- and postcourse assessment has become a very important tool for education research in physics and other areas. The web offers an attractive alternative to in-class paper administration, but concerns about web-based administration include reliability due to changes in medium, student compliance rates, and test security, both question leakage…

WebCN: A web-based computation tool for in situ-produced cosmogenic nuclides

NASA Astrophysics Data System (ADS)

Ma, Xiuzeng; Li, Yingkui; Bourgeois, Mike; Caffee, Marc; Elmore, David; Granger, Darryl; Muzikar, Paul; Smith, Preston

2007-06-01

Cosmogenic nuclide techniques are increasingly being utilized in geoscience research. For this it is critical to establish an effective, easily accessible and well defined tool for cosmogenic nuclide computations. We have been developing a web-based tool (WebCN) to calculate surface exposure ages and erosion rates based on the nuclide concentrations measured by the accelerator mass spectrometry. WebCN for 10Be and 26Al has been finished and published at http://www.physics.purdue.edu/primelab/for_users/rockage.html. WebCN for 36Cl is under construction. WebCN is designed as a three-tier client/server model and uses the open source PostgreSQL for the database management and PHP for the interface design and calculations. On the client side, an internet browser and Microsoft Access are used as application interfaces to access the system. Open Database Connectivity is used to link PostgreSQL and Microsoft Access. WebCN accounts for both spatial and temporal distributions of the cosmic ray flux to calculate the production rates of in situ-produced cosmogenic nuclides at the Earth's surface.

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.

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.

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

PubMed

Pretz, Jean E; Link, John A

2008-11-01

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

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/ .

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

NASA Astrophysics Data System (ADS)

Karno, Donna; Glassman, Michael

2013-12-01

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

Can Interactive Web-Based CAD Tools Improve the Learning of Engineering Drawing? A Case Study

ERIC Educational Resources Information Center

Pando Cerra, Pablo; Suárez González, Jesús M.; Busto Parra, Bernardo; Rodríguez Ortiz, Diana; Álvarez Peñín, Pedro I.

2014-01-01

Many current Web-based learning environments facilitate the theoretical teaching of a subject but this may not be sufficient for those disciplines that require a significant use of graphic mechanisms to resolve problems. This research study looks at the use of an environment that can help students learn engineering drawing with Web-based CAD…

The Promise of Technology to Confront Dilemmas in Teacher Education: The Use of WebQuests in Problem-Based Methods Courses

ERIC Educational Resources Information Center

Smith, Leigh K.; Draper, Roni Jo; Sabey, Brenda L.

2005-01-01

This qualitative study examined the use of WebQuests as a teaching tool in problem-based elementary methods courses. We explored the potential of WebQuests to address three dilemmas faced in teacher education: (a) modeling instruction that is based on current learning theory and research-based practices, (b) providing preservice teachers with…

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.

A web based tool for storing and visualising data generated within a smart home.

PubMed

McDonald, H A; Nugent, C D; Moore, G; Finlay, D D; Hallberg, J

2011-01-01

There is a growing need to re-assess the current approaches available to researchers for storing and managing heterogeneous data generated within a smart home environment. In our current work we have developed the homeML Application; a web based tool to support researchers engaged in the area of smart home research as they perform experiments. Within this paper the homeML Application is presented which includes the fundamental components of the homeML Repository and the homeML Toolkit. Results from a usability study conducted by 10 computer science researchers are presented; the initial results of which have been positive.

A new web-based modelling tool (Websim-MILQ) aimed at optimisation of thermal treatments in the dairy industry.

PubMed

Schutyser, M A I; Straatsma, J; Keijzer, P M; Verschueren, M; De Jong, P

2008-11-30

In the framework of a cooperative EU research project (MILQ-QC-TOOL) a web-based modelling tool (Websim-MILQ) was developed for optimisation of thermal treatments in the dairy industry. The web-based tool enables optimisation of thermal treatments with respect to product safety, quality and costs. It can be applied to existing products and processes but also to reduce time to market for new products. Important aspects of the tool are its user-friendliness and its specifications customised to the needs of small dairy companies. To challenge the web-based tool it was applied for optimisation of thermal treatments in 16 dairy companies producing yoghurt, fresh cream, chocolate milk and cheese. Optimisation with WebSim-MILQ resulted in concrete improvements with respect to risk of microbial contamination, cheese yield, fouling and production costs. In this paper we illustrate the use of WebSim-MILQ for optimisation of a cheese milk pasteurisation process where we could increase the cheese yield (1 extra cheese for each 100 produced cheeses from the same amount of milk) and reduced the risk of contamination of pasteurised cheese milk with thermoresistent streptococci from critical to negligible. In another case we demonstrate the advantage for changing from an indirect to a direct heating method for a UHT process resulting in 80% less fouling, while improving product quality and maintaining product safety.

The Faculty's Perception of Web-Based Instruction Application in Iran's Higher Education

ERIC Educational Resources Information Center

Gholami, Khalil; Sayadi, Yaser

2012-01-01

This paper addresses the faculty perception on web-based instruction in order to explain the nature of learning and instruction in this setting. Using a mixed method approach, the research studied a sample of 132 University Faculty (lecturers and professors) in University of Kurdistan. The research tools were interview and questionnaire. The…

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

The potential of the internet.

PubMed

Coleman, Jamie J; McDowell, Sarah E

2012-06-01

The internet and the World Wide Web have changed the ways that we function. As technologies grow and adapt, there is a huge potential for the internet to affect drug research and development, as well as many other aspects of clinical pharmacology. We review some of the areas of interest to date and discuss some of the potential areas in which internet-based technology can be exploited. Information retrieval from the web by health-care professionals is common, and bringing evidence-based medicine to the bedside affects the care of patients. As a primary research tool the web can provide a vast array of information in generating new ideas or exploring previous research findings. This has facilitated systematic reviewing, for example. The content of the web has become a subject of research in its own right. The web is also widely used as a research facilitator, including enhancement of communication between collaborators, provision of online research tools (such as questionnaires, management of large scale multicentre trials, registration of clinical trials) and distribution of information. Problems include information overload, ignorance of early data that are not indexed in databases, difficulties in keeping web sites up to date and assessing the validity of information retrieved. Some web-based activities are viewed with suspicion, including analysis by pharmaceutical companies of drug information to facilitate direct-to-consumer advertising of novel pharmaceuticals. Use of these technologies will continue to expand in often unexpected ways. Clinical pharmacologists must embrace internet technology and include it as a key priority in their research agenda. © 2012 The Authors. British Journal of Clinical Pharmacology © 2012 The British Pharmacological Society.

MyGeoHub: A Collaborative Geospatial Research and Education Platform

NASA Astrophysics Data System (ADS)

Kalyanam, R.; Zhao, L.; Biehl, L. L.; Song, C. X.; Merwade, V.; Villoria, N.

2017-12-01

Scientific research is increasingly collaborative and globally distributed; research groups now rely on web-based scientific tools and data management systems to simplify their day-to-day collaborative workflows. However, such tools often lack seamless interfaces, requiring researchers to contend with manual data transfers, annotation and sharing. MyGeoHub is a web platform that supports out-of-the-box, seamless workflows involving data ingestion, metadata extraction, analysis, sharing and publication. MyGeoHub is built on the HUBzero cyberinfrastructure platform and adds general-purpose software building blocks (GABBs), for geospatial data management, visualization and analysis. A data management building block iData, processes geospatial files, extracting metadata for keyword and map-based search while enabling quick previews. iData is pervasive, allowing access through a web interface, scientific tools on MyGeoHub or even mobile field devices via a data service API. GABBs includes a Python map library as well as map widgets that in a few lines of code, generate complete geospatial visualization web interfaces for scientific tools. GABBs also includes powerful tools that can be used with no programming effort. The GeoBuilder tool provides an intuitive wizard for importing multi-variable, geo-located time series data (typical of sensor readings, GPS trackers) to build visualizations supporting data filtering and plotting. MyGeoHub has been used in tutorials at scientific conferences and educational activities for K-12 students. MyGeoHub is also constantly evolving; the recent addition of Jupyter and R Shiny notebook environments enable reproducible, richly interactive geospatial analyses and applications ranging from simple pre-processing to published tools. MyGeoHub is not a monolithic geospatial science gateway, instead it supports diverse needs ranging from just a feature-rich data management system, to complex scientific tools and workflows.

Web-Based Virtual Laboratory for Food Analysis Course

NASA Astrophysics Data System (ADS)

Handayani, M. N.; Khoerunnisa, I.; Sugiarti, Y.

2018-02-01

Implementation of learning on food analysis course in Program Study of Agro-industrial Technology Education faced problems. These problems include the availability of space and tools in the laboratory that is not comparable with the number of students also lack of interactive learning tools. On the other hand, the information technology literacy of students is quite high as well the internet network is quite easily accessible on campus. This is a challenge as well as opportunities in the development of learning media that can help optimize learning in the laboratory. This study aims to develop web-based virtual laboratory as one of the alternative learning media in food analysis course. This research is R & D (research and development) which refers to Borg & Gall model. The results showed that assessment’s expert of web-based virtual labs developed, in terms of software engineering aspects; visual communication; material relevance; usefulness and language used, is feasible as learning media. The results of the scaled test and wide-scale test show that students strongly agree with the development of web based virtual laboratory. The response of student to this virtual laboratory was positive. Suggestions from students provided further opportunities for improvement web based virtual laboratory and should be considered for further research.

Web Apollo: a web-based genomic annotation editing platform.

PubMed

Lee, Eduardo; Helt, Gregg A; Reese, Justin T; Munoz-Torres, Monica C; Childers, Chris P; Buels, Robert M; Stein, Lincoln; Holmes, Ian H; Elsik, Christine G; Lewis, Suzanna E

2013-08-30

Web Apollo is the first instantaneous, collaborative genomic annotation editor available on the web. One of the natural consequences following from current advances in sequencing technology is that there are more and more researchers sequencing new genomes. These researchers require tools to describe the functional features of their newly sequenced genomes. With Web Apollo researchers can use any of the common browsers (for example, Chrome or Firefox) to jointly analyze and precisely describe the features of a genome in real time, whether they are in the same room or working from opposite sides of the world.

Web Apollo: a web-based genomic annotation editing platform

PubMed Central

2013-01-01

Web Apollo is the first instantaneous, collaborative genomic annotation editor available on the web. One of the natural consequences following from current advances in sequencing technology is that there are more and more researchers sequencing new genomes. These researchers require tools to describe the functional features of their newly sequenced genomes. With Web Apollo researchers can use any of the common browsers (for example, Chrome or Firefox) to jointly analyze and precisely describe the features of a genome in real time, whether they are in the same room or working from opposite sides of the world. PMID:24000942

Towards a collaborative, global infrastructure for biodiversity assessment

PubMed Central

Guralnick, Robert P; Hill, Andrew W; Lane, Meredith

2007-01-01

Biodiversity data are rapidly becoming available over the Internet in common formats that promote sharing and exchange. Currently, these data are somewhat problematic, primarily with regard to geographic and taxonomic accuracy, for use in ecological research, natural resources management and conservation decision-making. However, web-based georeferencing tools that utilize best practices and gazetteer databases can be employed to improve geographic data. Taxonomic data quality can be improved through web-enabled valid taxon names databases and services, as well as more efficient mechanisms to return systematic research results and taxonomic misidentification rates back to the biodiversity community. Both of these are under construction. A separate but related challenge will be developing web-based visualization and analysis tools for tracking biodiversity change. Our aim was to discuss how such tools, combined with data of enhanced quality, will help transform today's portals to raw biodiversity data into nexuses of collaborative creation and sharing of biodiversity knowledge. PMID:17594421

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

USGS Publications Warehouse

Signell, Richard; Camossi, E.

2016-01-01

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

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

NASA Astrophysics Data System (ADS)

Signell, Richard P.; Camossi, Elena

2016-05-01

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

Use of Web-Based Portfolios as Tools for Reflection in Preservice Teacher Education

ERIC Educational Resources Information Center

Oner, Diler; Adadan, Emine

2011-01-01

This mixed-methods study examined the use of web-based portfolios for developing preservice teachers' reflective skills. Building on the work of previous research, the authors proposed a set of reflection-based tasks to enrich preservice teachers' internship experiences. Their purpose was to identify (a) whether preservice teachers demonstrated…

Developing the online survey.

PubMed

Gordon, Jeffry S; McNew, Ryan

2008-12-01

Institutions of higher education are now using Internet-based technology tools to conduct surveys for data collection. Research shows that the type and quality of responses one receives with online surveys are comparable with what one receives in paper-based surveys. Data collection can take place on Web-based surveys, e-mail-based surveys, and personal digital assistants/Smartphone devices. Web surveys can be subscription templates, software packages installed on one's own server, or created from scratch using Web programming development tools. All of these approaches have their advantages and disadvantages. The survey owner must make informed decisions as to the right technology to implement. The correct choice can save hours of work in sorting, organizing, and analyzing data.

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…

NaviCell Web Service for network-based data visualization.

PubMed

Bonnet, Eric; Viara, Eric; Kuperstein, Inna; Calzone, Laurence; Cohen, David P A; Barillot, Emmanuel; Zinovyev, Andrei

2015-07-01

Data visualization is an essential element of biological research, required for obtaining insights and formulating new hypotheses on mechanisms of health and disease. NaviCell Web Service is a tool for network-based visualization of 'omics' data which implements several data visual representation methods and utilities for combining them together. NaviCell Web Service uses Google Maps and semantic zooming to browse large biological network maps, represented in various formats, together with different types of the molecular data mapped on top of them. For achieving this, the tool provides standard heatmaps, barplots and glyphs as well as the novel map staining technique for grasping large-scale trends in numerical values (such as whole transcriptome) projected onto a pathway map. The web service provides a server mode, which allows automating visualization tasks and retrieving data from maps via RESTful (standard HTTP) calls. Bindings to different programming languages are provided (Python and R). We illustrate the purpose of the tool with several case studies using pathway maps created by different research groups, in which data visualization provides new insights into molecular mechanisms involved in systemic diseases such as cancer and neurodegenerative diseases. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Web-Based Learning and Instruction Support System for Pneumatics

ERIC Educational Resources Information Center

Yen, Chiaming; Li, Wu-Jeng

2003-01-01

This research presents a Web-based learning and instructional system for Pneumatics. The system includes course material, remote data acquisition modules, and a pneumatic laboratory set. The course material is in the HTML format accompanied with text, still and animated images, simulation programs, and computer aided design tools. The data…

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…

Teaching Web 2.0 technologies using Web 2.0 technologies.

PubMed

Rethlefsen, Melissa L; Piorun, Mary; Prince, J Dale

2009-10-01

The research evaluated participant satisfaction with the content and format of the "Web 2.0 101: Introduction to Second Generation Web Tools" course and measured the impact of the course on participants' self-evaluated knowledge of Web 2.0 tools. The "Web 2.0 101" online course was based loosely on the Learning 2.0 model. Content was provided through a course blog and covered a wide range of Web 2.0 tools. All Medical Library Association members were invited to participate. Participants were asked to complete a post-course survey. Respondents who completed the entire course or who completed part of the course self-evaluated their knowledge of nine social software tools and concepts prior to and after the course using a Likert scale. Additional qualitative information about course strengths and weaknesses was also gathered. Respondents' self-ratings showed a significant change in perceived knowledge for each tool, using a matched pair Wilcoxon signed rank analysis (P<0.0001 for each tool/concept). Overall satisfaction with the course appeared high. Hands-on exercises were the most frequently identified strength of the course; the length and time-consuming nature of the course were considered weaknesses by some. Learning 2.0-style courses, though demanding time and self-motivation from participants, can increase knowledge of Web 2.0 tools.

Tools and Strategies for Engaging the Supervisor in Technology-Supported Work-Based Learning, Evaluation Research

ERIC Educational Resources Information Center

Bianco, Manuela; Collis, Betty

2004-01-01

This study reports the results of the formative evaluations of two computer-supported tools and the associated strategies for their use. Tools and strategies embedded in web-based courses can increase a supervisor's involvement in helping employees transfer learning onto the workplace. Issues relating to characteristics of the tools and strategies…

Pain Research Forum: application of scientific social media frameworks in neuroscience.

PubMed

Das, Sudeshna; McCaffrey, Patricia G; Talkington, Megan W T; Andrews, Neil A; Corlosquet, Stéphane; Ivinson, Adrian J; Clark, Tim

2014-01-01

Social media has the potential to accelerate the pace of biomedical research through online collaboration, discussions, and faster sharing of information. Focused web-based scientific social collaboratories such as the Alzheimer Research Forum have been successful in engaging scientists in open discussions of the latest research and identifying gaps in knowledge. However, until recently, tools to rapidly create such communities and provide high-bandwidth information exchange between collaboratories in related fields did not exist. We have addressed this need by constructing a reusable framework to build online biomedical communities, based on Drupal, an open-source content management system. The framework incorporates elements of Semantic Web technology combined with social media. Here we present, as an exemplar of a web community built on our framework, the Pain Research Forum (PRF) (http://painresearchforum.org). PRF is a community of chronic pain researchers, established with the goal of fostering collaboration and communication among pain researchers. Launched in 2011, PRF has over 1300 registered members with permission to submit content. It currently hosts over 150 topical news articles on research; more than 30 active or archived forum discussions and journal club features; a webinar series; an editor-curated weekly updated listing of relevant papers; and several other resources for the pain research community. All content is licensed for reuse under a Creative Commons license; the software is freely available. The framework was reused to develop other sites, notably the Multiple Sclerosis Discovery Forum (http://msdiscovery.org) and StemBook (http://stembook.org). Web-based collaboratories are a crucial integrative tool supporting rapid information transmission and translation in several important research areas. In this article, we discuss the success factors, lessons learned, and ongoing challenges in using PRF as a driving force to develop tools for online collaboration in neuroscience. We also indicate ways these tools can be applied to other areas and uses.

Pain Research Forum: application of scientific social media frameworks in neuroscience

PubMed Central

Das, Sudeshna; McCaffrey, Patricia G.; Talkington, Megan W. T.; Andrews, Neil A.; Corlosquet, Stéphane; Ivinson, Adrian J.; Clark, Tim

2014-01-01

Background: Social media has the potential to accelerate the pace of biomedical research through online collaboration, discussions, and faster sharing of information. Focused web-based scientific social collaboratories such as the Alzheimer Research Forum have been successful in engaging scientists in open discussions of the latest research and identifying gaps in knowledge. However, until recently, tools to rapidly create such communities and provide high-bandwidth information exchange between collaboratories in related fields did not exist. Methods: We have addressed this need by constructing a reusable framework to build online biomedical communities, based on Drupal, an open-source content management system. The framework incorporates elements of Semantic Web technology combined with social media. Here we present, as an exemplar of a web community built on our framework, the Pain Research Forum (PRF) (http://painresearchforum.org). PRF is a community of chronic pain researchers, established with the goal of fostering collaboration and communication among pain researchers. Results: Launched in 2011, PRF has over 1300 registered members with permission to submit content. It currently hosts over 150 topical news articles on research; more than 30 active or archived forum discussions and journal club features; a webinar series; an editor-curated weekly updated listing of relevant papers; and several other resources for the pain research community. All content is licensed for reuse under a Creative Commons license; the software is freely available. The framework was reused to develop other sites, notably the Multiple Sclerosis Discovery Forum (http://msdiscovery.org) and StemBook (http://stembook.org). Discussion: Web-based collaboratories are a crucial integrative tool supporting rapid information transmission and translation in several important research areas. In this article, we discuss the success factors, lessons learned, and ongoing challenges in using PRF as a driving force to develop tools for online collaboration in neuroscience. We also indicate ways these tools can be applied to other areas and uses. PMID:24653693

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

Study on Web-Based Tool for Regional Agriculture Industry Structure Optimization Using Ajax

NASA Astrophysics Data System (ADS)

Huang, Xiaodong; Zhu, Yeping

According to the research status of regional agriculture industry structure adjustment information system and the current development of information technology, this paper takes web-based regional agriculture industry structure optimization tool as research target. This paper introduces Ajax technology and related application frameworks to build an auxiliary toolkit of decision support system for agricultural policy maker and economy researcher. The toolkit includes a “one page” style component of regional agriculture industry structure optimization which provides agile arguments setting method that enables applying sensitivity analysis and usage of data and comparative advantage analysis result, and a component that can solve the linear programming model and its dual problem by simplex method.

STATWIZ - AN ELECTRONIC STATISTICAL TOOL (ABSTRACT)

EPA Science Inventory

StatWiz is a web-based, interactive, and dynamic statistical tool for researchers. It will allow researchers to input information and/or data and then receive experimental design options, or outputs from data analysis. StatWiz is envisioned as an expert system that will walk rese...

A web-based tree crown condition training and evaluation tool for urban and community forestry

Treesearch

Matthew F. Winn; Neil A. Clark; Philip A. Araman; Sang-Mook Lee

2007-01-01

Training personnel for natural resource related field work can be a costly and time-consuming process. For that reason, web-based training is considered by many to be a more attractive alternative to on-site training. The U.S. Forest Service Southern Research Station unit with Virginia Tech cooperators in Blacksburg, Va., are in the process of constructing a web site...

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 .

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.

OptoBase: A web platform for molecular optogenetics.

PubMed

Kolar, Katja; Knobloch, Christian; Stork, Hendrik; Žnidarič, Matej; Weber, Wilfried

2018-06-18

OptoBase is an online platform for molecular optogenetics. At its core is a hand-annotated and ontology-supported database that aims to cover all existing optogenetic switches and publications, which is further complemented with a collection of convenient optogenetics-related web tools. OptoBase is meant for both expert optogeneticists, to easily keep track of the field, as well as for all researchers who find optogenetics inviting as a powerful tool to address their biological questions of interest. It is available at https://www.optobase.org. This work also presents OptoBase-based analysis of the trends in molecular optogenetics.

Implementing Digital Tools to Support Student Questioning Abilities: A Collaborative Action Research Report

ERIC Educational Resources Information Center

Cadieux Bolden, Danielle; Hurt, June W.; Richardson, Mary Kathleen

2017-01-01

This collaborative action research project was conducted in a second-grade classroom to determine the impact that digital web-based tools would have in helping a school media coordinator scaffold her students' understanding of productive versus nonproductive questions. The digital tools Kahoot, Quizizz, and Socrative were used by the students to…

Conducting Guided Inquiry in Science Classes Using Authentic, Archived, Web-Based Data

ERIC Educational Resources Information Center

Ucar, Sedat; Trundle, Kathy Cabe

2011-01-01

Students are often unable to collect the real-time data necessary for conducting inquiry in science classrooms. Web-based, real-time data could, therefore, offer a promising tool for conducting scientific inquiries within classroom environments. This study used a quasi-experimental research design to investigate the effects of inquiry-based…

Monitoring Global Crop Condition Indicators Using a Web-Based Visualization Tool

Treesearch

Bob Tetrault; Bob Baldwin

2006-01-01

Global crop condition information for major agricultural regions in the world can be monitored using the web-based application called Crop Explorer. With this application, U.S. and international producers, traders, researchers, and the public can access remote sensing information used by agricultural economists and scientists who predict crop production worldwide. For...

Collaborative Learning and Knowledge-Construction through a Knowledge-Based WWW Authoring Tool.

ERIC Educational Resources Information Center

Haugsjaa, Erik

This paper outlines hurdles to using the World Wide Web for learning, specifically in a collaborative knowledge-construction environment. Theoretical solutions based directly on existing Web environments, as well as on research and system prototypes in the areas of Intelligent Tutoring Systems (ITS) and ITS authoring systems, are suggested. Topics…

Molecular beacon sequence design algorithm.

PubMed

Monroe, W Todd; Haselton, Frederick R

2003-01-01

A method based on Web-based tools is presented to design optimally functioning molecular beacons. Molecular beacons, fluorogenic hybridization probes, are a powerful tool for the rapid and specific detection of a particular nucleic acid sequence. However, their synthesis costs can be considerable. Since molecular beacon performance is based on its sequence, it is imperative to rationally design an optimal sequence before synthesis. The algorithm presented here uses simple Microsoft Excel formulas and macros to rank candidate sequences. This analysis is carried out using mfold structural predictions along with other free Web-based tools. For smaller laboratories where molecular beacons are not the focus of research, the public domain algorithm described here may be usefully employed to aid in molecular beacon design.

An Integrative Model of "Information Visibility" and "Information Seeking" on the Web

ERIC Educational Resources Information Center

Mansourian, Yazdan; Ford, Nigel; Webber, Sheila; Madden, Andrew

2008-01-01

Purpose: This paper aims to encapsulate the main procedure and key findings of a qualitative research on end-users' interactions with web-based search tools in order to demonstrate how the concept of "information visibility" emerged and how an integrative model of information visibility and information seeking on the web was constructed.…

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

Web-based analysis and publication of flow cytometry experiments.

PubMed

Kotecha, Nikesh; Krutzik, Peter O; Irish, Jonathan M

2010-07-01

Cytobank is a Web-based application for storage, analysis, and sharing of flow cytometry experiments. Researchers use a Web browser to log in and use a wide range of tools developed for basic and advanced flow cytometry. In addition to providing access to standard cytometry tools from any computer, Cytobank creates a platform and community for developing new analysis and publication tools. Figure layouts created on Cytobank are designed to allow transparent access to the underlying experiment annotation and data processing steps. Since all flow cytometry files and analysis data are stored on a central server, experiments and figures can be viewed or edited by anyone with the proper permission, from any computer with Internet access. Once a primary researcher has performed the initial analysis of the data, collaborators can engage in experiment analysis and make their own figure layouts using the gated, compensated experiment files. Cytobank is available to the scientific community at http://www.cytobank.org. (c) 2010 by John Wiley & Sons, Inc.

Web-Based Analysis and Publication of Flow Cytometry Experiments

PubMed Central

Kotecha, Nikesh; Krutzik, Peter O.; Irish, Jonathan M.

2014-01-01

Cytobank is a web-based application for storage, analysis, and sharing of flow cytometry experiments. Researchers use a web browser to log in and use a wide range of tools developed for basic and advanced flow cytometry. In addition to providing access to standard cytometry tools from any computer, Cytobank creates a platform and community for developing new analysis and publication tools. Figure layouts created on Cytobank are designed to allow transparent access to the underlying experiment annotation and data processing steps. Since all flow cytometry files and analysis data are stored on a central server, experiments and figures can be viewed or edited by anyone with the proper permissions from any computer with Internet access. Once a primary researcher has performed the initial analysis of the data, collaborators can engage in experiment analysis and make their own figure layouts using the gated, compensated experiment files. Cytobank is available to the scientific community at www.cytobank.org PMID:20578106

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.

Web 2.0 in Computer-Assisted Language Learning: A Research Synthesis and Implications for Instructional Design and Educational Practice

ERIC Educational Resources Information Center

Parmaxi, Antigoni; Zaphiris, Panayiotis

2017-01-01

This study explores the research development pertaining to the use of Web 2.0 technologies in the field of Computer-Assisted Language Learning (CALL). Published research manuscripts related to the use of Web 2.0 tools in CALL have been explored, and the following research foci have been determined: (1) Web 2.0 tools that dominate second/foreign…

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.

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.)…

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

Allen Brain Atlas-Driven Visualizations: a web-based gene expression energy visualization tool.

PubMed

Zaldivar, Andrew; Krichmar, Jeffrey L

2014-01-01

The Allen Brain Atlas-Driven Visualizations (ABADV) is a publicly accessible web-based tool created to retrieve and visualize expression energy data from the Allen Brain Atlas (ABA) across multiple genes and brain structures. Though the ABA offers their own search engine and software for researchers to view their growing collection of online public data sets, including extensive gene expression and neuroanatomical data from human and mouse brain, many of their tools limit the amount of genes and brain structures researchers can view at once. To complement their work, ABADV generates multiple pie charts, bar charts and heat maps of expression energy values for any given set of genes and brain structures. Such a suite of free and easy-to-understand visualizations allows for easy comparison of gene expression across multiple brain areas. In addition, each visualization links back to the ABA so researchers may view a summary of the experimental detail. ABADV is currently supported on modern web browsers and is compatible with expression energy data from the Allen Mouse Brain Atlas in situ hybridization data. By creating this web application, researchers can immediately obtain and survey numerous amounts of expression energy data from the ABA, which they can then use to supplement their work or perform meta-analysis. In the future, we hope to enable ABADV across multiple data resources.

Making Your Tools Useful to a Broader Audience

NASA Astrophysics Data System (ADS)

Lyness, M. D.; Broten, M. J.

2006-12-01

With the increasing growth of Web Services and SOAP the ability to connect and reuse computational and also visualization tools from all over the world via Web Interfaces that can be easily displayed in any current browser has provided the means to construct an ideal online research environment. The age-old question of usability is a major determining factor whether a particular tool would find great success in its community. An interface that can be understood purely by a user's intuition is desirable and more closely obtainable than ever before. Through the use of increasingly sophisticated web-oriented technologies including JavaScript, AJAX, and the DOM, web interfaces are able to harness the advantages of the Internet along with the functional capabilities of native applications such as menus, partial page changes, background processing, and visual effects to name a few. Also, with computers becoming a normal part of the educational process companies, such as Google and Microsoft, give us a synthetic intuition as a foundation for new designs. Understanding the way earth science researchers know how to use computers will allow the VLab portal (http://vlab.msi.umn.edu) and other projects to create interfaces that will get used. To provide detailed communication with the users of VLab's computational tools, projects like the Porky Portlet (http://www.gorerle.com/vlab-wiki/index.php?title=Porky_Portlet) spawned to empower users with a fully- detailed, interactive visual representation of progressing workflows. With the well-thought design of such tools and interfaces, researchers around the world will become accustomed to new highly engaging, visual web- based research environments.

Gamifying Learning Experiences: Practical Implications and Outcomes

ERIC Educational Resources Information Center

Dominguez, Adrian; Saenz-de-Navarrete, Joseba; de-Marcos, Luis; Fernandez-Sanz, Luis; Pages, Carmen; Martinez-Herraiz, Jose-Javier

2013-01-01

Gamification is the use of game design elements and game mechanics in non-game contexts. This idea has been used successfully in many web based businesses to increase user engagement. Some researchers suggest that it could also be used in web based education as a tool to increase student motivation and engagement. In an attempt to verify those…

Examining the Role of Web 2.0 Tools in Supporting Problem Solving during Case-Based Instruction

ERIC Educational Resources Information Center

Koehler, Adrie A.; Newby, Timothy J.; Ertmer, Peggy A.

2017-01-01

As learners solve complex problems, such as the ones present in case narratives, they need instructional support. Potentially, Web 2.0 applications can be useful to learners during case-based instruction (CBI), as their affordances offer creative and collaborative opportunities. However, there is limited research available on how the affordances…

A decade of Web Server updates at the Bioinformatics Links Directory: 2003-2012.

PubMed

Brazas, Michelle D; Yim, David; Yeung, Winston; Ouellette, B F Francis

2012-07-01

The 2012 Bioinformatics Links Directory update marks the 10th special Web Server issue from Nucleic Acids Research. Beginning with content from their 2003 publication, the Bioinformatics Links Directory in collaboration with Nucleic Acids Research has compiled and published a comprehensive list of freely accessible, online tools, databases and resource materials for the bioinformatics and life science research communities. The past decade has exhibited significant growth and change in the types of tools, databases and resources being put forth, reflecting both technology changes and the nature of research over that time. With the addition of 90 web server tools and 12 updates from the July 2012 Web Server issue of Nucleic Acids Research, the Bioinformatics Links Directory at http://bioinformatics.ca/links_directory/ now contains an impressive 134 resources, 455 databases and 1205 web server tools, mirroring the continued activity and efforts of our field.

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.

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.

Redesigning Instruction through Web-based Course Authoring Tools.

ERIC Educational Resources Information Center

Dabbagh, Nada H.; Schmitt, Jeff

1998-01-01

Examines the pedagogical implications of redesigning instruction for Web-based delivery through a case study of an undergraduate computer science course. Initially designed for a traditional learning environment, this course transformed to a Web-based course using WebCT, a Web-based course authoring tool. Discusses the specific features of WebCT.…

msBiodat analysis tool, big data analysis for high-throughput experiments.

PubMed

Muñoz-Torres, Pau M; Rokć, Filip; Belužic, Robert; Grbeša, Ivana; Vugrek, Oliver

2016-01-01

Mass spectrometry (MS) are a group of a high-throughput techniques used to increase knowledge about biomolecules. They produce a large amount of data which is presented as a list of hundreds or thousands of proteins. Filtering those data efficiently is the first step for extracting biologically relevant information. The filtering may increase interest by merging previous data with the data obtained from public databases, resulting in an accurate list of proteins which meet the predetermined conditions. In this article we present msBiodat Analysis Tool, a web-based application thought to approach proteomics to the big data analysis. With this tool, researchers can easily select the most relevant information from their MS experiments using an easy-to-use web interface. An interesting feature of msBiodat analysis tool is the possibility of selecting proteins by its annotation on Gene Ontology using its Gene Id, ensembl or UniProt codes. The msBiodat analysis tool is a web-based application that allows researchers with any programming experience to deal with efficient database querying advantages. Its versatility and user-friendly interface makes easy to perform fast and accurate data screening by using complex queries. Once the analysis is finished, the result is delivered by e-mail. msBiodat analysis tool is freely available at http://msbiodata.irb.hr.

Competency-Based Assessment for Clinical Supervisors: Design-Based Research on a Web-Delivered Program

PubMed Central

Williams, Lauren Therese; Grealish, Laurie; Jamieson, Maggie

2015-01-01

Background Clinicians need to be supported by universities to use credible and defensible assessment practices during student placements. Web-based delivery of clinical education in student assessment offers professional development regardless of the geographical location of placement sites. Objective This paper explores the potential for a video-based constructivist Web-based program to support site supervisors in their assessments of student dietitians during clinical placements. Methods This project was undertaken as design-based research in two stages. Stage 1 describes the research consultation, development of the prototype, and formative feedback. In Stage 2, the program was pilot-tested and evaluated by a purposeful sample of nine clinical supervisors. Data generated as a result of user participation during the pilot test is reported. Users’ experiences with the program were also explored via interviews (six in a focus group and three individually). The interviews were transcribed verbatim and thematic analysis conducted from a pedagogical perspective using van Manen’s highlighting approach. Results This research succeeded in developing a Web-based program, “Feed our Future”, that increased supervisors’ confidence with their competency-based assessments of students on clinical placements. Three pedagogical themes emerged: constructivist design supports transformative Web-based learning; videos make abstract concepts tangible; and accessibility, usability, and pedagogy are interdependent. Conclusions Web-based programs, such as Feed our Future, offer a viable means for universities to support clinical supervisors in their assessment practices during clinical placements. A design-based research approach offers a practical process for such Web-based tool development, highlighting pedagogical barriers for planning purposes. PMID:25803172

Survey Says? A Primer on Web-based Survey Design and Distribution

PubMed Central

Oppenheimer, Adam J.; Pannucci, Christopher J.; Kasten, Steven J.; Haase, Steven C.

2011-01-01

The internet has changed the way in which we gather and interpret information. While books were once the exclusive bearers of data, knowledge is now only a keystroke away. The internet has also facilitated the synthesis of new knowledge. Specifically, it has become a tool through which medical research is conducted. A review of the literature reveals that in the past year, over one-hundred medical publications have been based on web-based survey data alone. Due to emerging internet technologies, web-based surveys can now be launched with little computer knowledge. They may also be self-administered, eliminating personnel requirements. Ultimately, an investigator may build, implement, and analyze survey results with speed and efficiency, obviating the need for mass mailings and data processing. All of these qualities have rendered telephone and mail-based surveys virtually obsolete. Despite these capabilities, web-based survey techniques are not without their limitations, namely recall and response biases. When used properly, however, web-based surveys can greatly simplify the research process. This article discusses the implications of web-based surveys and provides guidelines for their effective design and distribution. PMID:21701347

NaviCell Web Service for network-based data visualization

PubMed Central

Bonnet, Eric; Viara, Eric; Kuperstein, Inna; Calzone, Laurence; Cohen, David P. A.; Barillot, Emmanuel; Zinovyev, Andrei

2015-01-01

Data visualization is an essential element of biological research, required for obtaining insights and formulating new hypotheses on mechanisms of health and disease. NaviCell Web Service is a tool for network-based visualization of ‘omics’ data which implements several data visual representation methods and utilities for combining them together. NaviCell Web Service uses Google Maps and semantic zooming to browse large biological network maps, represented in various formats, together with different types of the molecular data mapped on top of them. For achieving this, the tool provides standard heatmaps, barplots and glyphs as well as the novel map staining technique for grasping large-scale trends in numerical values (such as whole transcriptome) projected onto a pathway map. The web service provides a server mode, which allows automating visualization tasks and retrieving data from maps via RESTful (standard HTTP) calls. Bindings to different programming languages are provided (Python and R). We illustrate the purpose of the tool with several case studies using pathway maps created by different research groups, in which data visualization provides new insights into molecular mechanisms involved in systemic diseases such as cancer and neurodegenerative diseases. PMID:25958393

SMARTE: IMPROVING REVITALIZATION DECISIONS - OCTOBER 3, 2006

EPA Science Inventory

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

Web-based hydrodynamics computing

NASA Astrophysics Data System (ADS)

Shimoide, Alan; Lin, Luping; Hong, Tracie-Lynne; Yoon, Ilmi; Aragon, Sergio R.

2005-01-01

Proteins are long chains of amino acids that have a definite 3-d conformation and the shape of each protein is vital to its function. Since proteins are normally in solution, hydrodynamics (describes the movement of solvent around a protein as a function of shape and size of the molecule) can be used to probe the size and shape of proteins compared to those derived from X-ray crystallography. The computation chain needed for these hydrodynamics calculations consists of several separate programs by different authors on various platforms and often requires 3D visualizations of intermediate results. Due to the complexity, tools developed by a particular research group are not readily available for use by other groups, nor even by the non-experts within the same research group. To alleviate this situation, and to foment the easy and wide distribution of computational tools worldwide, we developed a web based interactive computational environment (WICE) including interactive 3D visualization that can be used with any web browser. Java based technologies were used to provide a platform neutral, user-friendly solution. Java Server Pages (JSP), Java Servlets, Java Beans, JOGL (Java bindings for OpenGL), and Java Web Start were used to create a solution that simplifies the computing chain for the user allowing the user to focus on their scientific research. WICE hides complexity from the user and provides robust and sophisticated visualization through a web browser.

Web-based hydrodynamics computing

NASA Astrophysics Data System (ADS)

Shimoide, Alan; Lin, Luping; Hong, Tracie-Lynne; Yoon, Ilmi; Aragon, Sergio R.

2004-12-01

Proteins are long chains of amino acids that have a definite 3-d conformation and the shape of each protein is vital to its function. Since proteins are normally in solution, hydrodynamics (describes the movement of solvent around a protein as a function of shape and size of the molecule) can be used to probe the size and shape of proteins compared to those derived from X-ray crystallography. The computation chain needed for these hydrodynamics calculations consists of several separate programs by different authors on various platforms and often requires 3D visualizations of intermediate results. Due to the complexity, tools developed by a particular research group are not readily available for use by other groups, nor even by the non-experts within the same research group. To alleviate this situation, and to foment the easy and wide distribution of computational tools worldwide, we developed a web based interactive computational environment (WICE) including interactive 3D visualization that can be used with any web browser. Java based technologies were used to provide a platform neutral, user-friendly solution. Java Server Pages (JSP), Java Servlets, Java Beans, JOGL (Java bindings for OpenGL), and Java Web Start were used to create a solution that simplifies the computing chain for the user allowing the user to focus on their scientific research. WICE hides complexity from the user and provides robust and sophisticated visualization through a web browser.

Web-Based Lecture Technologies: Blurring the Boundaries between Face-to-Face and Distance Learning

ERIC Educational Resources Information Center

Woo, Karen; Gosper, Maree; McNeill, Margot; Preston, Greg; Green, David; Phillips, Rob

2008-01-01

Web-based lecture technologies (WBLT) have gained popularity amongst universities in Australia as a tool for delivering lecture recordings to students in close to real time. This paper reports on a selection of results from a larger research project investigating the impact of WBLT on teaching and learning. Results show that while staff see the…

Developing the E-Delphi System: A Web-Based Forecasting Tool for Educational Research.

ERIC Educational Resources Information Center

Chou, Chien

2002-01-01

Discusses use of the Delphi technique and describes the development of an electronic version, called e-Delphi, in which questionnaire construction and communication with panel members was accomplished using the Web. Explains system function and interface and discusses evaluation of the e-Delphi system. (Author/LRW)

Integration of Geographical Information Systems and Geophysical Applications with Distributed Computing Technologies.

NASA Astrophysics Data System (ADS)

Pierce, M. E.; Aktas, M. S.; Aydin, G.; Fox, G. C.; Gadgil, H.; Sayar, A.

2005-12-01

We examine the application of Web Service Architectures and Grid-based distributed computing technologies to geophysics and geo-informatics. We are particularly interested in the integration of Geographical Information System (GIS) services with distributed data mining applications. GIS services provide the general purpose framework for building archival data services, real time streaming data services, and map-based visualization services that may be integrated with data mining and other applications through the use of distributed messaging systems and Web Service orchestration tools. Building upon on our previous work in these areas, we present our current research efforts. These include fundamental investigations into increasing XML-based Web service performance, supporting real time data streams, and integrating GIS mapping tools with audio/video collaboration systems for shared display and annotation.

