Arachne - A web-based event viewer for MINERvA

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

Tagg, N.; /Otterbein Coll.; Brangham, J.

2011-11-01

Neutrino interaction events in the MINERvA detector are visually represented with a web-based tool called Arachne. Data are retrieved from a central server via AJAX, and client-side JavaScript draws images into the user's browser window using the draft HTML 5 standard. These technologies allow neutrino interactions to be viewed by anyone with a web browser, allowing for easy hand-scanning of particle interactions. Arachne has been used in MINERvA to evaluate neutrino data in a prototype detector, to tune reconstruction algorithms, and for public outreach and education.

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

ERIC Educational Resources Information Center

Buckley, Patrick; Doyle, Elaine

2016-01-01

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

Encourage Students to Read through the Use of Data Visualization

ERIC Educational Resources Information Center

Bandeen, Heather M.; Sawin, Jason E.

2012-01-01

Instructors are always looking for new ways to engage students in reading assignments. The authors present a few techniques that rely on a web-based data visualization tool called Wordle (wordle.net). Wordle creates word frequency representations called word clouds. The larger a word appears within a cloud, the more frequently it occurs within a…

CASAS: A tool for composing automatically and semantically astrophysical services

NASA Astrophysics Data System (ADS)

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

2017-07-01

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

ToTem: a tool for variant calling pipeline optimization.

PubMed

Tom, Nikola; Tom, Ondrej; Malcikova, Jitka; Pavlova, Sarka; Kubesova, Blanka; Rausch, Tobias; Kolarik, Miroslav; Benes, Vladimir; Bystry, Vojtech; Pospisilova, Sarka

2018-06-26

High-throughput bioinformatics analyses of next generation sequencing (NGS) data often require challenging pipeline optimization. The key problem is choosing appropriate tools and selecting the best parameters for optimal precision and recall. Here we introduce ToTem, a tool for automated pipeline optimization. ToTem is a stand-alone web application with a comprehensive graphical user interface (GUI). ToTem is written in Java and PHP with an underlying connection to a MySQL database. Its primary role is to automatically generate, execute and benchmark different variant calling pipeline settings. Our tool allows an analysis to be started from any level of the process and with the possibility of plugging almost any tool or code. To prevent an over-fitting of pipeline parameters, ToTem ensures the reproducibility of these by using cross validation techniques that penalize the final precision, recall and F-measure. The results are interpreted as interactive graphs and tables allowing an optimal pipeline to be selected, based on the user's priorities. Using ToTem, we were able to optimize somatic variant calling from ultra-deep targeted gene sequencing (TGS) data and germline variant detection in whole genome sequencing (WGS) data. ToTem is a tool for automated pipeline optimization which is freely available as a web application at  https://totem.software .

Using Firefly Tools to Enhance Archive Web Pages

NASA Astrophysics Data System (ADS)

Roby, W.; Wu, X.; Ly, L.; Goldina, T.

2013-10-01

Astronomy web developers are looking for fast and powerful HTML 5/AJAX tools to enhance their web archives. We are exploring ways to make this easier for the developer. How could you have a full FITS visualizer or a Web 2.0 table that supports paging, sorting, and filtering in your web page in 10 minutes? Can it be done without even installing any software or maintaining a server? Firefly is a powerful, configurable system for building web-based user interfaces to access astronomy science archives. It has been in production for the past three years. Recently, we have made some of the advanced components available through very simple JavaScript calls. This allows a web developer, without any significant knowledge of Firefly, to have FITS visualizers, advanced table display, and spectrum plots on their web pages with minimal learning curve. Because we use cross-site JSONP, installing a server is not necessary. Web sites that use these tools can be created in minutes. Firefly was created in IRSA, the NASA/IPAC Infrared Science Archive (http://irsa.ipac.caltech.edu). We are using Firefly to serve many projects including Spitzer, Planck, WISE, PTF, LSST and others.

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)

Teachers' Emotional Responses to New Pedagogical Tools in High Challenge Settings: Illustrations from the Northern Territory

ERIC Educational Resources Information Center

Harper, Helen

2012-01-01

This paper explores the role of teachers' emotions in adopting new pedagogical tools in urban and remote schools in the Northern Territory. The discussion is illustrated through case study material of Northern Territory teachers who had taken up using a web-based early childhood literacy resource called ABRACADABRA. A sociocultural perspective is…

Designing Web 2.0 Based Constructivist-Oriented E-Learning Units

ERIC Educational Resources Information Center

Chai, Ching Sing; Woo, Huay Lit; Wang, Qiyun

2010-01-01

Purpose: The main purpose of this paper is to present how meaningful e-learning units can be created by using an online tool called Meaningful E-learning Units (MeLU). The paper also aims to describe how created e-learning units can be shared by teachers and students. Design/methodology/approach: This tool can help to produce e-learning units that…

Web-based volume slicer for 3D electron-microscopy data from EMDB

PubMed Central

Salavert-Torres, José; Iudin, Andrii; Lagerstedt, Ingvar; Sanz-García, Eduardo; Kleywegt, Gerard J.; Patwardhan, Ardan

2016-01-01

We describe the functionality and design of the Volume slicer – a web-based slice viewer for EMDB entries. This tool uniquely provides the facility to view slices from 3D EM reconstructions along the three orthogonal axes and to rapidly switch between them and navigate through the volume. We have employed multiple rounds of user-experience testing with members of the EM community to ensure that the interface is easy and intuitive to use and the information provided is relevant. The impetus to develop the Volume slicer has been calls from the EM community to provide web-based interactive visualisation of 2D slice data. This would be useful for quick initial checks of the quality of a reconstruction. Again in response to calls from the community, we plan to further develop the Volume slicer into a fully-fledged Volume browser that provides integrated visualisation of EMDB and PDB entries from the molecular to the cellular scale. PMID:26876163

Spitzer Space Telescope proposal process

NASA Astrophysics Data System (ADS)

Laine, S.; Silbermann, N. A.; Rebull, L. M.; Storrie-Lombardi, L. J.

2006-06-01

This paper discusses the Spitzer Space Telescope General Observer proposal process. Proposals, consisting of the scientific justification, basic contact information for the observer, and observation requests, are submitted electronically using a client-server Java package called Spot. The Spitzer Science Center (SSC) uses a one-phase proposal submission process, meaning that fully-planned observations are submitted for most proposals at the time of submission, not months after acceptance. Ample documentation and tools are available to the observers on SSC web pages to support the preparation of proposals, including an email-based Helpdesk. Upon submission proposals are immediately ingested into a database which can be queried at the SSC for program information, statistics, etc. at any time. Large proposals are checked for technical feasibility and all proposals are checked against duplicates of already approved observations. Output from these tasks is made available to the Time Allocation Committee (TAC) members. At the review meeting, web-based software is used to record reviewer comments and keep track of the voted scores. After the meeting, another Java-based web tool, Griffin, is used to track the approved programs as they go through technical reviews, duplication checks and minor modifications before the observations are released for scheduling. In addition to detailing the proposal process, lessons learned from the first two General Observer proposal calls are discussed.

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.

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.

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.

Combining Domain-driven Design and Mashups for Service Development

NASA Astrophysics Data System (ADS)

Iglesias, Carlos A.; Fernández-Villamor, José Ignacio; Del Pozo, David; Garulli, Luca; García, Boni

This chapter presents the Romulus project approach to Service Development using Java-based web technologies. Romulus aims at improving productivity of service development by providing a tool-supported model to conceive Java-based web applications. This model follows a Domain Driven Design approach, which states that the primary focus of software projects should be the core domain and domain logic. Romulus proposes a tool-supported model, Roma Metaframework, that provides an abstraction layer on top of existing web frameworks and automates the application generation from the domain model. This metaframework follows an object centric approach, and complements Domain Driven Design by identifying the most common cross-cutting concerns (security, service, view, ...) of web applications. The metaframework uses annotations for enriching the domain model with these cross-cutting concerns, so-called aspects. In addition, the chapter presents the usage of mashup technology in the metaframework for service composition, using the web mashup editor MyCocktail. This approach is applied to a scenario of the Mobile Phone Service Portability case study for the development of a new service.

Biotool2Web: creating simple Web interfaces for bioinformatics applications.

PubMed

Shahid, Mohammad; Alam, Intikhab; Fuellen, Georg

2006-01-01

Currently there are many bioinformatics applications being developed, but there is no easy way to publish them on the World Wide Web. We have developed a Perl script, called Biotool2Web, which makes the task of creating web interfaces for simple ('home-made') bioinformatics applications quick and easy. Biotool2Web uses an XML document containing the parameters to run the tool on the Web, and generates the corresponding HTML and common gateway interface (CGI) files ready to be published on a web server. This tool is available for download at URL http://www.uni-muenster.de/Bioinformatics/services/biotool2web/ Georg Fuellen (fuellen@alum.mit.edu).

WEBCAP: Web Scheduler for Distance Learning Multimedia Documents with Web Workload Considerations

ERIC Educational Resources Information Center

Habib, Sami; Safar, Maytham

2008-01-01

In many web applications, such as the distance learning, the frequency of refreshing multimedia web documents places a heavy burden on the WWW resources. Moreover, the updated web documents may encounter inordinate delays, which make it difficult to retrieve web documents in time. Here, we present an Internet tool called WEBCAP that can schedule…

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…

Web Development Simplified

ERIC Educational Resources Information Center

Becker, Bernd W.

2010-01-01

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

Introduction to the Watershed Central Web Site and Watershed Wiki Mini-Workshop

EPA Science Inventory

Many communities across the country struggle to find the right approaches, tools and data to include in their watershed plans. EPA recently posted a new web site called "Watershed Central,” a “one-stop" tool, to help watershed organizations and others find key resources to protec...

The Value of Interactive Assignments in the Online Learning Environment

ERIC Educational Resources Information Center

Florenthal, Bela

2016-01-01

The offerings of Web-based supplemental material for textbooks have been increasingly growing. When deciding to adopt a textbook, instructors examine the added value of the associated supplements, also called "e-learning tools," to enhance students' learning of course concepts. In this study, one such supplement, interactive assignments,…

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.

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.

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

Identification and Illustration of Insecure Direct Object References and their Countermeasures

NASA Astrophysics Data System (ADS)

KumarShrestha, Ajay; Singh Maharjan, Pradip; Paudel, Santosh

2015-03-01

The insecure direct object reference simply represents the flaws in the system design without the full protection mechanism for the sensitive system resources or data. It basically occurs when the web application developer provides direct access to objects in accordance with the user input. So any attacker can exploit this web vulnerability and gain access to privileged information by bypassing the authorization. The main aim of this paper is to demonstrate the real effect and the identification of the insecure direct object references and then to provide the feasible preventive solutions such that the web applications do not allow direct object references to be manipulated by attackers. The experiment of the insecure direct object referencing is carried out using the insecure J2EE web application called WebGoat and its security testing is being performed using another JAVA based tool called BURP SUITE. The experimental result shows that the access control check for gaining access to privileged information is a very simple problem but at the same time its correct implementation is a tricky task. The paper finally presents some ways to overcome this web vulnerability.

45 CFR 155.205 - Consumer assistance tools and programs of an Exchange.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Exchange. (a) Call center. The Exchange must provide for operation of a toll-free call center that...)(1), (c)(2)(i), and (c)(3) of this section. (b) Internet Web site. The Exchange must maintain an up-to-date Internet Web site that meets the requirements outlined in paragraph (c) of this section and...