Web-based visual analysis for high-throughput genomics

PubMed Central

2013-01-01

Background Visualization plays an essential role in genomics research by making it possible to observe correlations and trends in large datasets as well as communicate findings to others. Visual analysis, which combines visualization with analysis tools to enable seamless use of both approaches for scientific investigation, offers a powerful method for performing complex genomic analyses. However, there are numerous challenges that arise when creating rich, interactive Web-based visualizations/visual analysis applications for high-throughput genomics. These challenges include managing data flow from Web server to Web browser, integrating analysis tools and visualizations, and sharing visualizations with colleagues. Results We have created a platform simplifies the creation of Web-based visualization/visual analysis applications for high-throughput genomics. This platform provides components that make it simple to efficiently query very large datasets, draw common representations of genomic data, integrate with analysis tools, and share or publish fully interactive visualizations. Using this platform, we have created a Circos-style genome-wide viewer, a generic scatter plot for correlation analysis, an interactive phylogenetic tree, a scalable genome browser for next-generation sequencing data, and an application for systematically exploring tool parameter spaces to find good parameter values. All visualizations are interactive and fully customizable. The platform is integrated with the Galaxy (http://galaxyproject.org) genomics workbench, making it easy to integrate new visual applications into Galaxy. Conclusions Visualization and visual analysis play an important role in high-throughput genomics experiments, and approaches are needed to make it easier to create applications for these activities. Our framework provides a foundation for creating Web-based visualizations and integrating them into Galaxy. Finally, the visualizations we have created using the framework are useful tools for high-throughput genomics experiments. PMID:23758618

SMARTE: HELPING COMMUNITIES OVERCOME OBSTACLES TO REVITALIZATION - JUNE 28, 2006

EPA Science Inventory

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

SMARTE: HELPING COMMUNITIES EVALUATE REUSE OPTIONS AND OVERCOME REVITALIZATION OBSTACLES

EPA Science Inventory

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

NIH tools facilitate matching cancer drugs with gene targets

Cancer.gov

A new study details how a suite of web-based tools provides the research community with greatly improved capacity to compare data derived from large collections of genomic information against thousands of drugs. By comparing drugs and genetic targets, re

Building a Propulsion Experiment Project Management Environment

NASA Technical Reports Server (NTRS)

Keiser, Ken; Tanner, Steve; Hatcher, Danny; Graves, Sara

2004-01-01

What do you get when you cross rocket scientists with computer geeks? It is an interactive, distributed computing web of tools and services providing a more productive environment for propulsion research and development. The Rocket Engine Advancement Program 2 (REAP2) project involves researchers at several institutions collaborating on propulsion experiments and modeling. In an effort to facilitate these collaborations among researchers at different locations and with different specializations, researchers at the Information Technology and Systems Center,' University of Alabama in Huntsville, are creating a prototype web-based interactive information system in support of propulsion research. This system, to be based on experience gained in creating similar systems for NASA Earth science field experiment campaigns such as the Convection and Moisture Experiments (CAMEX), will assist in the planning and analysis of model and experiment results across REAP2 participants. The initial version of the Propulsion Experiment Project Management Environment (PExPM) consists of a controlled-access web portal facilitating the drafting and sharing of working documents and publications. Interactive tools for building and searching an annotated bibliography of publications related to REAP2 research topics have been created to help organize and maintain the results of literature searches. Also work is underway, with some initial prototypes in place, for interactive project management tools allowing project managers to schedule experiment activities, track status and report on results. This paper describes current successes, plans, and expected challenges for this project.

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.

Web-based routing assistance tool to reduce pavement damage by overweight and oversize vehicles.

DOT National Transportation Integrated Search

2016-10-30

This report documents the results of a completed project titled Web-Based Routing Assistance Tool to Reduce Pavement Damage by Overweight and Oversize Vehicles. The tasks involved developing a Web-based GIS routing assistance tool and evaluate ...

Web-Based Instruction and Learning: Analysis and Needs Assessment

NASA Technical Reports Server (NTRS)

Grabowski, Barbara; McCarthy, Marianne; Koszalka, Tiffany

1998-01-01

An analysis and needs assessment was conducted to identify kindergarten through grade 14 (K-14) customer needs with regard to using the World Wide Web (WWW) for instruction and to identify obstacles K-14 teachers face in utilizing NASA Learning Technologies products in the classroom. The needs assessment was conducted as part of the Dryden Learning Technologies Project which is a collaboration between Dryden Flight Research Center (DFRC), Edwards, California and Tne Pennsylvania State University (PSU), University Park, Pennsylvania. The overall project is a multiyear effort to conduct research in the development of teacher training and tools for Web-based science, mathematics and technology instruction and learning.

State Health Mapper: An Interactive, Web-Based Tool for Physician Workforce Planning, Recruitment, and Health Services Research.

PubMed

Krause, Denise D

2015-11-01

Health rankings in Mississippi are abysmal. Mississippi also has fewer physicians to serve its population compared with all other states. Many residents of this predominately rural state do not have access to healthcare providers. To better understand the demographics and distribution of the current health workforce in Mississippi, the main objective of the study was to design a Web-based, spatial, interactive application to visualize and explore the physician workforce. A Web application was designed to assist in health workforce planning. Secondary datasets of licensure and population information were obtained, and live feeds from licensure systems are being established. Several technologies were used to develop an intuitive, user-friendly application. Custom programming was completed in JavaScript so the application could run on most platforms, including mobile devices. The application allows users to identify and query geographic locations of individual or aggregated physicians based on attributes included in the licensure data, to perform drive time or buffer analyses, and to explore sociodemographic population data by geographic area of choice. This Web-based application with analytical tools visually represents the physician workforce licensed in Mississippi and its attributes, and provides access to much-needed information for statewide health workforce planning and research. The success of the application is not only based on the practicality of the tool but also on its ease of use. Feedback has been positive and has come from a wide variety of organizations across the state.

Enriching the trustworthiness of health-related web pages.

PubMed

Gaudinat, Arnaud; Cruchet, Sarah; Boyer, Celia; Chrawdhry, Pravir

2011-06-01

We present an experimental mechanism for enriching web content with quality metadata. This mechanism is based on a simple and well-known initiative in the field of the health-related web, the HONcode. The Resource Description Framework (RDF) format and the Dublin Core Metadata Element Set were used to formalize these metadata. The model of trust proposed is based on a quality model for health-related web pages that has been tested in practice over a period of thirteen years. Our model has been explored in the context of a project to develop a research tool that automatically detects the occurrence of quality criteria in health-related web pages.

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.

Implementing WebGL and HTML5 in Macromolecular Visualization and Modern Computer-Aided Drug Design.

PubMed

Yuan, Shuguang; Chan, H C Stephen; Hu, Zhenquan

2017-06-01

Web browsers have long been recognized as potential platforms for remote macromolecule visualization. However, the difficulty in transferring large-scale data to clients and the lack of native support for hardware-accelerated applications in the local browser undermine the feasibility of such utilities. With the introduction of WebGL and HTML5 technologies in recent years, it is now possible to exploit the power of a graphics-processing unit (GPU) from a browser without any third-party plugin. Many new tools have been developed for biological molecule visualization and modern drug discovery. In contrast to traditional offline tools, real-time computing, interactive data analysis, and cross-platform analyses feature WebGL- and HTML5-based tools, facilitating biological research in a more efficient and user-friendly way. Copyright © 2017 Elsevier Ltd. All rights reserved.

Working More Productively: Tools for Administrative Data

PubMed Central

Roos, Leslie L; Soodeen, Ruth-Ann; Bond, Ruth; Burchill, Charles

2003-01-01

Objective This paper describes a web-based resource () that contains a series of tools for working with administrative data. This work in knowledge management represents an effort to document, find, and transfer concepts and techniques, both within the local research group and to a more broadly defined user community. Concepts and associated computer programs are made as “modular” as possible to facilitate easy transfer from one project to another. Study Setting/Data Sources Tools to work with a registry, longitudinal administrative data, and special files (survey and clinical) from the Province of Manitoba, Canada in the 1990–2003 period. Data Collection Literature review and analyses of web site utilization were used to generate the findings. Principal Findings The Internet-based Concept Dictionary and SAS macros developed in Manitoba are being used in a growing number of research centers. Nearly 32,000 hits from more than 10,200 hosts in a recent month demonstrate broad interest in the Concept Dictionary. Conclusions The tools, taken together, make up a knowledge repository and research production system that aid local work and have great potential internationally. Modular software provides considerable efficiency. The merging of documentation and researcher-to-researcher dissemination keeps costs manageable. PMID:14596394

WebQuests as Language-Learning Tools

ERIC Educational Resources Information Center

Aydin, Selami

2016-01-01

This study presents a review of the literature that examines WebQuests as tools for second-language acquisition and foreign language-learning processes to guide teachers in their teaching activities and researchers in further research on the issue. The study first introduces the theoretical background behind WebQuest use in the mentioned…

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

Design of a Web-tool for diagnostic clinical trials handling medical imaging research.

PubMed

Baltasar Sánchez, Alicia; González-Sistal, Angel

2011-04-01

New clinical studies in medicine are based on patients and controls using different imaging diagnostic modalities. Medical information systems are not designed for clinical trials employing clinical imaging. Although commercial software and communication systems focus on storage of image data, they are not suitable for storage and mining of new types of quantitative data. We sought to design a Web-tool to support diagnostic clinical trials involving different experts and hospitals or research centres. The image analysis of this project is based on skeletal X-ray imaging. It involves a computerised image method using quantitative analysis of regions of interest in healthy bone and skeletal metastases. The database is implemented with ASP.NET 3.5 and C# technologies for our Web-based application. For data storage, we chose MySQL v.5.0, one of the most popular open source databases. User logins were necessary, and access to patient data was logged for auditing. For security, all data transmissions were carried over encrypted connections. This Web-tool is available to users scattered at different locations; it allows an efficient organisation and storage of data (case report form) and images and allows each user to know precisely what his task is. The advantages of our Web-tool are as follows: (1) sustainability is guaranteed; (2) network locations for collection of data are secured; (3) all clinical information is stored together with the original images and the results derived from processed images and statistical analysis that enable us to perform retrospective studies; (4) changes are easily incorporated because of the modular architecture; and (5) assessment of trial data collected at different sites is centralised to reduce statistical variance.

Using Web 2.0 tools to connect shore-based users to live science from the wide blue ocean

NASA Astrophysics Data System (ADS)

Cooper, S. K.; Peart, L.; Collins, J.

2009-12-01

The fast-expanding use of social networking tools, combined with improved connectivity available through satellite-provided internet on board the scientific ocean drilling vessel JOIDES Resolution (the JR), has allowed for a whole new kind of interaction. Unlike in the not-so-distant past, when non-participants were forced to wait for months to read about the results of ongoing research, web tools allow almost instantaneous participation in ship-based ocean science. Utilizing a brand new portal, joidesresolution.org, scientists and educators at sea can post daily blogs about their work and respond to questions and comments on those blogs, update the JR’s Facebook and Twitter pages, and post videos and photos to YouTube and Flickr regularly. Live video conferencing tools also allow for direct interaction with scientists and a view into the work being done on board in real time. These tools have allowed students, teachers and families, groups and individuals on shore to follow along with the expeditions of the ship and its exciting scientific explorations -- and become a part of them. Building this community provides a whole range of rich interactions and brings seafloor research and the real process of science to those who would never before have had access to it. This presentation will include an overview of the web portal and its associated social networking sites, as well as a discussion of the challenges and lessons learned over nearly a year of utilizing these new tools. The web portal joidesresolution.org home page.

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

Designing and Implementing Web-Based Scaffolding Tools for Technology-Enhanced Socioscientific Inquiry

ERIC Educational Resources Information Center

Shin, Suhkyung; Brush, Thomas A.; Glazewski, Krista D.

2017-01-01

This study explores how web-based scaffolding tools provide instructional support while implementing a socio-scientific inquiry (SSI) unit in a science classroom. This case study focused on how students used web-based scaffolding tools during SSI activities, and how students perceived the SSI unit and the scaffolding tools embedded in the SSI…

A Web-Based Lean Simulation Game for Office Operations: Training the Other Side of a Lean Enterprise

ERIC Educational Resources Information Center

Kuriger, Glenn W.; Wan, Huang-da; Mirehei, S. Moussa; Tamma, Saumya; Chen, F. Frank

2010-01-01

This research proposes a Web-based version of a lean office simulation game (WeBLOG). The game is designed to be used to train lean concepts to office and administrative personnel. This group belongs to the frequently forgotten side of a lean enterprise. Over four phases, the game presents the following seven lean tools: one-piece flow,…

An Examination of Teachers' Integration of Web 2.0 Technologies in Secondary Classrooms: A Phenomenological Study

ERIC Educational Resources Information Center

Wang, Ling

2013-01-01

Web 2.0 tools may be able to close the digital gap between teachers and students if teachers can integrate the tools and change their pedagogy. The TPACK framework has outlined the elements needed to effect change, and research on Web 2.0 tools shows its potential as a change agent, but little research has looked at how the two interrelate. Using…

Older Cancer Patients’ User Experiences With Web-Based Health Information Tools: A Think-Aloud Study

PubMed Central

Romijn, Geke; Smets, Ellen M A; Loos, Eugene F; Kunneman, Marleen; van Weert, Julia C M

2016-01-01

Background Health information is increasingly presented on the Internet. Several Web design guidelines for older Web users have been proposed; however, these guidelines are often not applied in website development. Furthermore, although we know that older individuals use the Internet to search for health information, we lack knowledge on how they use and evaluate Web-based health information. Objective This study evaluates user experiences with existing Web-based health information tools among older (≥ 65 years) cancer patients and survivors and their partners. The aim was to gain insight into usability issues and the perceived usefulness of cancer-related Web-based health information tools. Methods We conducted video-recorded think-aloud observations for 7 Web-based health information tools, specifically 3 websites providing cancer-related information, 3 Web-based question prompt lists (QPLs), and 1 values clarification tool, with colorectal cancer patients or survivors (n=15) and their partners (n=8) (median age: 73; interquartile range 70-79). Participants were asked to think aloud while performing search, evaluation, and application tasks using the Web-based health information tools. Results Overall, participants perceived Web-based health information tools as highly useful and indicated a willingness to use such tools. However, they experienced problems in terms of usability and perceived usefulness due to difficulties in using navigational elements, shortcomings in the layout, a lack of instructions on how to use the tools, difficulties with comprehensibility, and a large amount of variety in terms of the preferred amount of information. Although participants frequently commented that it was easy for them to find requested information, we observed that the large majority of the participants were not able to find it. Conclusions Overall, older cancer patients appreciate and are able to use cancer information websites. However, this study shows the importance of maintaining awareness of age-related problems such as cognitive and functional decline and navigation difficulties with this target group in mind. The results of this study can be used to design usable and useful Web-based health information tools for older (cancer) patients. PMID:27457709

Enabling Astronony Research in High Schools with the START Collaboratory

NASA Astrophysics Data System (ADS)

Greenberg, G. J.; Pennypacker, C. R.

2005-12-01

The START Collaboratory is a three-year, NSF funded project to create a Web-based national astronomy research collaboratory for high school students that will bring authentic scientific research to classrooms across the country. The project brings together the resources and experience of Hands-On Universe at the University of California at Berkeley, the Sloan Digital Sky Survey / National Virtual Observatory at Johns Hopkins University and the Northwestern University Collaboratory Project. The START Collaboratory seamlessly integrates access to gigabytes of searchable data and images from the Sloan Digital Sky Survey and the NVO into Web-based research notebooks and research reports that can be shared and discussed online. Requests for observations can be made through the START Telescope Request Broker. These observations can be viewed with the START Web Visualization Tool for visualization and measurement of FITS files. The project has developed a set of research scenarios to introduce students to the resources and tools available through the START Collaboratory, and to provide a model for network-based collaboration that engages students, teachers and professional scientists. Great attention has been paid to ensuring that the research scenarios result in accurate and authentic research products that are of real interest to working astronomers. In this panel presentation, we will describe the educational benefits and opportunities being seen in pilot testing with teachers and students, and in preparations for a teacher professional development project with the Adler Planetarium.

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…

Learning Register Variation. A Web-Based Platform for Developing Diaphasic Skills

ERIC Educational Resources Information Center

Allora, Adriano; Corino, Elisa; Onesti, Cristina

2012-01-01

The present paper shows the first results of a linguistic project devoted to the construction of web learning tools for reinforcing sensitivity to diaphasic varieties and for learning style variation in L2/LS learning. (Contains 1 figure and 1 footnote.) [Support for this research was provided by the VALERE Project.

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.

The START Collaboratory: Broadening Participation in Astronomy Research

NASA Astrophysics Data System (ADS)

Pennypacker, C. R.; Raddick, M. J.; Greenberg, G. J.; Hoette, V.; Meredith, K.

2005-12-01

The START Collaboratory is a three-year, NSF-funded project to create a Web-based national astronomy research collaboratory for high school students that will bring authentic scientific research to classrooms across the country. The project brings together the resources and experience of Hands-On Universe at the University of California at Berkeley, the Sloan Digital Sky Survey / National Virtual Observatory at Johns Hopkins University and the Northwestern University Collaboratory Project. START Collaboratory documents enable students to create, share and discuss Web-based astronomy research notebooks and research reports. These documents include seamless access to gigabytes of searchable data from the SDSS and the NVO. The START Collaboratory also supports observation requests to a "Telescope Request Broker" that automatically coordinates access to telescopes around the world, and a Web Visualization Tool for visualization and measurement of FITS files from professional observatories or user observations. The project has developed a set of research scenarios that use real astronomical problems to introduce students to the resources and tools available through the START Collaboratory. These scenarios also introduce a model for network-based collaboration that engages students, teachers and professional scientists. Great attention has been paid to ensuring that the research scenarios result in accurate and authentic research products that are of real interest to working astronomers. With the START Collaboratory, students will study science by doing science, generating useful scientific results just as professional astronomers do. As the third and last year of the project finalizes integrating tools and resources, an NSF-funded two-year CI-TEAM project with the Adler Planetarium will begin to create a professional development program for high school teachers interested in learning how to use the START Collaboratory to engage their students in astrophysical research. Through this program, we will begin to implement the tools and research scenarios that we have designed.

Hospital-based nurses' perceptions of the adoption of Web 2.0 tools for knowledge sharing, learning, social interaction and the production of collective intelligence.

PubMed

Lau, Adela S M

2011-11-11

Web 2.0 provides a platform or a set of tools such as blogs, wikis, really simple syndication (RSS), podcasts, tags, social bookmarks, and social networking software for knowledge sharing, learning, social interaction, and the production of collective intelligence in a virtual environment. Web 2.0 is also becoming increasingly popular in e-learning and e-social communities. The objectives were to investigate how Web 2.0 tools can be applied for knowledge sharing, learning, social interaction, and the production of collective intelligence in the nursing domain and to investigate what behavioral perceptions are involved in the adoption of Web 2.0 tools by nurses. The decomposed technology acceptance model was applied to construct the research model on which the hypotheses were based. A questionnaire was developed based on the model and data from nurses (n = 388) were collected from late January 2009 until April 30, 2009. Pearson's correlation analysis and t tests were used for data analysis. Intention toward using Web 2.0 tools was positively correlated with usage behavior (r = .60, P < .05). Behavioral intention was positively correlated with attitude (r = .72, P < .05), perceived behavioral control (r = .58, P < .05), and subjective norm (r = .45, P < .05). In their decomposed constructs, perceived usefulness (r = .7, P < .05), relative advantage (r = .64, P < .05), and compatibility (r = .60,P < .05) were positively correlated with attitude, but perceived ease of use was not significantly correlated (r = .004, P < .05) with it. Peer (r = .47, P < .05), senior management (r = .24,P < .05), and hospital (r = .45, P < .05) influences had positive correlations with subjective norm. Resource (r = .41,P < .05) and technological (r = .69,P < .05) conditions were positively correlated with perceived behavioral control. The identified behavioral perceptions may further health policy makers' understanding of nurses' concerns regarding and barriers to the adoption of Web 2.0 tools and enable them to better plan the strategy of implementation of Web 2.0 tools for knowledge sharing, learning, social interaction, and the production of collective intelligence.

Hospital-Based Nurses’ Perceptions of the Adoption of Web 2.0 Tools for Knowledge Sharing, Learning, Social Interaction and the Production of Collective Intelligence

PubMed Central

2011-01-01

Background Web 2.0 provides a platform or a set of tools such as blogs, wikis, really simple syndication (RSS), podcasts, tags, social bookmarks, and social networking software for knowledge sharing, learning, social interaction, and the production of collective intelligence in a virtual environment. Web 2.0 is also becoming increasingly popular in e-learning and e-social communities. Objectives The objectives were to investigate how Web 2.0 tools can be applied for knowledge sharing, learning, social interaction, and the production of collective intelligence in the nursing domain and to investigate what behavioral perceptions are involved in the adoption of Web 2.0 tools by nurses. Methods The decomposed technology acceptance model was applied to construct the research model on which the hypotheses were based. A questionnaire was developed based on the model and data from nurses (n = 388) were collected from late January 2009 until April 30, 2009. Pearson’s correlation analysis and t tests were used for data analysis. Results Intention toward using Web 2.0 tools was positively correlated with usage behavior (r = .60, P < .05). Behavioral intention was positively correlated with attitude (r = .72, P < .05), perceived behavioral control (r = .58, P < .05), and subjective norm (r = .45, P < .05). In their decomposed constructs, perceived usefulness (r = .7, P < .05), relative advantage (r = .64, P < .05), and compatibility (r = .60, P < .05) were positively correlated with attitude, but perceived ease of use was not significantly correlated (r = .004, P < .05) with it. Peer (r = .47, P < .05), senior management (r = .24, P < .05), and hospital (r = .45, P < .05) influences had positive correlations with subjective norm. Resource (r = .41, P < .05) and technological (r = .69, P < .05) conditions were positively correlated with perceived behavioral control. Conclusions The identified behavioral perceptions may further health policy makers’ understanding of nurses’ concerns regarding and barriers to the adoption of Web 2.0 tools and enable them to better plan the strategy of implementation of Web 2.0 tools for knowledge sharing, learning, social interaction, and the production of collective intelligence. PMID:22079851

CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research

PubMed Central

Sherif, Tarek; Rioux, Pierre; Rousseau, Marc-Etienne; Kassis, Nicolas; Beck, Natacha; Adalat, Reza; Das, Samir; Glatard, Tristan; Evans, Alan C.

2014-01-01

The Canadian Brain Imaging Research Platform (CBRAIN) is a web-based collaborative research platform developed in response to the challenges raised by data-heavy, compute-intensive neuroimaging research. CBRAIN offers transparent access to remote data sources, distributed computing sites, and an array of processing and visualization tools within a controlled, secure environment. Its web interface is accessible through any modern browser and uses graphical interface idioms to reduce the technical expertise required to perform large-scale computational analyses. CBRAIN's flexible meta-scheduling has allowed the incorporation of a wide range of heterogeneous computing sites, currently including nine national research High Performance Computing (HPC) centers in Canada, one in Korea, one in Germany, and several local research servers. CBRAIN leverages remote computing cycles and facilitates resource-interoperability in a transparent manner for the end-user. Compared with typical grid solutions available, our architecture was designed to be easily extendable and deployed on existing remote computing sites with no tool modification, administrative intervention, or special software/hardware configuration. As October 2013, CBRAIN serves over 200 users spread across 53 cities in 17 countries. The platform is built as a generic framework that can accept data and analysis tools from any discipline. However, its current focus is primarily on neuroimaging research and studies of neurological diseases such as Autism, Parkinson's and Alzheimer's diseases, Multiple Sclerosis as well as on normal brain structure and development. This technical report presents the CBRAIN Platform, its current deployment and usage and future direction. PMID:24904400

CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research.

PubMed

Sherif, Tarek; Rioux, Pierre; Rousseau, Marc-Etienne; Kassis, Nicolas; Beck, Natacha; Adalat, Reza; Das, Samir; Glatard, Tristan; Evans, Alan C

2014-01-01

The Canadian Brain Imaging Research Platform (CBRAIN) is a web-based collaborative research platform developed in response to the challenges raised by data-heavy, compute-intensive neuroimaging research. CBRAIN offers transparent access to remote data sources, distributed computing sites, and an array of processing and visualization tools within a controlled, secure environment. Its web interface is accessible through any modern browser and uses graphical interface idioms to reduce the technical expertise required to perform large-scale computational analyses. CBRAIN's flexible meta-scheduling has allowed the incorporation of a wide range of heterogeneous computing sites, currently including nine national research High Performance Computing (HPC) centers in Canada, one in Korea, one in Germany, and several local research servers. CBRAIN leverages remote computing cycles and facilitates resource-interoperability in a transparent manner for the end-user. Compared with typical grid solutions available, our architecture was designed to be easily extendable and deployed on existing remote computing sites with no tool modification, administrative intervention, or special software/hardware configuration. As October 2013, CBRAIN serves over 200 users spread across 53 cities in 17 countries. The platform is built as a generic framework that can accept data and analysis tools from any discipline. However, its current focus is primarily on neuroimaging research and studies of neurological diseases such as Autism, Parkinson's and Alzheimer's diseases, Multiple Sclerosis as well as on normal brain structure and development. This technical report presents the CBRAIN Platform, its current deployment and usage and future direction.

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

PubMed Central

Rhodes, S; Bowie, D; Hergenrather, K

2003-01-01

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

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

PubMed

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

2003-01-01

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

Examining Web 2.0 Tools Usage of Science Teacher Candidates

ERIC Educational Resources Information Center

Balkan Kiyici, Fatime

2012-01-01

Using technology in a science teaching is so important. Only the person, who can use these tools in expert level, can use these tools in their teaching activities. In this research it is aimed firstly identifying science teacher candidates web 2.0 tools usage experience level and factors affecting experience level. In this research survey method…

Dissemination of a Web-Based Tool for Supporting Health Insurance Plan Decisions (Show Me Health Plans): Cross-Sectional Observational Study.

PubMed

Zhao, Jingsong; Mir, Nageen; Ackermann, Nicole; Kaphingst, Kimberly A; Politi, Mary C

2018-06-20

The rate of uninsured people has decreased dramatically since the Affordable Care Act was passed. To make an informed decision, consumers need assistance to understand the advantages and disadvantages of health insurance plans. The Show Me Health Plans Web-based decision support tool was developed to improve the quality of health insurance selection. In response to the promising effectiveness of Show Me Health Plans in a randomized controlled trial (RCT) and the growing need for Web-based health insurance decision support, the study team used expert recommendations for dissemination and implementation, engaged external stakeholders, and made the Show Me Health Plans tool available to the public. The purpose of this study was to implement the public dissemination of the Show Me Health Plans tool in the state of Missouri and to evaluate its impact compared to the RCT. This study used a cross-sectional observational design. Dissemination phase users were compared with users in the RCT study across the same outcome measures. Time spent using the Show Me Health Plans tool, knowledge, importance rating of 9 health insurance features, and intended plan choice match with algorithm predictions were examined. During the dissemination phase (November 2016 to January 2017), 10,180 individuals visited the SMHP website, and the 1069 users who stayed on the tool for more than one second were included in our analyses. Dissemination phase users were more likely to live outside St. Louis City or County (P<.001), were less likely to be below the federal poverty level (P<.001), and had a higher income (P=.03). Overall, Show Me Health Plans users from St. Louis City or County spent more time on the Show Me Health Plans tool than those from other Missouri counties (P=.04); this association was not observed in the RCT. Total time spent on the tool was not correlated with knowledge scores, which were associated with lower poverty levels (P=.009). The users from the RCT phase were more likely to select an insurance plan that matched the tool's recommendations (P<.001) compared with the dissemination phase users. The study suggests that a higher income population may be more likely to seek information and online help when making a health insurance plan decision. We found that Show Me Health Plans users in the dissemination phase were more selective in the information they reviewed. This study illustrates one way of disseminating and implementing an empirically tested Web-based decision aid tool. Distributing Web-based tools is feasible and may attract a large number of potential users, educate them on basic health insurance information, and make recommendations based on personal information and preference. However, using Web-based tools may differ according to the demographics of the general public compared to research study participants. ©Jingsong Zhao, Nageen Mir, Nicole Ackermann, Kimberly A Kaphingst, Mary C Politi. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 20.06.2018.

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.

A web-based data visualization tool for the MIMIC-II database.

PubMed

Lee, Joon; Ribey, Evan; Wallace, James R

2016-02-04

Although MIMIC-II, a public intensive care database, has been recognized as an invaluable resource for many medical researchers worldwide, becoming a proficient MIMIC-II researcher requires knowledge of SQL programming and an understanding of the MIMIC-II database schema. These are challenging requirements especially for health researchers and clinicians who may have limited computer proficiency. In order to overcome this challenge, our objective was to create an interactive, web-based MIMIC-II data visualization tool that first-time MIMIC-II users can easily use to explore the database. The tool offers two main features: Explore and Compare. The Explore feature enables the user to select a patient cohort within MIMIC-II and visualize the distributions of various administrative, demographic, and clinical variables within the selected cohort. The Compare feature enables the user to select two patient cohorts and visually compare them with respect to a variety of variables. The tool is also helpful to experienced MIMIC-II researchers who can use it to substantially accelerate the cumbersome and time-consuming steps of writing SQL queries and manually visualizing extracted data. Any interested researcher can use the MIMIC-II data visualization tool for free to quickly and conveniently conduct a preliminary investigation on MIMIC-II with a few mouse clicks. Researchers can also use the tool to learn the characteristics of the MIMIC-II patients. Since it is still impossible to conduct multivariable regression inside the tool, future work includes adding analytics capabilities. Also, the next version of the tool will aim to utilize MIMIC-III which contains more data.

Brave New Media World: Science Communication Voyages through the Global Seas

NASA Astrophysics Data System (ADS)

Clark, C. L.; Reisewitz, A.

2010-12-01

By leveraging online tools, such as blogs, Twitter, Facebook, Google Earth, flickr, web-based discussion boards, and a bi-monthly electronic magazine for the non-scientist, Scripps Institution of Oceanography is taking science communications out of the static webpage to create interactive journeys that spark social dialogue and helped raise awareness of science-based research on global marine environmental issues. Several new initiatives are being chronicled through popular blogs and expedition web sites as researchers share interesting scientific facts and unusual findings in near real-time.

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.

Medicine 2.0: social networking, collaboration, participation, apomediation, and openness.

PubMed

Eysenbach, Gunther

2008-08-25

In a very significant development for eHealth, broad adoption of Web 2.0 technologies and approaches coincides with the more recent emergence of Personal Health Application Platforms and Personally Controlled Health Records such as Google Health, Microsoft HealthVault, and Dossia. "Medicine 2.0" applications, services and tools are defined as Web-based services for health care consumers, caregivers, patients, health professionals, and biomedical researchers, that use Web 2.0 technologies and/or semantic web and virtual reality approaches to enable and facilitate specifically 1) social networking, 2) participation, 3) apomediation, 4) openness and 5) collaboration, within and between these user groups. The Journal of Medical Internet Research (JMIR) publishes a Medicine 2.0 theme issue and sponsors a conference on "How Social Networking and Web 2.0 changes Health, Health Care, Medicine and Biomedical Research", to stimulate and encourage research in these five areas.

SUSTAINABLE MANAGEMENT APPROACHES AND REVITALIZATION TOOLS-ELECTRONIC (SMARTE)�A FREE TOOL FOR REVITALIZATION

EPA Science Inventory

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

Teachers' Perceptions and Attitudes toward the Implementation of Web 2.0 Tools in Secondary Education

ERIC Educational Resources Information Center

Quadri, Lekan Kamil

2014-01-01

Researchers have concluded that Web 2.0 technologies offered many educational benefits. However, many secondary teachers in a large northwestern school district were not using Web 2.0 tools in spite of its possibilities for teaching and learning. The purpose of this quantitative correlational research was to explore the relationships between the…

jsPsych: a JavaScript library for creating behavioral experiments in a Web browser.

PubMed

de Leeuw, Joshua R

2015-03-01

Online experiments are growing in popularity, and the increasing sophistication of Web technology has made it possible to run complex behavioral experiments online using only a Web browser. Unlike with offline laboratory experiments, however, few tools exist to aid in the development of browser-based experiments. This makes the process of creating an experiment slow and challenging, particularly for researchers who lack a Web development background. This article introduces jsPsych, a JavaScript library for the development of Web-based experiments. jsPsych formalizes a way of describing experiments that is much simpler than writing the entire experiment from scratch. jsPsych then executes these descriptions automatically, handling the flow from one task to another. The jsPsych library is open-source and designed to be expanded by the research community. The project is available online at www.jspsych.org .

How can scientists bring research to use: the HENVINET experience.

PubMed

Bartonova, Alena

2012-06-28

Health concerns have driven the European environmental policies of the last 25 years, with issues becoming more complex. Addressing these concerns requires an approach that is both interdisciplinary and engages scientists with society. In response to this requirement, the FP6 coordination action "Health and Environment Network" HENVINET was set up to create a permanent inter-disciplinary network of professionals in the field of health and environment tasked to bridge the communication gap between science and society. In this paper we describe how HENVINET delivered on this task. The HENVINET project approached the issue of inter-disciplinary collaboration in four ways. (1) The Drivers-Pressures-State-Exposure-Effect-Action framework was used to structure information gathering, collaboration and communication between scientists in the field of health and the environment. (2) Interactive web-based tools were developed to enhance methods for knowledge evaluation, and use these methods to formulate policy advice. (3) Quantification methods were adapted to measure scientific agreement. And (4) Open architecture web technology was used to develop an information repository and a web portal to facilitate collaboration and communication among scientists. Twenty-five organizations from Europe and five from outside Europe participated in the Health and Environment Network HENVINET, which lasted for 3.5 years. The consortium included partners in environmental research, public health and veterinary medicine; included medical practitioners and representatives of local administrations; and had access to national policy making and EEA and WHO expertise. Dedicated web-based tools for visualisation of environmental health issues and knowledge evaluation allowed remote expert elicitation, and were used as a basis for developing policy advice in five health areas (asthma and allergies; cancer; neurodevelopmental disorders; endocrine disruption; and engineered nanoparticles in the environment). An open searchable database of decision support tools was established and populated. A web based social networking tool was developed to enhance collaboration and communication between scientists and society. HENVINET addressed key issues that arise in inter-disciplinary research on health and environment and in communicating research results to policy makers and society. HENVINET went beyond traditional scientific tools and methods to bridge the communication gap between science and policy makers. The project identified the need for a common framework and delivered it. It developed and implemented a variety of novel methods and tools and, using several representative examples, demonstrated the process of producing politically relevant scientific advice based on an open participation of experts. It highlighted the need for, and benefits of, a liaison between health and environment professionals and professionals in the social sciences and liberal arts. By adopting critical complexity thinking, HENVINET extended the traditional approach to environment and health research, and set the standard for current approaches to bridge the gap between science and society.

Document-Centred Discourse on the Web: A Publishing Tool for Students, Tutors and Researchers.

ERIC Educational Resources Information Center

Shum, Simon Buckingham; Sumner, Tamara

This paper describes how the authors are exploiting the potential of interactive World Wide Web media to support a central part of academic life--the publishing, critiquing, and discussion of documents. The paper begins with an overview of documents in academic life and a discussion of paper-based or "papyrocentric" print and scholarly…

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.

Web-based Health Educational Program in Saudi Arabia.

PubMed

Bahkali, Salwa; Almaiman, Ahmad; Alsaleh, Mahassen; Elmetwally, Ashraf; Househ, Mowafa

2014-01-01

The purpose of this exploratory study is to provide an overview of a web-based health educational site created by the King Faisal Specialist Hospital and Research Center (KFSH&RC) in the Kingdom of Saudi Arabia (KSA). Sources of data included two interviews with Saudi IT personnel, three health educators, and two medical consultants working at KFSH&RC. The interviews ranged between 45 minutes and 120 minutes. The KFSH&RC website was also searched for the type of health information content posted. Results show that the KFSH&RC web-based health educational site provides health information through a medical encyclopedia, a social networking platform, health educational links, and targeted health information for children, which includes tools such as games and coloring books. Further research is needed on the effectiveness of the KFSH&RC web-based health education site in terms of improving knowledge and changing behavior of Saudi patients. The study recommends that targeted web-based health education strategies should be developed to reach large rural populations which have inadequate computer skills and limited access to the internet.

E-Moderating Personas

ERIC Educational Resources Information Center

Avgerinou, Maria D.; Andersson, Carina

2007-01-01

Web-based distance education has become a "real" teaching alternative which has instigated more research particularly in the past decade. This research has commonly focused on four major perspectives: (1) information-technology; (2) course management systems (including course communication tools); (3) information design; and (4) online…

Increasing efficiency of information dissemination and collection through the World Wide Web

Treesearch

Daniel P. Huebner; Malchus B. Baker; Peter F. Ffolliott

2000-01-01

Researchers, managers, and educators have access to revolutionary technology for information transfer through the World Wide Web (Web). Using the Web to effectively gather and distribute information is addressed in this paper. Tools, tips, and strategies are discussed. Companion Web sites are provided to guide users in selecting the most appropriate tool for searching...

CAS-viewer: web-based tool for splicing-guided integrative analysis of multi-omics cancer data.

PubMed

Han, Seonggyun; Kim, Dongwook; Kim, Youngjun; Choi, Kanghoon; Miller, Jason E; Kim, Dokyoon; Lee, Younghee

2018-04-20

The Cancer Genome Atlas (TCGA) project is a public resource that provides transcriptomic, DNA sequence, methylation, and clinical data for 33 cancer types. Transforming the large size and high complexity of TCGA cancer genome data into integrated knowledge can be useful to promote cancer research. Alternative splicing (AS) is a key regulatory mechanism of genes in human cancer development and in the interaction with epigenetic factors. Therefore, AS-guided integration of existing TCGA data sets will make it easier to gain insight into the genetic architecture of cancer risk and related outcomes. There are already existing tools analyzing and visualizing alternative mRNA splicing patterns for large-scale RNA-seq experiments. However, these existing web-based tools are limited to the analysis of individual TCGA data sets at a time, such as only transcriptomic information. We implemented CAS-viewer (integrative analysis of Cancer genome data based on Alternative Splicing), a web-based tool leveraging multi-cancer omics data from TCGA. It illustrates alternative mRNA splicing patterns along with methylation, miRNAs, and SNPs, and then provides an analysis tool to link differential transcript expression ratio to methylation, miRNA, and splicing regulatory elements for 33 cancer types. Moreover, one can analyze AS patterns with clinical data to identify potential transcripts associated with different survival outcome for each cancer. CAS-viewer is a web-based application for transcript isoform-driven integration of multi-omics data in multiple cancer types and will aid in the visualization and possible discovery of biomarkers for cancer by integrating multi-omics data from TCGA.

Simple Web-based interactive key development software (WEBiKEY) and an example key for Kuruna (Poaceae: Bambusoideae).

PubMed

Attigala, Lakshmi; De Silva, Nuwan I; Clark, Lynn G

2016-04-01

Programs that are user-friendly and freely available for developing Web-based interactive keys are scarce and most of the well-structured applications are relatively expensive. WEBiKEY was developed to enable researchers to easily develop their own Web-based interactive keys with fewer resources. A Web-based multiaccess identification tool (WEBiKEY) was developed that uses freely available Microsoft ASP.NET technologies and an SQL Server database for Windows-based hosting environments. WEBiKEY was tested for its usability with a sample data set, the temperate woody bamboo genus Kuruna (Poaceae). WEBiKEY is freely available to the public and can be used to develop Web-based interactive keys for any group of species. The interactive key we developed for Kuruna using WEBiKEY enables users to visually inspect characteristics of Kuruna and identify an unknown specimen as one of seven possible species in the genus.

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

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...

Marine and Hydrokinetic Research | Water Power | NREL

Science.gov Websites

. Resource Characterization and Maps NREL develops measurement systems, simulation tools, and web-based models and tools to evaluate the economic potential of power-generating devices for all technology Acceleration NREL analysts study the potential impacts that developing a robust MHK market could have on

GenePattern | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

GenePattern is a genomic analysis platform that provides access to hundreds of tools for the analysis and visualization of multiple data types. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. A new GenePattern Notebook environment allows users to combine GenePattern analyses with text, graphics, and code to create complete reproducible research narratives.

A midas plugin to enable construction of reproducible web-based image processing pipelines

PubMed Central

Grauer, Michael; Reynolds, Patrick; Hoogstoel, Marion; Budin, Francois; Styner, Martin A.; Oguz, Ipek

2013-01-01

Image processing is an important quantitative technique for neuroscience researchers, but difficult for those who lack experience in the field. In this paper we present a web-based platform that allows an expert to create a brain image processing pipeline, enabling execution of that pipeline even by those biomedical researchers with limited image processing knowledge. These tools are implemented as a plugin for Midas, an open-source toolkit for creating web based scientific data storage and processing platforms. Using this plugin, an image processing expert can construct a pipeline, create a web-based User Interface, manage jobs, and visualize intermediate results. Pipelines are executed on a grid computing platform using BatchMake and HTCondor. This represents a new capability for biomedical researchers and offers an innovative platform for scientific collaboration. Current tools work well, but can be inaccessible for those lacking image processing expertise. Using this plugin, researchers in collaboration with image processing experts can create workflows with reasonable default settings and streamlined user interfaces, and data can be processed easily from a lab environment without the need for a powerful desktop computer. This platform allows simplified troubleshooting, centralized maintenance, and easy data sharing with collaborators. These capabilities enable reproducible science by sharing datasets and processing pipelines between collaborators. In this paper, we present a description of this innovative Midas plugin, along with results obtained from building and executing several ITK based image processing workflows for diffusion weighted MRI (DW MRI) of rodent brain images, as well as recommendations for building automated image processing pipelines. Although the particular image processing pipelines developed were focused on rodent brain MRI, the presented plugin can be used to support any executable or script-based pipeline. PMID:24416016

A midas plugin to enable construction of reproducible web-based image processing pipelines.

PubMed

Grauer, Michael; Reynolds, Patrick; Hoogstoel, Marion; Budin, Francois; Styner, Martin A; Oguz, Ipek

2013-01-01

Image processing is an important quantitative technique for neuroscience researchers, but difficult for those who lack experience in the field. In this paper we present a web-based platform that allows an expert to create a brain image processing pipeline, enabling execution of that pipeline even by those biomedical researchers with limited image processing knowledge. These tools are implemented as a plugin for Midas, an open-source toolkit for creating web based scientific data storage and processing platforms. Using this plugin, an image processing expert can construct a pipeline, create a web-based User Interface, manage jobs, and visualize intermediate results. Pipelines are executed on a grid computing platform using BatchMake and HTCondor. This represents a new capability for biomedical researchers and offers an innovative platform for scientific collaboration. Current tools work well, but can be inaccessible for those lacking image processing expertise. Using this plugin, researchers in collaboration with image processing experts can create workflows with reasonable default settings and streamlined user interfaces, and data can be processed easily from a lab environment without the need for a powerful desktop computer. This platform allows simplified troubleshooting, centralized maintenance, and easy data sharing with collaborators. These capabilities enable reproducible science by sharing datasets and processing pipelines between collaborators. In this paper, we present a description of this innovative Midas plugin, along with results obtained from building and executing several ITK based image processing workflows for diffusion weighted MRI (DW MRI) of rodent brain images, as well as recommendations for building automated image processing pipelines. Although the particular image processing pipelines developed were focused on rodent brain MRI, the presented plugin can be used to support any executable or script-based pipeline.

Verification Tools Secure Online Shopping, Banking

NASA Technical Reports Server (NTRS)

2010-01-01

Just like rover or rocket technology sent into space, the software that controls these technologies must be extensively tested to ensure reliability and effectiveness. Ames Research Center invented the open-source Java Pathfinder (JPF) toolset for the deep testing of Java-based programs. Fujitsu Labs of America Inc., based in Sunnyvale, California, improved the capabilities of the JPF Symbolic Pathfinder tool, establishing the tool as a means of thoroughly testing the functionality and security of Web-based Java applications such as those used for Internet shopping and banking.

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

NASA Astrophysics Data System (ADS)

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

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

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.

Notepad Is NOT Bad: Employing Yahoo! Notepad as an Online Research Diary in Educational Enquiry Based on a PhD Study

ERIC Educational Resources Information Center

Abdallah, Mahmoud Mohammad Sayed

2011-01-01

Reflective tools have been gaining ground in educational research. Diaries, especially electronic ones, can be effective in enabling researchers to organise and reflect upon their research. Online diaries are flexible Web-based facilities since the recording process can be conducted quickly and smoothly. Here, I report on using Yahoo! Notepad as…

Maximizing Impact: Pairing interactive web visualizations with traditional print media

NASA Astrophysics Data System (ADS)

Read, E. K.; Appling, A.; Carr, L.; De Cicco, L.; Read, J. S.; Walker, J. I.; Winslow, L. A.

2016-12-01

Our Nation's rapidly growing store of environmental data makes new demands on researchers: to take on increasingly broad-scale, societally relevant analyses and to rapidly communicate findings to the public. Interactive web-based data visualizations now commonly supplement or comprise journalism, and science journalism has followed suit. To maximize the impact of US Geological Survey (USGS) science, the USGS Office of Water Information Data Science team builds tools and products that combine traditional static research products (e.g., print journal articles) with web-based, interactive data visualizations that target non-scientific audiences. We developed a lightweight, open-source framework for web visualizations to reduce time to production. The framework provides templates for a data visualization workflow and the packaging of text, interactive figures, and images into an appealing web interface with standardized look and feel, usage tracking, and responsiveness. By partnering with subject matter experts to focus on timely, societally relevant issues, we use these tools to produce appealing visual stories targeting specific audiences, including managers, the general public, and scientists, on diverse topics including drought, microplastic pollution, and fisheries response to climate change. We will describe the collaborative and technical methodologies used; describe some examples of how it's worked; and challenges and opportunities for the future.

The Availability of Web 2.0 Tools from Community College Libraries' Websites Serving Large Student Bodies

ERIC Educational Resources Information Center

Blummer, Barbara; Kenton, Jeffrey M.

2014-01-01

Web 2.0 tools offer academic libraries new avenues for delivering services and resources to students. In this research we report on a content analysis of 100 US community college libraries' Websites for the availability of Web 2.0 applications. We found Web 2.0 tools utilized by 97% of our sample population and many of these sites contained more…

P-MartCancer: A New Online Platform to Access CPTAC Datasets and Enable New Analyses | Office of Cancer Clinical Proteomics Research

Cancer.gov

The November 1, 2017 issue of Cancer Research is dedicated to a collection of computational resource papers in genomics, proteomics, animal models, imaging, and clinical subjects for non-bioinformaticists looking to incorporate computing tools into their work. Scientists at Pacific Northwest National Laboratory have developed P-MartCancer, an open, web-based interactive software tool that enables statistical analyses of peptide or protein data generated from mass-spectrometry (MS)-based global proteomics experiments.

English for Business: Student Responses to Language Learning through Social Networking Tools

ERIC Educational Resources Information Center

García Laborda, Jesús; Litzler, Mary Frances

2017-01-01

This action research based case study addresses the situation of a first year class of Business English students at Universidad de Alcalá and their attitudes towards using Web 2.0 tools and social media for language learning. During the semester, the students were asked to collaborate in the creation and use of some tools such as blogs, video…

Accessing the public MIMIC-II intensive care relational database for clinical research.

PubMed

Scott, Daniel J; Lee, Joon; Silva, Ikaro; Park, Shinhyuk; Moody, George B; Celi, Leo A; Mark, Roger G

2013-01-10

The Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC-II) database is a free, public resource for intensive care research. The database was officially released in 2006, and has attracted a growing number of researchers in academia and industry. We present the two major software tools that facilitate accessing the relational database: the web-based QueryBuilder and a downloadable virtual machine (VM) image. QueryBuilder and the MIMIC-II VM have been developed successfully and are freely available to MIMIC-II users. Simple example SQL queries and the resulting data are presented. Clinical studies pertaining to acute kidney injury and prediction of fluid requirements in the intensive care unit are shown as typical examples of research performed with MIMIC-II. In addition, MIMIC-II has also provided data for annual PhysioNet/Computing in Cardiology Challenges, including the 2012 Challenge "Predicting mortality of ICU Patients". QueryBuilder is a web-based tool that provides easy access to MIMIC-II. For more computationally intensive queries, one can locally install a complete copy of MIMIC-II in a VM. Both publicly available tools provide the MIMIC-II research community with convenient querying interfaces and complement the value of the MIMIC-II relational database.

SuML: A Survey Markup Language for Generalized Survey Encoding

PubMed Central

Barclay, MW; Lober, WB; Karras, BT

2002-01-01

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

Characterizing Aerosols over Southeast Asia using the AERONET Data Synergy Tool

NASA Technical Reports Server (NTRS)

Giles, David M.; Holben, Brent N.; Eck, Thomas F.; Slutsker, Ilya; Slutsker, Ilya; Welton, Ellsworth, J.; Chin, Mian; Kucsera, Thomas; Schmaltz, Jeffery E.; Diehl, Thomas;

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.

A web tool for STORET/WQX water quality data retrieval and Best Management Practice scenario suggestion.

PubMed

Park, Youn Shik; Engel, Bernie A; Kim, Jonggun; Theller, Larry; Chaubey, Indrajeet; Merwade, Venkatesh; Lim, Kyoung Jae

2015-03-01

Total Maximum Daily Load is a water quality standard to regulate water quality of streams, rivers and lakes. A wide range of approaches are used currently to develop TMDLs for impaired streams and rivers. Flow and load duration curves (FDC and LDC) have been used in many states to evaluate the relationship between flow and pollutant loading along with other models and approaches. A web-based LDC Tool was developed to facilitate development of FDC and LDC as well as to support other hydrologic analyses. In this study, the FDC and LDC tool was enhanced to allow collection of water quality data via the web and to assist in establishing cost-effective Best Management Practice (BMP) implementations. The enhanced web-based tool provides use of water quality data not only from the US Geological Survey but also from the Water Quality Portal for the U.S. via web access. Moreover, the web-based tool identifies required pollutant reductions to meet standard loads and suggests a BMP scenario based on ability of BMPs to reduce pollutant loads, BMP establishment and maintenance costs. In the study, flow and water quality data were collected via web access to develop LDC and to identify the required reduction. The suggested BMP scenario from the web-based tool was evaluated using the EPA Spreadsheet Tool for the Estimation of Pollutant Load model to attain the required pollutant reduction at least cost. Copyright © 2014 Elsevier Ltd. All rights reserved.

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.

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.

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Supporting Middle School Students' Online Reading of Scientific Resources: Moving beyond Cursory, Fragmented, and Opportunistic Reading

ERIC Educational Resources Information Center

Zhang, M.

2013-01-01

The abundant scientific resources on the Web provide great opportunities for students to expand their science learning, yet easy access to information does not ensure learning. Prior research has found that middle school students tend to read Web-based scientific resources in a shallow, superficial manner. A software tool was designed to support…

Experiences with the BSCW Shared Workspace System as the Backbone of a Virtual Learning Environment for Students.

ERIC Educational Resources Information Center

Appelt, Wolfgang; Mambrey, Peter

The GMD (German National Research Center for Information Technology) has developed the BSCW (Basic Support for Cooperative Work) Shared Workspace system within the last four years with the goal of transforming the Web from a primarily passive information repository to an active cooperation medium. The BSCW system is a Web-based groupware tool for…

Personalised and Self Regulated Learning in the Web 2.0 Era: International Exemplars of Innovative Pedagogy Using Social Software

ERIC Educational Resources Information Center

McLoughlin, Catherine; Lee, Mark J. W.

2010-01-01

Research findings in recent years provide compelling evidence of the importance of encouraging student control over the learning process as a whole. The socially based tools and technologies of the Web 2.0 movement are capable of supporting informal conversation, reflexive dialogue and collaborative content generation, enabling access to a wide…

On Recommending Web 2.0 Tools to Personalise Learning

ERIC Educational Resources Information Center

Juškeviciene, Anita; Kurilovas, Eugenijus

2014-01-01

The paper aims to present research results on using Web 2.0 tools for learning personalisation. In the work, personalised Web 2.0 tools selection method is presented. This method takes into account student's learning preferences for content and communication modes tailored to the learning activities with a view to help the learner to quickly and…

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

deepTools: a flexible platform for exploring deep-sequencing data.

PubMed

Ramírez, Fidel; Dündar, Friederike; Diehl, Sarah; Grüning, Björn A; Manke, Thomas

2014-07-01

We present a Galaxy based web server for processing and visualizing deeply sequenced data. The web server's core functionality consists of a suite of newly developed tools, called deepTools, that enable users with little bioinformatic background to explore the results of their sequencing experiments in a standardized setting. Users can upload pre-processed files with continuous data in standard formats and generate heatmaps and summary plots in a straight-forward, yet highly customizable manner. In addition, we offer several tools for the analysis of files containing aligned reads and enable efficient and reproducible generation of normalized coverage files. As a modular and open-source platform, deepTools can easily be expanded and customized to future demands and developments. The deepTools webserver is freely available at http://deeptools.ie-freiburg.mpg.de and is accompanied by extensive documentation and tutorials aimed at conveying the principles of deep-sequencing data analysis. The web server can be used without registration. deepTools can be installed locally either stand-alone or as part of Galaxy. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

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.

Medicine 2.0: Social Networking, Collaboration, Participation, Apomediation, and Openness

PubMed Central

2008-01-01

In a very significant development for eHealth, a broad adoption of Web 2.0 technologies and approaches coincides with the more recent emergence of Personal Health Application Platforms and Personally Controlled Health Records such as Google Health, Microsoft HealthVault, and Dossia. “Medicine 2.0” applications, services, and tools are defined as Web-based services for health care consumers, caregivers, patients, health professionals, and biomedical researchers, that use Web 2.0 technologies and/or semantic web and virtual reality approaches to enable and facilitate specifically 1) social networking, 2) participation, 3) apomediation, 4) openness, and 5) collaboration, within and between these user groups. The Journal of Medical Internet Research (JMIR) publishes a Medicine 2.0 theme issue and sponsors a conference on “How Social Networking and Web 2.0 changes Health, Health Care, Medicine, and Biomedical Research”, to stimulate and encourage research in these five areas. PMID:18725354

Randomized Comparison of Mobile and Web-Tools to Provide Dementia Risk Reduction Education: Use, Engagement and Participant Satisfaction

PubMed Central

O'Connor, Elodie; Hatherly, Chris

2014-01-01

Background Encouraging middle-aged adults to maintain their physical and cognitive health may have a significant impact on reducing the prevalence of dementia in the future. Mobile phone apps and interactive websites may be one effective way to target this age group. However, to date there has been little research investigating the user experience of dementia risk reduction tools delivered in this way. Objective The aim of this study was to explore participant engagement and evaluations of three different targeted smartphone and Web-based dementia risk reduction tools following a four-week intervention. Methods Participants completed a Web-based screening questionnaire to collect eligibility information. Eligible participants were asked to complete a Web-based baseline questionnaire and were then randomly assigned to use one of the three dementia risk reduction tools for a period of four weeks: (1) a mobile phone application; (2) an information-based website; and (3) an interactive website. User evaluations were obtained via a Web-based follow-up questionnaire after completion of the intervention. Results Of 415 eligible participants, 370 (89.16%) completed the baseline questionnaire and were assigned to an intervention group; 200 (54.05%) completed the post-intervention questionnaire. The average age of participants was 52 years, and 149 (75%) were female. Findings indicated that participants from all three intervention groups reported a generally positive impression of the tools across a range of domains. Participants using the information-based website reported higher ratings of their overall impression of the tool, F2,191=4.12, P=.02; how interesting the information was, F2,189=3.53, P=.03; how helpful the information was, F2,192=4.15, P=.02; and how much they learned, F2,188=3.86, P=.02. Group differences were significant between the mobile phone app and information-based website users, but not between the interactive website users and the other two groups. Additionally, participants using the information-based website reported significantly higher scores on their ratings of the ease of navigation, F2,190=4.20, P=.02, than those using the mobile phone app and the interactive website. There were no significant differences between groups on ratings of ease of understanding the information, F2,188=0.27, P=.76. Most participants from each of the three intervention groups indicated that they intended to keep using the dementia risk reduction eHealth tool. Conclusions Overall, results indicated that while participants across all three intervention groups reported a generally positive experience with the targeted dementia risk reduction tools, participants using the information-based website provided a more favorable evaluation across a range of areas than participants using the mobile phone app. Further research is required to investigate whether targeted dementia risk reduction tools, in the form of interactive websites and mobile apps, can be improved to provide benefits above those gained by providing static information alone. PMID:26543904

Randomized Comparison of Mobile and Web-Tools to Provide Dementia Risk Reduction Education: Use, Engagement and Participant Satisfaction.

PubMed

O'Connor, Elodie; Farrow, Maree; Hatherly, Chris

2014-01-01

Encouraging middle-aged adults to maintain their physical and cognitive health may have a significant impact on reducing the prevalence of dementia in the future. Mobile phone apps and interactive websites may be one effective way to target this age group. However, to date there has been little research investigating the user experience of dementia risk reduction tools delivered in this way. The aim of this study was to explore participant engagement and evaluations of three different targeted smartphone and Web-based dementia risk reduction tools following a four-week intervention. Participants completed a Web-based screening questionnaire to collect eligibility information. Eligible participants were asked to complete a Web-based baseline questionnaire and were then randomly assigned to use one of the three dementia risk reduction tools for a period of four weeks: (1) a mobile phone application; (2) an information-based website; and (3) an interactive website. User evaluations were obtained via a Web-based follow-up questionnaire after completion of the intervention. Of 415 eligible participants, 370 (89.16%) completed the baseline questionnaire and were assigned to an intervention group; 200 (54.05%) completed the post-intervention questionnaire. The average age of participants was 52 years, and 149 (75%) were female. Findings indicated that participants from all three intervention groups reported a generally positive impression of the tools across a range of domains. Participants using the information-based website reported higher ratings of their overall impression of the tool, F2,191=4.12, P=.02; how interesting the information was, F2,189=3.53, P=.03; how helpful the information was, F2,192=4.15, P=.02; and how much they learned, F2,188=3.86, P=.02. Group differences were significant between the mobile phone app and information-based website users, but not between the interactive website users and the other two groups. Additionally, participants using the information-based website reported significantly higher scores on their ratings of the ease of navigation, F2,190=4.20, P=.02, than those using the mobile phone app and the interactive website. There were no significant differences between groups on ratings of ease of understanding the information, F2,188=0.27, P=.76. Most participants from each of the three intervention groups indicated that they intended to keep using the dementia risk reduction eHealth tool. Overall, results indicated that while participants across all three intervention groups reported a generally positive experience with the targeted dementia risk reduction tools, participants using the information-based website provided a more favorable evaluation across a range of areas than participants using the mobile phone app. Further research is required to investigate whether targeted dementia risk reduction tools, in the form of interactive websites and mobile apps, can be improved to provide benefits above those gained by providing static information alone.

C3: A Collaborative Web Framework for NASA Earth Exchange

NASA Astrophysics Data System (ADS)

Foughty, E.; Fattarsi, C.; Hardoyo, C.; Kluck, D.; Wang, L.; Matthews, B.; Das, K.; Srivastava, A.; Votava, P.; Nemani, R. R.

2010-12-01

The NASA Earth Exchange (NEX) is a new collaboration platform for the Earth science community that provides a mechanism for scientific collaboration and knowledge sharing. NEX combines NASA advanced supercomputing resources, Earth system modeling, workflow management, NASA remote sensing data archives, and a collaborative communication platform to deliver a complete work environment in which users can explore and analyze large datasets, run modeling codes, collaborate on new or existing projects, and quickly share results among the Earth science communities. NEX is designed primarily for use by the NASA Earth science community to address scientific grand challenges. The NEX web portal component provides an on-line collaborative environment for sharing of Eearth science models, data, analysis tools and scientific results by researchers. In addition, the NEX portal also serves as a knowledge network that allows researchers to connect and collaborate based on the research they are involved in, specific geographic area of interest, field of study, etc. Features of the NEX web portal include: Member profiles, resource sharing (data sets, algorithms, models, publications), communication tools (commenting, messaging, social tagging), project tools (wikis, blogs) and more. The NEX web portal is built on the proven technologies and policies of DASHlink.arc.nasa.gov, (one of NASA's first science social media websites). The core component of the web portal is a C3 framework, which was built using Django and which is being deployed as a common framework for a number of collaborative sites throughout NASA.

PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes

PubMed Central

Fong, Christine; Rohmer, Laurence; Radey, Matthew; Wasnick, Michael; Brittnacher, Mitchell J

2008-01-01

Background The conservation of gene order among prokaryotic genomes can provide valuable insight into gene function, protein interactions, or events by which genomes have evolved. Although some tools are available for visualizing and comparing the order of genes between genomes of study, few support an efficient and organized analysis between large numbers of genomes. The Prokaryotic Sequence homology Analysis Tool (PSAT) is a web tool for comparing gene neighborhoods among multiple prokaryotic genomes. Results PSAT utilizes a database that is preloaded with gene annotation, BLAST hit results, and gene-clustering scores designed to help identify regions of conserved gene order. Researchers use the PSAT web interface to find a gene of interest in a reference genome and efficiently retrieve the sequence homologs found in other bacterial genomes. The tool generates a graphic of the genomic neighborhood surrounding the selected gene and the corresponding regions for its homologs in each comparison genome. Homologs in each region are color coded to assist users with analyzing gene order among various genomes. In contrast to common comparative analysis methods that filter sequence homolog data based on alignment score cutoffs, PSAT leverages gene context information for homologs, including those with weak alignment scores, enabling a more sensitive analysis. Features for constraining or ordering results are designed to help researchers browse results from large numbers of comparison genomes in an organized manner. PSAT has been demonstrated to be useful for helping to identify gene orthologs and potential functional gene clusters, and detecting genome modifications that may result in loss of function. Conclusion PSAT allows researchers to investigate the order of genes within local genomic neighborhoods of multiple genomes. A PSAT web server for public use is available for performing analyses on a growing set of reference genomes through any web browser with no client side software setup or installation required. Source code is freely available to researchers interested in setting up a local version of PSAT for analysis of genomes not available through the public server. Access to the public web server and instructions for obtaining source code can be found at . PMID:18366802

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.

Environmental Inquiry by College Students: Original Research and Peer Review Using Web-Based Collaborative Tools. Preliminary Quantitative Data Analysis.

ERIC Educational Resources Information Center

Cakir, Mustafa; Carlsen, William S.

The Environmental Inquiry (EI) program (Cornell University and Pennsylvania State University) supports inquiry based, student-centered science teaching on selected topics in the environmental sciences. Texts to support high school student research are published by the National Science Teachers Association (NSTA) in the domains of environmental…

SMARTE: SUSTAINABLE MANAGEMENT APPROACHES AND REVITALIZATION TOOLS ELECTRONIC (CINCINNATI, OHIO)

EPA Science Inventory

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

EPA’s EnviroAtlas: Identifying Nature’s Benefits, Deficits, and Opportunities for Equitable Distribution in Populated Places#

EPA Science Inventory

The web-based EnviroAtlas is an easy-to-use mapping and analysis tool built by the U.S. Environmental Protection Agency and its partners to provide information, data, and research on the relationships between ecosystems, built infrastructure, and societal well-being. The tool is ...

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.

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.

Selecting a Free Web-Hosted Survey Tool for Student Use

ERIC Educational Resources Information Center

Elbeck, Matt

2014-01-01

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

bioWeb3D: an online webGL 3D data visualisation tool.

PubMed

Pettit, Jean-Baptiste; Marioni, John C

2013-06-07

Data visualization is critical for interpreting biological data. However, in practice it can prove to be a bottleneck for non trained researchers; this is especially true for three dimensional (3D) data representation. Whilst existing software can provide all necessary functionalities to represent and manipulate biological 3D datasets, very few are easily accessible (browser based), cross platform and accessible to non-expert users. An online HTML5/WebGL based 3D visualisation tool has been developed to allow biologists to quickly and easily view interactive and customizable three dimensional representations of their data along with multiple layers of information. Using the WebGL library Three.js written in Javascript, bioWeb3D allows the simultaneous visualisation of multiple large datasets inputted via a simple JSON, XML or CSV file, which can be read and analysed locally thanks to HTML5 capabilities. Using basic 3D representation techniques in a technologically innovative context, we provide a program that is not intended to compete with professional 3D representation software, but that instead enables a quick and intuitive representation of reasonably large 3D datasets.

PhytoCRISP-Ex: a web-based and stand-alone application to find specific target sequences for CRISPR/CAS editing.

PubMed

Rastogi, Achal; Murik, Omer; Bowler, Chris; Tirichine, Leila

2016-07-01

With the emerging interest in phytoplankton research, the need to establish genetic tools for the functional characterization of genes is indispensable. The CRISPR/Cas9 system is now well recognized as an efficient and accurate reverse genetic tool for genome editing. Several computational tools have been published allowing researchers to find candidate target sequences for the engineering of the CRISPR vectors, while searching possible off-targets for the predicted candidates. These tools provide built-in genome databases of common model organisms that are used for CRISPR target prediction. Although their predictions are highly sensitive, the applicability to non-model genomes, most notably protists, makes their design inadequate. This motivated us to design a new CRISPR target finding tool, PhytoCRISP-Ex. Our software offers CRIPSR target predictions using an extended list of phytoplankton genomes and also delivers a user-friendly standalone application that can be used for any genome. The software attempts to integrate, for the first time, most available phytoplankton genomes information and provide a web-based platform for Cas9 target prediction within them with high sensitivity. By offering a standalone version, PhytoCRISP-Ex maintains an independence to be used with any organism and widens its applicability in high throughput pipelines. PhytoCRISP-Ex out pars all the existing tools by computing the availability of restriction sites over the most probable Cas9 cleavage sites, which can be ideal for mutant screens. PhytoCRISP-Ex is a simple, fast and accurate web interface with 13 pre-indexed and presently updating phytoplankton genomes. The software was also designed as a UNIX-based standalone application that allows the user to search for target sequences in the genomes of a variety of other species.

Using a Learning Styles Inventory to Examine Student Satisfaction with Web-Based Instruction: A 15-Year Study of One Professor's Web-Based Course Instruction

ERIC Educational Resources Information Center

Olliges, Ralph

2017-01-01

This article examines Active Engagement, Active Communication, and Peer Engagement learning practices among various student groups. It examines which tools are most important for increasing student satisfaction with web-based and web-enhanced instruction. Second, it looks at how different tools lead to greater satisfaction among different types of…

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

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

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.

Web based tools for data manipulation, visualisation and validation with interactive georeferenced graphs

NASA Astrophysics Data System (ADS)

Ivankovic, D.; Dadic, V.

2009-04-01

Some of oceanographic parameters have to be manually inserted into database; some (for example data from CTD probe) are inserted from various files. All this parameters requires visualization, validation and manipulation from research vessel or scientific institution, and also public presentation. For these purposes is developed web based system, containing dynamic sql procedures and java applets. Technology background is Oracle 10g relational database, and Oracle application server. Web interfaces are developed using PL/SQL stored database procedures (mod PL/SQL). Additional parts for data visualization include use of Java applets and JavaScript. Mapping tool is Google maps API (javascript) and as alternative java applet. Graph is realized as dynamically generated web page containing java applet. Mapping tool and graph are georeferenced. That means that click on some part of graph, automatically initiate zoom or marker onto location where parameter was measured. This feature is very useful for data validation. Code for data manipulation and visualization are partially realized with dynamic SQL and that allow as to separate data definition and code for data manipulation. Adding new parameter in system requires only data definition and description without programming interface for this kind of data.

A web-based program to increase knowledge and reduce cigarette and nargila smoking among Arab university students in Israel: mixed-methods study to test acceptability.

PubMed

Essa-Hadad, Jumanah; Linn, Shai; Rafaeli, Sheizaf

2015-02-20

Among Arab citizens in Israel, cigarette and nargila (hookah, waterpipe) smoking is a serious public health problem, particularly among the young adult population. With the dramatic increase of Internet and computer use among Arab college and university students, a Web-based program may provide an easy, accessible tool to reduce smoking rates without heavy resource demands required by traditional methods. The purpose of this research was to examine the acceptability and feasibility of a pilot Web-based program that provides tailored feedback to increase smoking knowledge and reduce cigarette and nargila smoking behaviors among Arab college/university students in Israel. A pilot Web-based program was developed, consisting of a self-administered questionnaire and feedback system on cigarette and nargila smoking. Arab university students were recruited to participate in a mixed-methods study, using both quantitative (pre-/posttest study design) and qualitative tools. A posttest was implemented at 1 month following participation in the intervention to assess any changes in smoking knowledge and behaviors. Focus group sessions were implemented to assess acceptability and preferences related to the Web-based program. A total of 225 participants-response rate of 63.2% (225/356)-completed the intervention at baseline and at 1-month poststudy, and were used for the comparative analysis. Statistically significant reductions in nargila smoking among participants (P=.001) were found. The intervention did not result in reductions in cigarette smoking. However, the tailored Web intervention resulted in statistically significant increases in the intention to quit smoking (P=.021). No statistically significant increases in knowledge were seen at 1-month poststudy. Participants expressed high satisfaction with the intervention and 93.8% (211/225) of those who completed the intervention at both time intervals reported that they would recommend the program to their friends, indicating excellent acceptability and feasibility of the intervention. This was further emphasized in the focus group sessions. A tailored Web-based program may be a promising tool to reduce nargila smoking among Arab university students in Israel. The tailored Web intervention was not successful at significantly reducing cigarette smoking or increasing knowledge. However, the intervention did increase participants' intention to quit smoking. Participants considered the Web-based tool to be an interesting, feasible, and highly acceptable strategy. ISRCTN registry ISRCTN59207794; http://www.isrctn.com/ISRCTN59207794 (Archived by WebCite at http://www.webcitation.org/6VkYOBNOJ).

A Web-Based Program to Increase Knowledge and Reduce Cigarette and Nargila Smoking Among Arab University Students in Israel: Mixed-Methods Study to Test Acceptability

PubMed Central

Linn, Shai; Rafaeli, Sheizaf

2015-01-01

Background Among Arab citizens in Israel, cigarette and nargila (hookah, waterpipe) smoking is a serious public health problem, particularly among the young adult population. With the dramatic increase of Internet and computer use among Arab college and university students, a Web-based program may provide an easy, accessible tool to reduce smoking rates without heavy resource demands required by traditional methods. Objective The purpose of this research was to examine the acceptability and feasibility of a pilot Web-based program that provides tailored feedback to increase smoking knowledge and reduce cigarette and nargila smoking behaviors among Arab college/university students in Israel. Methods A pilot Web-based program was developed, consisting of a self-administered questionnaire and feedback system on cigarette and nargila smoking. Arab university students were recruited to participate in a mixed-methods study, using both quantitative (pre-/posttest study design) and qualitative tools. A posttest was implemented at 1 month following participation in the intervention to assess any changes in smoking knowledge and behaviors. Focus group sessions were implemented to assess acceptability and preferences related to the Web-based program. Results A total of 225 participants—response rate of 63.2% (225/356)—completed the intervention at baseline and at 1-month poststudy, and were used for the comparative analysis. Statistically significant reductions in nargila smoking among participants (P=.001) were found. The intervention did not result in reductions in cigarette smoking. However, the tailored Web intervention resulted in statistically significant increases in the intention to quit smoking (P=.021). No statistically significant increases in knowledge were seen at 1-month poststudy. Participants expressed high satisfaction with the intervention and 93.8% (211/225) of those who completed the intervention at both time intervals reported that they would recommend the program to their friends, indicating excellent acceptability and feasibility of the intervention. This was further emphasized in the focus group sessions. Conclusions A tailored Web-based program may be a promising tool to reduce nargila smoking among Arab university students in Israel. The tailored Web intervention was not successful at significantly reducing cigarette smoking or increasing knowledge. However, the intervention did increase participants’ intention to quit smoking. Participants considered the Web-based tool to be an interesting, feasible, and highly acceptable strategy. Trial Registration Trial Registration: ISRCTN registry ISRCTN59207794; http://www.isrctn.com/ISRCTN59207794 (Archived by WebCite at http://www.webcitation.org/6VkYOBNOJ). PMID:25707034

An online planning tool for designing terrace layouts

USDA-ARS?s Scientific Manuscript database

A web-based conservation planning tool, WebTERLOC (web-based Terrace Location Program), was developed to provide multiple terrace layout options using digital elevation model (DEM) and geographic information systems (GIS). Development of a terrace system is complicated by the time-intensive manual ...

Web-Based Course Delivery and Administration Using Scheme.

ERIC Educational Resources Information Center

Salustri, Filippo A.

This paper discusses the use at the University of Windsor (Ontario) of a small World Wide Web-based tool for course delivery and administration called HAL (HTML-based Administrative Lackey), written in the Scheme programming language. This tool was developed by the author to provide Web-based services for a large first-year undergraduate course in…

ORD'S BROWNFIELDS RESEARCH

EPA Science Inventory

SMARTe is a web-based,decision support tool for developing and evaluating plans for redevelopment/revitalization of potentially contaminated sites. Brownfield project stakeholders should use SMARTe to: (1) Assess both market and non-market costs and benefits of potential redevelo...

ASA24 enables multiple automatically coded self-administered 24-hour recalls and food records

Cancer.gov

A freely available web-based tool for epidemiologic, interventional, behavioral, or clinical research from NCI that enables multiple automatically coded self-administered 24-hour recalls and food records.

Laura Jackson, Ph.D.

EPA Pesticide Factsheets

Research Biologist with the EPA. Her current work involves linking natural and built infrastructure to human health and well-being at multiple spatial scales, in order to develop interpretive maps and analytical tools for an interactive, web-based Atlas.

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

PubMed

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

2014-04-01

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

TU-CD-304-11: Veritas 2.0: A Cloud-Based Tool to Facilitate Research and Innovation

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

Mishra, P; Patankar, A; Etmektzoglou, A

Purpose: We introduce Veritas 2.0, a cloud-based, non-clinical research portal, to facilitate translation of radiotherapy research ideas to new delivery techniques. The ecosystem of research tools includes web apps for a research beam builder for TrueBeam Developer Mode, an image reader for compressed and uncompressed XIM files, and a trajectory log file based QA/beam delivery analyzer. Methods: The research beam builder can generate TrueBeam readable XML file either from scratch or from pre-existing DICOM-RT plans. DICOM-RT plan is first converted to XML format and then researcher can interactively modify or add control points to them. Delivered beam can be verifiedmore » via reading generated images and analyzing trajectory log files. Image reader can read both uncompressed and HND-compressed XIM images. The trajectory log analyzer lets researchers plot expected vs. actual values and deviations among 30 mechanical axes. The analyzer gives an animated view of MLC patterns for the beam delivery. Veritas 2.0 is freely available and its advantages versus standalone software are i) No software installation or maintenance needed, ii) easy accessibility across all devices iii) seamless upgrades and iv) OS independence. Veritas is written using open-source tools like twitter bootstrap, jQuery, flask, and Python-based modules. Results: In the first experiment, an anonymized 7-beam DICOM-RT IMRT plan was converted to XML beam containing 1400 control points. kV and MV imaging points were inserted into this XML beam. In another experiment, a binary log file was analyzed to compare actual vs expected values and deviations among axes. Conclusions: Veritas 2.0 is a public cloud-based web app that hosts a pool of research tools for facilitating research from conceptualization to verification. It is aimed at providing a platform for facilitating research and collaboration. I am full time employee at Varian Medical systems, Palo Alto.« less

Developing creativity and problem-solving skills of engineering students: a comparison of web- and pen-and-paper-based approaches

NASA Astrophysics Data System (ADS)

Valentine, Andrew; Belski, Iouri; Hamilton, Margaret

2017-11-01

Problem-solving is a key engineering skill, yet is an area in which engineering graduates underperform. This paper investigates the potential of using web-based tools to teach students problem-solving techniques without the need to make use of class time. An idea generation experiment involving 90 students was designed. Students were surveyed about their study habits and reported they use electronic-based materials more than paper-based materials while studying, suggesting students may engage with web-based tools. Students then generated solutions to a problem task using either a paper-based template or an equivalent web interface. Students who used the web-based approach performed as well as students who used the paper-based approach, suggesting the technique can be successfully adopted and taught online. Web-based tools may therefore be adopted as supplementary material in a range of engineering courses as a way to increase students' options for enhancing problem-solving skills.

A Performance-Based Web Budget Tool

ERIC Educational Resources Information Center

Abou-Sayf, Frank K.; Lau, Wilson

2007-01-01

A web-based formula-driven tool has been developed for the purpose of performing two distinct academic department budgeting functions: allocation funding to the department, and budget management by the department. The tool's major features are discussed and its uses demonstrated. The tool's advantages are presented. (Contains 10 figures.)

BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.

PubMed

Moreno, Pablo; Beisken, Stephan; Harsha, Bhavana; Muthukrishnan, Venkatesh; Tudose, Ilinca; Dekker, Adriano; Dornfeldt, Stefanie; Taruttis, Franziska; Grosse, Ivo; Hastings, Janna; Neumann, Steffen; Steinbeck, Christoph

2015-02-21

Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biological entities, enrichment analysis methods assess whether there is a significant over or under representation of entities for ontology classes. While many tools exist that run enrichment analysis for protein sets annotated with the Gene Ontology, there are only a few that can be used for small molecules enrichment analysis. We describe BiNChE, an enrichment analysis tool for small molecules based on the ChEBI Ontology. BiNChE displays an interactive graph that can be exported as a high-resolution image or in network formats. The tool provides plain, weighted and fragment analysis based on either the ChEBI Role Ontology or the ChEBI Structural Ontology. BiNChE aids in the exploration of large sets of small molecules produced within Metabolomics or other Systems Biology research contexts. The open-source tool provides easy and highly interactive web access to enrichment analysis with the ChEBI ontology tool and is additionally available as a standalone library.

Simple Web-based interactive key development software (WEBiKEY) and an example key for Kuruna (Poaceae: Bambusoideae)1

PubMed Central

Attigala, Lakshmi; De Silva, Nuwan I.; Clark, Lynn G.

2016-01-01

Premise of the study: Programs that are user-friendly and freely available for developing Web-based interactive keys are scarce and most of the well-structured applications are relatively expensive. WEBiKEY was developed to enable researchers to easily develop their own Web-based interactive keys with fewer resources. Methods and Results: A Web-based multiaccess identification tool (WEBiKEY) was developed that uses freely available Microsoft ASP.NET technologies and an SQL Server database for Windows-based hosting environments. WEBiKEY was tested for its usability with a sample data set, the temperate woody bamboo genus Kuruna (Poaceae). Conclusions: WEBiKEY is freely available to the public and can be used to develop Web-based interactive keys for any group of species. The interactive key we developed for Kuruna using WEBiKEY enables users to visually inspect characteristics of Kuruna and identify an unknown specimen as one of seven possible species in the genus. PMID:27144109

LandEx - Fast, FOSS-Based Application for Query and Retrieval of Land Cover Patterns

NASA Astrophysics Data System (ADS)

Netzel, P.; Stepinski, T.

2012-12-01

The amount of satellite-based spatial data is continuously increasing making a development of efficient data search tools a priority. The bulk of existing research on searching satellite-gathered data concentrates on images and is based on the concept of Content-Based Image Retrieval (CBIR); however, available solutions are not efficient and robust enough to be put to use as deployable web-based search tools. Here we report on development of a practical, deployable tool that searches classified, rather than raw image. LandEx (Landscape Explorer) is a GeoWeb-based tool for Content-Based Pattern Retrieval (CBPR) contained within the National Land Cover Dataset 2006 (NLCD2006). The USGS-developed NLCD2006 is derived from Landsat multispectral images; it covers the entire conterminous U.S. with the resolution of 30 meters/pixel and it depicts 16 land cover classes. The size of NLCD2006 is about 10 Gpixels (161,000 x 100,000 pixels). LandEx is a multi-tier GeoWeb application based on Open Source Software. Main components are: GeoExt/OpenLayers (user interface), GeoServer (OGC WMS, WCS and WPS server), and GRASS (calculation engine). LandEx performs search using query-by-example approach: user selects a reference scene (exhibiting a chosen pattern of land cover classes) and the tool produces, in real time, a map indicating a degree of similarity between the reference pattern and all local patterns across the U.S. Scene pattern is encapsulated by a 2D histogram of classes and sizes of single-class clumps. Pattern similarity is based on the notion of mutual information. The resultant similarity map can be viewed and navigated in a web browser, or it can download as a GeoTiff file for more in-depth analysis. The LandEx is available at http://sil.uc.edu

The Impact of Self-Efficacy and Professional Development on Implementation of Web 2.0 Tools in Elementary Classrooms

ERIC Educational Resources Information Center

Ward, Stephen

2015-01-01

This study sought to understand the impact of self-efficacy and professional development on the implementation of specific Web 2.0 tools in the elementary classroom. There were three research questions addressed in this QUAN-Qual study. Quantitative data were collected through three surveys with 48 total participants: the Web 2.0 tools Utilization…

NASA-Langley Web-Based Operational Real-time Cloud Retrieval Products from Geostationary Satellites

NASA Technical Reports Server (NTRS)

Palikonda, Rabindra; Minnis, Patrick; Spangenberg, Douglas A.; Khaiyer, Mandana M.; Nordeen, Michele L.; Ayers, Jeffrey K.; Nguyen, Louis; Yi, Yuhong; Chan, P. K.; Trepte, Qing Z.;

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.

Terminal Restriction Fragment Length Polymorphism Analysis Program, a Web-Based Research Tool for Microbial Community Analysis

PubMed Central

Marsh, Terence L.; Saxman, Paul; Cole, James; Tiedje, James

2000-01-01

Rapid analysis of microbial communities has proven to be a difficult task. This is due, in part, to both the tremendous diversity of the microbial world and the high complexity of many microbial communities. Several techniques for community analysis have emerged over the past decade, and most take advantage of the molecular phylogeny derived from 16S rRNA comparative sequence analysis. We describe a web-based research tool located at the Ribosomal Database Project web site (http://www.cme.msu.edu/RDP/html/analyses.html) that facilitates microbial community analysis using terminal restriction fragment length polymorphism of 16S ribosomal DNA. The analysis function (designated TAP T-RFLP) permits the user to perform in silico restriction digestions of the entire 16S sequence database and derive terminal restriction fragment sizes, measured in base pairs, from the 5′ terminus of the user-specified primer to the 3′ terminus of the restriction endonuclease target site. The output can be sorted and viewed either phylogenetically or by size. It is anticipated that the site will guide experimental design as well as provide insight into interpreting results of community analysis with terminal restriction fragment length polymorphisms. PMID:10919828

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

NASA Astrophysics Data System (ADS)

Clements, Oliver; Walker, Peter

2017-04-01

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

Arctic Logistics Information and Support: ALIAS

NASA Astrophysics Data System (ADS)

Warnick, W. K.