45 CFR 155.205 - Consumer assistance tools and programs of an Exchange.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Exchange. (a) Call center. The Exchange must provide for operation of a toll-free call center that...)(1), (c)(2)(i), and (c)(3) of this section. (b) Internet Web site. The Exchange must maintain an up-to-date Internet Web site that meets the requirements outlined in paragraph (c) of this section and...

45 CFR 155.205 - Consumer assistance tools and programs of an Exchange.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Exchange. (a) Call center. The Exchange must provide for operation of a toll-free call center that...)(1), (c)(2)(i), and (c)(3) of this section. (b) Internet Web site. The Exchange must maintain an up-to-date Internet Web site that meets the requirements outlined in paragraph (c) of this section and...

An advanced web query interface for biological databases

PubMed Central

Latendresse, Mario; Karp, Peter D.

2010-01-01

Although most web-based biological databases (DBs) offer some type of web-based form to allow users to author DB queries, these query forms are quite restricted in the complexity of DB queries that they can formulate. They can typically query only one DB, and can query only a single type of object at a time (e.g. genes) with no possible interaction between the objects—that is, in SQL parlance, no joins are allowed between DB objects. Writing precise queries against biological DBs is usually left to a programmer skillful enough in complex DB query languages like SQL. We present a web interface for building precise queries for biological DBs that can construct much more precise queries than most web-based query forms, yet that is user friendly enough to be used by biologists. It supports queries containing multiple conditions, and connecting multiple object types without using the join concept, which is unintuitive to biologists. This interactive web interface is called the Structured Advanced Query Page (SAQP). Users interactively build up a wide range of query constructs. Interactive documentation within the SAQP describes the schema of the queried DBs. The SAQP is based on BioVelo, a query language based on list comprehension. The SAQP is part of the Pathway Tools software and is available as part of several bioinformatics web sites powered by Pathway Tools, including the BioCyc.org site that contains more than 500 Pathway/Genome DBs. PMID:20624715

Pediatric Price Transparency: Still Opaque With Opportunities for Improvement.

PubMed

Faherty, Laura J; Wong, Charlene A; Feingold, Jordyn; Li, Joan; Town, Robert; Fieldston, Evan; Werner, Rachel M

2017-10-01

Price transparency is gaining importance as families' portion of health care costs rise. We describe (1) online price transparency data for pediatric care on children's hospital Web sites and state-based price transparency Web sites, and (2) the consumer experience of obtaining an out-of-pocket estimate from children's hospitals for a common procedure. From 2015 to 2016, we audited 45 children's hospital Web sites and 38 state-based price transparency Web sites, describing availability and characteristics of health care prices and personalized cost estimate tools. Using secret shopper methodology, we called children's hospitals and submitted online estimate requests posing as a self-paying family requesting an out-of-pocket estimate for a tonsillectomy-adenoidectomy. Eight children's hospital Web sites (18%) listed prices. Twelve (27%) provided personalized cost estimate tool (online form n = 5 and/or phone number n = 9). All 9 hospitals with a phone number for estimates provided the estimated patient liability for a tonsillectomy-adenoidectomy (mean $6008, range $2622-$9840). Of the remaining 36 hospitals without a dedicated price estimate phone number, 21 (58%) provided estimates (mean $7144, range $1200-$15 360). Two of 4 hospitals with online forms provided estimates. Fifteen (39%) state-based Web sites distinguished between prices for pediatric and adult care. One had a personalized cost estimate tool. Meaningful prices for pediatric care were not widely available online through children's hospital or state-based price transparency Web sites. A phone line or online form for price estimates were effective strategies for hospitals to provide out-of-pocket price information. Opportunities exist to improve pediatric price transparency. Copyright © 2017 by the American Academy of Pediatrics.

Assisting Tutors to Utilize Web 2.0 Tools in Education

ERIC Educational Resources Information Center

Perikos, Isidoros; Grivokostopoulou, Foteini; Kovas, Konstantinos; Hatzilygeroudis, Ioannis

2015-01-01

Over the last decade, web has changed the way that educational procedures are delivered to students and has brought innovative learning technologies and possibilities that were not available before. The Web has evolved to a worldwide platform for collaboration, sharing and innovation, constituting what is called Web 2.0. Social media are an…

A Good Teaching Technique: WebQuests

ERIC Educational Resources Information Center

Halat, Erdogan

2008-01-01

In this article, the author first introduces and describes a new teaching tool called WebQuests to practicing teachers. He then provides detailed information about the structure of a good WebQuest. Third, the author shows the strengths and weaknesses of using Web-Quests in teaching and learning. Last, he points out the challenges for practicing…

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

NASA Astrophysics Data System (ADS)

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

2014-03-01

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

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

ERIC Educational Resources Information Center

Johnson, Lynn E.; Tang, Michael

2005-01-01

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

Usability of Browser-Based Tools for Web-Search Privacy

DTIC Science & Technology

2010-03-01

What might Italians call maize? — Polenta From which country do french fries originate? — Belgium In Peru, which color potatoes are grown, in addition...What is kartofflen? — Potato Dumplings What is the name of the flatbread eaten with most Indian cuisine ? — Naan What type of cuisine offers Dim Sum

The relation between media promotions and service volume for a statewide tobacco quitline and a web-based cessation program