2004-12-01

The ALIAS web site is a gateway to logistics information for arctic research, funded by the U.S. National Science Foundation, and created and maintained by the Arctic Research Consortium of the United States (ARCUS). ALIAS supports the collaborative development and efficient use of all arctic logistics resources. It presents information from a searchable database, including both arctic terrestrial resources and arctic-capable research vessels, on a circumpolar scale. With this encompassing scope, ALIAS is uniquely valuable as a tool to promote and facilitate international collaboration between researchers, which is of increasing importance for vessel-based research due to the high cost and limited number of platforms. Users of the web site can identify vessels which are potential platforms for their research, examine and compare vessel specifications and facilities, learn about research cruises the vessel has performed in the past, and find contact information for scientists who have used the vessel, as well as for the owners and operators of the vessel. The purpose of this poster presentation is to inform the scientific community about the ALIAS website as a tool for planning arctic research generally, and particularly for identifying and contacting vessels which may be suitable for planned ship-based research projects in arctic seas.

Weather forecasting with open source software

NASA Astrophysics Data System (ADS)

Rautenhaus, Marc; Dörnbrack, Andreas

2013-04-01

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

WaveNet: A Web-Based Metocean Data Access, Processing and Analysis Tool. Part 4 - GLOS/GLCFS Database

DTIC Science & Technology

2014-06-01

and Coastal Data Information Program ( CDIP ). This User’s Guide includes step-by-step instructions for accessing the GLOS/GLCFS database via WaveNet...access, processing and analysis tool; part 3 – CDIP database. ERDC/CHL CHETN-xx-14. Vicksburg, MS: U.S. Army Engineer Research and Development Center

SMARTE: RESTORING THE ENVIRONMENT, REVITALIZING COMMUNITIES - NOV. 15, 2006 - ELECTRONIC TOOLS AND RESOURCES SESSION

EPA Science Inventory

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

Managing Epilepsy Well: Emerging e-Tools for epilepsy self-management.

PubMed

Shegog, Ross; Bamps, Yvan A; Patel, Archna; Kakacek, Jody; Escoffery, Cam; Johnson, Erica K; Ilozumba, Ukwuoma O

2013-10-01

The Managing Epilepsy Well (MEW) Network was established in 2007 by the Centers for Disease Control and Prevention Epilepsy Program to expand epilepsy self-management research. The network has employed collaborative research strategies to develop, test, and disseminate evidence-based, community-based, and e-Health interventions (e-Tools) for epilepsy self-management for people with epilepsy, caregivers, and health-care providers. Since its inception, MEW Network collaborators have conducted formative studies (n=7) investigating the potential of e-Health to support epilepsy self-management and intervention studies evaluating e-Tools (n=5). The MEW e-Tools (the MEW website, WebEase, UPLIFT, MINDSET, and PEARLS online training) and affiliated e-Tools (Texting 4 Control) are designed to complement self-management practices in each phase of the epilepsy care continuum. These tools exemplify a concerted research agenda, shared methodological principles and models for epilepsy self-management, and a communal knowledge base for implementing e-Health to improve quality of life for people with epilepsy. © 2013.

Web-Based Tools for Text-Based Patient-Provider Communication in Chronic Conditions: Scoping Review.

PubMed

Voruganti, Teja; Grunfeld, Eva; Makuwaza, Tutsirai; Bender, Jacqueline L

2017-10-27

Patients with chronic conditions require ongoing care which not only necessitates support from health care providers outside appointments but also self-management. Web-based tools for text-based patient-provider communication, such as secure messaging, allow for sharing of contextual information and personal narrative in a simple accessible medium, empowering patients and enabling their providers to address emerging care needs. The objectives of this study were to (1) conduct a systematic search of the published literature and the Internet for Web-based tools for text-based communication between patients and providers; (2) map tool characteristics, their intended use, contexts in which they were used, and by whom; (3) describe the nature of their evaluation; and (4) understand the terminology used to describe the tools. We conducted a scoping review using the MEDLINE (Medical Literature Analysis and Retrieval System Online) and EMBASE (Excerpta Medica Database) databases. We summarized information on the characteristics of the tools (structure, functions, and communication paradigm), intended use, context and users, evaluation (study design and outcomes), and terminology. We performed a parallel search of the Internet to compare with tools identified in the published literature. We identified 54 papers describing 47 unique tools from 13 countries studied in the context of 68 chronic health conditions. The majority of tools (77%, 36/47) had functions in addition to communication (eg, viewable care plan, symptom diary, or tracker). Eight tools (17%, 8/47) were described as allowing patients to communicate with the team or multiple health care providers. Most of the tools were intended to support communication regarding symptom reporting (49%, 23/47), and lifestyle or behavior modification (36%, 17/47). The type of health care providers who used tools to communicate with patients were predominantly allied health professionals of various disciplines (30%, 14/47), nurses (23%, 11/47), and physicians (19%, 9/47), among others. Over half (52%, 25/48) of the tools were evaluated in randomized controlled trials, and 23 tools (48%, 23/48) were evaluated in nonrandomized studies. Terminology of tools varied by intervention type and functionality and did not consistently reflect a theme of communication. The majority of tools found in the Internet search were patient portals from 6 developers; none were found among published articles. Web-based tools for text-based patient-provider communication were identified from a wide variety of clinical contexts and with varied functionality. Tools were most prevalent in contexts where intended use was self-management. Few tools for team-based communication were found, but this may become increasingly important as chronic disease care becomes more interdisciplinary. ©Teja Voruganti, Eva Grunfeld, Tutsirai Makuwaza, Jacqueline L Bender. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 27.10.2017.

Introduction of a web portal for an Individual Health Management and observational health data sciences.

PubMed

Melchart, Dieter; Eustachi, Axel; Gronwald, Stephan; Wühr, Erich; Wifling, Kristina; Bachmeier, Beatrice E

2018-01-01

There is a global trend to a stronger active involvement of persons in the maintenance and restoring of health. The Competence Centre for Complementary Medicine and Naturopathy (CoCoNat) of the Technical University of Munich (TUM) has developed a lifestyle concept to enable each individual to manage his or her health - Individual Health Management (IHM) - and a web-based health portal named Virtual Tool for Education, Reporting, Information and Outcomes (VITERIO ® ), which addresses these needs for practice and research. The objectives of this study were to establish a core set of questionnaires for a self-assessment program on certain risk indications and comprehensive protection factors of health and to develop and enhance 1) tools for individual feedback, longitudinal self-monitoring, self-assessment, and (self-)care-planning; 2) training packages; 3) open notes and records for provider and patient; and 4) tools for monitoring groups and single participants in various indicators for individual coaching and scientific evaluation. The CoCoNat of TUM, Faculty for Applied Health Science of Technische Hochschule Deggendorf, VITERIO ® company, IHM campus network, and Erich Rothenfußer Foundation, Munich, provide a consortium responsible for content, research strategy, technical production and implication, postgraduate education for IHM coaches, implementation of IHM in various settings, and funding resources. A data set of indicators for health screening and self-monitoring of findings, symptoms, health behavior, and attitudes are integrated into a web-based health portal named VITERIO ® . The article introduces some implemented graphical solutions of developed tools and gives examples for daily use. Behavioral change and adaptation in attitudes and personal values are difficult issues of health education and lifestyle medicine. To address this problem best, the implementation of a patient-centric, performance measures-based program including open records and a blended learning concept were elaborated. The combination of an individual web-based health portal with personal coaching allows the implementation of IHM in everyday practice.

Applying Web-Based Tools for Research, Engineering, and Operations

NASA Technical Reports Server (NTRS)

Ivancic, William D.

2011-01-01

Personnel in the NASA Glenn Research Center Network and Architectures branch have performed a variety of research related to space-based sensor webs, network centric operations, security and delay tolerant networking (DTN). Quality documentation and communications, real-time monitoring and information dissemination are critical in order to perform quality research while maintaining low cost and utilizing multiple remote systems. This has been accomplished using a variety of Internet technologies often operating simultaneously. This paper describes important features of various technologies and provides a number of real-world examples of how combining Internet technologies can enable a virtual team to act efficiently as one unit to perform advanced research in operational systems. Finally, real and potential abuses of power and manipulation of information and information access is addressed.

Teaching with technology: automatically receiving information from the internet and web.

PubMed

Wink, Diane M

2010-01-01

In this bimonthly series, the author examines how nurse educators can use the Internet and Web-based computer technologies such as search, communication, and collaborative writing tools, social networking and social bookmarking sites, virtual worlds, and Web-based teaching and learning programs. This article presents information and tools related to automatically receiving information from the Internet and Web.

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.

Assessing the Effect of Web-Based Learning Tools on Student Understanding of Stoichiometry Using Knowledge Space Theory

ERIC Educational Resources Information Center

Arasasingham, Ramesh D.; Taagepera, Mare; Potter, Frank; Martorell, Ingrid; Lonjers, Stacy

2005-01-01

Student achievement in web-based learning tools is assessed by using in-class examination, pretests, and posttests. The study reveals that using mastering chemistry web software in large-scale instruction provides an overall benefit to introductory chemistry students.

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

Adding tools to the open source toolbox: The Internet

NASA Technical Reports Server (NTRS)

Porth, Tricia

1994-01-01

The Internet offers researchers additional sources of information not easily available from traditional sources such as print volumes or commercial data bases. Internet tools such as e-mail and file transfer protocol (ftp) speed up the way researchers communicate and transmit data. Mosaic, one of the newest additions to the Internet toolbox, allows users to combine tools such as ftp, gopher, wide area information server, and the world wide web with multimedia capabilities. Mosaic has quickly become a popular means of making information available on the Internet because it is versatile and easily customizable.

Accessing the public MIMIC-II intensive care relational database for clinical research

PubMed Central

2013-01-01

Background The Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC-II) database is a free, public resource for intensive care research. The database was officially released in 2006, and has attracted a growing number of researchers in academia and industry. We present the two major software tools that facilitate accessing the relational database: the web-based QueryBuilder and a downloadable virtual machine (VM) image. Results QueryBuilder and the MIMIC-II VM have been developed successfully and are freely available to MIMIC-II users. Simple example SQL queries and the resulting data are presented. Clinical studies pertaining to acute kidney injury and prediction of fluid requirements in the intensive care unit are shown as typical examples of research performed with MIMIC-II. In addition, MIMIC-II has also provided data for annual PhysioNet/Computing in Cardiology Challenges, including the 2012 Challenge “Predicting mortality of ICU Patients”. Conclusions QueryBuilder is a web-based tool that provides easy access to MIMIC-II. For more computationally intensive queries, one can locally install a complete copy of MIMIC-II in a VM. Both publicly available tools provide the MIMIC-II research community with convenient querying interfaces and complement the value of the MIMIC-II relational database. PMID:23302652

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.

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

PubMed Central

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

2006-01-01

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

enoLOGOS: a versatile web tool for energy normalized sequence logos

PubMed Central

Workman, Christopher T.; Yin, Yutong; Corcoran, David L.; Ideker, Trey; Stormo, Gary D.; Benos, Panayiotis V.

2005-01-01

enoLOGOS is a web-based tool that generates sequence logos from various input sources. Sequence logos have become a popular way to graphically represent DNA and amino acid sequence patterns from a set of aligned sequences. Each position of the alignment is represented by a column of stacked symbols with its total height reflecting the information content in this position. Currently, the available web servers are able to create logo images from a set of aligned sequences, but none of them generates weighted sequence logos directly from energy measurements or other sources. With the advent of high-throughput technologies for estimating the contact energy of different DNA sequences, tools that can create logos directly from binding affinity data are useful to researchers. enoLOGOS generates sequence logos from a variety of input data, including energy measurements, probability matrices, alignment matrices, count matrices and aligned sequences. Furthermore, enoLOGOS can represent the mutual information of different positions of the consensus sequence, a unique feature of this tool. Another web interface for our software, C2H2-enoLOGOS, generates logos for the DNA-binding preferences of the C2H2 zinc-finger transcription factor family members. enoLOGOS and C2H2-enoLOGOS are accessible over the web at . PMID:15980495

Web-Based-Research as Critical Pedagogy: A Reflection on Its Application to Undergraduate Management Education

ERIC Educational Resources Information Center

Coronado, Gabriela

2011-01-01

In disciplines such as Management, where research capacity is not seen as an obvious workplace skill, it is difficult to get students to engage in research activities. They see them as too difficult and without value. However, research activities in undergraduate Management education are vital as tools for developing key learning attributes such…

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.

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

A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data

PubMed Central

2014-01-01

Abstract ChIP-Seq (chromatin immunoprecipitation sequencing) has provided the advantage for finding motifs as ChIP-Seq experiments narrow down the motif finding to binding site locations. Recent motif finding tools facilitate the motif detection by providing user-friendly Web interface. In this work, we reviewed nine motif finding Web tools that are capable for detecting binding site motifs in ChIP-Seq data. We showed each motif finding Web tool has its own advantages for detecting motifs that other tools may not discover. We recommended the users to use multiple motif finding Web tools that implement different algorithms for obtaining significant motifs, overlapping resemble motifs, and non-overlapping motifs. Finally, we provided our suggestions for future development of motif finding Web tool that better assists researchers for finding motifs in ChIP-Seq data. Reviewers This article was reviewed by Prof. Sandor Pongor, Dr. Yuriy Gusev, and Dr. Shyam Prabhakar (nominated by Prof. Limsoon Wong). PMID:24555784

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

Clinical software development for the Web: lessons learned from the BOADICEA project

PubMed Central

2012-01-01

Background In the past 20 years, society has witnessed the following landmark scientific advances: (i) the sequencing of the human genome, (ii) the distribution of software by the open source movement, and (iii) the invention of the World Wide Web. Together, these advances have provided a new impetus for clinical software development: developers now translate the products of human genomic research into clinical software tools; they use open-source programs to build them; and they use the Web to deliver them. Whilst this open-source component-based approach has undoubtedly made clinical software development easier, clinical software projects are still hampered by problems that traditionally accompany the software process. This study describes the development of the BOADICEA Web Application, a computer program used by clinical geneticists to assess risks to patients with a family history of breast and ovarian cancer. The key challenge of the BOADICEA Web Application project was to deliver a program that was safe, secure and easy for healthcare professionals to use. We focus on the software process, problems faced, and lessons learned. Our key objectives are: (i) to highlight key clinical software development issues; (ii) to demonstrate how software engineering tools and techniques can facilitate clinical software development for the benefit of individuals who lack software engineering expertise; and (iii) to provide a clinical software development case report that can be used as a basis for discussion at the start of future projects. Results We developed the BOADICEA Web Application using an evolutionary software process. Our approach to Web implementation was conservative and we used conventional software engineering tools and techniques. The principal software development activities were: requirements, design, implementation, testing, documentation and maintenance. The BOADICEA Web Application has now been widely adopted by clinical geneticists and researchers. BOADICEA Web Application version 1 was released for general use in November 2007. By May 2010, we had > 1200 registered users based in the UK, USA, Canada, South America, Europe, Africa, Middle East, SE Asia, Australia and New Zealand. Conclusions We found that an evolutionary software process was effective when we developed the BOADICEA Web Application. The key clinical software development issues identified during the BOADICEA Web Application project were: software reliability, Web security, clinical data protection and user feedback. PMID:22490389

Clinical software development for the Web: lessons learned from the BOADICEA project.

PubMed

Cunningham, Alex P; Antoniou, Antonis C; Easton, Douglas F

2012-04-10

In the past 20 years, society has witnessed the following landmark scientific advances: (i) the sequencing of the human genome, (ii) the distribution of software by the open source movement, and (iii) the invention of the World Wide Web. Together, these advances have provided a new impetus for clinical software development: developers now translate the products of human genomic research into clinical software tools; they use open-source programs to build them; and they use the Web to deliver them. Whilst this open-source component-based approach has undoubtedly made clinical software development easier, clinical software projects are still hampered by problems that traditionally accompany the software process. This study describes the development of the BOADICEA Web Application, a computer program used by clinical geneticists to assess risks to patients with a family history of breast and ovarian cancer. The key challenge of the BOADICEA Web Application project was to deliver a program that was safe, secure and easy for healthcare professionals to use. We focus on the software process, problems faced, and lessons learned. Our key objectives are: (i) to highlight key clinical software development issues; (ii) to demonstrate how software engineering tools and techniques can facilitate clinical software development for the benefit of individuals who lack software engineering expertise; and (iii) to provide a clinical software development case report that can be used as a basis for discussion at the start of future projects. We developed the BOADICEA Web Application using an evolutionary software process. Our approach to Web implementation was conservative and we used conventional software engineering tools and techniques. The principal software development activities were: requirements, design, implementation, testing, documentation and maintenance. The BOADICEA Web Application has now been widely adopted by clinical geneticists and researchers. BOADICEA Web Application version 1 was released for general use in November 2007. By May 2010, we had > 1200 registered users based in the UK, USA, Canada, South America, Europe, Africa, Middle East, SE Asia, Australia and New Zealand. We found that an evolutionary software process was effective when we developed the BOADICEA Web Application. The key clinical software development issues identified during the BOADICEA Web Application project were: software reliability, Web security, clinical data protection and user feedback.

Developing a Web-Based Ppgis, as AN Environmental Reporting Service

NASA Astrophysics Data System (ADS)

Ranjbar Nooshery, N.; Taleai, M.; Kazemi, R.; Ebadi, K.

2017-09-01

Today municipalities are searching for new tools to empower locals for changing the future of their own areas by increasing their participation in different levels of urban planning. These tools should involve the community in planning process using participatory approaches instead of long traditional top-down planning models and help municipalities to obtain proper insight about major problems of urban neighborhoods from the residents' point of view. In this matter, public participation GIS (PPGIS) which enables citizens to record and following up their feeling and spatial knowledge regarding problems of the city in the form of maps have been introduced. In this research, a tool entitled CAER (Collecting & Analyzing of Environmental Reports) is developed. In the first step, a software framework based on Web-GIS tool, called EPGIS (Environmental Participatory GIS) has been designed to support public participation in reporting urban environmental problems and to facilitate data flow between citizens and municipality. A web-based cartography tool was employed for geo-visualization and dissemination of map-based reports. In the second step of CAER, a subsystem is developed based on SOLAP (Spatial On-Line Analytical Processing), as a data mining tools to elicit the local knowledge facilitating bottom-up urban planning practices and to help urban managers to find hidden relations among the recorded reports. This system is implemented in a case study area in Boston, Massachusetts and its usability was evaluated. The CAER should be considered as bottom-up planning tools to collect people's problems and views about their neighborhood and transmits them to the city officials. It also helps urban planners to find solutions for better management from citizen's viewpoint and gives them this chance to develop good plans to the neighborhoods that should be satisfied the citizens.

Mining Hidden Gems Beneath the Surface: A Look At the Invisible Web.

ERIC Educational Resources Information Center

Carlson, Randal D.; Repman, Judi

2002-01-01

Describes resources for researchers called the Invisible Web that are hidden from the usual search engines and other tools and contrasts them with those resources available on the surface Web. Identifies specialized search tools, databases, and strategies that can be used to locate credible in-depth information. (Author/LRW)

Bipolar disorder research 2.0: Web technologies for research capacity and knowledge translation.

PubMed

Michalak, Erin E; McBride, Sally; Barnes, Steven J; Wood, Chanel S; Khatri, Nasreen; Balram Elliott, Nusha; Parikh, Sagar V

2017-12-01

Current Web technologies offer bipolar disorder (BD) researchers many untapped opportunities for conducting research and for promoting knowledge exchange. In the present paper, we document our experiences with a variety of Web 2.0 technologies in the context of an international BD research network: The Collaborative RESearch Team to Study psychosocial issues in BD (CREST.BD). Three technologies were used as tools for enabling research within CREST.BD and for encouraging the dissemination of the results of our research: (1) the crestbd.ca website, (2) social networking tools (ie, Facebook, Twitter), and (3) several sorts of file sharing (ie YouTube, FileShare). For each Web technology, we collected quantitative assessments of their effectiveness (in reach, exposure, and engagement) over a 6-year timeframe (2010-2016). In general, many of our strategies were deemed successful for promoting knowledge exchange and other network goals. We discuss how we applied our Web analytics to inform adaptations and refinements of our Web 2.0 platforms to maximise knowledge exchange with people with BD, their supporters, and health care providers. We conclude with some general recommendations for other mental health researchers and research networks interested in pursuing Web 2.0 strategies. © 2017 John Wiley & Sons, Ltd.

BrucellaBase: Genome information resource.

PubMed

Sankarasubramanian, Jagadesan; Vishnu, Udayakumar S; Khader, L K M Abdul; Sridhar, Jayavel; Gunasekaran, Paramasamy; Rajendhran, Jeyaprakash

2016-09-01

Brucella sp. causes a major zoonotic disease, brucellosis. Brucella belongs to the family Brucellaceae under the order Rhizobiales of Alphaproteobacteria. We present BrucellaBase, a web-based platform, providing features of a genome database together with unique analysis tools. We have developed a web version of the multilocus sequence typing (MLST) (Whatmore et al., 2007) and phylogenetic analysis of Brucella spp. BrucellaBase currently contains genome data of 510 Brucella strains along with the user interfaces for BLAST, VFDB, CARD, pairwise genome alignment and MLST typing. Availability of these tools will enable the researchers interested in Brucella to get meaningful information from Brucella genome sequences. BrucellaBase will regularly be updated with new genome sequences, new features along with improvements in genome annotations. BrucellaBase is available online at http://www.dbtbrucellosis.in/brucellabase.html or http://59.99.226.203/brucellabase/homepage.html. Copyright © 2016 Elsevier B.V. All rights reserved.

Watershed Dynamics: Using Web-based GIS to Access Data and Study the Hydrosphere

NASA Astrophysics Data System (ADS)

Buzby, C. K.; Jona, K.

2010-12-01

The Watershed Dynamics project has developed online GIS tools and curriculum to provide high school earth science students with access to data and analysis tools to perform investigations on their local watershed. Using FieldScope web-based GIS tools from National Geographic, students investigate precipitation, stream discharge, and land cover data for the US. Students use the data to study water availability across the US and the world, human impacts on the watershed, and more. Curriculum developers at the Office of STEM Education Partnerships (OSEP) at Northwestern University and the GLOBE Program have created two complete units which scaffold students on their way to independent research using GIS. In the Water Availability unit, students work with precipitation, evaporation, and surface runoff to investigate the water cycle and how it varies regionally and seasonally. In the Human Impact unit, students analyze land cover change over time and investigate stream discharge to figure out how humans are impacting their watershed. These units can be used together or individually, but provide students progressively more research independence, leading them to ask their own questions about the watershed using GIS data. Both units have been pilot tested in high school classrooms and found to be successful at increasing student content knowledge about the water cycle. They are being modified for use at the undergraduate level. The web-based GIS interface has the functionality of desktop GIS, but allows for a simpler user-experience and direct links to relevant data. Students can use these tools to learn scientific content and as a stepping-stone for further GIS investigations.

Free and Easy to Use Web Based Presentation and Classroom Tools

ERIC Educational Resources Information Center

Jensen, Jennifer; Tunon, Johanna

2012-01-01

A number of free Web-based tools are available for distance librarians to create presentations and online assignments. The relative merits of presentation tools like Dabbleboard, Jing, Prezi, Tildee, 280 Slides, and Glogster, and classroom tools like Make Beliefs Comix, Picviewer, Photopeach, and Wordle are assessed for ease of use by distance…

Using Six-Sigma To Change and Measure Improvement.

ERIC Educational Resources Information Center

Feld, Karl G.; Stone, William K.

2002-01-01

Explains why Honeywell's Market Research Department replaced its traditional data collection and paper-based tabulation with blended modes, including electronic interviewing and real-time reporting. Describes how the Six-Sigma quality control process demonstrated that a hybrid approach with blended modes and Web-based reporting tools could deliver…

Prototyping Tool for Web-Based Multiuser Online Role-Playing Game

NASA Astrophysics Data System (ADS)

Okamoto, Shusuke; Kamada, Masaru; Yonekura, Tatsuhiro

This letter proposes a prototyping tool for Web-based Multiuser Online Role-Playing Game (MORPG). The design goal is to make this tool simple and powerful. The tool is comprised of a GUI editor, a translator and a runtime environment. The GUI editor is used to edit state-transition diagrams, each of which defines the behavior of the fictional characters. The state-transition diagrams are translated into C program codes, which plays the role of a game engine in RPG system. The runtime environment includes PHP, JavaScript with Ajax and HTML. So the prototype system can be played on the usual Web browser, such as Fire-fox, Safari and IE. On a click or key press by a player, the Web browser sends it to the Web server to reflect its consequence on the screens which other players are looking at. Prospected users of this tool include programming novices and schoolchildren. The knowledge or skill of any specific programming languages is not required to create state-transition diagrams. Its structure is not only suitable for the definition of a character behavior but also intuitive to help novices understand. Therefore, the users can easily create Web-based MORPG system with the tool.

The University of Washington Health Sciences Library BioCommons: an evolving Northwest biomedical research information support infrastructure

PubMed Central

Minie, Mark; Bowers, Stuart; Tarczy-Hornoch, Peter; Roberts, Edward; James, Rose A.; Rambo, Neil; Fuller, Sherrilynne

2006-01-01

Setting: The University of Washington Health Sciences Libraries and Information Center BioCommons serves the bioinformatics needs of researchers at the university and in the vibrant for-profit and not-for-profit biomedical research sector in the Washington area and region. Program Components: The BioCommons comprises services addressing internal University of Washington, not-for-profit, for-profit, and regional and global clientele. The BioCommons is maintained and administered by the BioResearcher Liaison Team. The BioCommons architecture provides a highly flexible structure for adapting to rapidly changing resources and needs. Evaluation Mechanisms: BioCommons uses Web-based pre- and post-course evaluations and periodic user surveys to assess service effectiveness. Recent surveys indicate substantial usage of BioCommons services and a high level of effectiveness and user satisfaction. Next Steps/Future Directions: BioCommons is developing novel collaborative Web resources to distribute bioinformatics tools and is experimenting with Web-based competency training in bioinformation resource use. PMID:16888667

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

Vang, Leng; Prescott, Steven R; Smith, Curtis

In collaborating scientific research arena it is important to have an environment where analysts have access to a shared of information documents, software tools and be able to accurately maintain and track historical changes in models. A new cloud-based environment would be accessible remotely from anywhere regardless of computing platforms given that the platform has available of Internet access and proper browser capabilities. Information stored at this environment would be restricted based on user assigned credentials. This report reviews development of a Cloud-based Architecture Capabilities (CAC) as a web portal for PRA tools.

Web Surveys to Digital Movies: Technological Tools of the Trade.

ERIC Educational Resources Information Center

Fetterman, David M.

2002-01-01

Highlights some of the technological tools used by educational researchers today, focusing on data collection related tools such as Web surveys, digital photography, voice recognition and transcription, file sharing and virtual office, videoconferencing on the Internet, instantaneous chat and chat rooms, reporting and dissemination, and digital…

NGL Viewer: Web-based molecular graphics for large complexes.

PubMed

Rose, Alexander S; Bradley, Anthony R; Valasatava, Yana; Duarte, Jose M; Prlic, Andreas; Rose, Peter W

2018-05-29

The interactive visualization of very large macromolecular complexes on the web is becoming a challenging problem as experimental techniques advance at an unprecedented rate and deliver structures of increasing size. We have tackled this problem by developing highly memory-efficient and scalable extensions for the NGL WebGL-based molecular viewer and by using MMTF, a binary and compressed Macromolecular Transmission Format. These enable NGL to download and render molecular complexes with millions of atoms interactively on desktop computers and smartphones alike, making it a tool of choice for web-based molecular visualization in research and education. The source code is freely available under the MIT license at github.com/arose/ngl and distributed on NPM (npmjs.com/package/ngl). MMTF-JavaScript encoders and decoders are available at github.com/rcsb/mmtf-javascript. asr.moin@gmail.com.

Resource Disambiguator for the Web: Extracting Biomedical Resources and Their Citations from the Scientific Literature.

PubMed

Ozyurt, Ibrahim Burak; Grethe, Jeffrey S; Martone, Maryann E; Bandrowski, Anita E

2016-01-01

The NIF Registry developed and maintained by the Neuroscience Information Framework is a cooperative project aimed at cataloging research resources, e.g., software tools, databases and tissue banks, funded largely by governments and available as tools to research scientists. Although originally conceived for neuroscience, the NIF Registry has over the years broadened in the scope to include research resources of general relevance to biomedical research. The current number of research resources listed by the Registry numbers over 13K. The broadening in scope to biomedical science led us to re-christen the NIF Registry platform as SciCrunch. The NIF/SciCrunch Registry has been cataloging the resource landscape since 2006; as such, it serves as a valuable dataset for tracking the breadth, fate and utilization of these resources. Our experience shows research resources like databases are dynamic objects, that can change location and scope over time. Although each record is entered manually and human-curated, the current size of the registry requires tools that can aid in curation efforts to keep content up to date, including when and where such resources are used. To address this challenge, we have developed an open source tool suite, collectively termed RDW: Resource Disambiguator for the (Web). RDW is designed to help in the upkeep and curation of the registry as well as in enhancing the content of the registry by automated extraction of resource candidates from the literature. The RDW toolkit includes a URL extractor from papers, resource candidate screen, resource URL change tracker, resource content change tracker. Curators access these tools via a web based user interface. Several strategies are used to optimize these tools, including supervised and unsupervised learning algorithms as well as statistical text analysis. The complete tool suite is used to enhance and maintain the resource registry as well as track the usage of individual resources through an innovative literature citation index honed for research resources. Here we present an overview of the Registry and show how the RDW tools are used in curation and usage tracking.

Resource Disambiguator for the Web: Extracting Biomedical Resources and Their Citations from the Scientific Literature

PubMed Central

Ozyurt, Ibrahim Burak; Grethe, Jeffrey S.; Martone, Maryann E.; Bandrowski, Anita E.

2016-01-01

The NIF Registry developed and maintained by the Neuroscience Information Framework is a cooperative project aimed at cataloging research resources, e.g., software tools, databases and tissue banks, funded largely by governments and available as tools to research scientists. Although originally conceived for neuroscience, the NIF Registry has over the years broadened in the scope to include research resources of general relevance to biomedical research. The current number of research resources listed by the Registry numbers over 13K. The broadening in scope to biomedical science led us to re-christen the NIF Registry platform as SciCrunch. The NIF/SciCrunch Registry has been cataloging the resource landscape since 2006; as such, it serves as a valuable dataset for tracking the breadth, fate and utilization of these resources. Our experience shows research resources like databases are dynamic objects, that can change location and scope over time. Although each record is entered manually and human-curated, the current size of the registry requires tools that can aid in curation efforts to keep content up to date, including when and where such resources are used. To address this challenge, we have developed an open source tool suite, collectively termed RDW: Resource Disambiguator for the (Web). RDW is designed to help in the upkeep and curation of the registry as well as in enhancing the content of the registry by automated extraction of resource candidates from the literature. The RDW toolkit includes a URL extractor from papers, resource candidate screen, resource URL change tracker, resource content change tracker. Curators access these tools via a web based user interface. Several strategies are used to optimize these tools, including supervised and unsupervised learning algorithms as well as statistical text analysis. The complete tool suite is used to enhance and maintain the resource registry as well as track the usage of individual resources through an innovative literature citation index honed for research resources. Here we present an overview of the Registry and show how the RDW tools are used in curation and usage tracking. PMID:26730820

bioWeb3D: an online webGL 3D data visualisation tool

PubMed Central

2013-01-01

Background Data visualization is critical for interpreting biological data. However, in practice it can prove to be a bottleneck for non trained researchers; this is especially true for three dimensional (3D) data representation. Whilst existing software can provide all necessary functionalities to represent and manipulate biological 3D datasets, very few are easily accessible (browser based), cross platform and accessible to non-expert users. Results An online HTML5/WebGL based 3D visualisation tool has been developed to allow biologists to quickly and easily view interactive and customizable three dimensional representations of their data along with multiple layers of information. Using the WebGL library Three.js written in Javascript, bioWeb3D allows the simultaneous visualisation of multiple large datasets inputted via a simple JSON, XML or CSV file, which can be read and analysed locally thanks to HTML5 capabilities. Conclusions Using basic 3D representation techniques in a technologically innovative context, we provide a program that is not intended to compete with professional 3D representation software, but that instead enables a quick and intuitive representation of reasonably large 3D datasets. PMID:23758781

INTRODUCTION TO SUSTAINABLE MANAGEMENT APPROACHES AND REVITALIZATION TOOLS-ELECTRONIC (SMARTE): IMPROVING REVITALIZATION DECISIONS IN DAKOTA CITY, NEBRASKA

EPA Science Inventory

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

INTRODUCTION TO SUSTAINABLE MANAGEMENT APPROACHES AND REVITALIZATION TOOLS-ELECTRONIC (SMARTE): IMPROVING REVITALIZATION DECISIONS IN STELLA, MISSOURI

EPA Science Inventory

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

TrAVis to Enhance Online Tutoring and Learning Activities: Real-Time Visualization of Students Tracking Data

ERIC Educational Resources Information Center

May, Madeth; George, Sebastien; Prevot, Patrick

2011-01-01

Purpose: This paper presents a part of our research work that places an emphasis on Tracking Data Analysis and Visualization (TrAVis) tools, a web-based system, designed to enhance online tutoring and learning activities, supported by computer-mediated communication (CMC) tools. TrAVis is particularly dedicated to assist both tutors and students…

Reducing Information Overload in Large Seismic Data Sets

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

HAMPTON,JEFFERY W.; YOUNG,CHRISTOPHER J.; MERCHANT,BION J.

2000-08-02

Event catalogs for seismic data can become very large. Furthermore, as researchers collect multiple catalogs and reconcile them into a single catalog that is stored in a relational database, the reconciled set becomes even larger. The sheer number of these events makes searching for relevant events to compare with events of interest problematic. Information overload in this form can lead to the data sets being under-utilized and/or used incorrectly or inconsistently. Thus, efforts have been initiated to research techniques and strategies for helping researchers to make better use of large data sets. In this paper, the authors present their effortsmore » to do so in two ways: (1) the Event Search Engine, which is a waveform correlation tool and (2) some content analysis tools, which area combination of custom-built and commercial off-the-shelf tools for accessing, managing, and querying seismic data stored in a relational database. The current Event Search Engine is based on a hierarchical clustering tool known as the dendrogram tool, which is written as a MatSeis graphical user interface. The dendrogram tool allows the user to build dendrogram diagrams for a set of waveforms by controlling phase windowing, down-sampling, filtering, enveloping, and the clustering method (e.g. single linkage, complete linkage, flexible method). It also allows the clustering to be based on two or more stations simultaneously, which is important to bridge gaps in the sparsely recorded event sets anticipated in such a large reconciled event set. Current efforts are focusing on tools to help the researcher winnow the clusters defined using the dendrogram tool down to the minimum optimal identification set. This will become critical as the number of reference events in the reconciled event set continually grows. The dendrogram tool is part of the MatSeis analysis package, which is available on the Nuclear Explosion Monitoring Research and Engineering Program Web Site. As part of the research into how to winnow the reference events in these large reconciled event sets, additional database query approaches have been developed to provide windows into these datasets. These custom built content analysis tools help identify dataset characteristics that can potentially aid in providing a basis for comparing similar reference events in these large reconciled event sets. Once these characteristics can be identified, algorithms can be developed to create and add to the reduced set of events used by the Event Search Engine. These content analysis tools have already been useful in providing information on station coverage of the referenced events and basic statistical, information on events in the research datasets. The tools can also provide researchers with a quick way to find interesting and useful events within the research datasets. The tools could also be used as a means to review reference event datasets as part of a dataset delivery verification process. There has also been an effort to explore the usefulness of commercially available web-based software to help with this problem. The advantages of using off-the-shelf software applications, such as Oracle's WebDB, to manipulate, customize and manage research data are being investigated. These types of applications are being examined to provide access to large integrated data sets for regional seismic research in Asia. All of these software tools would provide the researcher with unprecedented power without having to learn the intricacies and complexities of relational database systems.« less

Design and Testing of a Tool for Evaluating the Quality of Diabetes Consumer-Information Web Sites

PubMed Central

Steinwachs, Donald; Rubin, Haya R

2003-01-01

Background Most existing tools for measuring the quality of Internet health information focus almost exclusively on structural criteria or other proxies for quality information rather than evaluating actual accuracy and comprehensiveness. Objective This research sought to develop a new performance-measurement tool for evaluating the quality of Internet health information, test the validity and reliability of the tool, and assess the variability in diabetes Web site quality. Methods An objective, systematic tool was developed to evaluate Internet diabetes information based on a quality-of-care measurement framework. The principal investigator developed an abstraction tool and trained an external reviewer on its use. The tool included 7 structural measures and 34 performance measures created by using evidence-based practice guidelines and experts' judgments of accuracy and comprehensiveness. Results Substantial variation existed in all categories, with overall scores following a normal distribution and ranging from 15% to 95% (mean was 50% and median was 51%). Lin's concordance correlation coefficient to assess agreement between raters produced a rho of 0.761 (Pearson's r of 0.769), suggesting moderate to high agreement. The average agreement between raters for the performance measures was 0.80. Conclusions Diabetes Web site quality varies widely. Alpha testing of this new tool suggests that it could become a reliable and valid method for evaluating the quality of Internet health sites. Such an instrument could help lay people distinguish between beneficial and misleading information. PMID:14713658

AAVSO Target Tool: A Web-Based Service for Tracking Variable Star Observations (Abstract)

NASA Astrophysics Data System (ADS)

Burger, D.; Stassun, K. G.; Barnes, C.; Kafka, S.; Beck, S.; Li, K.

2018-06-01

(Abstract only) The AAVSO Target Tool is a web-based interface for bringing stars in need of observation to the attention of AAVSOís network of amateur and professional astronomers. The site currently tracks over 700 targets of interest, collecting data from them on a regular basis from AAVSOís servers and sorting them based on priority. While the target tool does not require a login, users can obtain visibility times for each target by signing up and entering a telescope location. Other key features of the site include filtering by AAVSO observing section, sorting by different variable types, formatting the data for printing, and exporting the data to a CSV file. The AAVSO Target Tool builds upon seven years of experience developing web applications for astronomical data analysis, most notably on Filtergraph (Burger, D., et al. 2013, Astronomical Data Analysis Software and Systems XXII, Astronomical Society of the Pacific, San Francisco, 399), and is built using the web2py web framework based on the python programming language. The target tool is available at http://filtergraph.com/aavso.

Introducing the Forensic Research/Reference on Genetics knowledge base, FROG-kb.

PubMed

Rajeevan, Haseena; Soundararajan, Usha; Pakstis, Andrew J; Kidd, Kenneth K

2012-09-01

Online tools and databases based on multi-allelic short tandem repeat polymorphisms (STRPs) are actively used in forensic teaching, research, and investigations. The Fst value of each CODIS marker tends to be low across the populations of the world and most populations typically have all the common STRP alleles present diminishing the ability of these systems to discriminate ethnicity. Recently, considerable research is being conducted on single nucleotide polymorphisms (SNPs) to be considered for human identification and description. However, online tools and databases that can be used for forensic research and investigation are limited. The back end DBMS (Database Management System) for FROG-kb is Oracle version 10. The front end is implemented with specific code using technologies such as Java, Java Servlet, JSP, JQuery, and GoogleCharts. We present an open access web application, FROG-kb (Forensic Research/Reference on Genetics-knowledge base, http://frog.med.yale.edu), that is useful for teaching and research relevant to forensics and can serve as a tool facilitating forensic practice. The underlying data for FROG-kb are provided by the already extensively used and referenced ALlele FREquency Database, ALFRED (http://alfred.med.yale.edu). In addition to displaying data in an organized manner, computational tools that use the underlying allele frequencies with user-provided data are implemented in FROG-kb. These tools are organized by the different published SNP/marker panels available. This web tool currently has implemented general functions possible for two types of SNP panels, individual identification and ancestry inference, and a prediction function specific to a phenotype informative panel for eye color. The current online version of FROG-kb already provides new and useful functionality. We expect FROG-kb to grow and expand in capabilities and welcome input from the forensic community in identifying datasets and functionalities that will be most helpful and useful. Thus, the structure and functionality of FROG-kb will be revised in an ongoing process of improvement. This paper describes the state as of early June 2012.

Measuring participant rurality in Web-based interventions.

PubMed

Danaher, Brian G; Hart, L Gary; McKay, H Garth; Severson, Herbert H

2007-08-31

Web-based health behavior change programs can reach large groups of disparate participants and thus they provide promise of becoming important public health tools. Data on participant rurality can complement other demographic measures to deepen our understanding of the success of these programs. Specifically, analysis of participant rurality can inform recruitment and social marketing efforts, and facilitate the targeting and tailoring of program content. Rurality analysis can also help evaluate the effectiveness of interventions across population groupings. We describe how the RUCAs (Rural-Urban Commuting Area Codes) methodology can be used to examine results from two Randomized Controlled Trials of Web-based tobacco cessation programs: the ChewFree.com project for smokeless tobacco cessation and the Smokers' Health Improvement Program (SHIP) project for smoking cessation. Using RUCAs methodology helped to highlight the extent to which both Web-based interventions reached a substantial percentage of rural participants. The ChewFree program was found to have more rural participation which is consistent with the greater prevalence of smokeless tobacco use in rural settings as well as ChewFree's multifaceted recruitment program that specifically targeted rural settings. Researchers of Web-based health behavior change programs targeted to the US should routinely include RUCAs as a part of analyzing participant demographics. Researchers in other countries should examine rurality indices germane to their country.

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.

OLTARIS: On-Line Tool for the Assessment of Radiation in Space

NASA Technical Reports Server (NTRS)

Singleterry, Robert C., Jr.; Blattnig, Steve R.; Clowdsley, Martha S.; Qualls, Garry D.; Sandridge, Christopher A.; Simonsen, Lisa C.; Norbury, John W.; Slaba, Tony C.; Walker, Steven A.; Badavi, Francis F.;

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

Design and evaluation of a web-based decision support tool for district-level disease surveillance in a low-resource setting

PubMed Central

Pore, Meenal; Sengeh, David M.; Mugambi, Purity; Purswani, Nuri V.; Sesay, Tom; Arnold, Anna Lena; Tran, Anh-Minh A.; Myers, Ralph

2017-01-01

During the 2014 West African Ebola Virus outbreak it became apparent that the initial response to the outbreak was hampered by limitations in the collection, aggregation, analysis and use of data for intervention planning. As part of the post-Ebola recovery phase, IBM Research Africa partnered with the Port Loko District Health Management Team (DHMT) in Sierra Leone and GOAL Global, to design, implement and deploy a web-based decision support tool for district-level disease surveillance. This paper discusses the design process and the functionality of the first version of the system. The paper presents evaluation results prior to a pilot deployment and identifies features for future iterations. A qualitative assessment of the tool prior to pilot deployment indicates that it improves the timeliness and ease of using data for making decisions at the DHMT level. PMID:29854209

Doctoral Supervision in Virtual Spaces: A Review of Research of Web-Based Tools to Develop Collaborative Supervision

ERIC Educational Resources Information Center

Maor, Dorit; Ensor, Jason D.; Fraser, Barry J.

2016-01-01

Supervision of doctoral students needs to be improved to increase completion rates, reduce attrition rates (estimated to be at 25% or more) and improve quality of research. The current literature review aimed to explore the contribution that technology can make to higher degree research supervision. The articles selected included empirical studies…

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.

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).

The IHMC CmapTools software in research and education: a multi-level use case in Space Meteorology

NASA Astrophysics Data System (ADS)

Messerotti, Mauro

2010-05-01

The IHMC (Institute for Human and Machine Cognition, Florida University System, USA) CmapTools software is a powerful multi-platform tool for knowledge modelling in graphical form based on concept maps. In this work we present its application for the high-level development of a set of multi-level concept maps in the framework of Space Meteorology to act as the kernel of a space meteorology domain ontology. This is an example of a research use case, as a domain ontology coded in machine-readable form via e.g. OWL (Web Ontology Language) is suitable to be an active layer of any knowledge management system embedded in a Virtual Observatory (VO). Apart from being manageable at machine level, concept maps developed via CmapTools are intrinsically human-readable and can embed hyperlinks and objects of many kinds. Therefore they are suitable to be published on the web: the coded knowledge can be exploited for educational purposes by the students and the public, as the level of information can be naturally organized among linked concept maps in progressively increasing complexity levels. Hence CmapTools and its advanced version COE (Concept-map Ontology Editor) represent effective and user-friendly software tools for high-level knowledge represention in research and education.

FRAT-up, a Web-based fall-risk assessment tool for elderly people living in the community.

PubMed

Cattelani, Luca; Palumbo, Pierpaolo; Palmerini, Luca; Bandinelli, Stefania; Becker, Clemens; Chesani, Federico; Chiari, Lorenzo

2015-02-18

About 30% of people over 65 are subject to at least one unintentional fall a year. Fall prevention protocols and interventions can decrease the number of falls. To be effective, a prevention strategy requires a prior step to evaluate the fall risk of the subjects. Despite extensive research, existing assessment tools for fall risk have been insufficient for predicting falls. The goal of this study is to present a novel web-based fall-risk assessment tool (FRAT-up) and to evaluate its accuracy in predicting falls, within a context of community-dwelling persons aged 65 and up. FRAT-up is based on the assumption that a subject's fall risk is given by the contribution of their exposure to each of the known fall-risk factors. Many scientific studies have investigated the relationship between falls and risk factors. The majority of these studies adopted statistical approaches, usually providing quantitative information such as odds ratios. FRAT-up exploits these numerical results to compute how each single factor contributes to the overall fall risk. FRAT-up is based on a formal ontology that enlists a number of known risk factors, together with quantitative findings in terms of odds ratios. From such information, an automatic algorithm generates a rule-based probabilistic logic program, that is, a set of rules for each risk factor. The rule-based program takes the health profile of the subject (in terms of exposure to the risk factors) and computes the fall risk. A Web-based interface allows users to input health profiles and to visualize the risk assessment for the given subject. FRAT-up has been evaluated on the InCHIANTI Study dataset, a representative population-based study of older persons living in the Chianti area (Tuscany, Italy). We compared reported falls with predicted ones and computed performance indicators. The obtained area under curve of the receiver operating characteristic was 0.642 (95% CI 0.614-0.669), while the Brier score was 0.174. The Hosmer-Lemeshow test indicated statistical significance of miscalibration. FRAT-up is a web-based tool for evaluating the fall risk of people aged 65 or up living in the community. Validation results of fall risks computed by FRAT-up show that its performance is comparable to externally validated state-of-the-art tools. A prototype is freely available through a web-based interface. ClinicalTrials.gov NCT01331512 (The InChianti Follow-Up Study); http://clinicaltrials.gov/show/NCT01331512 (Archived by WebCite at http://www.webcitation.org/6UDrrRuaR).

EVpedia: a community web portal for extracellular vesicles research.

PubMed

Kim, Dae-Kyum; Lee, Jaewook; Kim, Sae Rom; Choi, Dong-Sic; Yoon, Yae Jin; Kim, Ji Hyun; Go, Gyeongyun; Nhung, Dinh; Hong, Kahye; Jang, Su Chul; Kim, Si-Hyun; Park, Kyong-Su; Kim, Oh Youn; Park, Hyun Taek; Seo, Ji Hye; Aikawa, Elena; Baj-Krzyworzeka, Monika; van Balkom, Bas W M; Belting, Mattias; Blanc, Lionel; Bond, Vincent; Bongiovanni, Antonella; Borràs, Francesc E; Buée, Luc; Buzás, Edit I; Cheng, Lesley; Clayton, Aled; Cocucci, Emanuele; Dela Cruz, Charles S; Desiderio, Dominic M; Di Vizio, Dolores; Ekström, Karin; Falcon-Perez, Juan M; Gardiner, Chris; Giebel, Bernd; Greening, David W; Gross, Julia Christina; Gupta, Dwijendra; Hendrix, An; Hill, Andrew F; Hill, Michelle M; Nolte-'t Hoen, Esther; Hwang, Do Won; Inal, Jameel; Jagannadham, Medicharla V; Jayachandran, Muthuvel; Jee, Young-Koo; Jørgensen, Malene; Kim, Kwang Pyo; Kim, Yoon-Keun; Kislinger, Thomas; Lässer, Cecilia; Lee, Dong Soo; Lee, Hakmo; van Leeuwen, Johannes; Lener, Thomas; Liu, Ming-Lin; Lötvall, Jan; Marcilla, Antonio; Mathivanan, Suresh; Möller, Andreas; Morhayim, Jess; Mullier, François; Nazarenko, Irina; Nieuwland, Rienk; Nunes, Diana N; Pang, Ken; Park, Jaesung; Patel, Tushar; Pocsfalvi, Gabriella; Del Portillo, Hernando; Putz, Ulrich; Ramirez, Marcel I; Rodrigues, Marcio L; Roh, Tae-Young; Royo, Felix; Sahoo, Susmita; Schiffelers, Raymond; Sharma, Shivani; Siljander, Pia; Simpson, Richard J; Soekmadji, Carolina; Stahl, Philip; Stensballe, Allan; Stępień, Ewa; Tahara, Hidetoshi; Trummer, Arne; Valadi, Hadi; Vella, Laura J; Wai, Sun Nyunt; Witwer, Kenneth; Yáñez-Mó, María; Youn, Hyewon; Zeidler, Reinhard; Gho, Yong Song

2015-03-15

Extracellular vesicles (EVs) are spherical bilayered proteolipids, harboring various bioactive molecules. Due to the complexity of the vesicular nomenclatures and components, online searches for EV-related publications and vesicular components are currently challenging. We present an improved version of EVpedia, a public database for EVs research. This community web portal contains a database of publications and vesicular components, identification of orthologous vesicular components, bioinformatic tools and a personalized function. EVpedia includes 6879 publications, 172 080 vesicular components from 263 high-throughput datasets, and has been accessed more than 65 000 times from more than 750 cities. In addition, about 350 members from 73 international research groups have participated in developing EVpedia. This free web-based database might serve as a useful resource to stimulate the emerging field of EV research. The web site was implemented in PHP, Java, MySQL and Apache, and is freely available at http://evpedia.info. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Web-based assessments of physical activity in youth: considerations for design and scale calibration.

PubMed

Saint-Maurice, Pedro F; Welk, Gregory J

2014-12-01

This paper describes the design and methods involved in calibrating a Web-based self-report instrument to estimate physical activity behavior. The limitations of self-report measures are well known, but calibration methods enable the reported information to be equated to estimates obtained from objective data. This paper summarizes design considerations for effective development and calibration of physical activity self-report measures. Each of the design considerations is put into context and followed by a practical application based on our ongoing calibration research with a promising online self-report tool called the Youth Activity Profile (YAP). We first describe the overall concept of calibration and how this influences the selection of appropriate self-report tools for this population. We point out the advantages and disadvantages of different monitoring devices since the choice of the criterion measure and the strategies used to minimize error in the measure can dramatically improve the quality of the data. We summarize strategies to ensure quality control in data collection and discuss analytical considerations involved in group- vs individual-level inference. For cross-validation procedures, we describe the advantages of equivalence testing procedures that directly test and quantify agreement. Lastly, we introduce the unique challenges encountered when transitioning from paper to a Web-based tool. The Web offers considerable potential for broad adoption but an iterative calibration approach focused on continued refinement is needed to ensure that estimates are generalizable across individuals, regions, seasons and countries.

Can trainees design and deliver a national audit of epistaxis management? A pilot of a secure web-based audit tool and research trainee collaboratives.

PubMed

Mehta, N; Williams, R J; Smith, M E; Hall, A; Hardman, J C; Cheung, L; Ellis, M P; Fussey, J M; Lakhani, R; McLaren, O; Nankivell, P C; Sharma, N; Yeung, W; Carrie, S; Hopkins, C

2017-06-01

To investigate the feasibility of a national audit of epistaxis management led and delivered by a multi-region trainee collaborative using a web-based interface to capture patient data. Six trainee collaboratives across England nominated one site each and worked together to carry out this pilot. An encrypted data capture tool was adapted and installed within the infrastructure of a university secure server. Site-lead feedback was assessed through questionnaires. Sixty-three patients with epistaxis were admitted over a two-week period. Site leads reported an average of 5 minutes to complete questionnaires and described the tool as easy to use. Data quality was high, with little missing data. Site-lead feedback showed high satisfaction ratings for the project (mean, 4.83 out of 5). This pilot showed that trainee collaboratives can work together to deliver an audit using an encrypted data capture tool cost-effectively, whilst maintaining the highest levels of data quality.

Internet (WWW) based system of ultrasonic image processing tools for remote image analysis.

PubMed

Zeng, Hong; Fei, Ding-Yu; Fu, Cai-Ting; Kraft, Kenneth A

2003-07-01

Ultrasonic Doppler color imaging can provide anatomic information and simultaneously render flow information within blood vessels for diagnostic purpose. Many researchers are currently developing ultrasound image processing algorithms in order to provide physicians with accurate clinical parameters from the images. Because researchers use a variety of computer languages and work on different computer platforms to implement their algorithms, it is difficult for other researchers and physicians to access those programs. A system has been developed using World Wide Web (WWW) technologies and HTTP communication protocols to publish our ultrasonic Angle Independent Doppler Color Image (AIDCI) processing algorithm and several general measurement tools on the Internet, where authorized researchers and physicians can easily access the program using web browsers to carry out remote analysis of their local ultrasonic images or images provided from the database. In order to overcome potential incompatibility between programs and users' computer platforms, ActiveX technology was used in this project. The technique developed may also be used for other research fields.

A Software Engineering Approach based on WebML and BPMN to the Mediation Scenario of the SWS Challenge

NASA Astrophysics Data System (ADS)

Brambilla, Marco; Ceri, Stefano; Valle, Emanuele Della; Facca, Federico M.; Tziviskou, Christina

Although Semantic Web Services are expected to produce a revolution in the development of Web-based systems, very few enterprise-wide design experiences are available; one of the main reasons is the lack of sound Software Engineering methods and tools for the deployment of Semantic Web applications. In this chapter, we present an approach to software development for the Semantic Web based on classical Software Engineering methods (i.e., formal business process development, computer-aided and component-based software design, and automatic code generation) and on semantic methods and tools (i.e., ontology engineering, semantic service annotation and discovery).

3Drefine: an interactive web server for efficient protein structure refinement.

PubMed

Bhattacharya, Debswapna; Nowotny, Jackson; Cao, Renzhi; Cheng, Jianlin

2016-07-08

3Drefine is an interactive web server for consistent and computationally efficient protein structure refinement with the capability to perform web-based statistical and visual analysis. The 3Drefine refinement protocol utilizes iterative optimization of hydrogen bonding network combined with atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields for efficient protein structure refinement. The method has been extensively evaluated on blind CASP experiments as well as on large-scale and diverse benchmark datasets and exhibits consistent improvement over the initial structure in both global and local structural quality measures. The 3Drefine web server allows for convenient protein structure refinement through a text or file input submission, email notification, provided example submission and is freely available without any registration requirement. The server also provides comprehensive analysis of submissions through various energy and statistical feedback and interactive visualization of multiple refined models through the JSmol applet that is equipped with numerous protein model analysis tools. The web server has been extensively tested and used by many users. As a result, the 3Drefine web server conveniently provides a useful tool easily accessible to the community. The 3Drefine web server has been made publicly available at the URL: http://sysbio.rnet.missouri.edu/3Drefine/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

A Field Test of Web-Based Screening for Dry Eye Disease to Enhance Awareness of Eye Problems Among General Internet Users: A Latent Strategy to Promote Health

PubMed Central

Uchino, Miki; Kawazoe, Takashi; Kamiyashiki, Masaaki; Sano, Kokoro; Tsubota, Kazuo

2013-01-01

Background A Web-based self-check system including a brief questionnaire would seem to be a suitable tool for rapid disease screening. Objective The purpose of this preliminary study was to test a Web-based self-screening questionnaire for drawing attention to dry eye disease among general Internet users and identifying those with a higher risk of developing the condition. Methods A survey website was launched and used to recruit participants from general Internet users. In the first phase, volunteers were asked to complete a Web-based self-screening questionnaire containing 12 questions on dry eye symptoms. The second phase focused on the respondents who reported five or more dry eye symptoms and expressed their intention to seek medical attention. These participants performed the Schirmer test, for evaluating tear production, and completed a paper-based lifestyle questionnaire to provide relevant background data. Results Of the 1689 visitors to the website, 980 (58.0%) volunteers completed the Web-based self-screening questionnaire. Among these, 355 (36.2%) respondents reported five or more dry eye symptoms. Then, 99 (27.9%) of the symptomatic participants performed the Schirmer test and completed the paper-based lifestyle questionnaire. Out of these, 32 (32.2%) had abnormal tear production (≤5 mm). Conclusions The proposed Web-based self-screening questionnaire seems to be a promising tool for raising awareness of dry eye disease among general Internet users and identifying those with a higher risk of developing the condition, although further research is needed to validate its effectiveness. PMID:24072379

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

Utilizing Web 2.0 Technologies for Library Web Tutorials: An Examination of Instruction on Community College Libraries' Websites Serving Large Student Bodies

ERIC Educational Resources Information Center

Blummer, Barbara; Kenton, Jeffrey M.

2015-01-01

This is the second part of a series on Web 2.0 tools available from community college libraries' Websites. The first article appeared in an earlier volume of this journal and it illustrated the wide variety of Web 2.0 tools on community college libraries' Websites serving large student bodies (Blummer and Kenton 2014). The research found many of…

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.

Developing a Web-Based Nursing Practice and Research Information Management System: A Pilot Study.

PubMed

Choi, Jeeyae; Lapp, Cathi; Hagle, Mary E

2015-09-01

Many hospital information systems have been developed and implemented to collect clinical data from the bedside and have used the information to improve patient care. Because of a growing awareness that the use of clinical information improves quality of care and patient outcomes, measuring tools (electronic and paper based) have been developed, but most of them require multiple steps of data collection and analysis. This necessitated the development of a Web-based Nursing Practice and Research Information Management System that processes clinical nursing data to measure nurses' delivery of care and its impact on patient outcomes and provides useful information to clinicians, administrators, researchers, and policy makers at the point of care. This pilot study developed a computer algorithm based on a falls prevention protocol and programmed the prototype Web-based Nursing Practice and Research Information Management System. It successfully measured performance of nursing care delivered and its impact on patient outcomes successfully using clinical nursing data from the study site. Although Nursing Practice and Research Information Management System was tested with small data sets, results of study revealed that it has the potential to measure nurses' delivery of care and its impact on patient outcomes, while pinpointing components of nursing process in need of improvement.

A Comparison of Web 2.0 Tools in a Doctoral Course

ERIC Educational Resources Information Center

Meyer, Katrina A.

2010-01-01

Adult, professional students in a doctoral-level course used Web 2.0 tools such as wikis, blogs, and online discussions to develop answers to six "Big Questions" related to higher education finance and also produced a research paper that used original data or the research literature to improve understanding of a specific topic. At the close of the…

Sharik 1.0: User Needs and System Requirements for a Web-Based Tool to Support Collaborative Sensemaking

DTIC Science & Technology

2016-05-01

Sharik 1.0: User Needs and System Requirements for a Web -Based Tool to Support Collaborative Sensemaking Shadi Ghajar-Khosravi...share the new intelligence items with their peers. In this report, the authors describe Sharik (SHAring Resources, Information, and Knowledge), a web ...SHAring Resources, Information and Knowledge, soit le partage des ressources, de l’information et des connaissances), un outil Web qui facilite le

ResearchMaps.org for integrating and planning research.

PubMed

Matiasz, Nicholas J; Wood, Justin; Doshi, Pranay; Speier, William; Beckemeyer, Barry; Wang, Wei; Hsu, William; Silva, Alcino J

2018-01-01

To plan experiments, a biologist needs to evaluate a growing set of empirical findings and hypothetical assertions from diverse fields that use increasingly complex techniques. To address this problem, we operationalized principles (e.g., convergence and consistency) that biologists use to test causal relations and evaluate experimental evidence. With the framework we derived, we then created a free, open-source web application that allows biologists to create research maps, graph-based representations of empirical evidence and hypothetical assertions found in research articles, reviews, and other sources. With our ResearchMaps web application, biologists can systematically reason through the research that is most important to them, as well as evaluate and plan experiments with a breadth and precision that are unlikely without such a tool.

ResearchMaps.org for integrating and planning research

PubMed Central

Speier, William; Beckemeyer, Barry; Wang, Wei; Hsu, William; Silva, Alcino J.

2018-01-01

To plan experiments, a biologist needs to evaluate a growing set of empirical findings and hypothetical assertions from diverse fields that use increasingly complex techniques. To address this problem, we operationalized principles (e.g., convergence and consistency) that biologists use to test causal relations and evaluate experimental evidence. With the framework we derived, we then created a free, open-source web application that allows biologists to create research maps, graph-based representations of empirical evidence and hypothetical assertions found in research articles, reviews, and other sources. With our ResearchMaps web application, biologists can systematically reason through the research that is most important to them, as well as evaluate and plan experiments with a breadth and precision that are unlikely without such a tool. PMID:29723213

Assessing Learning, Quality and Engagement in Learning Objects: The Learning Object Evaluation Scale for Students (LOES-S)

ERIC Educational Resources Information Center

Kay, Robin H.; Knaack, Liesel

2009-01-01

Learning objects are interactive web-based tools that support the learning of specific concepts by enhancing, amplifying, and/or guiding the cognitive processes of learners. Research on the impact, effectiveness, and usefulness of learning objects is limited, partially because comprehensive, theoretically based, reliable, and valid evaluation…

Original Research and Peer Review Using Web-Based Collaborative Tools by College Students

ERIC Educational Resources Information Center

Cakir, Mustafa; Carlsen, William S.

2007-01-01

The Environmental Inquiry program supports inquiry based, student-centered science teaching on selected topics in the environmental sciences. Many teachers are unfamiliar with both the underlying science of toxicology, and the process and importance of peer review in scientific method. The protocol and peer review process was tested with college…

Using Web 2.0 Tools to Facilitate Case-Based Instruction: Considering the Possibilities

ERIC Educational Resources Information Center

Koehler, Adrie A.; Ertmer, Peggy A.

2016-01-01

Case-based instruction (CBI) offers a promising method for promoting problem-solving skills in learners. However, during CBI, the instructor shoulders major responsibility for shaping the learning that takes place. Research indicates that the facilitation techniques used during case discussions influence what gets covered, and to what extent,…

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

PubMed

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

2015-02-01

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

DAVID-WS: a stateful web service to facilitate gene/protein list analysis

PubMed Central

Jiao, Xiaoli; Sherman, Brad T.; Huang, Da Wei; Stephens, Robert; Baseler, Michael W.; Lane, H. Clifford; Lempicki, Richard A.

2012-01-01

Summary: The database for annotation, visualization and integrated discovery (DAVID), which can be freely accessed at http://david.abcc.ncifcrf.gov/, is a web-based online bioinformatics resource that aims to provide tools for the functional interpretation of large lists of genes/proteins. It has been used by researchers from more than 5000 institutes worldwide, with a daily submission rate of ∼1200 gene lists from ∼400 unique researchers, and has been cited by more than 6000 scientific publications. However, the current web interface does not support programmatic access to DAVID, and the uniform resource locator (URL)-based application programming interface (API) has a limit on URL size and is stateless in nature as it uses URL request and response messages to communicate with the server, without keeping any state-related details. DAVID-WS (web service) has been developed to automate user tasks by providing stateful web services to access DAVID programmatically without the need for human interactions. Availability: The web service and sample clients (written in Java, Perl, Python and Matlab) are made freely available under the DAVID License at http://david.abcc.ncifcrf.gov/content.jsp?file=WS.html. Contact: xiaoli.jiao@nih.gov; rlempicki@nih.gov PMID:22543366

DAVID-WS: a stateful web service to facilitate gene/protein list analysis.

PubMed

Jiao, Xiaoli; Sherman, Brad T; Huang, Da Wei; Stephens, Robert; Baseler, Michael W; Lane, H Clifford; Lempicki, Richard A

2012-07-01

The database for annotation, visualization and integrated discovery (DAVID), which can be freely accessed at http://david.abcc.ncifcrf.gov/, is a web-based online bioinformatics resource that aims to provide tools for the functional interpretation of large lists of genes/proteins. It has been used by researchers from more than 5000 institutes worldwide, with a daily submission rate of ∼1200 gene lists from ∼400 unique researchers, and has been cited by more than 6000 scientific publications. However, the current web interface does not support programmatic access to DAVID, and the uniform resource locator (URL)-based application programming interface (API) has a limit on URL size and is stateless in nature as it uses URL request and response messages to communicate with the server, without keeping any state-related details. DAVID-WS (web service) has been developed to automate user tasks by providing stateful web services to access DAVID programmatically without the need for human interactions. The web service and sample clients (written in Java, Perl, Python and Matlab) are made freely available under the DAVID License at http://david.abcc.ncifcrf.gov/content.jsp?file=WS.html.

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.

Biowep: a workflow enactment portal for bioinformatics applications.

PubMed

Romano, Paolo; Bartocci, Ezio; Bertolini, Guglielmo; De Paoli, Flavio; Marra, Domenico; Mauri, Giancarlo; Merelli, Emanuela; Milanesi, Luciano

2007-03-08

The huge amount of biological information, its distribution over the Internet and the heterogeneity of available software tools makes the adoption of new data integration and analysis network tools a necessity in bioinformatics. ICT standards and tools, like Web Services and Workflow Management Systems (WMS), can support the creation and deployment of such systems. Many Web Services are already available and some WMS have been proposed. They assume that researchers know which bioinformatics resources can be reached through a programmatic interface and that they are skilled in programming and building workflows. Therefore, they are not viable to the majority of unskilled researchers. A portal enabling these to take profit from new technologies is still missing. We designed biowep, a web based client application that allows for the selection and execution of a set of predefined workflows. The system is available on-line. Biowep architecture includes a Workflow Manager, a User Interface and a Workflow Executor. The task of the Workflow Manager is the creation and annotation of workflows. These can be created by using either the Taverna Workbench or BioWMS. Enactment of workflows is carried out by FreeFluo for Taverna workflows and by BioAgent/Hermes, a mobile agent-based middleware, for BioWMS ones. Main workflows' processing steps are annotated on the basis of their input and output, elaboration type and application domain by using a classification of bioinformatics data and tasks. The interface supports users authentication and profiling. Workflows can be selected on the basis of users' profiles and can be searched through their annotations. Results can be saved. We developed a web system that support the selection and execution of predefined workflows, thus simplifying access for all researchers. The implementation of Web Services allowing specialized software to interact with an exhaustive set of biomedical databases and analysis software and the creation of effective workflows can significantly improve automation of in-silico analysis. Biowep is available for interested researchers as a reference portal. They are invited to submit their workflows to the workflow repository. Biowep is further being developed in the sphere of the Laboratory of Interdisciplinary Technologies in Bioinformatics - LITBIO.

Biowep: a workflow enactment portal for bioinformatics applications

PubMed Central

Romano, Paolo; Bartocci, Ezio; Bertolini, Guglielmo; De Paoli, Flavio; Marra, Domenico; Mauri, Giancarlo; Merelli, Emanuela; Milanesi, Luciano

2007-01-01

Background The huge amount of biological information, its distribution over the Internet and the heterogeneity of available software tools makes the adoption of new data integration and analysis network tools a necessity in bioinformatics. ICT standards and tools, like Web Services and Workflow Management Systems (WMS), can support the creation and deployment of such systems. Many Web Services are already available and some WMS have been proposed. They assume that researchers know which bioinformatics resources can be reached through a programmatic interface and that they are skilled in programming and building workflows. Therefore, they are not viable to the majority of unskilled researchers. A portal enabling these to take profit from new technologies is still missing. Results We designed biowep, a web based client application that allows for the selection and execution of a set of predefined workflows. The system is available on-line. Biowep architecture includes a Workflow Manager, a User Interface and a Workflow Executor. The task of the Workflow Manager is the creation and annotation of workflows. These can be created by using either the Taverna Workbench or BioWMS. Enactment of workflows is carried out by FreeFluo for Taverna workflows and by BioAgent/Hermes, a mobile agent-based middleware, for BioWMS ones. Main workflows' processing steps are annotated on the basis of their input and output, elaboration type and application domain by using a classification of bioinformatics data and tasks. The interface supports users authentication and profiling. Workflows can be selected on the basis of users' profiles and can be searched through their annotations. Results can be saved. Conclusion We developed a web system that support the selection and execution of predefined workflows, thus simplifying access for all researchers. The implementation of Web Services allowing specialized software to interact with an exhaustive set of biomedical databases and analysis software and the creation of effective workflows can significantly improve automation of in-silico analysis. Biowep is available for interested researchers as a reference portal. They are invited to submit their workflows to the workflow repository. Biowep is further being developed in the sphere of the Laboratory of Interdisciplinary Technologies in Bioinformatics – LITBIO. PMID:17430563

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

PubMed

Garaizar, Pablo; Reips, Ulf-Dietrich

2015-09-01

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

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

DECISION SUPPORT FOR REVITALIZATION PRACTITIONERS: SUSTAINABLE MANAGEMENT APPROACHES AND REVITALIZATION TOOLS-ELECTRONIC (SMARTE-TRAINING FOR OH EPA - APRIL 13, 2006

EPA Science Inventory

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

Usability testing of a Falls Prevention Tool Kit for an inpatient acute care setting.

PubMed

Goldsmith, Denise; Zuyev, Lyubov; Benoit, Angie; Chang, Frank Y; Horsky, Jan; Dykes, Patricia

2009-01-01

Efforts to prevent falls in the hospital setting involves identifying patients at risk of falling and implementing fall prevention strategies. This poster describes the method and results of Performance Usability Testing on a web-based Fall Prevention Tool Kit (FPTK) developed as part of a research study, (Falls TIPS-Tailoring Interventions for Patient Safety) funded by The Robert Wood Johnson Foundation.

Genomics for Everyone

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

Chain, Patrick

Genomics — the genetic mapping and DNA sequencing of sets of genes or the complete genomes of organisms, along with related genome analysis and database work — is emerging as one of the transformative sciences of the 21st century. But current bioinformatics tools are not accessible to most biological researchers. Now, a new computational and web-based tool called EDGE Bioinformatics is working to fulfill the promise of democratizing genomics.

I-Maculaweb: A Tool to Support Data Reuse in Ophthalmology

PubMed Central

Bonetto, Monica; Nicolò, Massimo; Gazzarata, Roberta; Fraccaro, Paolo; Rosa, Raffaella; Musetti, Donatella; Musolino, Maria; Traverso, Carlo E.

2016-01-01

This paper intends to present a Web-based application to collect and manage clinical data and clinical trials together in a unique tool. I-maculaweb is a user-friendly Web-application designed to manage, share, and analyze clinical data from patients affected by degenerative and vascular diseases of the macula. The unique and innovative scientific and technological elements of this project are the integration with individual and population data, relevant for degenerative and vascular diseases of the macula. Clinical records can also be extracted for statistical purposes and used for clinical decision support systems. I-maculaweb is based on an existing multilevel and multiscale data management model, which includes general principles that are suitable for several different clinical domains. The database structure has been specifically built to respect laterality, a key aspect in ophthalmology. Users can add and manage patient records, follow-up visits, treatment, diagnoses, and clinical history. There are two different modalities to extract records: one for the patient’s own center, in which personal details are shown and the other for statistical purposes, where all center’s anonymized data are visible. The Web-platform allows effective management, sharing, and reuse of information within primary care and clinical research. Clear and precise clinical data will improve understanding of real-life management of degenerative and vascular diseases of the macula as well as increasing precise epidemiologic and statistical data. Furthermore, this Web-based application can be easily employed as an electronic clinical research file in clinical studies. PMID:27170913

EPA MODELING TOOLS FOR CAPTURE ZONE DELINEATION

EPA Science Inventory

The EPA Office of Research and Development supports a step-wise modeling approach for design of wellhead protection areas for water supply wells. A web-based WellHEDSS (wellhead decision support system) is under development for determining when simple capture zones (e.g., centri...

Omics AnalySIs System for PRecision Oncology (OASISPRO): A Web-based Omics Analysis Tool for Clinical Phenotype Prediction.

PubMed

Yu, Kun-Hsing; Fitzpatrick, Michael R; Pappas, Luke; Chan, Warren; Kung, Jessica; Snyder, Michael

2017-09-12

Precision oncology is an approach that accounts for individual differences to guide cancer management. Omics signatures have been shown to predict clinical traits for cancer patients. However, the vast amount of omics information poses an informatics challenge in systematically identifying patterns associated with health outcomes, and no general-purpose data-mining tool exists for physicians, medical researchers, and citizen scientists without significant training in programming and bioinformatics. To bridge this gap, we built the Omics AnalySIs System for PRecision Oncology (OASISPRO), a web-based system to mine the quantitative omics information from The Cancer Genome Atlas (TCGA). This system effectively visualizes patients' clinical profiles, executes machine-learning algorithms of choice on the omics data, and evaluates the prediction performance using held-out test sets. With this tool, we successfully identified genes strongly associated with tumor stage, and accurately predicted patients' survival outcomes in many cancer types, including mesothelioma and adrenocortical carcinoma. By identifying the links between omics and clinical phenotypes, this system will facilitate omics studies on precision cancer medicine and contribute to establishing personalized cancer treatment plans. This web-based tool is available at http://tinyurl.com/oasispro ;source codes are available at http://tinyurl.com/oasisproSourceCode . © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

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.

GEM-TREND: a web tool for gene expression data mining toward relevant network discovery

PubMed Central

Feng, Chunlai; Araki, Michihiro; Kunimoto, Ryo; Tamon, Akiko; Makiguchi, Hiroki; Niijima, Satoshi; Tsujimoto, Gozoh; Okuno, Yasushi

2009-01-01

Background DNA microarray technology provides us with a first step toward the goal of uncovering gene functions on a genomic scale. In recent years, vast amounts of gene expression data have been collected, much of which are available in public databases, such as the Gene Expression Omnibus (GEO). To date, most researchers have been manually retrieving data from databases through web browsers using accession numbers (IDs) or keywords, but gene-expression patterns are not considered when retrieving such data. The Connectivity Map was recently introduced to compare gene expression data by introducing gene-expression signatures (represented by a set of genes with up- or down-regulated labels according to their biological states) and is available as a web tool for detecting similar gene-expression signatures from a limited data set (approximately 7,000 expression profiles representing 1,309 compounds). In order to support researchers to utilize the public gene expression data more effectively, we developed a web tool for finding similar gene expression data and generating its co-expression networks from a publicly available database. Results GEM-TREND, a web tool for searching gene expression data, allows users to search data from GEO using gene-expression signatures or gene expression ratio data as a query and retrieve gene expression data by comparing gene-expression pattern between the query and GEO gene expression data. The comparison methods are based on the nonparametric, rank-based pattern matching approach of Lamb et al. (Science 2006) with the additional calculation of statistical significance. The web tool was tested using gene expression ratio data randomly extracted from the GEO and with in-house microarray data, respectively. The results validated the ability of GEM-TREND to retrieve gene expression entries biologically related to a query from GEO. For further analysis, a network visualization interface is also provided, whereby genes and gene annotations are dynamically linked to external data repositories. Conclusion GEM-TREND was developed to retrieve gene expression data by comparing query gene-expression pattern with those of GEO gene expression data. It could be a very useful resource for finding similar gene expression profiles and constructing its gene co-expression networks from a publicly available database. GEM-TREND was designed to be user-friendly and is expected to support knowledge discovery. GEM-TREND is freely available at . PMID:19728865

GEM-TREND: a web tool for gene expression data mining toward relevant network discovery.

PubMed

Feng, Chunlai; Araki, Michihiro; Kunimoto, Ryo; Tamon, Akiko; Makiguchi, Hiroki; Niijima, Satoshi; Tsujimoto, Gozoh; Okuno, Yasushi

2009-09-03

DNA microarray technology provides us with a first step toward the goal of uncovering gene functions on a genomic scale. In recent years, vast amounts of gene expression data have been collected, much of which are available in public databases, such as the Gene Expression Omnibus (GEO). To date, most researchers have been manually retrieving data from databases through web browsers using accession numbers (IDs) or keywords, but gene-expression patterns are not considered when retrieving such data. The Connectivity Map was recently introduced to compare gene expression data by introducing gene-expression signatures (represented by a set of genes with up- or down-regulated labels according to their biological states) and is available as a web tool for detecting similar gene-expression signatures from a limited data set (approximately 7,000 expression profiles representing 1,309 compounds). In order to support researchers to utilize the public gene expression data more effectively, we developed a web tool for finding similar gene expression data and generating its co-expression networks from a publicly available database. GEM-TREND, a web tool for searching gene expression data, allows users to search data from GEO using gene-expression signatures or gene expression ratio data as a query and retrieve gene expression data by comparing gene-expression pattern between the query and GEO gene expression data. The comparison methods are based on the nonparametric, rank-based pattern matching approach of Lamb et al. (Science 2006) with the additional calculation of statistical significance. The web tool was tested using gene expression ratio data randomly extracted from the GEO and with in-house microarray data, respectively. The results validated the ability of GEM-TREND to retrieve gene expression entries biologically related to a query from GEO. For further analysis, a network visualization interface is also provided, whereby genes and gene annotations are dynamically linked to external data repositories. GEM-TREND was developed to retrieve gene expression data by comparing query gene-expression pattern with those of GEO gene expression data. It could be a very useful resource for finding similar gene expression profiles and constructing its gene co-expression networks from a publicly available database. GEM-TREND was designed to be user-friendly and is expected to support knowledge discovery. GEM-TREND is freely available at http://cgs.pharm.kyoto-u.ac.jp/services/network.

Building Professional Learning Communities in Special Education through Social Networking: Directions for Future Research

ERIC Educational Resources Information Center

Hardman, Elizabeth L.

2011-01-01

This paper examines the challenges inherent in building professional learning communities (PLCs) in special education and describes how two Web 2.0 tools were used to build a community that engages general and special education teachers, school administrators, and teacher educators in implementing research based inclusive practices that are known…

An Electronic Portfolio to Support Learning

ERIC Educational Resources Information Center

Wade, Anne; Abrami, Philip C.; Sclater, Jennifer

2005-01-01

In this paper, we provide a description of a CSLP research project that looked at portfolio use within a middle school, the web-based e-portfolio software we have developed within the context of the Quebec educational system, our plans for further development of the tool, and our research plans related to the use of portfolios to support learning.…

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.

Students' Reaction to WebCT: Implications for Designing On-Line Learning Environments

ERIC Educational Resources Information Center

Osman, Mohamed Eltahir

2005-01-01

There is a growing number of web-based and web-assisted course development tools and products that can be used to create on-line learning environment. The utility of these products, however, varies greatly depending on their feasibility, prerequisite infrastructure, technical features, interface, and course development and management tools. WebCT…

Using a web-based survey tool to undertake a Delphi study: application for nurse education research.

PubMed

Gill, Fenella J; Leslie, Gavin D; Grech, Carol; Latour, Jos M

2013-11-01

The Internet is increasingly being used as a data collection medium to access research participants. This paper reports on the experience and value of using web-survey software to conduct an eDelphi study to develop Australian critical care course graduate practice standards. The eDelphi technique used involved the iterative process of administering three rounds of surveys to a national expert panel. The survey was developed online using SurveyMonkey. Panel members responded to statements using one rating scale for round one and two scales for rounds two and three. Text boxes for panel comments were provided. For each round, the SurveyMonkey's email tool was used to distribute an individualized email invitation containing the survey web link. The distribution of panel responses, individual responses and a summary of comments were emailed to panel members. Stacked bar charts representing the distribution of responses were generated using the SurveyMonkey software. Panel response rates remained greater than 85% over all rounds. An online survey provided numerous advantages over traditional survey approaches including high quality data collection, ease and speed of survey administration, direct communication with the panel and rapid collation of feedback allowing data collection to be undertaken in 12 weeks. Only minor challenges were experienced using the technology. Ethical issues, specific to using the Internet to conduct research and external hosting of web-based software, lacked formal guidance. High response rates and an increased level of data quality were achieved in this study using web-survey software and the process was efficient and user-friendly. However, when considering online survey software, it is important to match the research design with the computer capabilities of participants and recognize that ethical review guidelines and processes have not yet kept pace with online research practices. Copyright © 2013 Elsevier Ltd. All rights reserved.

Providing Knowledge Recommendations: An Approach for Informal Electronic Mentoring

ERIC Educational Resources Information Center

Colomo-Palacios, Ricardo; Casado-Lumbreras, Cristina; Soto-Acosta, Pedro; Misra, Sanjay

2014-01-01

The use of Web 2.0 technologies for knowledge management is invading the corporate sphere. The Web 2.0 is the most adopted knowledge transfer tool within knowledge intensive firms and is starting to be used for mentoring. This paper presents IM-TAG, a Web 2.0 tool, based on semantic technologies, for informal mentoring. The tool offers…

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.

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

ERIC Educational Resources Information Center

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

2010-01-01

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

Methodological and Ethical Challenges in a Web-Based Randomized Controlled Trial of a Domestic Violence Intervention

PubMed Central

Valpied, Jodie; Koziol-McLain, Jane; Glass, Nancy; Hegarty, Kelsey

2017-01-01

The use of Web-based methods to deliver and evaluate interventions is growing in popularity, particularly in a health care context. They have shown particular promise in responding to sensitive or stigmatized issues such as mental health and sexually transmitted infections. In the field of domestic violence (DV), however, the idea of delivering and evaluating interventions via the Web is still relatively new. Little is known about how to successfully navigate several challenges encountered by the researchers while working in this area. This paper uses the case study of I-DECIDE, a Web-based healthy relationship tool and safety decision aid for women experiencing DV, developed in Australia. The I-DECIDE website has recently been evaluated through a randomized controlled trial, and we outline some of the methodological and ethical challenges encountered during recruitment, retention, and evaluation. We suggest that with careful consideration of these issues, randomized controlled trials can be safely conducted via the Web in this sensitive area. PMID:28351830

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.