PubMed Central

2011-01-01

Background This observational study assessed the relation between mass media campaigns and service volume for a statewide tobacco cessation quitline and stand-alone web-based cessation program. Methods Multivariate regression analysis was used to identify how weekly calls to a cessation quitline and weekly registrations to a web-based cessation program are related to levels of broadcast media, media campaigns, and media types, controlling for the impact of external and earned media events. Results There was a positive relation between weekly broadcast targeted rating points and the number of weekly calls to a cessation quitline and the number of weekly registrations to a web-based cessation program. Additionally, print secondhand smoke ads and online cessation ads were positively related to weekly quitline calls. Television and radio cessation ads and radio smoke-free law ads were positively related to web program registration levels. There was a positive relation between the number of web registrations and the number of calls to the cessation quitline, with increases in registrations to the web in 1 week corresponding to increases in calls to the quitline in the subsequent week. Web program registration levels were more highly influenced by earned media and other external events than were quitline call volumes. Conclusion Overall, broadcast advertising had a greater impact on registrations for the web program than calls to the quitline. Furthermore, registrations for the web program influenced calls to the quitline. These two findings suggest the evolving roles of web-based cessation programs and Internet-use practices should be considered when creating cessation programs and media campaigns to promote them. Additionally, because different types of media and campaigns were positively associated with calls to the quitline and web registrations, developing mass media campaigns that offer a variety of messages and communicate through different types of media to motivate tobacco users to seek services appears important to reach tobacco users. Further research is needed to better understand the complexities and opportunities involved in simultaneous promotion of quitline and web-based cessation services. PMID:22177237

The relation between media promotions and service volume for a statewide tobacco quitline and a web-based cessation program.

PubMed

Schillo, Barbara A; Mowery, Andrea; Greenseid, Lija O; Luxenberg, Michael G; Zieffler, Andrew; Christenson, Matthew; Boyle, Raymond G

2011-12-16

This observational study assessed the relation between mass media campaigns and service volume for a statewide tobacco cessation quitline and stand-alone web-based cessation program. Multivariate regression analysis was used to identify how weekly calls to a cessation quitline and weekly registrations to a web-based cessation program are related to levels of broadcast media, media campaigns, and media types, controlling for the impact of external and earned media events. There was a positive relation between weekly broadcast targeted rating points and the number of weekly calls to a cessation quitline and the number of weekly registrations to a web-based cessation program. Additionally, print secondhand smoke ads and online cessation ads were positively related to weekly quitline calls. Television and radio cessation ads and radio smoke-free law ads were positively related to web program registration levels. There was a positive relation between the number of web registrations and the number of calls to the cessation quitline, with increases in registrations to the web in 1 week corresponding to increases in calls to the quitline in the subsequent week. Web program registration levels were more highly influenced by earned media and other external events than were quitline call volumes. Overall, broadcast advertising had a greater impact on registrations for the web program than calls to the quitline. Furthermore, registrations for the web program influenced calls to the quitline. These two findings suggest the evolving roles of web-based cessation programs and Internet-use practices should be considered when creating cessation programs and media campaigns to promote them. Additionally, because different types of media and campaigns were positively associated with calls to the quitline and web registrations, developing mass media campaigns that offer a variety of messages and communicate through different types of media to motivate tobacco users to seek services appears important to reach tobacco users. Further research is needed to better understand the complexities and opportunities involved in simultaneous promotion of quitline and web-based cessation services.

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

PubMed

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

2014-01-01

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

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

PubMed Central

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

1997-01-01

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

The semantic web and computer vision: old AI meets new AI

NASA Astrophysics Data System (ADS)

Mundy, J. L.; Dong, Y.; Gilliam, A.; Wagner, R.

2018-04-01

There has been vast process in linking semantic information across the billions of web pages through the use of ontologies encoded in the Web Ontology Language (OWL) based on the Resource Description Framework (RDF). A prime example is the Wikipedia where the knowledge contained in its more than four million pages is encoded in an ontological database called DBPedia http://wiki.dbpedia.org/. Web-based query tools can retrieve semantic information from DBPedia encoded in interlinked ontologies that can be accessed using natural language. This paper will show how this vast context can be used to automate the process of querying images and other geospatial data in support of report changes in structures and activities. Computer vision algorithms are selected and provided with context based on natural language requests for monitoring and analysis. The resulting reports provide semantically linked observations from images and 3D surface models.

The national web-based outbreak rapid alert system in Norway: eight years of experience, 2006-2013.

PubMed

Guzman-Herrador, B; Vold, L; Berg, T; Berglund, T M; Heier, B; Kapperud, G; Lange, H; Nygård, K

2016-01-01

In 2005, the Norwegian Institute of Public Health established a web-based outbreak rapid alert system called Vesuv. The system is used for mandatory outbreak alerts from municipal medical officers, healthcare institutions, and food safety authorities. As of 2013, 1426 outbreaks have been reported, involving 32913 cases. More than half of the outbreaks occurred in healthcare institutions (759 outbreaks, 53·2%). A total of 474 (33·2%) outbreaks were associated with food or drinking water. The web-based rapid alert system has proved to be a helpful tool by enhancing reporting and enabling rapid and efficient information sharing between different authorities at both the local and national levels. It is also an important tool for event-based reporting, as required by the International Health Regulations (IHR) 2005. Collecting information from all the outbreak alerts and reports in a national database is also useful for analysing trends, such as occurrence of certain microorganisms, places or sources of infection, or route of transmission. This can facilitate the identification of specific areas where more general preventive measures are needed.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Examining A Health Care Price Transparency Tool: Who Uses It, And How They Shop For Care.

PubMed

Sinaiko, Anna D; Rosenthal, Meredith B

2016-04-01

Calls for transparency in health care prices are increasing, in an effort to encourage and enable patients to make value-based decisions. Yet there is very little evidence of whether and how patients use health care price transparency tools. We evaluated the experiences, in the period 2011-12, of an insured population of nonelderly adults with Aetna's Member Payment Estimator, a web-based tool that provides real-time, personalized, episode-level price estimates. Overall, use of the tool increased during the study period but remained low. Nonetheless, for some procedures the number of people searching for prices of services (called searchers) was high relative to the number of people who received the service (called patients). Among Aetna patients who had an imaging service, childbirth, or one of several outpatient procedures, searchers for price information were significantly more likely to be younger and healthier and to have incurred higher annual deductible spending than patients who did not search for price information. A campaign to deliver price information to consumers may be important to increase patients' engagement with price transparency tools. Project HOPE—The People-to-People Health Foundation, Inc.