An open source, web based, simple solution for seismic data dissemination and collaborative research

NASA Astrophysics Data System (ADS)

Diviacco, Paolo

2005-06-01

Collaborative research and data dissemination in the field of geophysical exploration need network tools that can access large amounts of data from anywhere using any PC or workstation. Simple solutions based on a combination of Open Source software can be developed to address such requests, exploiting the possibilities offered by the web technologies, and at the same time avoiding the costs and inflexibility of commercial systems. A viable solution consists of MySQL for data storage and retrieval, CWP/SU and GMT for data visualisation and a scripting layer driven by PHP that allows users to access the system via an Apache web server. In the light of the experience building the on-line archive of seismic data of the Istituto Nazionale di Oceanografia e di Geofisica Sperimentale (OGS), we describe the solutions and the methods adopted, with a view to stimulate both the attitude of network collaborative research of other institutions similar to ours, and the development of different applications.

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

NASA Astrophysics Data System (ADS)

Sundaravel, A.; Wilkinson, D. C.

2010-12-01

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

Learning Tools for Knowledge Nomads: Using Personal Digital Assistants (PDAs) in Web-based Learning Environments.

ERIC Educational Resources Information Center

Loh, Christian Sebastian

2001-01-01

Examines how mobile computers, or personal digital assistants (PDAs), can be used in a Web-based learning environment. Topics include wireless networks on college campuses; online learning; Web-based learning technologies; synchronous and asynchronous communication via the Web; content resources; Web connections; and collaborative learning. (LRW)

Effective collaborative learning in biomedical education using a web-based infrastructure.

PubMed

Wu, Yunfeng; Zheng, Fang; Cai, Suxian; Xiang, Ning; Zhong, Zhangting; He, Jia; Xu, Fang

2012-01-01

This paper presents a feature-rich web-based system used for biomedical education at the undergraduate level. With the powerful groupware features provided by the wiki system, the instructors are able to establish a community-centered mentoring environment that capitalizes on local expertise to create a sense of online collaborative learning among students. The web-based infrastructure can help the instructors effectively organize and coordinate student research projects, and the groupware features may support the interactive activities, such as interpersonal communications and data sharing. The groupware features also provide the web-based system with a wide range of additional ways of organizing collaboratively developed materials, which makes it become an effective tool for online active learning. Students are able to learn the ability to work effectively in teams, with an improvement of project management, design collaboration, and technical writing skills. With the fruitful outcomes in recent years, it is positively thought that the web-based collaborative learning environment can perform an excellent shift away from the conventional instructor-centered teaching to community- centered collaborative learning in the undergraduate education.

Software Tools to Support Research on Airport Departure Planning

NASA Technical Reports Server (NTRS)

Carr, Francis; Evans, Antony; Feron, Eric; Clarke, John-Paul

2003-01-01

A simple, portable and useful collection of software tools has been developed for the analysis of airport surface traffic. The tools are based on a flexible and robust traffic-flow model, and include calibration, validation and simulation functionality for this model. Several different interfaces have been developed to help promote usage of these tools, including a portable Matlab(TM) implementation of the basic algorithms; a web-based interface which provides online access to automated analyses of airport traffic based on a database of real-world operations data which covers over 250 U.S. airports over a 5-year period; and an interactive simulation-based tool currently in use as part of a college-level educational module. More advanced applications for airport departure traffic include taxi-time prediction and evaluation of "windowing" congestion control.

Decision Support and the Effectiveness of Web-based Delivery and Information Tailoring for Bowel Cancer Screening: An Exploratory Study

PubMed Central

Wilson, Carlene J; Zajac, Ian T; Hart, Elizabeth; McGillivray, Jane A

2012-01-01

Background Colorectal cancer (CRC) is the third most commonly diagnosed cancer in males and the second in females throughout the developed world. Population screening using fecal occult blood tests (FOBTs) facilitates early detection and greater chance of survival, but participation rates are low. We developed a Web-based decision tool to provide information tailored to an individual’s decision stage for CRC screening and attitude toward screening utilizing the Preventive Health Model (PHM) and Precaution Adoption Process Model (PAPM) as theoretical frameworks for screening behavior. We describe the practical steps employed in the tool’s design and the subsequent conduct of an exploratory study. Objective To design a decision tool for CRC screening and conduct an exploratory study among average-risk men and women to (1) test the impact of message type (tailored vs non-tailored) and message delivery modality (Web-based vs paper-based) on attitudes toward screening and screening uptake, and (2) investigate the acceptability of the decision tool and relevance of materials. Methods Participants (n = 100), recruited from a population sample of men and women aged 50-76 residing in urban Adelaide, Australia, were randomly assigned to a control group or one of 4 interventions: (1) Web-based and tailored information, (2) paper-based and tailored information, (3) Web-based and non-tailored (generic) information, or (4) paper-based and non-tailored information. Participation was augmented by snowball recruitment (n = 19). Questionnaires based on PHM variables were administered pre- and post-intervention. Participants were given the opportunity to request an FOBT. Following the intervention, participants discussed the acceptability of the tool. Results Full data were available for 87.4% (104/119) of participants. Post-intervention, perceived susceptibility scores for individuals receiving tailored information increased from mean 10.6 (SD 2.1) to mean 11.8 (SD 2.2). Scores on self-efficacy increased in the tailored group from mean 11.7 (SD 2.0) to mean 12.6 (SD 1.8). There were significant time x modality x message effects for social influence and salience and coherence, reflecting an increase in these scores for tailored Web-based participants only; social influence scores increased from mean 11.7 (SD 2.6) to mean 14.9 (SD 2.3), and salience and coherence scores increased from mean 16.0 (SD 2.2) to mean 17.7 (SD 2.1). There was no greater influence of modality or message type on movement toward a decision to screen or screening uptake, indicating that neither tailored messages nor a Web modality had superior effect. Overall, participants regarded tailored messages positively, but thought that the Web tool lacked “media richness.” Conclusions This exploratory study confirms that tailoring on PHM predictors of CRC screening has the potential to positively address attitudes toward screening. However, tailoring on these variables did not result in significantly increased screening uptake. Future research should consider other possible psychosocial influences. Mode of delivery did not affect outcomes, but as a delivery medium, the Web has economic and logistical advantages over paper. PMID:23611950

Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web.

PubMed

Miller, Chase A; Anthony, Jon; Meyer, Michelle M; Marth, Gabor

2013-02-01

High-throughput biological research requires simultaneous visualization as well as analysis of genomic data, e.g. read alignments, variant calls and genomic annotations. Traditionally, such integrative analysis required desktop applications operating on locally stored data. Many current terabyte-size datasets generated by large public consortia projects, however, are already only feasibly stored at specialist genome analysis centers. As even small laboratories can afford very large datasets, local storage and analysis are becoming increasingly limiting, and it is likely that most such datasets will soon be stored remotely, e.g. in the cloud. These developments will require web-based tools that enable users to access, analyze and view vast remotely stored data with a level of sophistication and interactivity that approximates desktop applications. As rapidly dropping cost enables researchers to collect data intended to answer questions in very specialized contexts, developers must also provide software libraries that empower users to implement customized data analyses and data views for their particular application. Such specialized, yet lightweight, applications would empower scientists to better answer specific biological questions than possible with general-purpose genome browsers currently available. Using recent advances in core web technologies (HTML5), we developed Scribl, a flexible genomic visualization library specifically targeting coordinate-based data such as genomic features, DNA sequence and genetic variants. Scribl simplifies the development of sophisticated web-based graphical tools that approach the dynamism and interactivity of desktop applications. Software is freely available online at http://chmille4.github.com/Scribl/ and is implemented in JavaScript with all modern browsers supported.

Consumer e-health education in HIV/AIDS: a pilot study of a web-based video workshop

PubMed Central

O'Grady, Laura A

2006-01-01

Background Members of the HIV/AIDS community are known to use web-based tools to support learning about treatment issues. Initial research indicated components such as message forums or web-based documentation were effectively used by persons with HIV/AIDS. Video has also shown promise as a technology to aid consumer health education. However, no research has been published thus far investigating the impact of web-based environments combining these components in an educational workshop format. Methods In this qualitative study HIV/AIDS community members provided feedback on an integrated web-based consumer health education environment. Participants were recruited through organizations that serve the HIV/AIDS community located in Toronto, Canada. Demographics, data on Internet use, including messages exchanged in the study environment were collected. A group interview provided feedback on usability of the study environment, preferences for information formats, use of the message forum, and other sources for learning about treatment information. Results In this pilot study analysis of the posted messages did not demonstrate use for learning of the workshop content. Participants did not generally find the environment of value for learning about treatment information. However, participants did share how they were meeting these needs. It was indicated that a combination of resources are being used to find and discuss treatment information, including in-person sources. Conclusion More research on the ways in which treatment information needs are being met by HIV/AIDS community members and how technology fits in this process is necessary before investing large amounts of money into web-based interventions. Although this study had a limited number of participants, the findings were unexpected and, therefore, of interest to those who intend to implement online consumer health education initiatives or interventions. PMID:16504148

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.

Students' Perceptions of the Effectiveness of the World Wide Web as a Research and Teaching Tool in Science Learning.

ERIC Educational Resources Information Center

Ng, Wan; Gunstone, Richard

2002-01-01

Investigates the use of the World Wide Web (WWW) as a research and teaching tool in promoting self-directed learning groups of 15-year-old students. Discusses the perceptions of students of the effectiveness of the WWW in assisting them with the construction of knowledge on photosynthesis and respiration. (Contains 33 references.) (Author/YDS)

Web Based Personal Nutrition Management Tool

NASA Astrophysics Data System (ADS)

Bozkurt, Selen; Zayim, Neşe; Gülkesen, Kemal Hakan; Samur, Mehmet Kemal

Internet is being used increasingly as a resource for accessing health-related information because of its several advantages. Therefore, Internet tailoring becomes quite preferable in health education and personal health management recently. Today, there are many web based health programs de-signed for individuals. Among these studies nutrition and weight management is popular because, obesity has become a heavy burden for populations worldwide. In this study, we designed a web based personal nutrition education and management tool, The Nutrition Web Portal, in order to enhance patients’ nutrition knowledge, and provide behavioral change against obesity. The present paper reports analysis, design and development processes of The Nutrition Web Portal.

Framework Development Supporting the Safety Portal

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

Prescott, Steven Ralph; Kvarfordt, Kellie Jean; Vang, Leng

2015-07-01

In a collaborating scientific research arena it is important to have an environment where analysts have access to a shared repository of information, documents, and software tools, and be able to accurately maintain and track historical changes in models. The new Safety Portal cloud-based environment will be accessible remotely from anywhere regardless of computing platforms given that the platform has available Internet access and proper browser capabilities. Information stored at this environment would be restricted based on user assigned credentials. This report discusses current development of a cloud-based web portal for PRA tools.

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.

Advancing translational research with the Semantic Web.

PubMed

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

2007-05-09

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

Advancing translational research with the Semantic Web

PubMed Central

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

2007-01-01

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

Identifying Audiences of E-Infrastructures - Tools for Measuring Impact

PubMed Central

van den Besselaar, Peter

2012-01-01

Research evaluation should take into account the intended scholarly and non-scholarly audiences of the research output. This holds too for research infrastructures, which often aim at serving a large variety of audiences. With research and research infrastructures moving to the web, new possibilities are emerging for evaluation metrics. This paper proposes a feasible indicator for measuring the scope of audiences who use web-based e-infrastructures, as well as the frequency of use. In order to apply this indicator, a method is needed for classifying visitors to e-infrastructures into relevant user categories. The paper proposes such a method, based on an inductive logic program and a Bayesian classifier. The method is tested, showing that the visitors are efficiently classified with 90% accuracy into the selected categories. Consequently, the method can be used to evaluate the use of the e-infrastructure within and outside academia. PMID:23239995

Using WebCT as a Supplemental Tool to Enhance Critical Thinking and Engagement among Developmental Reading Students

ERIC Educational Resources Information Center

Burgess, Melissa L.

2009-01-01

The purpose of this research was to examine possible outcomes of developmental students' critical thinking and motivation to read when the online learning community, WebCT, was implemented. My role, in addition to instructor, was that of participant-observer. I implemented WebCT tools, such as discussion board and chat, over a four-month period…

Models and Simulations as a Service: Exploring the Use of Galaxy for Delivering Computational Models

PubMed Central

Walker, Mark A.; Madduri, Ravi; Rodriguez, Alex; Greenstein, Joseph L.; Winslow, Raimond L.

2016-01-01

We describe the ways in which Galaxy, a web-based reproducible research platform, can be used for web-based sharing of complex computational models. Galaxy allows users to seamlessly customize and run simulations on cloud computing resources, a concept we refer to as Models and Simulations as a Service (MaSS). To illustrate this application of Galaxy, we have developed a tool suite for simulating a high spatial-resolution model of the cardiac Ca2+ spark that requires supercomputing resources for execution. We also present tools for simulating models encoded in the SBML and CellML model description languages, thus demonstrating how Galaxy’s reproducible research features can be leveraged by existing technologies. Finally, we demonstrate how the Galaxy workflow editor can be used to compose integrative models from constituent submodules. This work represents an important novel approach, to our knowledge, to making computational simulations more accessible to the broader scientific community. PMID:26958881

Effectiveness of a Technology-Based Intervention to Teach Evidence-Based Practice: The EBR Tool.

PubMed

Long, JoAnn D; Gannaway, Paula; Ford, Cindy; Doumit, Rita; Zeeni, Nadine; Sukkarieh-Haraty, Ola; Milane, Aline; Byers, Beverly; Harrison, LaNell; Hatch, Daniel; Brown, Justin; Proper, Sharlan; White, Patricia; Song, Huaxin

2016-02-01

As the world becomes increasingly digital, advances in technology have changed how students access evidence-based information. Research suggests that students overestimate their ability to locate quality online research and lack the skills needed to evaluate the scientific literature. Clinical nurses report relying on personal experience to answer clinical questions rather than searching evidence-based sources. To address the problem, a web-based, evidence-based research (EBR) tool that is usable from a computer, smartphone, or iPad was developed and tested. The purpose of the EBR tool is to guide students through the basic steps needed to locate and critically appraise the online scientific literature while linking users to quality electronic resources to support evidence-based practice (EBP). Testing of the tool took place in a mixed-method, quasi-experimental, and two-population randomized controlled trial (RCT) design in a U.S. and Middle East university. A statistically significant improvement in overall research skills was supported in the quasi-experimental nursing student group and RCT nutrition student group using the EBR tool. A statistically significant proportional difference was supported in the RCT nutrition and PharmD intervention groups in participants' ability to distinguish the credibility of online source materials compared with controls. The majority of participants could correctly apply PICOTS to a case study when using the tool. The data from this preliminary study suggests that the EBR tool enhanced student overall research skills and selected EBP skills while generating data for assessment of learning outcomes. The EBR tool places evidence-based resources at the fingertips of users by addressing some of the most commonly cited barriers to research utilization while exposing users to information and online literacy standards of practice, meeting a growing need within nursing curricula. © 2016 Sigma Theta Tau International.

AncestrySNPminer: A bioinformatics tool to retrieve and develop ancestry informative SNP panels

PubMed Central

Amirisetty, Sushil; Khurana Hershey, Gurjit K.; Baye, Tesfaye M.

2012-01-01

A wealth of genomic information is available in public and private databases. However, this information is underutilized for uncovering population specific and functionally relevant markers underlying complex human traits. Given the huge amount of SNP data available from the annotation of human genetic variation, data mining is a faster and cost effective approach for investigating the number of SNPs that are informative for ancestry. In this study, we present AncestrySNPminer, the first web-based bioinformatics tool specifically designed to retrieve Ancestry Informative Markers (AIMs) from genomic data sets and link these informative markers to genes and ontological annotation classes. The tool includes an automated and simple “scripting at the click of a button” functionality that enables researchers to perform various population genomics statistical analyses methods with user friendly querying and filtering of data sets across various populations through a single web interface. AncestrySNPminer can be freely accessed at https://research.cchmc.org/mershalab/AncestrySNPminer/login.php. PMID:22584067

SOAP based web services and their future role in VO projects

NASA Astrophysics Data System (ADS)

Topf, F.; Jacquey, C.; Génot, V.; Cecconi, B.; André, N.; Zhang, T. L.; Kallio, E.; Lammer, H.; Facsko, G.; Stöckler, R.; Khodachenko, M.

2011-10-01

Modern state-of-the-art web services are from crucial importance for the interoperability of different VO tools existing in the planetary community. SOAP based web services assure the interconnectability between different data sources and tools by providing a common protocol for communication. This paper will point out a best practice approach with the Automated Multi-Dataset Analysis Tool (AMDA) developed by CDPP, Toulouse and the provision of VEX/MAG data from a remote database located at IWF, Graz. Furthermore a new FP7 project IMPEx will be introduced with a potential usage example of AMDA web services in conjunction with simulation models.

The AIChE "Concept Warehouse": A Web-Based Tool to Promote Concept-Based Instruction

ERIC Educational Resources Information Center

Koretsky, Milo D.; Falconer, John L.; Brooks, Bill J.; Gilbuena, Debra M.; Silverstein, David L.; Smith, Christina; Miletic, Marina

2014-01-01

This paper describes the "AIChE Concept Warehouse," a recently developed web-based instructional tool that enables faculty within the discipline of chemical engineering to better provide their students concept-based instruction. It currently houses over 2,000 concept questions and 10 concept inventories pertinent to courses throughout…

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).

UceWeb: a web-based collaborative tool for collecting and sharing quality of life data.

PubMed

Parimbelli, E; Sacchi, L; Rubrichi, S; Mazzanti, A; Quaglini, S

2015-01-01

This work aims at building a platform where quality-of-life data, namely utility coefficients, can be elicited not only for immediate use, but also systematically stored together with patient profiles to build a public repository to be further exploited in studies on specific target populations (e.g. cost/utility analyses). We capitalized on utility theory and previous experience to define a set of desirable features such a tool should show to facilitate sound elicitation of quality of life. A set of visualization tools and algorithms has been developed to this purpose. To make it easily accessible for potential users, the software has been designed as a web application. A pilot validation study has been performed on 20 atrial fibrillation patients. A collaborative platform, UceWeb, has been developed and tested. It implements the standard gamble, time trade-off and rating-scale utility elicitation methods. It allows doctors and patients to choose the mode of interaction to maximize patients’ comfort in answering difficult questions. Every utility elicitation may contribute to the growth of the repository. UceWeb can become a unique source of data allowing researchers both to perform more reliable comparisons among healthcare interventions and build statistical models to gain deeper insight into quality of life data.

Use of StreamStats in the Upper French Broad River Basin, North Carolina: A Pilot Water-Resources Web Application

USGS Publications Warehouse

Wagner, Chad R.; Tighe, Kirsten C.; Terziotti, Silvia

2009-01-01

StreamStats is a Web-based Geographic Information System (GIS) application that was developed by the U.S. Geological Survey (USGS) in cooperation with Environmental Systems Research Institute, Inc. (ESRI) to provide access to an assortment of analytical tools that are useful for water-resources planning and management. StreamStats allows users to easily obtain streamflow statistics, basin characteristics, and descriptive information for USGS data-collection sites and selected ungaged sites. StreamStats also allows users to identify stream reaches upstream and downstream from user-selected sites and obtain information for locations along streams where activities occur that can affect streamflow conditions. This functionality can be accessed through a map-based interface with the user's Web browser or through individual functions requested remotely through other Web applications.

Enhancing Thematic Units Using the World Wide Web: Tools and Strategies for Students with Mild Disabilities.

ERIC Educational Resources Information Center

Gardner, J. Emmett; Wissick, Cheryl A.

2002-01-01

This article presents principles for using Web-based activities to support curriculum accommodations for students with mild disabilities. Tools, resources, and strategies are identified to help teachers construct meaningful and Web-enhanced thematic units. Web sites are listed in the areas of math, science, language arts, and social studies;…

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.

Novel Problem Solving - The NASA Solution Mechanism Guide

NASA Technical Reports Server (NTRS)

Keeton, Kathryn E.; Richard, Elizabeth E.; Davis, Jeffrey R.

2014-01-01

Over the past five years, the Human Health and Performance (HH&P) Directorate at the NASA Johnson Space Center (JSC) has conducted a number of pilot and ongoing projects in collaboration and open innovation. These projects involved the use of novel open innovation competitions that sought solutions from "the crowd", non-traditional problem solvers. The projects expanded to include virtual collaboration centers such as the NASA Human Health and Performance Center (NHHPC) and more recently a collaborative research project between NASA and the National Science Foundation (NSF). These novel problem-solving tools produced effective results and the HH&P wanted to capture the knowledge from these new tools, to teach the results to the directorate, and to implement new project management tools and coursework. The need to capture and teach the results of these novel problem solving tools, the HH&P decided to create a web-based tool to capture best practices and case studies, to teach novice users how to use new problem solving tools and to change project management training/. This web-based tool was developed with a small, multi-disciplinary group and named the Solution Mechanism Guide (SMG). An alpha version was developed that was tested against several sessions of user groups to get feedback on the SMG and determine a future course for development. The feedback was very positive and the HH&P decided to move to the beta-phase of development. To develop the web-based tool, the HH&P utilized the NASA Tournament Lab (NTL) to develop the software with TopCoder under an existing contract. In this way, the HH&P is using one new tool (the NTL and TopCoder) to develop the next generation tool, the SMG. The beta-phase of the SMG is planed for release in the spring of 2014 and results of the beta-phase testing will be available for the IAC meeting in September. The SMG is intended to disrupt the way problem solvers and project managers approach problem solving and to increase the use of novel and more cost and time effective problem solving tools such as open innovation, collaborative research, and virtual collaborative project centers. The HH&P envisions changing project management coursework by including the SMG in the teaching of project management problem solving tools.

Development of a data mining and imaging informatics display tool for a multiple sclerosis e-folder system

NASA Astrophysics Data System (ADS)

Liu, Margaret; Loo, Jerry; Ma, Kevin; Liu, Brent

2011-03-01

Multiple sclerosis (MS) is a debilitating autoimmune disease of the central nervous system that damages axonal pathways through inflammation and demyelination. In order to address the need for a centralized application to manage and study MS patients, the MS e-Folder - a web-based, disease-specific electronic medical record system - was developed. The e-Folder has a PHP and MySQL based graphical user interface (GUI) that can serve as both a tool for clinician decision support and a data mining tool for researchers. This web-based GUI gives the e-Folder a user friendly interface that can be securely accessed through the internet and requires minimal software installation on the client side. The e-Folder GUI displays and queries patient medical records--including demographic data, social history, past medical history, and past MS history. In addition, DICOM format imaging data, and computer aided detection (CAD) results from a lesion load algorithm are also displayed. The GUI interface is dynamic and allows manipulation of the DICOM images, such as zoom, pan, and scrolling, and the ability to rotate 3D images. Given the complexity of clinical management and the need to bolster research in MS, the MS e-Folder system will improve patient care and provide MS researchers with a function-rich patient data hub.

K-12 Student Use of Web 2.0 Tools: A Global Study

ERIC Educational Resources Information Center

Toledo, Cheri; Shepard, MaryFriend

2011-01-01

Over the past decade, Internet use has increased 445% worldwide. This boom has enabled widespread access to online tools and digital spaces for educational practices. The results of this study of Web 2.0 tool use in kindergarten through high school (K-12) classrooms around the world will be presented. A web-based survey was sent out through online…

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/

Discover Space Weather and Sun's Superpowers: Using CCMC's innovative tools and applications

NASA Astrophysics Data System (ADS)

Mendoza, A. M. M.; Maddox, M. M.; Kuznetsova, M. M.; Chulaki, A.; Rastaetter, L.; Mullinix, R.; Weigand, C.; Boblitt, J.; Taktakishvili, A.; MacNeice, P. J.; Pulkkinen, A. A.; Pembroke, A. D.; Mays, M. L.; Zheng, Y.; Shim, J. S.

2015-12-01

Community Coordinated Modeling Center (CCMC) has developed a comprehensive set of tools and applications that are directly applicable to space weather and space science education. These tools, some of which were developed by our student interns, are capable of serving a wide range of student audiences, from middle school to postgraduate research. They include a web-based point of access to sophisticated space physics models and visualizations, and a powerful space weather information dissemination system, available on the web and as a mobile app. In this demonstration, we will use CCMC's innovative tools to engage the audience in real-time space weather analysis and forecasting and will share some of our interns' hands-on experiences while being trained as junior space weather forecasters. The main portals to CCMC's educational material are ccmc.gsfc.nasa.gov and iswa.gsfc.nasa.gov

Web-Based Machine Translation as a Tool for Promoting Electronic Literacy and Language Awareness

ERIC Educational Resources Information Center

Williams, Lawrence

2006-01-01

This article addresses a pervasive problem of concern to teachers of many foreign languages: the use of Web-Based Machine Translation (WBMT) by students who do not understand the complexities of this relatively new tool. Although networked technologies have greatly increased access to many language and communication tools, WBMT is still…

Experiences From a Web- and App-Based Workplace Health Promotion Intervention Among Employees in the Social and Health Care Sector Based on Use-Data and Qualitative Interviews.

PubMed

Balk-Møller, Nina Charlotte; Larsen, Thomas Meinert; Holm, Lotte

2017-10-19

An increasing number of Web- and app-based tools for health promotion are being developed at the moment. The ambition is generally to reach out to a larger part of the population and to help users improve their lifestyle and develop healthier habits, and thereby improve their health status. However, the positive effects are generally modest. To understand why the effects are modest, further investigation into the participants' experiences and the social aspects of using Web- and app-based health promotion tools is needed. The objectives of this study were to investigate the motivation behind taking part in and using a Web- and app-based health promotion tool (SoSu-life) at the workplace and to explore the participants' experiences with using the tool. Qualitative interviews with 26 participants who participated in a 38-week randomized controlled trial of a workplace Web- and app-based tool for health promotion were conducted. Data were supplemented with tracking the frequency of use. The basic features of the tool investigated in the trial were self-reporting of diet and exercise, personalized feedback, suggestions for activities and programs, practical tips and tricks, and a series of social features designed to support and build interactions among the participants at the workplace. The respondents reported typically one of the two reasons for signing up to participate in the study: either a personal wish to attain some health benefits or the more social reason that participants did not want to miss out on the social interaction with colleagues. Peer pressure from colleagues had made some participants to sign up even though they did not believe they had an unhealthy behavior. Of the total of 355 participants in the intervention group, 203 (57.2%) left the intervention before it ended. Of the remaining participants, most did not use the tool after the competition at the end of the initial 16-week period. The actual number of active users of the tool throughout the whole intervention period was low; however, the participants reported that lifestyle habits became a topic of conversation. A tool that addresses group interactions at workplaces appears to initiate peer pressure, which helped recruitment for participation. However, active participation was low. A social change was indicated, allowing for more interaction among colleagues around healthy lifestyle issues. Future and more long-term studies are needed to determine whether such social changes could lead to sustained improvements of health. ©Nina Charlotte Balk-Møller, Thomas Meinert Larsen, Lotte Holm. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 19.10.2017.

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

PubMed

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

2016-01-01

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

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

USGS Publications Warehouse

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

2009-01-01

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

WebPresent: a World Wide Web-based telepresentation tool for physicians

NASA Astrophysics Data System (ADS)

Sampath-Kumar, Srihari; Banerjea, Anindo; Moshfeghi, Mehran

1997-05-01

In this paper, we present the design architecture and the implementation status of WebPresent - a world wide web based tele-presentation tool. This tool allows a physician to use a conference server workstation and make a presentation of patient cases to a geographically distributed audience. The audience consists of other physicians collaborating on patients' health care management and physicians participating in continuing medical education. These physicians are at several locations with networks of different bandwidth and capabilities connecting them. Audiences also receive the patient case information on different computers ranging form high-end display workstations to laptops with low-resolution displays. WebPresent is a scalable networked multimedia tool which supports the presentation of hypertext, images, audio, video, and a white-board to remote physicians with hospital Intranet access. WebPresent allows the audience to receive customized information. The data received can differ in resolution and bandwidth, depending on the availability of resources such as display resolution and network bandwidth.

CoryneBase: Corynebacterium Genomic Resources and Analysis Tools at Your Fingertips

PubMed Central

Tan, Mui Fern; Jakubovics, Nick S.; Wee, Wei Yee; Mutha, Naresh V. R.; Wong, Guat Jah; Ang, Mia Yang; Yazdi, Amir Hessam; Choo, Siew Woh

2014-01-01

Corynebacteria are used for a wide variety of industrial purposes but some species are associated with human diseases. With increasing number of corynebacterial genomes having been sequenced, comparative analysis of these strains may provide better understanding of their biology, phylogeny, virulence and taxonomy that may lead to the discoveries of beneficial industrial strains or contribute to better management of diseases. To facilitate the ongoing research of corynebacteria, a specialized central repository and analysis platform for the corynebacterial research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. Here we present CoryneBase, a genomic database for Corynebacterium with diverse functionality for the analysis of genomes aimed to provide: (1) annotated genome sequences of Corynebacterium where 165,918 coding sequences and 4,180 RNAs can be found in 27 species; (2) access to comprehensive Corynebacterium data through the use of advanced web technologies for interactive web interfaces; and (3) advanced bioinformatic analysis tools consisting of standard BLAST for homology search, VFDB BLAST for sequence homology search against the Virulence Factor Database (VFDB), Pairwise Genome Comparison (PGC) tool for comparative genomic analysis, and a newly designed Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomic analysis. CoryneBase offers the access of a range of Corynebacterium genomic resources as well as analysis tools for comparative genomics and pathogenomics. It is publicly available at http://corynebacterium.um.edu.my/. PMID:24466021

Website Analysis as a Tool for Task-Based Language Learning and Higher Order Thinking in an EFL Context

ERIC Educational Resources Information Center

Roy, Debopriyo

2014-01-01

Besides focusing on grammar, writing skills, and web-based language learning, researchers in "CALL" and second language acquisition have also argued for the importance of promoting higher-order thinking skills in ESL (English as Second Language) and EFL (English as Foreign Language) classrooms. There is solid evidence supporting the…

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".

Opal web services for biomedical applications.

PubMed

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

2010-07-01

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

CoP Sensing Framework on Web-Based Environment

NASA Astrophysics Data System (ADS)

Mustapha, S. M. F. D. Syed

The Web technologies and Web applications have shown similar high growth rate in terms of daily usages and user acceptance. The Web applications have not only penetrated in the traditional domains such as education and business but have also encroached into areas such as politics, social, lifestyle, and culture. The emergence of Web technologies has enabled Web access even to the person on the move through PDAs or mobile phones that are connected using Wi-Fi, HSDPA, or other communication protocols. These two phenomena are the inducement factors toward the need of building Web-based systems as the supporting tools in fulfilling many mundane activities. In doing this, one of the many focuses in research has been to look at the implementation challenges in building Web-based support systems in different types of environment. This chapter describes the implementation issues in building the community learning framework that can be supported on the Web-based platform. The Community of Practice (CoP) has been chosen as the community learning theory to be the case study and analysis as it challenges the creativity of the architectural design of the Web system in order to capture the presence of learning activities. The details of this chapter describe the characteristics of the CoP to understand the inherent intricacies in modeling in the Web-based environment, the evidences of CoP that need to be traced automatically in a slick manner such that the evidence-capturing process is unobtrusive, and the technologies needed to embrace a full adoption of Web-based support system for the community learning framework.

Improving nutrition surveillance and public health research in Central and Eastern Europe/Balkan Countries using the Balkan Food Platform and dietary tools.

PubMed

Gurinović, Mirjana; Milešević, Jelena; Novaković, Romana; Kadvan, Agnes; Djekić-Ivanković, Marija; Šatalić, Zvonimir; Korošec, Mojca; Spiroski, Igor; Ranić, Marija; Dupouy, Eleonora; Oshaug, Arne; Finglas, Paul; Glibetić, Maria

2016-02-15

The objective of this paper is to share experience and provide updated information on Capacity Development in the Central and Eastern Europe/Balkan Countries (CEE/BC) region relevant to public health nutrition, particularly in creation of food composition databases (FCDBs), applying dietary intake assessment and monitoring tools, and harmonizing methodology for nutrition surveillance. Balkan Food Platform was established by a Memorandum of Understanding among EuroFIR AISBL, Institute for Medical Research, Belgrade, Capacity Development Network in Nutrition in CEE - CAPNUTRA and institutions from nine countries in the region. Inventory on FCDB status identified lack of harmonized and standardized research tools. To strengthen harmonization in CEE/BC in line with European research trends, the Network members collaborated in development of a Regional FCDB, using web-based food composition data base management software following EuroFIR standards. Comprehensive nutrition assessment and planning tool - DIET ASSESS & PLAN could enable synchronization of nutrition surveillance across countries. Copyright © 2015 Elsevier Ltd. All rights reserved.

Easily configured real-time CPOE Pick Off Tool supporting focused clinical research and quality improvement.

PubMed

Rosenbaum, Benjamin P; Silkin, Nikolay; Miller, Randolph A

2014-01-01

Real-time alerting systems typically warn providers about abnormal laboratory results or medication interactions. For more complex tasks, institutions create site-wide 'data warehouses' to support quality audits and longitudinal research. Sophisticated systems like i2b2 or Stanford's STRIDE utilize data warehouses to identify cohorts for research and quality monitoring. However, substantial resources are required to install and maintain such systems. For more modest goals, an organization desiring merely to identify patients with 'isolation' orders, or to determine patients' eligibility for clinical trials, may adopt a simpler, limited approach based on processing the output of one clinical system, and not a data warehouse. We describe a limited, order-entry-based, real-time 'pick off' tool, utilizing public domain software (PHP, MySQL). Through a web interface the tool assists users in constructing complex order-related queries and auto-generates corresponding database queries that can be executed at recurring intervals. We describe successful application of the tool for research and quality monitoring.

Genomics for Everyone

ScienceCinema

Chain, Patrick

2018-05-31

Genomics — the genetic mapping and DNA sequencing of sets of genes or the complete genomes of organisms, along with related genome analysis and database work — is emerging as one of the transformative sciences of the 21st century. But current bioinformatics tools are not accessible to most biological researchers. Now, a new computational and web-based tool called EDGE Bioinformatics is working to fulfill the promise of democratizing genomics.

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.

What deters nurses from participating in web-based graduate nursing programs?: A cross-sectional survey research study.

PubMed

Carpenter, Suzanne H

2016-01-01

A graduate degree is required of nursing faculty in America. Because of the nursing faculty shortage, web-based graduate nursing programs are being offered to encourage nurses to return to school. The identification of deterrents to participating in these programs is an important step in increasing enrollment. To identify deterrents to participation in web-based graduate nursing programs. Descriptive survey research. Louisiana Two hundred and eighty-one registered nurse members of the Louisiana Nurses' Association. The 54-item four-point Likert-type interval scale Deterrents to Participation in Web-Based Graduate Nursing Programs Survey Instrument was used. Data were collected over 8weeks using SurveyMonkey.com to administer the web survey tool to all members of the Louisiana State Nurses' Association. A factor analysis revealed a three-factor solution that explained 55.436% of the total variance in deterrents to participation in web-based graduate nursing programs. The factors were labeled "concerns about quality, cost, and time," "concerns about access to resources: technological and personal," and "concerns about electronic mediated communication." Multiple regression analysis revealed an overall model of three predictors of deterrents to participation in web-based graduate nursing programs: no computer literacy, annual household income between 20,000 and 50,000 dollars, and having the current educational status of graduating from a diploma RN program. This model accounted for 21% of the variance in the deterrents to participation scores. Since these three significant predictors of deterrents to participation in web-based graduate nursing programs were identified, web-based nursing graduate program administrators might consider an outreach to RN diploma graduates in an effort to make them aware of available technology support programs to foster participation. Scholarships for lower income nursing students are recommended, and programs to support computer literacy within the nursing community should be considered. Copyright © 2015 Elsevier Ltd. All rights reserved.

AirLab: a cloud-based platform to manage and share antibody-based single-cell research.

PubMed

Catena, Raúl; Özcan, Alaz; Jacobs, Andrea; Chevrier, Stephane; Bodenmiller, Bernd

2016-06-29

Single-cell analysis technologies are essential tools in research and clinical diagnostics. These methods include flow cytometry, mass cytometry, and other microfluidics-based technologies. Most laboratories that employ these methods maintain large repositories of antibodies. These ever-growing collections of antibodies, their multiple conjugates, and the large amounts of data generated in assays using specific antibodies and conditions makes a dedicated software solution necessary. We have developed AirLab, a cloud-based tool with web and mobile interfaces, for the organization of these data. AirLab streamlines the processes of antibody purchase, organization, and storage, antibody panel creation, results logging, and antibody validation data sharing and distribution. Furthermore, AirLab enables inventory of other laboratory stocks, such as primers or clinical samples, through user-controlled customization. Thus, AirLab is a mobile-powered and flexible tool that harnesses the capabilities of mobile tools and cloud-based technology to facilitate inventory and sharing of antibody and sample collections and associated validation data.

Life Cycle Project Plan Outline: Web Sites and Web-based Applications

EPA Pesticide Factsheets

This tool is a guideline for planning and checking for 508 compliance on web sites and web based applications. Determine which EIT components are covered or excepted, which 508 standards and requirements apply, and how to implement them.

75 FR 27182 - Energy Conservation Program: Web-Based Compliance and Certification Management System

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-14

... Conservation Program: Web-Based Compliance and Certification Management System AGENCY: Office of Energy... certification reports to the Department of Energy (DOE) through an electronic Web-based tool, the Compliance and... following means: 1. Compliance and Certification Management System (CCMS)--via the Web portal: http...

The Sydney West Knowledge Portal: Evaluating the Growth of a Knowledge Portal to Support Translational Research.

PubMed

Janssen, Anna; Robinson, Tracy Elizabeth; Provan, Pamela; Shaw, Tim

2016-06-29

The Sydney West Translational Cancer Research Centre is an organization funded to build capacity for translational research in cancer. Translational research is essential for ensuring the integration of best available evidence into practice and for improving patient outcomes. However, there is a low level of awareness regarding what it is and how to conduct it optimally. One solution to addressing this gap is the design and deployment of web-based knowledge portals to disseminate new knowledge and engage with and connect dispersed networks of researchers. A knowledge portal is an web-based platform for increasing knowledge dissemination and management in a specialized area. To measure the design and growth of an web-based knowledge portal for increasing individual awareness of translational research and to build organizational capacity for the delivery of translational research projects in cancer. An adaptive methodology was used to capture the design and growth of an web-based knowledge portal in cancer. This involved stakeholder consultations to inform initial design of the portal. Once the portal was live, site analytics were reviewed to evaluate member usage of the portal and to measure growth in membership. Knowledge portal membership grew consistently for the first 18 months after deployment, before leveling out. Analysis of site metrics revealed members were most likely to visit portal pages with community-generated content, particularly pages with a focus on translational research. This was closely followed by pages that disseminated educational material about translational research. Preliminary data from this study suggest that knowledge portals may be beneficial tools for translating new evidence and fostering an environment of communication and collaboration.

The Sydney West Knowledge Portal: Evaluating the Growth of a Knowledge Portal to Support Translational Research

PubMed Central

2016-01-01

Background The Sydney West Translational Cancer Research Centre is an organization funded to build capacity for translational research in cancer. Translational research is essential for ensuring the integration of best available evidence into practice and for improving patient outcomes. However, there is a low level of awareness regarding what it is and how to conduct it optimally. One solution to addressing this gap is the design and deployment of web-based knowledge portals to disseminate new knowledge and engage with and connect dispersed networks of researchers. A knowledge portal is an web-based platform for increasing knowledge dissemination and management in a specialized area. Objective To measure the design and growth of an web-based knowledge portal for increasing individual awareness of translational research and to build organizational capacity for the delivery of translational research projects in cancer. Methods An adaptive methodology was used to capture the design and growth of an web-based knowledge portal in cancer. This involved stakeholder consultations to inform initial design of the portal. Once the portal was live, site analytics were reviewed to evaluate member usage of the portal and to measure growth in membership. Results Knowledge portal membership grew consistently for the first 18 months after deployment, before leveling out. Analysis of site metrics revealed members were most likely to visit portal pages with community-generated content, particularly pages with a focus on translational research. This was closely followed by pages that disseminated educational material about translational research. Conclusions Preliminary data from this study suggest that knowledge portals may be beneficial tools for translating new evidence and fostering an environment of communication and collaboration. PMID:27357641

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.

Analysis of Utility and Use of a Web-Based Tool for Digital Signal Processing Teaching by Means of a Technological Acceptance Model

ERIC Educational Resources Information Center

Toral, S. L.; Barrero, F.; Martinez-Torres, M. R.

2007-01-01

This paper presents an exploratory study about the development of a structural and measurement model for the technological acceptance (TAM) of a web-based educational tool. The aim consists of measuring not only the use of this tool, but also the external variables with a significant influence in its use for planning future improvements. The tool,…

Using Web Database Tools To Facilitate the Construction of Knowledge in Online Courses.

ERIC Educational Resources Information Center

McNeil, Sara G.; Robin, Bernard R.

This paper presents an overview of database tools that dynamically generate World Wide Web materials and focuses on the use of these tools to support research activities, as well as teaching and learning. Database applications have been used in classrooms to support learning activities for over a decade, but, although business and e-commerce have…

CCDST: A free Canadian climate data scraping tool

NASA Astrophysics Data System (ADS)

Bonifacio, Charmaine; Barchyn, Thomas E.; Hugenholtz, Chris H.; Kienzle, Stefan W.