A New Tool for Managing Students' Self-Evaluations in Traditional and Distance Education Courses.

ERIC Educational Resources Information Center

Contreras-Castillo, Juan; Block, Arthur Edwards

This paper describes a Web-based question-answering system called E-teacher that can be used in both traditional and distance learning courses to review academic contents. E-teacher is a self-editing template-based system that consists of a set of PHP scripts that generate the HTML code dynamically, or "on the fly." The entire E-teacher…

Climate Model Diagnostic Analyzer Web Service System

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

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

PubMed

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

2016-11-16

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

Easy Web Interfaces to IDL Code for NSTX Data Analysis

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

W.M. Davis

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

SLIDE - a web-based tool for interactive visualization of large-scale -omics data.

PubMed

Ghosh, Soumita; Datta, Abhik; Tan, Kaisen; Choi, Hyungwon

2018-06-28

Data visualization is often regarded as a post hoc step for verifying statistically significant results in the analysis of high-throughput data sets. This common practice leaves a large amount of raw data behind, from which more information can be extracted. However, existing solutions do not provide capabilities to explore large-scale raw datasets using biologically sensible queries, nor do they allow user interaction based real-time customization of graphics. To address these drawbacks, we have designed an open-source, web-based tool called Systems-Level Interactive Data Exploration, or SLIDE to visualize large-scale -omics data interactively. SLIDE's interface makes it easier for scientists to explore quantitative expression data in multiple resolutions in a single screen. SLIDE is publicly available under BSD license both as an online version as well as a stand-alone version at https://github.com/soumitag/SLIDE. Supplementary Information are available at Bioinformatics online.

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.

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

ERIC Educational Resources Information Center

1996

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

Web-based training: a new paradigm in computer-assisted instruction in medicine.

PubMed

Haag, M; Maylein, L; Leven, F J; Tönshoff, B; Haux, R

1999-01-01

Computer-assisted instruction (CAI) programs based on internet technologies, especially on the world wide web (WWW), provide new opportunities in medical education. The aim of this paper is to examine different aspects of such programs, which we call 'web-based training (WBT) programs', and to differentiate them from conventional CAI programs. First, we will distinguish five different interaction types: presentation; browsing; tutorial dialogue; drill and practice; and simulation. In contrast to conventional CAI, there are four architectural types of WBT programs: client-based; remote data and knowledge; distributed teaching; and server-based. We will discuss the implications of the different architectures for developing WBT software. WBT programs have to meet other requirements than conventional CAI programs. The most important tools and programming languages for developing WBT programs will be listed and assigned to the architecture types. For the future, we expect a trend from conventional CAI towards WBT programs.

The Electron Microscopy Outreach Program: A Web-based resource for research and education.

PubMed

Sosinsky, G E; Baker, T S; Hand, G; Ellisman, M H

1999-01-01

We have developed a centralized World Wide Web (WWW)-based environment that serves as a resource of software tools and expertise for biological electron microscopy. A major focus is molecular electron microscopy, but the site also includes information and links on structural biology at all levels of resolution. This site serves to help integrate or link structural biology techniques in accordance with user needs. The WWW site, called the Electron Microscopy (EM) Outreach Program (URL: http://emoutreach.sdsc.edu), provides scientists with computational and educational tools for their research and edification. In particular, we have set up a centralized resource containing course notes, references, and links to image analysis and three-dimensional reconstruction software for investigators wanting to learn about EM techniques either within or outside of their fields of expertise. Copyright 1999 Academic Press.

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

NASA Astrophysics Data System (ADS)

Kurui, P. K.; Mutua, F.

2016-12-01

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

Depression and work performance: an ecological study using web-based screening.

PubMed

Harvey, S B; Glozier, N; Henderson, M; Allaway, S; Litchfield, P; Holland-Elliott, K; Hotopf, M

2011-05-01

Depression is reported to be a major cause of illness-related sub-optimal work performance (presenteeism). However, the majority of studies examining presenteeism have relied on self-report measures of work performance. Furthermore, employers currently face a number of practical challenges in attempting to facilitate early identification of depression. To test whether a web-based screening tool for depression could be used successfully in the workplace and whether it was possible to detect an association between rates of depression and objective measures of impaired workgroup performance. All permanent employees of a telecommunications company with UK-based call centres were encouraged to complete a web-based psychological assessment using the Patient Health Questionnaire depression scale (PHQ-9). In addition to confidential individual level results, the tool was able to provide anonymized summary statistics for each workgroup. Four objective measures of work performance were collected for each workgroup. During the study period, 1161 web-based PHQ-9 questionnaires were completed. There was a negative linear relationship between rates of depressive symptoms and the overall performance of a workgroup (P < 0.001). The linear relationship between depression and workgroup performance remained after controlling for gender balance, percent of temporary staff, employees' perceived level of engagement and satisfaction with their line manager (P < 0.01). Workgroups with high levels of depressive symptoms tend to perform poorly. Computer-aided web-based screening for symptoms of depression is feasible in a work setting.

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.

WebViz: A web browser based application for collaborative analysis of 3D data

NASA Astrophysics Data System (ADS)

Ruegg, C. S.

2011-12-01

In the age of high speed Internet where people can interact instantly, scientific tools have lacked technology which can incorporate this concept of communication using the web. To solve this issue a web application for geological studies has been created, tentatively titled WebViz. This web application utilizes tools provided by Google Web Toolkit to create an AJAX web application capable of features found in non web based software. Using these tools, a web application can be created to act as piece of software from anywhere in the globe with a reasonably speedy Internet connection. An application of this technology can be seen with data regarding the recent tsunami from the major japan earthquakes. After constructing the appropriate data to fit a computer render software called HVR, WebViz can request images of the tsunami data and display it to anyone who has access to the application. This convenience alone makes WebViz a viable solution, but the option to interact with this data with others around the world causes WebViz to be taken as a serious computational tool. WebViz also can be used on any javascript enabled browser such as those found on modern tablets and smart phones over a fast wireless connection. Due to the fact that WebViz's current state is built using Google Web Toolkit the portability of the application is in it's most efficient form. Though many developers have been involved with the project, each person has contributed to increase the usability and speed of the application. In the project's most recent form a dramatic speed increase has been designed as well as a more efficient user interface. The speed increase has been informally noticed in recent uses of the application in China and Australia with the hosting server being located at the University of Minnesota. The user interface has been improved to not only look better but the functionality has been improved. Major functions of the application are rotating the 3D object using buttons. These buttons have been replaced with a new layout that is easier to understand the function and is also easy to use with mobile devices. With these new changes, WebViz is easier to control and use for general use.

Epidemiology of operative burns at Kijabe Hospital from 2006 to 2010: Pilot study of a web-based tool for creation of the Kenya Burn Repository

PubMed Central

Dale, Elizabeth L.; Mueller, Melissa A.; Wang, Li; Fogerty, Mary D.; Guy, Jeffrey S.; Nthumba, Peter M.

2013-01-01

Introduction In order to implement effective burn prevention strategies, the WHO has called for improved data collection to better characterize burn injuries in low and middle income countries (LMIC). This study was designed to gather information on burn injury in Kenya and to test a model for such data collection. Methods The study was designed as a retrospective case series study utilizing an electronic data collection tool to assess the scope of burn injuries requiring operation at Kijabe Hospital from January 2006 to May 2010. Data were entered into a web-based tool to test its utility as the potential Kenya Burn Repository (KBR). Results 174 patients were included. The median age was 10 years. There was a male predominance (59% vs. 41%). Findings included that timing of presentation was associated with burn etiology (p = 0.009). Length of stay (LOS) was associated with burn etiology (p < 0.001). Etiology differed depending on the age group, with scald being most prominent in children (p = 0.002). Conclusions Burn injuries in Kenya show similarities with other LMIC in etiology and pediatric predominance. Late presentation for care and prolonged LOS are areas for further investigation. The web-based database is an effective tool for data collection and international collaboration. PMID:23040425

Epidemiology of operative burns at Kijabe Hospital from 2006 to 2010: pilot study of a web-based tool for creation of the Kenya Burn Repository.

PubMed

Dale, Elizabeth L; Mueller, Melissa A; Wang, Li; Fogerty, Mary D; Guy, Jeffrey S; Nthumba, Peter M

2013-06-01

In order to implement effective burn prevention strategies, the WHO has called for improved data collection to better characterize burn injuries in low and middle income countries (LMIC). This study was designed to gather information on burn injury in Kenya and to test a model for such data collection. The study was designed as a retrospective case series study utilizing an electronic data collection tool to assess the scope of burn injuries requiring operation at Kijabe Hospital from January 2006 to May 2010. Data were entered into a web-based tool to test its utility as the potential Kenya Burn Repository (KBR). 174 patients were included. The median age was 10 years. There was a male predominance (59% vs. 41%). Findings included that timing of presentation was associated with burn etiology (p=0.009). Length of stay (LOS) was associated with burn etiology (p<0.001). Etiology differed depending on the age group, with scald being most prominent in children (p=0.002). Burn injuries in Kenya show similarities with other LMIC in etiology and pediatric predominance. Late presentation for care and prolonged LOS are areas for further investigation. The web-based database is an effective tool for data collection and international collaboration. Copyright © 2012 Elsevier Ltd and ISBI. All rights reserved.

RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes.

PubMed

Ono, Hiromasa; Ogasawara, Osamu; Okubo, Kosaku; Bono, Hidemasa

2017-08-29

Gene expression data are exponentially accumulating; thus, the functional annotation of such sequence data from metadata is urgently required. However, life scientists have difficulty utilizing the available data due to its sheer magnitude and complicated access. We have developed a web tool for browsing reference gene expression pattern of mammalian tissues and cell lines measured using different methods, which should facilitate the reuse of the precious data archived in several public databases. The web tool is called Reference Expression dataset (RefEx), and RefEx allows users to search by the gene name, various types of IDs, chromosomal regions in genetic maps, gene family based on InterPro, gene expression patterns, or biological categories based on Gene Ontology. RefEx also provides information about genes with tissue-specific expression, and the relative gene expression values are shown as choropleth maps on 3D human body images from BodyParts3D. Combined with the newly incorporated Functional Annotation of Mammals (FANTOM) dataset, RefEx provides insight regarding the functional interpretation of unfamiliar genes. RefEx is publicly available at http://refex.dbcls.jp/.

RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes

PubMed Central

Ono, Hiromasa; Ogasawara, Osamu; Okubo, Kosaku; Bono, Hidemasa

2017-01-01

Gene expression data are exponentially accumulating; thus, the functional annotation of such sequence data from metadata is urgently required. However, life scientists have difficulty utilizing the available data due to its sheer magnitude and complicated access. We have developed a web tool for browsing reference gene expression pattern of mammalian tissues and cell lines measured using different methods, which should facilitate the reuse of the precious data archived in several public databases. The web tool is called Reference Expression dataset (RefEx), and RefEx allows users to search by the gene name, various types of IDs, chromosomal regions in genetic maps, gene family based on InterPro, gene expression patterns, or biological categories based on Gene Ontology. RefEx also provides information about genes with tissue-specific expression, and the relative gene expression values are shown as choropleth maps on 3D human body images from BodyParts3D. Combined with the newly incorporated Functional Annotation of Mammals (FANTOM) dataset, RefEx provides insight regarding the functional interpretation of unfamiliar genes. RefEx is publicly available at http://refex.dbcls.jp/. PMID:28850115

Using Collaborative Web Technology to Construct the Health Information National Trends Survey (HINTS)

PubMed Central

MOSER, RICHARD P.; BECKJORD, ELLEN BURKE; RUTTEN, LILA J. FINNEY; BLAKE, KELLY; HESSE, BRADFORD W.