2015-02-01

In this paper we present a new software tool that automatically fetches, downloads and consolidates climate data from a Web database where the data are contained on multiple Web pages. The tool is called the Canadian Climate Data Scraping Tool (CCDST) and was developed to enhance access and simplify analysis of climate data from Canada's National Climate Data and Information Archive (NCDIA). The CCDST deconstructs a URL for a particular climate station in the NCDIA and then iteratively modifies the date parameters to download large volumes of data, remove individual file headers, and merge data files into one output file. This automated sequence enhances access to climate data by substantially reducing the time needed to manually download data from multiple Web pages. To this end, we present a case study of the temporal dynamics of blowing snow events that resulted in ~3.1 weeks time savings. Without the CCDST, the time involved in manually downloading climate data limits access and restrains researchers and students from exploring climate trends. The tool is coded as a Microsoft Excel macro and is available to researchers and students for free. The main concept and structure of the tool can be modified for other Web databases hosting geophysical data.

Current concepts in clinical research: web-based, automated, arthroscopic surgery prospective database registry.

PubMed

Lubowitz, James H; Smith, Patrick A

2012-03-01

In 2011, postsurgical patient outcome data may be compiled in a research registry, allowing comparative-effectiveness research and cost-effectiveness analysis by use of Health Insurance Portability and Accountability Act-compliant, institutional review board-approved, Food and Drug Administration-approved, remote, Web-based data collection systems. Computerized automation minimizes cost and minimizes surgeon time demand. A research registry can be a powerful tool to observe and understand variations in treatment and outcomes, to examine factors that influence prognosis and quality of life, to describe care patterns, to assess effectiveness, to monitor safety, and to change provider practice through feedback of data. Registry of validated, prospective outcome data is required for arthroscopic and related researchers and the public to advocate with governments and health payers. The goal is to develop evidence-based data to determine the best methods for treating patients. Copyright © 2012 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

Computing tools for implementing standards for single-case designs.

PubMed

Chen, Li-Ting; Peng, Chao-Ying Joanne; Chen, Ming-E

2015-11-01

In the single-case design (SCD) literature, five sets of standards have been formulated and distinguished: design standards, assessment standards, analysis standards, reporting standards, and research synthesis standards. This article reviews computing tools that can assist researchers and practitioners in meeting the analysis standards recommended by the What Works Clearinghouse: Procedures and Standards Handbook-the WWC standards. These tools consist of specialized web-based calculators or downloadable software for SCD data, and algorithms or programs written in Excel, SAS procedures, SPSS commands/Macros, or the R programming language. We aligned these tools with the WWC standards and evaluated them for accuracy and treatment of missing data, using two published data sets. All tools were tested to be accurate. When missing data were present, most tools either gave an error message or conducted analysis based on the available data. Only one program used a single imputation method. This article concludes with suggestions for an inclusive computing tool or environment, additional research on the treatment of missing data, and reasonable and flexible interpretations of the WWC standards. © The Author(s) 2015.

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).

New Web-Based Tools Make Systems Pharmacology More Accessible Using Data from the NCI-60 | Center for Cancer Research

Cancer.gov

High-throughput biological techniques, like microarrays and drug screens, generate an enormous amount of data that may be critically important for cancer researchers and clinicians. Being able to manipulate the data to extract those pieces of interest, however, can require computational or bioinformatics skills beyond those of the average scientist.

Exploring Dialogue in a Virtual Space: Blogging to Learn in an Undergraduate Black Studies Course

ERIC Educational Resources Information Center

Stewart, Anissa R.

2011-01-01

A growing number of researchers claim that web-based communication tools, such as weblogs (blogs for short), have the potential to transform teaching and learning in schools across grade levels. Yet, much of this research lacks evidence of what instructors and students are actually doing with the technology, including the circumstances under which…

Training Aide: Research and Guidance for Effective Training User Guide

DTIC Science & Technology

2013-12-01

Research Product 2014-02 Training Aide: Research and Guidance for Effective Training User Guide Beth Plott Shaun...Effective Training User Guide 5a. CONTRACT OR GRANT NUMBER W91WAW-07-C-0081 5b. PROGRAM ELEMENT NUMBER 611102 6. AUTHOR(S) Beth Plott...Representative and Subject Matter POC: Karin A. Orvis 14. ABSTRACT: This is a user guide for the web-based tool called Training Aide: Research and Guidance

Clearing your Desk! Software and Data Services for Collaborative Web Based GIS Analysis

NASA Astrophysics Data System (ADS)

Tarboton, D. G.; Idaszak, R.; Horsburgh, J. S.; Ames, D. P.; Goodall, J. L.; Band, L. E.; Merwade, V.; Couch, A.; Hooper, R. P.; Maidment, D. R.; Dash, P. K.; Stealey, M.; Yi, H.; Gan, T.; Gichamo, T.; Yildirim, A. A.; Liu, Y.

2015-12-01

Can your desktop computer crunch the large GIS datasets that are becoming increasingly common across the geosciences? Do you have access to or the know-how to take advantage of advanced high performance computing (HPC) capability? Web based cyberinfrastructure takes work off your desk or laptop computer and onto infrastructure or "cloud" based data and processing servers. This talk will describe the HydroShare collaborative environment and web based services being developed to support the sharing and processing of hydrologic data and models. HydroShare supports the upload, storage, and sharing of a broad class of hydrologic data including time series, geographic features and raster datasets, multidimensional space-time data, and other structured collections of data. Web service tools and a Python client library provide researchers with access to HPC resources without requiring them to become HPC experts. This reduces the time and effort spent in finding and organizing the data required to prepare the inputs for hydrologic models and facilitates the management of online data and execution of models on HPC systems. This presentation will illustrate the use of web based data and computation services from both the browser and desktop client software. These web-based services implement the Terrain Analysis Using Digital Elevation Model (TauDEM) tools for watershed delineation, generation of hydrology-based terrain information, and preparation of hydrologic model inputs. They allow users to develop scripts on their desktop computer that call analytical functions that are executed completely in the cloud, on HPC resources using input datasets stored in the cloud, without installing specialized software, learning how to use HPC, or transferring large datasets back to the user's desktop. These cases serve as examples for how this approach can be extended to other models to enhance the use of web and data services in the geosciences.

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.

Community-based primary care: improving and assessing diabetes management.

PubMed

Gannon, Meghan; Qaseem, Amir; Snow, Vincenza

2010-01-01

Morbidity and mortality associated with diabetes make it a prime target for quality improvement research. Quality gaps and racial/gender disparities persist throughout this population of patients necessitating a sustainable improvement in the clinical management of diabetes. The authors of this study sought (1) to provide a population perspective on diabetes management, and (2) to reinforce evidence-based clinical guidelines through a Web-based educational module.The project also aimed to gain insight into working remotely with a community of rural physicians. This longitudinal pre-post intervention study involved 18 internal medicine physicians and included 3 points of medical record data abstraction over 24 months. A Web-based educational module was introduced after the baseline data abstraction. This module contained chapters on clinical education, practice tools, and self-assessment. The results showed a sustained improvement in most clinical outcomes and demonstrated the effectiveness of using Web-based mediums to reinforce clinical guidelines and change physician behavior.

Development of the Diabetes Indicators and Data Sources Internet Tool (DIDIT).

PubMed

Mukhtar, Qaiser; Mehta, Prachi; Brody, Erica R; Camponeschi, Jenny; Friedrichs, Michael; Kemple, Angela M; Ralls, Brenda

2006-01-01

Developing a Web-based tool that involves the input, buy-in, and collaboration of multiple stakeholders and contractors is a complex process. Several elements facilitated the development of the Web-based Diabetes Indicators and Data Sources Internet Tool (DIDIT). The DIDIT is designed to enhance the ability of staff within the state-based Diabetes Prevention and Control Programs (DPCPs) and the Centers for Disease Control and Prevention (CDC) to perform diabetes surveillance. It contains information on 38 diabetes indicators (measures of health or factors associated with health) and 12 national- and state-level data sources. Developing the DIDIT required one contractor to conduct research on content for diabetes indicators and data sources and another contractor to develop the Web-based application to house and manage the information. During 3 years, a work group composed of representatives from the DPCPs and the Division of Diabetes Translation (DDT) at the CDC guided the development process by 1) gathering information on and communicating the needs of users and their vision for the DIDIT, 2) reviewing and approving content, and 3) providing input into the design and system functions. Strong leadership and vision of the project lead, clear communication and collaboration among all team members, and a commitment from the management of the DDT were essential elements in developing and implementing the DIDIT. Expertise in diabetes surveillance and software development, enthusiasm, and dedication were also instrumental in developing the DIDIT.

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

Nursing's role in nutrition.

PubMed

Henning, Michael

2009-01-01

There are not enough dietitians and nutritionists available to serve the entire healthcare industry. That means that nurses often fill the role of nutrition counselors. Nurses do not receive extensive education about nutrition, but there are great opportunities for nurses in nutrition, both as educators and researchers. One way this can happen is through the use of nutrition assessment tools. This article introduces a freeware nutritional assessment tool for use on Windows-based computers (available at http://nursing.jmu.edu). Unlike currently available tools, the Nutrition Analyzer is a stand-alone, Web-independent product, which builds a database of client data that can be manipulated for analysis and research.

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…

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

FRAT-up, a Web-based Fall-Risk Assessment Tool for Elderly People Living in the Community

PubMed Central

Cattelani, Luca; Palumbo, Pierpaolo; Palmerini, Luca; Bandinelli, Stefania; Becker, Clemens; Chiari, Lorenzo

2015-01-01

Background About 30% of people over 65 are subject to at least one unintentional fall a year. Fall prevention protocols and interventions can decrease the number of falls. To be effective, a prevention strategy requires a prior step to evaluate the fall risk of the subjects. Despite extensive research, existing assessment tools for fall risk have been insufficient for predicting falls. Objective The goal of this study is to present a novel web-based fall-risk assessment tool (FRAT-up) and to evaluate its accuracy in predicting falls, within a context of community-dwelling persons aged 65 and up. Methods FRAT-up is based on the assumption that a subject’s fall risk is given by the contribution of their exposure to each of the known fall-risk factors. Many scientific studies have investigated the relationship between falls and risk factors. The majority of these studies adopted statistical approaches, usually providing quantitative information such as odds ratios. FRAT-up exploits these numerical results to compute how each single factor contributes to the overall fall risk. FRAT-up is based on a formal ontology that enlists a number of known risk factors, together with quantitative findings in terms of odds ratios. From such information, an automatic algorithm generates a rule-based probabilistic logic program, that is, a set of rules for each risk factor. The rule-based program takes the health profile of the subject (in terms of exposure to the risk factors) and computes the fall risk. A Web-based interface allows users to input health profiles and to visualize the risk assessment for the given subject. FRAT-up has been evaluated on the InCHIANTI Study dataset, a representative population-based study of older persons living in the Chianti area (Tuscany, Italy). We compared reported falls with predicted ones and computed performance indicators. Results The obtained area under curve of the receiver operating characteristic was 0.642 (95% CI 0.614-0.669), while the Brier score was 0.174. The Hosmer-Lemeshow test indicated statistical significance of miscalibration. Conclusions FRAT-up is a web-based tool for evaluating the fall risk of people aged 65 or up living in the community. Validation results of fall risks computed by FRAT-up show that its performance is comparable to externally validated state-of-the-art tools. A prototype is freely available through a web-based interface. Trial Registration ClinicalTrials.gov NCT01331512 (The InChianti Follow-Up Study); http://clinicaltrials.gov/show/NCT01331512 (Archived by WebCite at http://www.webcitation.org/6UDrrRuaR). PMID:25693419

Education and Technology in the 21st Century Experiences of Adult Online Learners Using Web 2.0

ERIC Educational Resources Information Center

Bryant, Wanda L.

2014-01-01

The emergence of a knowledge-based and technology-driven economy has prompted adults to seek additional knowledge and skills that will enable them to participate effectively in society. The rapid growth and popularity of the internet tools such as Web 2.0 tools have revolutionized adult learning. Through the rich support of Web 2.0 tools, adult…

Web-based tailored nutrition education: results of a randomized controlled trial.

PubMed

Oenema, A; Brug, J; Lechner, L

2001-12-01

There is ample evidence that printed, computer-tailored nutrition education is a more effective tool for motivating people to change to healthier diets than general nutrition education. New technology is now providing more advanced ways of delivering tailored messages, e.g. via the World Wide Web (WWW). Before disseminating a tailored intervention via the web, it is important to investigate the potential of web-based tailored nutrition education. The present study investigated the immediate impact of web-based computer-tailored nutrition education on personal awareness and intentions related to intake of fat, fruit and vegetables. A randomized controlled trial, with a pre-test-post-test control group design was conducted. Significant differences in awareness and intention to change were found between the intervention and control group at post-test. The tailored intervention was appreciated better, was rated as more personally relevant, and had more subjective impact on opinion and intentions to change than the general nutrition information. Computer literacy had no effect on these ratings. The results indicate that interactive, web-based computer-tailored nutrition education can lead to changes in determinants of behavior. Future research should be aimed at longer-term (behavioral) effects and the practicability of distributing tailored interventions via the WWW.

An Integrated Web-Based Assessment Tool for Assessing Pesticide Exposure and Risks

EPA Science Inventory

Background/Question/Methods We have created an integrated web-based tool designed to estimate exposure doses and ecological risks under the Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) and the Endangered Species Act. This involved combining a number of disparat...

Web-based applications for building, managing and analysing kinetic models of biological systems.

PubMed

Lee, Dong-Yup; Saha, Rajib; Yusufi, Faraaz Noor Khan; Park, Wonjun; Karimi, Iftekhar A

2009-01-01

Mathematical modelling and computational analysis play an essential role in improving our capability to elucidate the functions and characteristics of complex biological systems such as metabolic, regulatory and cell signalling pathways. The modelling and concomitant simulation render it possible to predict the cellular behaviour of systems under various genetically and/or environmentally perturbed conditions. This motivates systems biologists/bioengineers/bioinformaticians to develop new tools and applications, allowing non-experts to easily conduct such modelling and analysis. However, among a multitude of systems biology tools developed to date, only a handful of projects have adopted a web-based approach to kinetic modelling. In this report, we evaluate the capabilities and characteristics of current web-based tools in systems biology and identify desirable features, limitations and bottlenecks for further improvements in terms of usability and functionality. A short discussion on software architecture issues involved in web-based applications and the approaches taken by existing tools is included for those interested in developing their own simulation applications.

An online model composition tool for system biology models

PubMed Central

2013-01-01

Background There are multiple representation formats for Systems Biology computational models, and the Systems Biology Markup Language (SBML) is one of the most widely used. SBML is used to capture, store, and distribute computational models by Systems Biology data sources (e.g., the BioModels Database) and researchers. Therefore, there is a need for all-in-one web-based solutions that support advance SBML functionalities such as uploading, editing, composing, visualizing, simulating, querying, and browsing computational models. Results We present the design and implementation of the Model Composition Tool (Interface) within the PathCase-SB (PathCase Systems Biology) web portal. The tool helps users compose systems biology models to facilitate the complex process of merging systems biology models. We also present three tools that support the model composition tool, namely, (1) Model Simulation Interface that generates a visual plot of the simulation according to user’s input, (2) iModel Tool as a platform for users to upload their own models to compose, and (3) SimCom Tool that provides a side by side comparison of models being composed in the same pathway. Finally, we provide a web site that hosts BioModels Database models and a separate web site that hosts SBML Test Suite models. Conclusions Model composition tool (and the other three tools) can be used with little or no knowledge of the SBML document structure. For this reason, students or anyone who wants to learn about systems biology will benefit from the described functionalities. SBML Test Suite models will be a nice starting point for beginners. And, for more advanced purposes, users will able to access and employ models of the BioModels Database as well. PMID:24006914

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.

CoCoFolio: A Web-Based Electronic Portfolio for Enriching Students' Learning by Collaboration.

ERIC Educational Resources Information Center

Sugiyama, Takeshi; Kakehi, Naoyuki; Kura, Tsuneko; Takahashi Tokiichiro

A Web-based electronic portfolio, CoCoFolio, was developed for enriching students' learning by collaboration. CoCoFolio consists of two collaboration tools: a multi-layer drawing tool, CoCoBoard, and a small bulletin board, Discussion Board, for each student's submission. These tools support a series of expression activities: expression, sharing,…

Visible Earthquakes: a web-based tool for visualizing and modeling InSAR earthquake data

NASA Astrophysics Data System (ADS)

Funning, G. J.; Cockett, R.

2012-12-01

InSAR (Interferometric Synthetic Aperture Radar) is a technique for measuring the deformation of the ground using satellite radar data. One of the principal applications of this method is in the study of earthquakes; in the past 20 years over 70 earthquakes have been studied in this way, and forthcoming satellite missions promise to enable the routine and timely study of events in the future. Despite the utility of the technique and its widespread adoption by the research community, InSAR does not feature in the teaching curricula of most university geoscience departments. This is, we believe, due to a lack of accessibility to software and data. Existing tools for the visualization and modeling of interferograms are often research-oriented, command line-based and/or prohibitively expensive. Here we present a new web-based interactive tool for comparing real InSAR data with simple elastic models. The overall design of this tool was focused on ease of access and use. This tool should allow interested nonspecialists to gain a feel for the use of such data and greatly facilitate integration of InSAR into upper division geoscience courses, giving students practice in comparing actual data to modeled results. The tool, provisionally named 'Visible Earthquakes', uses web-based technologies to instantly render the displacement field that would be observable using InSAR for a given fault location, geometry, orientation, and slip. The user can adjust these 'source parameters' using a simple, clickable interface, and see how these affect the resulting model interferogram. By visually matching the model interferogram to a real earthquake interferogram (processed separately and included in the web tool) a user can produce their own estimates of the earthquake's source parameters. Once satisfied with the fit of their models, users can submit their results and see how they compare with the distribution of all other contributed earthquake models, as well as the mean and median models. We envisage that the ensemble of contributed models will be useful both as a research resource and in the classroom. Locations of earthquakes derived from InSAR data have already been demonstrated to differ significantly from those obtained from global seismic networks (Weston et al., 2011), and the locations obtained by our users will enable us to identify systematic mislocations that are likely due to errors in Earth velocity models used to locate earthquakes. If the tool is incorporated into geophysics, tectonics and/or structural geology classes, in addition to familiarizing students with InSAR and elastic deformation modeling, the spread of different results for each individual earthquake will allow the teaching of concepts such as model uncertainty and non-uniqueness when modeling real scientific data. Additionally, the process students go through to optimize their estimates of fault parameters can easily be tied into teaching about the concepts of forward and inverse problems, which are common in geophysics.

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.

AMP: a science-driven web-based application for the TeraGrid

NASA Astrophysics Data System (ADS)

Woitaszek, M.; Metcalfe, T.; Shorrock, I.

The Asteroseismic Modeling Portal (AMP) provides a web-based interface for astronomers to run and view simulations that derive the properties of Sun-like stars from observations of their pulsation frequencies. In this paper, we describe the architecture and implementation of AMP, highlighting the lightweight design principles and tools used to produce a functional fully-custom web-based science application in less than a year. Targeted as a TeraGrid science gateway, AMP's architecture and implementation are intended to simplify its orchestration of TeraGrid computational resources. AMP's web-based interface was developed as a traditional standalone database-backed web application using the Python-based Django web development framework, allowing us to leverage the Django framework's capabilities while cleanly separating the user interface development from the grid interface development. We have found this combination of tools flexible and effective for rapid gateway development and deployment.

Web-based CERES Clouds QC Property Viewing Tool

NASA Astrophysics Data System (ADS)

Smith, R. A.

2015-12-01

Churngwei Chu1, Rita Smith1, Sunny Sun-Mack1, Yan Chen1, Elizabeth Heckert1, Patrick Minnis21 Science Systems and Applications, Inc., Hampton, Virginia2 NASA Langley Research Center, Hampton, Virginia This presentation will display the capabilities of a web-based CERES cloud property viewer. Aqua/Terra/NPP data will be chosen for examples. It will demonstrate viewing of cloud properties in gridded global maps, histograms, time series displays, latitudinal zonal images, binned data charts, data frequency graphs, and ISCCP plots. Images can be manipulated by the user to narrow boundaries of the map as well as color bars and value ranges, compare datasets, view data values, and more. Other atmospheric studies groups will be encouraged to put their data into the underlying NetCDF data format and view their data with the tool.

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.

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.

Development of a data dictionary for the Strategies for Post Arrest Resuscitation Care (SPARC) network for post cardiac arrest research.

PubMed

Lin, Steve; Morrison, Laurie J; Brooks, Steven C

2011-04-01

The widely accepted Utstein style has standardized data collection and analysis in resuscitation and post resuscitation research. However, collection of many of these variables poses significant practical challenges. In addition, several important variables in post resuscitation research are missing. Our aim was to develop a comprehensive data dictionary and web-based data collection tool as part of the Strategies for Post Arrest Resuscitation Care (SPARC) Network project, which implemented a knowledge translation program for post cardiac arrest therapeutic hypothermia in 37 Ontario hospitals. A list of data variables was generated based on the current Utstein style, previous studies and expert opinion within our group of investigators. We developed a data dictionary by creating clear definitions and establishing abstraction instructions for each variable. The data dictionary was integrated into a web-based collection form allowing for interactive data entry. Two blinded investigators piloted the data collection tool, by performing a retrospective chart review. A total of 454 variables were included of which 400 were Utstein, 2 were adapted from existing studies and 52 were added to address missing elements. Kappa statistics for two outcome variables, survival to discharge and induction of therapeutic hypothermia were 0.86 and 0.64, respectively. This is the first attempt in the literature to develop a data dictionary as part of a standardized, pragmatic data collection tool for post cardiac arrest research patients. In addition, our dataset defined important variables that were previously missing. This data collection tool can serve as a reference for future trials in post cardiac arrest care. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

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

Trial Promoter: A Web-Based Tool for Boosting the Promotion of Clinical Research Through Social Media.

PubMed

Reuter, Katja; Ukpolo, Francis; Ward, Edward; Wilson, Melissa L; Angyan, Praveen

2016-06-29

Scarce information about clinical research, in particular clinical trials, is among the top reasons why potential participants do not take part in clinical studies. Without volunteers, on the other hand, clinical research and the development of novel approaches to preventing, diagnosing, and treating disease are impossible. Promising digital options such as social media have the potential to work alongside traditional methods to boost the promotion of clinical research. However, investigators and research institutions are challenged to leverage these innovations while saving time and resources. To develop and test the efficiency of a Web-based tool that automates the generation and distribution of user-friendly social media messages about clinical trials. Trial Promoter is developed in Ruby on Rails, HTML, cascading style sheet (CSS), and JavaScript. In order to test the tool and the correctness of the generated messages, clinical trials (n=46) were randomized into social media messages and distributed via the microblogging social media platform Twitter and the social network Facebook. The percent correct was calculated to determine the probability with which Trial Promoter generates accurate messages. During a 10-week testing phase, Trial Promoter automatically generated and published 525 user-friendly social media messages on Twitter and Facebook. On average, Trial Promoter correctly used the message templates and substituted the message parameters (text, URLs, and disease hashtags) 97.7% of the time (1563/1600). Trial Promoter may serve as a promising tool to render clinical trial promotion more efficient while requiring limited resources. It supports the distribution of any research or other types of content. The Trial Promoter code and installation instructions are freely available online.

Trial Promoter: A Web-Based Tool for Boosting the Promotion of Clinical Research Through Social Media

PubMed Central

Ukpolo, Francis; Ward, Edward; Wilson, Melissa L

2016-01-01

Background Scarce information about clinical research, in particular clinical trials, is among the top reasons why potential participants do not take part in clinical studies. Without volunteers, on the other hand, clinical research and the development of novel approaches to preventing, diagnosing, and treating disease are impossible. Promising digital options such as social media have the potential to work alongside traditional methods to boost the promotion of clinical research. However, investigators and research institutions are challenged to leverage these innovations while saving time and resources. Objective To develop and test the efficiency of a Web-based tool that automates the generation and distribution of user-friendly social media messages about clinical trials. Methods Trial Promoter is developed in Ruby on Rails, HTML, cascading style sheet (CSS), and JavaScript. In order to test the tool and the correctness of the generated messages, clinical trials (n=46) were randomized into social media messages and distributed via the microblogging social media platform Twitter and the social network Facebook. The percent correct was calculated to determine the probability with which Trial Promoter generates accurate messages. Results During a 10-week testing phase, Trial Promoter automatically generated and published 525 user-friendly social media messages on Twitter and Facebook. On average, Trial Promoter correctly used the message templates and substituted the message parameters (text, URLs, and disease hashtags) 97.7% of the time (1563/1600). Conclusions Trial Promoter may serve as a promising tool to render clinical trial promotion more efficient while requiring limited resources. It supports the distribution of any research or other types of content. The Trial Promoter code and installation instructions are freely available online. PMID:27357424

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.

A study of the development of critical thinking skills using an innovative web 2.0 tool.

PubMed

Eales-Reynolds, Lesley-Jane; Gillham, David; Grech, Carol; Clarke, Colin; Cornell, Jacqueline

2012-10-01

Healthcare educators face numerous challenges including technological change, information overload, and the need to maintain clinical expertise and research knowledge across multiple specialities. Students also need to develop their capacity for critical thinking, using and discriminating between diverse sources of knowledge in order to advance their own practice. To investigate student perceptions of the affordances of a novel web 2.0-based tool--the Web Resource Appraisal Process (WRAP), designed to support the development of critical thinking skills, and to identify how student's understanding of critical thinking and their use of web 2.0 resources might inform the cross-disciplinary development of the WRAP. A two phase, action research study of student perceptions of the WRAP and their ability to source and identify valid information sources. Implemented at the University of South Australia, development of the WRAP is an international project with the University of Westminster, UK. Students from international locations participated in the project. A mixed methods approach was adopted involving a two phase action research study. In phase one, student perceptions of the WRAP were obtained using a modified course feedback questionnaire. This informed the development of a subsequent questionnaire used to survey student perceptions of their usage of online resources, the ease of access of such resources and their approaches to determining their validity. Results suggest that students mainly use traditional resources when preparing work for assessment and they either do not understand the concept of, or do not exercise, critical thinking skills in such activities. However, the feedback from students using the WRAP, demonstrated that they found it instructive and useful. To ensure that practice developments are based on authoritative evidence, students need to develop critical thinking skills which may be facilitated by tools such as the WRAP. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

CartograTree: connecting tree genomes, phenotypes and environment.

PubMed

Vasquez-Gross, Hans A; Yu, John J; Figueroa, Ben; Gessler, Damian D G; Neale, David B; Wegrzyn, Jill L

2013-05-01

Today, researchers spend a tremendous amount of time gathering, formatting, filtering and visualizing data collected from disparate sources. Under the umbrella of forest tree biology, we seek to provide a platform and leverage modern technologies to connect biotic and abiotic data. Our goal is to provide an integrated web-based workspace that connects environmental, genomic and phenotypic data via geo-referenced coordinates. Here, we connect the genomic query web-based workspace, DiversiTree and a novel geographical interface called CartograTree to data housed on the TreeGenes database. To accomplish this goal, we implemented Simple Semantic Web Architecture and Protocol to enable the primary genomics database, TreeGenes, to communicate with semantic web services regardless of platform or back-end technologies. The novelty of CartograTree lies in the interactive workspace that allows for geographical visualization and engagement of high performance computing (HPC) resources. The application provides a unique tool set to facilitate research on the ecology, physiology and evolution of forest tree species. CartograTree can be accessed at: http://dendrome.ucdavis.edu/cartogratree. © 2013 Blackwell Publishing Ltd.

Work of the Web Weavers: Web Development in Academic Libraries

ERIC Educational Resources Information Center

Bundza, Maira; Vander Meer, Patricia Fravel; Perez-Stable, Maria A.

2009-01-01

Although the library's Web site has become a standard tool for seeking information and conducting research in academic institutions, there are a variety of ways libraries approach the often challenging--and sometimes daunting--process of Web site development and maintenance. Three librarians at Western Michigan University explored issues related…

Share2Quit: Web-Based Peer-Driven Referrals for Smoking Cessation

PubMed Central

2013-01-01

Background Smoking is the number one preventable cause of death in the United States. Effective Web-assisted tobacco interventions are often underutilized and require new and innovative engagement approaches. Web-based peer-driven chain referrals successfully used outside health care have the potential for increasing the reach of Internet interventions. Objective The objective of our study was to describe the protocol for the development and testing of proactive Web-based chain-referral tools for increasing the access to Decide2Quit.org, a Web-assisted tobacco intervention system. Methods We will build and refine proactive chain-referral tools, including email and Facebook referrals. In addition, we will implement respondent-driven sampling (RDS), a controlled chain-referral sampling technique designed to remove inherent biases in chain referrals and obtain a representative sample. We will begin our chain referrals with an initial recruitment of former and current smokers as seeds (initial participants) who will be trained to refer current smokers from their social network using the developed tools. In turn, these newly referred smokers will also be provided the tools to refer other smokers from their social networks. We will model predictors of referral success using sample weights from the RDS to estimate the success of the system in the targeted population. Results This protocol describes the evaluation of proactive Web-based chain-referral tools, which can be used in tobacco interventions to increase the access to hard-to-reach populations, for promoting smoking cessation. Conclusions Share2Quit represents an innovative advancement by capitalizing on naturally occurring technology trends to recruit smokers to Web-assisted tobacco interventions. PMID:24067329

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.

Plug and Play web-based visualization of mobile air monitoring data (Abstract)

EPA Science Inventory

EPA’s Real-Time Geospatial (RETIGO) Data Viewer web-based tool is a new program reducing the technical barrier to visualize and understand geospatial air data time series collected using wearable, bicycle-mounted, or vehicle-mounted air sensors. The RETIGO tool, with anticipated...

vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments

PubMed Central

2010-01-01

Background The replication rate (or fitness) between viral variants has been investigated in vivo and in vitro for human immunodeficiency virus (HIV). HIV fitness plays an important role in the development and persistence of drug resistance. The accurate estimation of viral fitness relies on complicated computations based on statistical methods. This calls for tools that are easy to access and intuitive to use for various experiments of viral fitness. Results Based on a mathematical model and several statistical methods (least-squares approach and measurement error models), a Web-based computing tool has been developed for improving estimation of virus fitness in growth competition assays of human immunodeficiency virus type 1 (HIV-1). Conclusions Unlike the two-point calculation used in previous studies, the estimation here uses linear regression methods with all observed data in the competition experiment to more accurately estimate relative viral fitness parameters. The dilution factor is introduced for making the computational tool more flexible to accommodate various experimental conditions. This Web-based tool is implemented in C# language with Microsoft ASP.NET, and is publicly available on the Web at http://bis.urmc.rochester.edu/vFitness/. PMID:20482791

vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments.

PubMed

Ma, Jingming; Dykes, Carrie; Wu, Tao; Huang, Yangxin; Demeter, Lisa; Wu, Hulin

2010-05-18

The replication rate (or fitness) between viral variants has been investigated in vivo and in vitro for human immunodeficiency virus (HIV). HIV fitness plays an important role in the development and persistence of drug resistance. The accurate estimation of viral fitness relies on complicated computations based on statistical methods. This calls for tools that are easy to access and intuitive to use for various experiments of viral fitness. Based on a mathematical model and several statistical methods (least-squares approach and measurement error models), a Web-based computing tool has been developed for improving estimation of virus fitness in growth competition assays of human immunodeficiency virus type 1 (HIV-1). Unlike the two-point calculation used in previous studies, the estimation here uses linear regression methods with all observed data in the competition experiment to more accurately estimate relative viral fitness parameters. The dilution factor is introduced for making the computational tool more flexible to accommodate various experimental conditions. This Web-based tool is implemented in C# language with Microsoft ASP.NET, and is publicly available on the Web at http://bis.urmc.rochester.edu/vFitness/.

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...

Facilitating Spatial Thinking in World Geography Using Web-Based GIS

ERIC Educational Resources Information Center

Jo, Injeong; Hong, Jung Eun; Verma, Kanika

2016-01-01

Advocates for geographic information system (GIS) education contend that learning about GIS promotes students' spatial thinking. Empirical studies are still needed to elucidate the potential of GIS as an instructional tool to support spatial thinking in other geography courses. Using a non-equivalent control group research design, this study…

SMARTE: IMPROVING REVITALIZATION DECISIONS (CINCINNATI, OHIO)

EPA Science Inventory

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

Mapping International Cancer Activities – Global Cancer Project Map Launch

Cancer.gov

CGH’s Dr. Sudha Sivaram, Dr. Makeda Williams, and Ms. Kalina Duncan have partnered with Drs. Ami Bhatt and Franklin Huang at Global Oncology, Inc. (GO) to develop the Global Cancer Project Map - a web-based tool designed to facilitate cancer research and control activity planning.

Products and Processes: Synergistic Relationships

ERIC Educational Resources Information Center

Wallace, Virginia; Husid, Whitney

2013-01-01

Most people agree that products are the culmination of what students have studied. For this article, "product" will refer to students' abilities to create outcomes and design artifacts. Those abilities are guided by four processes: inquiry-based learning, use of a research model, use of Web 2.0 tools, and appropriate assessments.…

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…

The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface.

PubMed

Chen, Josephine; Zhao, Po; Massaro, Donald; Clerch, Linda B; Almon, Richard R; DuBois, Debra C; Jusko, William J; Hoffman, Eric P

2004-01-01

Publicly accessible DNA databases (genome browsers) are rapidly accelerating post-genomic research (see http://www.genome.ucsc.edu/), with integrated genomic DNA, gene structure, EST/ splicing and cross-species ortholog data. DNA databases have relatively low dimensionality; the genome is a linear code that anchors all associated data. In contrast, RNA expression and protein databases need to be able to handle very high dimensional data, with time, tissue, cell type and genes, as interrelated variables. The high dimensionality of microarray expression profile data, and the lack of a standard experimental platform have complicated the development of web-accessible databases and analytical tools. We have designed and implemented a public resource of expression profile data containing 1024 human, mouse and rat Affymetrix GeneChip expression profiles, generated in the same laboratory, and subject to the same quality and procedural controls (Public Expression Profiling Resource; PEPR). Our Oracle-based PEPR data warehouse includes a novel time series query analysis tool (SGQT), enabling dynamic generation of graphs and spreadsheets showing the action of any transcript of interest over time. In this report, we demonstrate the utility of this tool using a 27 time point, in vivo muscle regeneration series. This data warehouse and associated analysis tools provides access to multidimensional microarray data through web-based interfaces, both for download of all types of raw data for independent analysis, and also for straightforward gene-based queries. Planned implementations of PEPR will include web-based remote entry of projects adhering to quality control and standard operating procedure (QC/SOP) criteria, and automated output of alternative probe set algorithms for each project (see http://microarray.cnmcresearch.org/pgadatatable.asp).

The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface

PubMed Central

Chen, Josephine; Zhao, Po; Massaro, Donald; Clerch, Linda B.; Almon, Richard R.; DuBois, Debra C.; Jusko, William J.; Hoffman, Eric P.

2004-01-01

Publicly accessible DNA databases (genome browsers) are rapidly accelerating post-genomic research (see http://www.genome.ucsc.edu/), with integrated genomic DNA, gene structure, EST/ splicing and cross-species ortholog data. DNA databases have relatively low dimensionality; the genome is a linear code that anchors all associated data. In contrast, RNA expression and protein databases need to be able to handle very high dimensional data, with time, tissue, cell type and genes, as interrelated variables. The high dimensionality of microarray expression profile data, and the lack of a standard experimental platform have complicated the development of web-accessible databases and analytical tools. We have designed and implemented a public resource of expression profile data containing 1024 human, mouse and rat Affymetrix GeneChip expression profiles, generated in the same laboratory, and subject to the same quality and procedural controls (Public Expression Profiling Resource; PEPR). Our Oracle-based PEPR data warehouse includes a novel time series query analysis tool (SGQT), enabling dynamic generation of graphs and spreadsheets showing the action of any transcript of interest over time. In this report, we demonstrate the utility of this tool using a 27 time point, in vivo muscle regeneration series. This data warehouse and associated analysis tools provides access to multidimensional microarray data through web-based interfaces, both for download of all types of raw data for independent analysis, and also for straightforward gene-based queries. Planned implementations of PEPR will include web-based remote entry of projects adhering to quality control and standard operating procedure (QC/SOP) criteria, and automated output of alternative probe set algorithms for each project (see http://microarray.cnmcresearch.org/pgadatatable.asp). PMID:14681485

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

Introducing the Forensic Research/Reference on Genetics knowledge base, FROG-kb

PubMed Central

2012-01-01

Background Online tools and databases based on multi-allelic short tandem repeat polymorphisms (STRPs) are actively used in forensic teaching, research, and investigations. The Fst value of each CODIS marker tends to be low across the populations of the world and most populations typically have all the common STRP alleles present diminishing the ability of these systems to discriminate ethnicity. Recently, considerable research is being conducted on single nucleotide polymorphisms (SNPs) to be considered for human identification and description. However, online tools and databases that can be used for forensic research and investigation are limited. Methods The back end DBMS (Database Management System) for FROG-kb is Oracle version 10. The front end is implemented with specific code using technologies such as Java, Java Servlet, JSP, JQuery, and GoogleCharts. Results We present an open access web application, FROG-kb (Forensic Research/Reference on Genetics-knowledge base, http://frog.med.yale.edu), that is useful for teaching and research relevant to forensics and can serve as a tool facilitating forensic practice. The underlying data for FROG-kb are provided by the already extensively used and referenced ALlele FREquency Database, ALFRED (http://alfred.med.yale.edu). In addition to displaying data in an organized manner, computational tools that use the underlying allele frequencies with user-provided data are implemented in FROG-kb. These tools are organized by the different published SNP/marker panels available. This web tool currently has implemented general functions possible for two types of SNP panels, individual identification and ancestry inference, and a prediction function specific to a phenotype informative panel for eye color. Conclusion The current online version of FROG-kb already provides new and useful functionality. We expect FROG-kb to grow and expand in capabilities and welcome input from the forensic community in identifying datasets and functionalities that will be most helpful and useful. Thus, the structure and functionality of FROG-kb will be revised in an ongoing process of improvement. This paper describes the state as of early June 2012. PMID:22938150

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.

Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web

PubMed Central

Miller, Chase A.; Anthony, Jon; Meyer, Michelle M.; Marth, Gabor

2013-01-01

Motivation: High-throughput biological research requires simultaneous visualization as well as analysis of genomic data, e.g. read alignments, variant calls and genomic annotations. Traditionally, such integrative analysis required desktop applications operating on locally stored data. Many current terabyte-size datasets generated by large public consortia projects, however, are already only feasibly stored at specialist genome analysis centers. As even small laboratories can afford very large datasets, local storage and analysis are becoming increasingly limiting, and it is likely that most such datasets will soon be stored remotely, e.g. in the cloud. These developments will require web-based tools that enable users to access, analyze and view vast remotely stored data with a level of sophistication and interactivity that approximates desktop applications. As rapidly dropping cost enables researchers to collect data intended to answer questions in very specialized contexts, developers must also provide software libraries that empower users to implement customized data analyses and data views for their particular application. Such specialized, yet lightweight, applications would empower scientists to better answer specific biological questions than possible with general-purpose genome browsers currently available. Results: Using recent advances in core web technologies (HTML5), we developed Scribl, a flexible genomic visualization library specifically targeting coordinate-based data such as genomic features, DNA sequence and genetic variants. Scribl simplifies the development of sophisticated web-based graphical tools that approach the dynamism and interactivity of desktop applications. Availability and implementation: Software is freely available online at http://chmille4.github.com/Scribl/ and is implemented in JavaScript with all modern browsers supported. Contact: gabor.marth@bc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23172864

Providing Web Interfaces to the NSF EarthScope USArray Transportable Array

NASA Astrophysics Data System (ADS)

Vernon, Frank; Newman, Robert; Lindquist, Kent

2010-05-01

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

The Web Resource Collaboration Center

ERIC Educational Resources Information Center

Dunlap, Joanna C.

2004-01-01

The Web Resource Collaboration Center (WRCC) is a web-based tool developed to help software engineers build their own web-based learning and performance support systems. Designed using various online communication and collaboration technologies, the WRCC enables people to: (1) build a learning and professional development resource that provides…

GDSCalc: A Web-Based Application for Evaluating Discrete Graph Dynamical Systems

PubMed Central

Elmeligy Abdelhamid, Sherif H.; Kuhlman, Chris J.; Marathe, Madhav V.; Mortveit, Henning S.; Ravi, S. S.

2015-01-01

Discrete dynamical systems are used to model various realistic systems in network science, from social unrest in human populations to regulation in biological networks. A common approach is to model the agents of a system as vertices of a graph, and the pairwise interactions between agents as edges. Agents are in one of a finite set of states at each discrete time step and are assigned functions that describe how their states change based on neighborhood relations. Full characterization of state transitions of one system can give insights into fundamental behaviors of other dynamical systems. In this paper, we describe a discrete graph dynamical systems (GDSs) application called GDSCalc for computing and characterizing system dynamics. It is an open access system that is used through a web interface. We provide an overview of GDS theory. This theory is the basis of the web application; i.e., an understanding of GDS provides an understanding of the software features, while abstracting away implementation details. We present a set of illustrative examples to demonstrate its use in education and research. Finally, we compare GDSCalc with other discrete dynamical system software tools. Our perspective is that no single software tool will perform all computations that may be required by all users; tools typically have particular features that are more suitable for some tasks. We situate GDSCalc within this space of software tools. PMID:26263006

GDSCalc: A Web-Based Application for Evaluating Discrete Graph Dynamical Systems.

PubMed

Elmeligy Abdelhamid, Sherif H; Kuhlman, Chris J; Marathe, Madhav V; Mortveit, Henning S; Ravi, S S

2015-01-01

Discrete dynamical systems are used to model various realistic systems in network science, from social unrest in human populations to regulation in biological networks. A common approach is to model the agents of a system as vertices of a graph, and the pairwise interactions between agents as edges. Agents are in one of a finite set of states at each discrete time step and are assigned functions that describe how their states change based on neighborhood relations. Full characterization of state transitions of one system can give insights into fundamental behaviors of other dynamical systems. In this paper, we describe a discrete graph dynamical systems (GDSs) application called GDSCalc for computing and characterizing system dynamics. It is an open access system that is used through a web interface. We provide an overview of GDS theory. This theory is the basis of the web application; i.e., an understanding of GDS provides an understanding of the software features, while abstracting away implementation details. We present a set of illustrative examples to demonstrate its use in education and research. Finally, we compare GDSCalc with other discrete dynamical system software tools. Our perspective is that no single software tool will perform all computations that may be required by all users; tools typically have particular features that are more suitable for some tasks. We situate GDSCalc within this space of software tools.

CsSNP: A Web-Based Tool for the Detecting of Comparative Segments SNPs.

PubMed

Wang, Yi; Wang, Shuangshuang; Zhou, Dongjie; Yang, Shuai; Xu, Yongchao; Yang, Chao; Yang, Long

2016-07-01

SNP (single nucleotide polymorphism) is a popular tool for the study of genetic diversity, evolution, and other areas. Therefore, it is necessary to develop a convenient, utility, robust, rapid, and open source detecting-SNP tool for all researchers. Since the detection of SNPs needs special software and series steps including alignment, detection, analysis and present, the study of SNPs is limited for nonprofessional users. CsSNP (Comparative segments SNP, http://biodb.sdau.edu.cn/cssnp/ ) is a freely available web tool based on the Blat, Blast, and Perl programs to detect comparative segments SNPs and to show the detail information of SNPs. The results are filtered and presented in the statistics figure and a Gbrowse map. This platform contains the reference genomic sequences and coding sequences of 60 plant species, and also provides new opportunities for the users to detect SNPs easily. CsSNP is provided a convenient tool for nonprofessional users to find comparative segments SNPs in their own sequences, and give the users the information and the analysis of SNPs, and display these data in a dynamic map. It provides a new method to detect SNPs and may accelerate related studies.

Web-Based Tools for Modelling and Analysis of Multivariate Data: California Ozone Pollution Activity

ERIC Educational Resources Information Center

Dinov, Ivo D.; Christou, Nicolas

2011-01-01

This article presents a hands-on web-based activity motivated by the relation between human health and ozone pollution in California. This case study is based on multivariate data collected monthly at 20 locations in California between 1980 and 2006. Several strategies and tools for data interrogation and exploratory data analysis, model fitting…

Web-Based Learning Design Tool

ERIC Educational Resources Information Center

Bruno, F. B.; Silva, T. L. K.; Silva, R. P.; Teixeira, F. G.

2012-01-01

Purpose: The purpose of this paper is to propose a web-based tool that enables the development and provision of learning designs and its reuse and re-contextualization as generative learning objects, aimed at developing educational materials. Design/methodology/approach: The use of learning objects can facilitate the process of production and…

BioTapestry now provides a web application and improved drawing and layout tools

PubMed Central

Paquette, Suzanne M.; Leinonen, Kalle; Longabaugh, William J.R.

2016-01-01

Gene regulatory networks (GRNs) control embryonic development, and to understand this process in depth, researchers need to have a detailed understanding of both the network architecture and its dynamic evolution over time and space. Interactive visualization tools better enable researchers to conceptualize, understand, and share GRN models. BioTapestry is an established application designed to fill this role, and recent enhancements released in Versions 6 and 7 have targeted two major facets of the program. First, we introduced significant improvements for network drawing and automatic layout that have now made it much easier for the user to create larger, more organized network drawings. Second, we revised the program architecture so it could continue to support the current Java desktop Editor program, while introducing a new BioTapestry GRN Viewer that runs as a JavaScript web application in a browser. We have deployed a number of GRN models using this new web application. These improvements will ensure that BioTapestry remains viable as a research tool in the face of the continuing evolution of web technologies, and as our understanding of GRN models grows. PMID:27134726

BioTapestry now provides a web application and improved drawing and layout tools.

PubMed

Paquette, Suzanne M; Leinonen, Kalle; Longabaugh, William J R

2016-01-01

Gene regulatory networks (GRNs) control embryonic development, and to understand this process in depth, researchers need to have a detailed understanding of both the network architecture and its dynamic evolution over time and space. Interactive visualization tools better enable researchers to conceptualize, understand, and share GRN models. BioTapestry is an established application designed to fill this role, and recent enhancements released in Versions 6 and 7 have targeted two major facets of the program. First, we introduced significant improvements for network drawing and automatic layout that have now made it much easier for the user to create larger, more organized network drawings. Second, we revised the program architecture so it could continue to support the current Java desktop Editor program, while introducing a new BioTapestry GRN Viewer that runs as a JavaScript web application in a browser. We have deployed a number of GRN models using this new web application. These improvements will ensure that BioTapestry remains viable as a research tool in the face of the continuing evolution of web technologies, and as our understanding of GRN models grows.

The Motivating Power of Social Obligation: An Investigation into the Pedagogical Affordances of Mobile Learning Integrated with Facebook

ERIC Educational Resources Information Center

Sazalli, Nurhasmiza; Wegerif, Rupert; Kleine-Staarman, Judith

2014-01-01

We report on the provisional findings of an ongoing research project investigating the pedagogical affordances of mobile learning in combination with Web 2.0 tools for the learning of English for English as a Second Language (ESL) learners. Using Design Based Research (DBR) as an approach to conduct this study, this paper will first present the…

Networking and Information Technology Research and Development. Supplement to the President’s Budget for FY 2002

DTIC Science & Technology

2001-07-01

Web-based applications to improve health data systems and quality of care; innovative strategies for data collection in clinical settings; approaches...research to increase interoperability and integration of software in distributed systems ; protocols and tools for data annotation and management; and...Generation National Defense and National Security Systems .......................... 27 Improved Health Care Systems for All Citizens

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…

Change Management Meets Web 2.0

ERIC Educational Resources Information Center

Gale, Doug

2008-01-01

Web 2.0 is the term used to describe a group of web-based creativity, information-sharing, and collaboration tools including wikis, blogs, social networks, and folksonomies. The common thread in all of these tools is twofold: They enable collaboration and information sharing, and their impact on higher education has been dramatic. A recent study…

Comprehensive Analysis of Semantic Web Reasoners and Tools: A Survey

ERIC Educational Resources Information Center

Khamparia, Aditya; Pandey, Babita

2017-01-01

Ontologies are emerging as best representation techniques for knowledge based context domains. The continuing need for interoperation, collaboration and effective information retrieval has lead to the creation of semantic web with the help of tools and reasoners which manages personalized information. The future of semantic web lies in an ontology…

Web Search Studies: Multidisciplinary Perspectives on Web Search Engines

NASA Astrophysics Data System (ADS)

Zimmer, Michael

Perhaps the most significant tool of our internet age is the web search engine, providing a powerful interface for accessing the vast amount of information available on the world wide web and beyond. While still in its infancy compared to the knowledge tools that precede it - such as the dictionary or encyclopedia - the impact of web search engines on society and culture has already received considerable attention from a variety of academic disciplines and perspectives. This article aims to organize a meta-discipline of “web search studies,” centered around a nucleus of major research on web search engines from five key perspectives: technical foundations and evaluations; transaction log analyses; user studies; political, ethical, and cultural critiques; and legal and policy analyses.

A Web Based Collaborative Design Environment for Spacecraft

NASA Technical Reports Server (NTRS)

Dunphy, Julia

1998-01-01

In this era of shrinking federal budgets in the USA we need to dramatically improve our efficiency in the spacecraft engineering design process. We have come up with a method which captures much of the experts' expertise in a dataflow design graph: Seamlessly connectable set of local and remote design tools; Seamlessly connectable web based design tools; and Web browser interface to the developing spacecraft design. We have recently completed our first web browser interface and demonstrated its utility in the design of an aeroshell using design tools located at web sites at three NASA facilities. Multiple design engineers and managers are now able to interrogate the design engine simultaneously and find out what the design looks like at any point in the design cycle, what its parameters are, and how it reacts to adverse space environments.

ChemVoyage: A Web-Based, Simulated Learning Environment with Scaffolding and Linking Visualization to Conceptualization

ERIC Educational Resources Information Center

McRae, Christopher; Karuso, Peter; Liu, Fei

2012-01-01

The Web is now a standard tool for information access and dissemination in higher education. The prospect of Web-based, simulated learning platforms and technologies, however, remains underexplored. We have developed a Web-based tutorial program (ChemVoyage) for a third-year organic chemistry class on the topic of pericyclic reactions to…

Creative Networks of Practice Using Web 2.0 Tools

ERIC Educational Resources Information Center

Orava, Jukka; Worrall, Pete

2011-01-01

This paper examines the professional implications for teachers and managers in new and evolving forms of professional development using Web 2.0 tools in a European context. Research findings are presented from the "Creative Use of Media" learning event developed through a European eTwinning Learning Lab initiative in spring of 2009. The…

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.

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

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.

Web-Based Course Management and Web Services

ERIC Educational Resources Information Center

Mandal, Chittaranjan; Sinha, Vijay Luxmi; Reade, Christopher M. P.

2004-01-01

The architecture of a web-based course management tool that has been developed at IIT [Indian Institute of Technology], Kharagpur and which manages the submission of assignments is discussed. Both the distributed architecture used for data storage and the client-server architecture supporting the web interface are described. Further developments…

Visual Based Retrieval Systems and Web Mining--Introduction.

ERIC Educational Resources Information Center

Iyengar, S. S.

2001-01-01

Briefly discusses Web mining and image retrieval techniques, and then presents a summary of articles in this special issue. Articles focus on Web content mining, artificial neural networks as tools for image retrieval, content-based image retrieval systems, and personalizing the Web browsing experience using media agents. (AEF)

From Web 2.0 to Teacher 2.0

ERIC Educational Resources Information Center

Thomas, David A.; Li, Qing

2008-01-01

The World Wide Web is evolving in response to users who demand faster and more efficient access to information, portability, and reusability of digital objects between Web-based and computer-based applications and powerful communication, publication, collaboration, and teaching and learning tools. This article reviews current uses of Web-based…

Utilization of two web-based continuing education courses evaluated by Markov chain model.

PubMed

Tian, Hao; Lin, Jin-Mann S; Reeves, William C

2012-01-01

To evaluate the web structure of two web-based continuing education courses, identify problems and assess the effects of web site modifications. Markov chain models were built from 2008 web usage data to evaluate the courses' web structure and navigation patterns. The web site was then modified to resolve identified design issues and the improvement in user activity over the subsequent 12 months was quantitatively evaluated. Web navigation paths were collected between 2008 and 2010. The probability of navigating from one web page to another was analyzed. The continuing education courses' sequential structure design was clearly reflected in the resulting actual web usage models, and none of the skip transitions provided was heavily used. The web navigation patterns of the two different continuing education courses were similar. Two possible design flaws were identified and fixed in only one of the two courses. Over the following 12 months, the drop-out rate in the modified course significantly decreased from 41% to 35%, but remained unchanged in the unmodified course. The web improvement effects were further verified via a second-order Markov chain model. The results imply that differences in web content have less impact than web structure design on how learners navigate through continuing education courses. Evaluation of user navigation can help identify web design flaws and guide modifications. This study showed that Markov chain models provide a valuable tool to evaluate web-based education courses. Both the results and techniques in this study would be very useful for public health education and research specialists.

Utilization of two web-based continuing education courses evaluated by Markov chain model

PubMed Central

Lin, Jin-Mann S; Reeves, William C

2011-01-01

Objectives To evaluate the web structure of two web-based continuing education courses, identify problems and assess the effects of web site modifications. Design Markov chain models were built from 2008 web usage data to evaluate the courses' web structure and navigation patterns. The web site was then modified to resolve identified design issues and the improvement in user activity over the subsequent 12 months was quantitatively evaluated. Measurements Web navigation paths were collected between 2008 and 2010. The probability of navigating from one web page to another was analyzed. Results The continuing education courses' sequential structure design was clearly reflected in the resulting actual web usage models, and none of the skip transitions provided was heavily used. The web navigation patterns of the two different continuing education courses were similar. Two possible design flaws were identified and fixed in only one of the two courses. Over the following 12 months, the drop-out rate in the modified course significantly decreased from 41% to 35%, but remained unchanged in the unmodified course. The web improvement effects were further verified via a second-order Markov chain model. Conclusions The results imply that differences in web content have less impact than web structure design on how learners navigate through continuing education courses. Evaluation of user navigation can help identify web design flaws and guide modifications. This study showed that Markov chain models provide a valuable tool to evaluate web-based education courses. Both the results and techniques in this study would be very useful for public health education and research specialists. PMID:21976027

Paired peer review of university classroom teaching in a school of nursing and midwifery.

PubMed

Bennett, Paul N; Parker, Steve; Smigiel, Heather

2012-08-01

Peer review of university classroom teaching can increase the quality of teaching but is not universally practiced in Australian universities. To report an evaluation of paired peer-review process using both paper and web based teaching evaluation tools. Twenty university teachers in one metropolitan Australian School of Nursing and Midwifery were randomly paired and then randomly assigned to a paper based or web-based peer review tool. Each teacher reviewed each other's classroom teaching as part of a peer review program. The participants then completed an 18 question survey evaluating the peer review tool and paired evaluation process. Responses were analyzed using frequencies and percentages. Regardless of the tool used, participants found this process of peer review positive (75%), collegial (78%), supportive (61%) and non-threatening (71%). Participants reported that the peer review will improve their own classroom delivery (61%), teaching evaluation (61%) and planning (53%). The web-based tool was found to be easier to use and allowed more space than the paper-based tool. Implementation of a web-based paired peer review system can be a positive method of peer review of university classroom teaching. Pairing of teachers to review each other's classroom teaching is a promising strategy and has the potential to improve teaching in teaching universities. Copyright © 2011 Elsevier Ltd. All rights reserved.

The Legacy Archive for Microwave Background Data Analysis (LAMBDA)

NASA Astrophysics Data System (ADS)

Miller, Nathan; LAMBDA

2018-01-01

The Legacy Archive for Microwave Background Data Analysis (LAMBDA) provides CMB researchers with archival data for cosmology missions, software tools, and links to other sites of interest. LAMBDA is one-stop shopping for CMB researchers. It hosts data from WMAP along with many suborbital experiments. Over the past year, LAMBDA has acquired new data from SPTpol, SPIDER and ACTPol. In addition to the primary CMB, LAMBDA also provides foreground data.LAMBDA has several ongoing efforts to provide tools for CMB researchers. These tools include a web interface for CAMB and a web interface for a CMB survey footprint database and plotting tool. Additionally, we have recently developed a Docker container with standard CMB analysis tools and demonstrations in the form of Jupyter notebooks. These containers will be publically available through Docker's container repository and the source will be available on github.

Free web-based modelling platform for managed aquifer recharge (MAR) applications

NASA Astrophysics Data System (ADS)

Stefan, Catalin; Junghanns, Ralf; Glaß, Jana; Sallwey, Jana; Fatkhutdinov, Aybulat; Fichtner, Thomas; Barquero, Felix; Moreno, Miguel; Bonilla, José; Kwoyiga, Lydia

2017-04-01

Managed aquifer recharge represents a valuable instrument for sustainable water resources management. The concept implies purposeful infiltration of surface water into underground for later recovery or environmental benefits. Over decades, MAR schemes were successfully installed worldwide for a variety of reasons: to maximize the natural storage capacity of aquifers, physical aquifer management, water quality management, and ecological benefits. The INOWAS-DSS platform provides a collection of free web-based tools for planning, management and optimization of main components of MAR schemes. The tools are grouped into 13 specific applications that cover most relevant challenges encountered at MAR sites, both from quantitative and qualitative perspectives. The applications include among others the optimization of MAR site location, the assessment of saltwater intrusion, the restoration of groundwater levels in overexploited aquifers, the maximization of natural storage capacity of aquifers, the improvement of water quality, the design and operational optimization of MAR schemes, clogging development and risk assessment. The platform contains a collection of about 35 web-based tools of various degrees of complexity, which are either included in application specific workflows or used as standalone modelling instruments. Among them are simple tools derived from data mining and empirical equations, analytical groundwater related equations, as well as complex numerical flow and transport models (MODFLOW, MT3DMS and SEAWAT). Up to now, the simulation core of the INOWAS-DSS, which is based on the finite differences groundwater flow model MODFLOW, is implemented and runs on the web. A scenario analyser helps to easily set up and evaluate new management options as well as future development such as land use and climate change and compare them to previous scenarios. Additionally simple tools such as analytical equations to assess saltwater intrusion are already running online. Besides the simulation tools, a web-based data base is under development where geospatial and time series data can be stored, managed, and processed. Furthermore, a web-based information system containing user guides for the various developed tools and applications as well as basic information on MAR and related topics is published and will be regularly expanded as new tools are getting implemented. The INOWAS-DSS including its simulation tools, data base and information system provides an extensive framework to manage, plan and optimize MAR facilities. As the INOWAS-DSS is an open-source software accessible via the internet using standard web browsers, it offers new ways for data sharing and collaboration among various partners and decision makers.

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

NASA Astrophysics Data System (ADS)

Signell, R. P.; Camossi, E.

2015-11-01

Work over the last decade has resulted in standardized web-services and tools that can significantly improve the efficiency and effectiveness of working with meteorological and ocean model data. While many operational modelling centres have enabled query and access to data via common web services, most small research groups have not. The penetration of this approach into the research community, where IT resources are limited, can be dramatically improved by: (1) making it simple for providers to enable web service access to existing output files; (2) using technology that is free, and that is easy to deploy and configure; and (3) providing tools to communicate with web services that work in existing research environments. We present a simple, local brokering approach that lets modelers continue producing custom data, but virtually aggregates and standardizes the data using NetCDF Markup Language. The THREDDS Data Server is used for data delivery, pycsw for data search, NCTOOLBOX (Matlab®1) and Iris (Python) for data access, and Ocean Geospatial Consortium Web Map Service for data preview. We illustrate the effectiveness of this approach with two use cases involving small research modelling groups at NATO and USGS.1 Mention of trade names or commercial products does not constitute endorsement or recommendation for use by the US Government.

The Online Bioinformatics Resources Collection at the University of Pittsburgh Health Sciences Library System--a one-stop gateway to online bioinformatics databases and software tools.

PubMed

Chen, Yi-Bu; Chattopadhyay, Ansuman; Bergen, Phillip; Gadd, Cynthia; Tannery, Nancy

2007-01-01

To bridge the gap between the rising information needs of biological and medical researchers and the rapidly growing number of online bioinformatics resources, we have created the Online Bioinformatics Resources Collection (OBRC) at the Health Sciences Library System (HSLS) at the University of Pittsburgh. The OBRC, containing 1542 major online bioinformatics databases and software tools, was constructed using the HSLS content management system built on the Zope Web application server. To enhance the output of search results, we further implemented the Vivísimo Clustering Engine, which automatically organizes the search results into categories created dynamically based on the textual information of the retrieved records. As the largest online collection of its kind and the only one with advanced search results clustering, OBRC is aimed at becoming a one-stop guided information gateway to the major bioinformatics databases and software tools on the Web. OBRC is available at the University of Pittsburgh's HSLS Web site (http://www.hsls.pitt.edu/guides/genetics/obrc).

OWLing Clinical Data Repositories With the Ontology Web Language

PubMed Central

Pastor, Xavier; Lozano, Esther

2014-01-01

Background The health sciences are based upon information. Clinical information is usually stored and managed by physicians with precarious tools, such as spreadsheets. The biomedical domain is more complex than other domains that have adopted information and communication technologies as pervasive business tools. Moreover, medicine continuously changes its corpus of knowledge because of new discoveries and the rearrangements in the relationships among concepts. This scenario makes it especially difficult to offer good tools to answer the professional needs of researchers and constitutes a barrier that needs innovation to discover useful solutions. Objective The objective was to design and implement a framework for the development of clinical data repositories, capable of facing the continuous change in the biomedicine domain and minimizing the technical knowledge required from final users. Methods We combined knowledge management tools and methodologies with relational technology. We present an ontology-based approach that is flexible and efficient for dealing with complexity and change, integrated with a solid relational storage and a Web graphical user interface. Results Onto Clinical Research Forms (OntoCRF) is a framework for the definition, modeling, and instantiation of data repositories. It does not need any database design or programming. All required information to define a new project is explicitly stated in ontologies. Moreover, the user interface is built automatically on the fly as Web pages, whereas data are stored in a generic repository. This allows for immediate deployment and population of the database as well as instant online availability of any modification. Conclusions OntoCRF is a complete framework to build data repositories with a solid relational storage. Driven by ontologies, OntoCRF is more flexible and efficient to deal with complexity and change than traditional systems and does not require very skilled technical people facilitating the engineering of clinical software systems. PMID:25599697

OWLing Clinical Data Repositories With the Ontology Web Language.

PubMed

Lozano-Rubí, Raimundo; Pastor, Xavier; Lozano, Esther

2014-08-01

The health sciences are based upon information. Clinical information is usually stored and managed by physicians with precarious tools, such as spreadsheets. The biomedical domain is more complex than other domains that have adopted information and communication technologies as pervasive business tools. Moreover, medicine continuously changes its corpus of knowledge because of new discoveries and the rearrangements in the relationships among concepts. This scenario makes it especially difficult to offer good tools to answer the professional needs of researchers and constitutes a barrier that needs innovation to discover useful solutions. The objective was to design and implement a framework for the development of clinical data repositories, capable of facing the continuous change in the biomedicine domain and minimizing the technical knowledge required from final users. We combined knowledge management tools and methodologies with relational technology. We present an ontology-based approach that is flexible and efficient for dealing with complexity and change, integrated with a solid relational storage and a Web graphical user interface. Onto Clinical Research Forms (OntoCRF) is a framework for the definition, modeling, and instantiation of data repositories. It does not need any database design or programming. All required information to define a new project is explicitly stated in ontologies. Moreover, the user interface is built automatically on the fly as Web pages, whereas data are stored in a generic repository. This allows for immediate deployment and population of the database as well as instant online availability of any modification. OntoCRF is a complete framework to build data repositories with a solid relational storage. Driven by ontologies, OntoCRF is more flexible and efficient to deal with complexity and change than traditional systems and does not require very skilled technical people facilitating the engineering of clinical software systems.

A WebGL Tool for Visualizing the Topology of the Sun's Coronal Magnetic Field

NASA Astrophysics Data System (ADS)

Duffy, A.; Cheung, C.; DeRosa, M. L.

2012-12-01

We present a web-based, topology-viewing tool that allows users to visualize the geometry and topology of the Sun's 3D coronal magnetic field in an interactive manner. The tool is implemented using, open-source, mature, modern web technologies including WebGL, jQuery, HTML 5, and CSS 3, which are compatible with nearly all modern web browsers. As opposed to the traditional method of visualization, which involves the downloading and setup of various software packages-proprietary and otherwise-the tool presents a clean interface that allows the user to easily load and manipulate the model, while also offering great power to choose which topological features are displayed. The tool accepts data encoded in the JSON open format that has libraries available for nearly every major programming language, making it simple to generate the data.

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.

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.

Using participatory design to develop (public) health decision support systems through GIS.

PubMed

Dredger, S Michelle; Kothari, Anita; Morrison, Jason; Sawada, Michael; Crighton, Eric J; Graham, Ian D

2007-11-27

Organizations that collect substantial data for decision-making purposes are often characterized as being 'data rich' but 'information poor'. Maps and mapping tools can be very useful for research transfer in converting locally collected data into information. Challenges involved in incorporating GIS applications into the decision-making process within the non-profit (public) health sector include a lack of financial resources for software acquisition and training for non-specialists to use such tools. This on-going project has two primary phases. This paper critically reflects on Phase 1: the participatory design (PD) process of developing a collaborative web-based GIS tool. A case study design is being used whereby the case is defined as the data analyst and manager dyad (a two person team) in selected Ontario Early Year Centres (OEYCs). Multiple cases are used to support the reliability of findings. With nine producer/user pair participants, the goal in Phase 1 was to identify barriers to map production, and through the participatory design process, develop a web-based GIS tool suited for data analysts and their managers. This study has been guided by the Ottawa Model of Research Use (OMRU) conceptual framework. Due to wide variations in OEYC structures, only some data analysts used mapping software and there was no consistency or standardization in the software being used. Consequently, very little sharing of maps and data occurred among data analysts. Using PD, this project developed a web-based mapping tool (EYEMAP) that was easy to use, protected proprietary data, and permit limited and controlled sharing between participants. By providing data analysts with training on its use, the project also ensured that data analysts would not break cartographic conventions (e.g. using a chloropleth map for count data). Interoperability was built into the web-based solution; that is, EYEMAP can read many different standard mapping file formats (e.g. ESRI, MapInfo, CSV). Based on the evaluation of Phase 1, the PD process has served both as a facilitator and a barrier. In terms of successes, the PD process identified two key components that are important to users: increased data/map sharing functionality and interoperability. Some of the challenges affected developers and users; both individually and as a collective. From a development perspective, this project experienced difficulties in obtaining personnel skilled in web application development and GIS. For users, some data sharing barriers are beyond what a technological tool can address (e.g. third party data). Lastly, the PD process occurs in real time; both a strength and a limitation. Programmatic changes at the provincial level and staff turnover at the organizational level made it difficult to maintain buy-in as participants changed over time. The impacts of these successes and challenges will be evaluated more concretely at the end of Phase 2. PD approaches, by their very nature, encourage buy-in to the development process, better addresses user-needs, and creates a sense of user-investment and ownership.

A Web-Based Decision Tool to Improve Contraceptive Counseling for Women With Chronic Medical Conditions: Protocol For a Mixed Methods Implementation Study.

PubMed

Wu, Justine P; Damschroder, Laura J; Fetters, Michael D; Zikmund-Fisher, Brian J; Crabtree, Benjamin F; Hudson, Shawna V; Ruffin, Mack T; Fucinari, Juliana; Kang, Minji; Taichman, L Susan; Creswell, John W

2018-04-18

Women with chronic medical conditions, such as diabetes and hypertension, have a higher risk of pregnancy-related complications compared with women without medical conditions and should be offered contraception if desired. Although evidence based guidelines for contraceptive selection in the presence of medical conditions are available via the United States Medical Eligibility Criteria (US MEC), these guidelines are underutilized. Research also supports the use of decision tools to promote shared decision making between patients and providers during contraceptive counseling. The overall goal of the MiHealth, MiChoice project is to design and implement a theory-driven, Web-based tool that incorporates the US MEC (provider-level intervention) within the vehicle of a contraceptive decision tool for women with chronic medical conditions (patient-level intervention) in community-based primary care settings (practice-level intervention). This will be a 3-phase study that includes a predesign phase, a design phase, and a testing phase in a randomized controlled trial. This study protocol describes phase 1 and aim 1, which is to determine patient-, provider-, and practice-level factors that are relevant to the design and implementation of the contraceptive decision tool. This is a mixed methods implementation study. To customize the delivery of the US MEC in the decision tool, we selected high-priority constructs from the Consolidated Framework for Implementation Research and the Theoretical Domains Framework to drive data collection and analysis at the practice and provider level, respectively. A conceptual model that incorporates constructs from the transtheoretical model and the health beliefs model undergirds patient-level data collection and analysis and will inform customization of the decision tool for this population. We will recruit 6 community-based primary care practices and conduct quantitative surveys and semistructured qualitative interviews with women who have chronic medical conditions, their primary care providers (PCPs), and clinic staff, as well as field observations of practice activities. Quantitative survey data will be summarized with simple descriptive statistics and relationships between participant characteristics and contraceptive recommendations (for PCPs), and current contraceptive use (for patients) will be examined using Fisher exact test. We will conduct thematic analysis of qualitative data from interviews and field observations. The integration of data will occur by comparing, contrasting, and synthesizing qualitative and quantitative findings to inform the future development and implementation of the intervention. We are currently enrolling practices and anticipate study completion in 15 months. This protocol describes the first phase of a multiphase mixed methods study to develop and implement a Web-based decision tool that is customized to meet the needs of women with chronic medical conditions in primary care settings. Study findings will promote contraceptive counseling via shared decision making and reflect evidence-based guidelines for contraceptive selection. ClinicalTrials.gov NCT03153644; https://clinicaltrials.gov/ct2/show/NCT03153644 (Archived by WebCite at http://www.webcitation.org/6yUkA5lK8). ©Justine P Wu, Laura J Damschroder, Michael D Fetters, Brian J Zikmund-Fisher, Benjamin F Crabtree, Shawna V Hudson, Mack T Ruffin IV, Juliana Fucinari, Minji Kang, L Susan Taichman, John W Creswell. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 18.04.2018.

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/

BIRCH: a user-oriented, locally-customizable, bioinformatics system.

PubMed

Fristensky, Brian

2007-02-09

Molecular biologists need sophisticated analytical tools which often demand extensive computational resources. While finding, installing, and using these tools can be challenging, pipelining data from one program to the next is particularly awkward, especially when using web-based programs. At the same time, system administrators tasked with maintaining these tools do not always appreciate the needs of research biologists. BIRCH (Biological Research Computing Hierarchy) is an organizational framework for delivering bioinformatics resources to a user group, scaling from a single lab to a large institution. The BIRCH core distribution includes many popular bioinformatics programs, unified within the GDE (Genetic Data Environment) graphic interface. Of equal importance, BIRCH provides the system administrator with tools that simplify the job of managing a multiuser bioinformatics system across different platforms and operating systems. These include tools for integrating locally-installed programs and databases into BIRCH, and for customizing the local BIRCH system to meet the needs of the user base. BIRCH can also act as a front end to provide a unified view of already-existing collections of bioinformatics software. Documentation for the BIRCH and locally-added programs is merged in a hierarchical set of web pages. In addition to manual pages for individual programs, BIRCH tutorials employ step by step examples, with screen shots and sample files, to illustrate both the important theoretical and practical considerations behind complex analytical tasks. BIRCH provides a versatile organizational framework for managing software and databases, and making these accessible to a user base. Because of its network-centric design, BIRCH makes it possible for any user to do any task from anywhere.

BIRCH: A user-oriented, locally-customizable, bioinformatics system

PubMed Central

Fristensky, Brian

2007-01-01

Background Molecular biologists need sophisticated analytical tools which often demand extensive computational resources. While finding, installing, and using these tools can be challenging, pipelining data from one program to the next is particularly awkward, especially when using web-based programs. At the same time, system administrators tasked with maintaining these tools do not always appreciate the needs of research biologists. Results BIRCH (Biological Research Computing Hierarchy) is an organizational framework for delivering bioinformatics resources to a user group, scaling from a single lab to a large institution. The BIRCH core distribution includes many popular bioinformatics programs, unified within the GDE (Genetic Data Environment) graphic interface. Of equal importance, BIRCH provides the system administrator with tools that simplify the job of managing a multiuser bioinformatics system across different platforms and operating systems. These include tools for integrating locally-installed programs and databases into BIRCH, and for customizing the local BIRCH system to meet the needs of the user base. BIRCH can also act as a front end to provide a unified view of already-existing collections of bioinformatics software. Documentation for the BIRCH and locally-added programs is merged in a hierarchical set of web pages. In addition to manual pages for individual programs, BIRCH tutorials employ step by step examples, with screen shots and sample files, to illustrate both the important theoretical and practical considerations behind complex analytical tasks. Conclusion BIRCH provides a versatile organizational framework for managing software and databases, and making these accessible to a user base. Because of its network-centric design, BIRCH makes it possible for any user to do any task from anywhere. PMID:17291351

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.

Electronic toolkit for nursing education.

PubMed

Trangenstein, Patricia A

2008-12-01

In an ever-increasing hectic and mobile society, Web-based instructional tools can enhance and supplement student learning and improve communication and collaboration among participants, give rapid feedback on one's progress, and address diverse ways of learning. Web-based formats offer distinct advantages by allowing the learner to view course materials when they choose, from any Internet connection, and as often as they want. The challenge for nurse educators is to assimilate the knowledge and expertise to understand and appropriately use these tools. A variety of Web-based instructional tools are described in this article. As nurse educators increase their awareness of these potential adjuncts they can select appropriate applications that are supported by their institution to construct their own "toolkit."

geneCommittee: a web-based tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification.

PubMed

Reboiro-Jato, Miguel; Arrais, Joel P; Oliveira, José Luis; Fdez-Riverola, Florentino

2014-01-30

The diagnosis and prognosis of several diseases can be shortened through the use of different large-scale genome experiments. In this context, microarrays can generate expression data for a huge set of genes. However, to obtain solid statistical evidence from the resulting data, it is necessary to train and to validate many classification techniques in order to find the best discriminative method. This is a time-consuming process that normally depends on intricate statistical tools. geneCommittee is a web-based interactive tool for routinely evaluating the discriminative classification power of custom hypothesis in the form of biologically relevant gene sets. While the user can work with different gene set collections and several microarray data files to configure specific classification experiments, the tool is able to run several tests in parallel. Provided with a straightforward and intuitive interface, geneCommittee is able to render valuable information for diagnostic analyses and clinical management decisions based on systematically evaluating custom hypothesis over different data sets using complementary classifiers, a key aspect in clinical research. geneCommittee allows the enrichment of microarrays raw data with gene functional annotations, producing integrated datasets that simplify the construction of better discriminative hypothesis, and allows the creation of a set of complementary classifiers. The trained committees can then be used for clinical research and diagnosis. Full documentation including common use cases and guided analysis workflows is freely available at http://sing.ei.uvigo.es/GC/.

The National Center for Biomedical Ontology

PubMed Central

Noy, Natalya F; Shah, Nigam H; Whetzel, Patricia L; Chute, Christopher G; Story, Margaret-Anne; Smith, Barry

2011-01-01

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. PMID:22081220

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.

A Web Tool for Research in Nonlinear Optics

NASA Astrophysics Data System (ADS)

Prikhod'ko, Nikolay V.; Abramovsky, Viktor A.; Abramovskaya, Natalia V.; Demichev, Andrey P.; Kryukov, Alexandr P.; Polyakov, Stanislav P.

2016-02-01

This paper presents a project of developing the web platform called WebNLO for computer modeling of nonlinear optics phenomena. We discuss a general scheme of the platform and a model for interaction between the platform modules. The platform is built as a set of interacting RESTful web services (SaaS approach). Users can interact with the platform through a web browser or command line interface. Such a resource has no analogues in the field of nonlinear optics and will be created for the first time therefore allowing researchers to access high-performance computing resources that will significantly reduce the cost of the research and development process.

NCBI GEO: archive for functional genomics data sets--update.

PubMed

Barrett, Tanya; Wilhite, Stephen E; Ledoux, Pierre; Evangelista, Carlos; Kim, Irene F; Tomashevsky, Maxim; Marshall, Kimberly A; Phillippy, Katherine H; Sherman, Patti M; Holko, Michelle; Yefanov, Andrey; Lee, Hyeseung; Zhang, Naigong; Robertson, Cynthia L; Serova, Nadezhda; Davis, Sean; Soboleva, Alexandra

2013-01-01

The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) is an international public repository for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community. The resource supports archiving of raw data, processed data and metadata which are indexed, cross-linked and searchable. All data are freely available for download in a variety of formats. GEO also provides several web-based tools and strategies to assist users to query, analyse and visualize data. This article reports current status and recent database developments, including the release of GEO2R, an R-based web application that helps users analyse GEO data.

A Worldwide Web-portal for Aquatic Mesocosm Facilities: WWW.MESOCOSM.EU

NASA Astrophysics Data System (ADS)

Berger, S. A.; Nejstgaard, J. C.

2016-02-01

Experimental mesocosms are valuable tools to fill the gap between highly controlled/replicated lab experiments and uncontrolled/non-replicated natural environments such as rivers, lakes and oceans. WWW.MESOCOSM.EU is an open web-portal for leading aquatic mesocosm facilities around the world. It was created within the FP7 EU-project MESOAQUA (A network of leading MESOcosm facilities to advance the studies of future AQUAtic ecosystems from the Arctic to the Mediterranean). The goal of the portal is to increase international knowledge about existing mesocosm facilities, including information on locations, environment, equipment, contacts, research opportunities and mesocosm-based publications. MESOCOSM.EU specifically aims to be a tool to enhance the quality of research by facilitating international cooperative network building, announcement of new research initiatives, transfer of best practice, and dissemination of knowledge, public information and press releases. As an open platform for all aquatic ecosystem scale science (marine and freshwater), MESOCOSM.EU aims to fill the lack of a centralized, coordinating virtual infrastructure for international aquatic mesocosm research, from the mountains to the ocean and from polar to tropical regions.

Primers-4-Yeast: a comprehensive web tool for planning primers for Saccharomyces cerevisiae.

PubMed

Yofe, Ido; Schuldiner, Maya

2014-02-01

The budding yeast Saccharomyces cerevisiae is a key model organism of functional genomics, due to its ease and speed of genetic manipulations. In fact, in this yeast, the requirement for homologous sequences for recombination purposes is so small that 40 base pairs (bp) are sufficient. Hence, an enormous variety of genetic manipulations can be performed by simply planning primers with the correct homology, using a defined set of transformation plasmids. Although designing primers for yeast transformations and for the verification of their correct insertion is a common task in all yeast laboratories, primer planning is usually done manually and a tool that would enable easy, automated primer planning for the yeast research community is still lacking. Here we introduce Primers-4-Yeast, a web tool that allows primers to be designed in batches for S. cerevisiae gene-targeting transformations, and for the validation of correct insertions. This novel tool enables fast, automated, accurate primer planning for large sets of genes, introduces consistency in primer planning and is therefore suggested to serve as a standard in yeast research. Primers-4-Yeast is available at: http://www.weizmann.ac.il/Primers-4-Yeast Copyright © 2013 John Wiley & Sons, Ltd.

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

Research and Publication on the World Wide Web: A Fifth Grade Class' Experience.

ERIC Educational Resources Information Center

Neal, Nancy L.

The World Wide Web (WWW) has become a major presence on the Internet, and teachers are just beginning to discover many valuable applications the Web can have in their classrooms. This study explored use of WWW as a research and publication tool in a fifth grade class project on the formation of the United States. Students were given instruction in…

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.

Design, construction, and technical implementation of a web-based interdisciplinary symptom evaluation (WISE) - a heuristic proposal for orofacial pain and temporomandibular disorders.

PubMed

Ettlin, Dominik A; Sommer, Isabelle; Brönnimann, Ben; Maffioletti, Sergio; Scheidt, Jörg; Hou, Mei-Yin; Lukic, Nenad; Steiger, Beat

2016-12-01

Medical symptoms independent of body location burden individuals to varying degrees and may require care by more than one expert. Various paper and computer-based tools exist that aim to comprehensively capture data for optimal clinical management and research. A web-based interdisciplinary symptom evaluation (WISE) was newly designed, constructed, and technically implemented. For worldwide applicability and to avoid copyright infringements, open source software tools and free validated questionnaires available in multiple languages were used. Highly secure data storage limits access strictly to those who use the tool for collecting, storing, and evaluating their data. Concept and implementation is illustrated by a WISE sample tailored for the requirements of a single center in Switzerland providing interdisciplinary care to orofacial pain and temporomandibular disorder patients. By combining a symptom- burden checklist with in-depth questionnaires serving as case-finding instruments, an algorithm was developed that assists in clarifying case complexity and need for targeted expert evaluation. This novel modular approach provides a personalized, response-tailored instrument for the time- and cost-effective collection of symptom-burden focused quantitative data. The tool includes body drawing options and instructional videos. It is applicable for biopsychosocial evaluation in a variety of clinical settings and offers direct feedback by a case report summary. In clinical practice, the new instrument assists in clarifying case complexity and referral need, based on symptom burden and response -tailored case finding. It provides single-case summary reports from a biopsychosocial perspective and includes graphical symptom maps. Secure, centrally stored data collection of anonymous data is possible. The tool enables personalized medicine, facilitates interprofessional education and collaboration, and allows for multicenter patient-reported outcomes research.

A web-based genomic sequence database for the Streptomycetaceae: a tool for systematics and genome mining

USDA-ARS?s Scientific Manuscript database

The ARS Microbial Genome Sequence Database (http://199.133.98.43), a web-based database server, was established utilizing the BIGSdb (Bacterial Isolate Genomics Sequence Database) software package, developed at Oxford University, as a tool to manage multi-locus sequence data for the family Streptomy...

A Web-Based Learning Tool Improves Student Performance in Statistics: A Randomized Masked Trial

ERIC Educational Resources Information Center

Gonzalez, Jose A.; Jover, Lluis; Cobo, Erik; Munoz, Pilar

2010-01-01

Background: e-status is a web-based tool able to generate different statistical exercises and to provide immediate feedback to students' answers. Although the use of Information and Communication Technologies (ICTs) is becoming widespread in undergraduate education, there are few experimental studies evaluating its effects on learning. Method: All…