2012-01-01

Scientists are taking advantage of web-based technology to work in new collaborative environments, a phenomenon known as Science 2.0. The National Cancer Institute (NCI) created a web-based tool called HINTS-GEM that allows a diverse group of stakeholders to collaborate in a virtual environment by providing input on content for the Health Information National Trends Survey (HINTS). This involved stakeholders providing new suggested content and commenting and rating on existing content. HINTS is a nationally-representative survey of the US non-institutionalized adult population (see Finney Rutten et al. [this journal] for more information about the HINTS program). This paper describes the conceptual development of HINTS-GEM and provides results of its use by stakeholders in creating an improved survey instrument. PMID:23020764

DRIFTER Web App Development Support

NASA Technical Reports Server (NTRS)

Davis, Derrick D.; Armstrong, Curtis D.

2015-01-01

During my 2015 internship at Stennis Space Center (SSC) I supported the development of a web based tool to enable user interaction with a low-cost environmental monitoring buoy called the DRIFTER. DRIFTERs are designed by SSC's Applied Science and Technology Projects branch and are used to measure parameters such as water temperature and salinity. Data collected by the buoys help verify measurements by NASA satellites, which contributes to NASA's mission to advance understanding of the Earth by developing technologies to improve the quality of life on or home planet. My main objective during this internship was to support the development of the DRIFTER by writing web-based software that allows the public to view and access data collected by the buoys. In addition, this software would enable DRIFTER owners to configure and control the devices.

The Impact of Oral and Written Feedback on EFL Writers with the Use of Screencasts

ERIC Educational Resources Information Center

Alvira, Roberto

2016-01-01

This article, based on an action research study performed at a Colombian middle-sized private university, proposes specific strategies to provide feedback to English as a foreign language learners and uses a Web 2.0 tool called "screencasting." The findings of the study suggest that the use of coded, written, and oral feedback is widely…

"Heart of Darkness" Webquest: Using Technology To Teach Literary Criticism.

ERIC Educational Resources Information Center

Rozema, Robert

This paper shows how literary criticism can enrich the high school English classroom. Specifically, the paper focuses on how an Internet teaching tool called the WebQuest helped one educator's students learn about literary criticism and apply it to "Heart of Darkness" by Joseph Conrad. The WebQuest homepage defines a WebQuest as "an…

Appreciating Hubble at Hyper-speed: A Web-tool for Students and Teachers

NASA Astrophysics Data System (ADS)

Will, Lisa M.; Mechtley, M.; Cohen, S.; Windhorst, R. A.; Malhotra, S.; Rhoads, J.; Pirzkal, N.; Summers, F.

2006-12-01

Even post-instruction, many high school students and non-science college majors lack a firm understanding of the basic concepts of physics and astronomy necessary to appreciate our expanding universe. To mitigate this trend, we are developing a state-of-the-art Web-tool called "Appreciating Hubble at Hyper-speed" (AHaH ) that uses the HST Cycle 14 Treasury Project "PEARS" (Probing Evolution And Reionization through Spectra) data. AHaH will span the fully 3-dimensional PEARS database of the GOODS/HUDF galaxy distribution from redshifts z = 0.05 to z = 6.5, spanning nearly 90% of the history of the Universe. The web-tool AHaH will allow students to interactively zoom in/out of this PEARS data base, rotate, and accelerate/decelerate towards a specified target, and travel forward or backwards in time. Hence, students can make a complete interactive journey in look-back time. AHaH will help students learn and visually understand basic concepts of physics and astronomy, and at the same time allow them to explore how galaxies change when traveling back in time, how their light is redshifted, and how they are formed and clustered in the expanding Universe. This poster will describe the features of the web-tool and the services that will be offered to help teachers implement this tool in their classrooms.

Use of Web Technology to Access and Update College Plans

ERIC Educational Resources Information Center

Valeau, Edward J.; Luan, Jing

2007-01-01

In this study, the process and outcome of a web-based planning application, called Ports of Call, are discussed. The application allows college management to create, edit, and report out activities relating to college plans, all through a web browser. Its design was based on best practices in modern web technology and the application can be easily…

REopt Lite Web Tool Evaluates Photovoltaics and Battery Storage

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

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

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

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

Using Web Logs in the Science Classroom

ERIC Educational Resources Information Center

Duplichan, Staycle C.

2009-01-01

As educators we must ask ourselves if we are meeting the needs of today's students. The science world is adapting to our ever-changing society; are the methodology and philosophy of our educational system keeping up? In this article, you'll learn why web logs (also called blogs) are an important Web 2.0 tool in your science classroom and how they…

Automated MeSH indexing of the World-Wide Web.

PubMed Central

Fowler, J.; Kouramajian, V.; Maram, S.; Devadhar, V.

1995-01-01

To facilitate networked discovery and information retrieval in the biomedical domain, we have designed a system for automatic assignment of Medical Subject Headings to documents retrieved from the World-Wide Web. Our prototype implementations show significant promise. We describe our methods and discuss the further development of a completely automated indexing tool called the "Web-MeSH Medibot." PMID:8563421

Visualization and interaction tools for aerial photograph mosaics

NASA Astrophysics Data System (ADS)

Fernandes, João Pedro; Fonseca, Alexandra; Pereira, Luís; Faria, Adriano; Figueira, Helder; Henriques, Inês; Garção, Rita; Câmara, António

1997-05-01

This paper describes the development of a digital spatial library based on mosaics of digital orthophotos, called Interactive Portugal, that will enable users both to retrieve geospatial information existing in the Portuguese National System for Geographic Information World Wide Web server, and to develop local databases connected to the main system. A set of navigation, interaction, and visualization tools are proposed and discussed. They include sketching, dynamic sketching, and navigation capabilities over the digital orthophotos mosaics. Main applications of this digital spatial library are pointed out and discussed, namely for education, professional, and tourism markets. Future developments are considered. These developments are related to user reactions, technological advancements, and projects that also aim at delivering and exploring digital imagery on the World Wide Web. Future capabilities for site selection and change detection are also considered.

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.)…

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.

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.

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.…

Rapid Response to Decision Making for Complex Issues - How Technologies of Cooperation Can Help

DTIC Science & Technology

2005-11-01

creating bottom–up taxonomies—called folksonomies —using metadata tools like del.icio.us (in which users create their own tags for bookmarking Web...tools such as RSS, tagging (and the consequent development of folksonomies ), wikis, and group visualization tools all help multiply the individual

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.

C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms

PubMed Central

Alam, Zaid; Peddinti, Gopal

2017-01-01

Abstract The advent of polypharmacology paradigm in drug discovery calls for novel chemoinformatic tools for analyzing compounds’ multi-targeting activities. Such tools should provide an intuitive representation of the chemical space through capturing and visualizing underlying patterns of compound similarities linked to their polypharmacological effects. Most of the existing compound-centric chemoinformatics tools lack interactive options and user interfaces that are critical for the real-time needs of chemical biologists carrying out compound screening experiments. Toward that end, we introduce C-SPADE, an open-source exploratory web-tool for interactive analysis and visualization of drug profiling assays (biochemical, cell-based or cell-free) using compound-centric similarity clustering. C-SPADE allows the users to visually map the chemical diversity of a screening panel, explore investigational compounds in terms of their similarity to the screening panel, perform polypharmacological analyses and guide drug-target interaction predictions. C-SPADE requires only the raw drug profiling data as input, and it automatically retrieves the structural information and constructs the compound clusters in real-time, thereby reducing the time required for manual analysis in drug development or repurposing applications. The web-tool provides a customizable visual workspace that can either be downloaded as figure or Newick tree file or shared as a hyperlink with other users. C-SPADE is freely available at http://cspade.fimm.fi/. PMID:28472495

A Web-based cost-effective training tool with possible application to brain injury rehabilitation.

PubMed

Wang, Peijun; Kreutzer, Ina Anna; Bjärnemo, Robert; Davies, Roy C

2004-06-01

Virtual reality (VR) has provoked enormous interest in the medical community. In particular, VR offers therapists new approaches for improving rehabilitation effects. However, most of these VR assistant tools are not very portable, extensible or economical. Due to the vast amount of 3D data, they are not suitable for Internet transfer. Furthermore, in order to run these VR systems smoothly, special hardware devices are needed. As a result, existing VR assistant tools tend to be available in hospitals but not in patients' homes. To overcome these disadvantages, as a case study, this paper proposes a Web-based Virtual Ticket Machine, called WBVTM, using VRML [VRML Consortium, The Virtual Reality Modeling Language: International Standard ISO/IEC DIS 14772-1, 1997, available at ], Java and EAI (External Authoring Interface) [Silicon Graphics, Inc., The External Authoring Interface (EAI), available at ], to help people with acquired brain injury (ABI) to relearn basic living skills at home at a low cost. As these technologies are open standard and feature usability on the Internet, WBVTM achieves the goals of portability, easy accessibility and cost-effectiveness.

A tool for improving the Web accessibility of visually handicapped persons.

PubMed

Fujiki, Tadayoshi; Hanada, Eisuke; Yamada, Tomomi; Noda, Yoshihiro; Antoku, Yasuaki; Nakashima, Naoki; Nose, Yoshiaki

2006-04-01

Abstract Much has been written concerning the difficulties faced by visually handicapped persons when they access the internet. To solve some of the problems and to make web pages more accessible, we developed a tool we call the "Easy Bar," which works as a toolbar on the web browser. The functions of the Easy Bar are to change the size of web texts and images, to adjust the color, and to clear cached data that is automatically saved by the web browser. These functions are executed with ease by clicking buttons and operating a pull-down list. Since the icons built into Easy Bar are quite large, it is not necessary for the user to deal with delicate operations. The functions of Easy Bar run on any web page without increasing the processing time. For the visually handicapped, Easy Bar would contribute greatly to improved web accessibility to medical information.

Principal Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool

PubMed Central

Clark, Neil R.; Szymkiewicz, Maciej; Wang, Zichen; Monteiro, Caroline D.; Jones, Matthew R.; Ma’ayan, Avi

2016-01-01

Gene set analysis of differential expression, which identifies collectively differentially expressed gene sets, has become an important tool for biology. The power of this approach lies in its reduction of the dimensionality of the statistical problem and its incorporation of biological interpretation by construction. Many approaches to gene set analysis have been proposed, but benchmarking their performance in the setting of real biological data is difficult due to the lack of a gold standard. In a previously published work we proposed a geometrical approach to differential expression which performed highly in benchmarking tests and compared well to the most popular methods of differential gene expression. As reported, this approach has a natural extension to gene set analysis which we call Principal Angle Enrichment Analysis (PAEA). PAEA employs dimensionality reduction and a multivariate approach for gene set enrichment analysis. However, the performance of this method has not been assessed nor its implementation as a web-based tool. Here we describe new benchmarking protocols for gene set analysis methods and find that PAEA performs highly. The PAEA method is implemented as a user-friendly web-based tool, which contains 70 gene set libraries and is freely available to the community. PMID:26848405

Principal Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool.

PubMed

Clark, Neil R; Szymkiewicz, Maciej; Wang, Zichen; Monteiro, Caroline D; Jones, Matthew R; Ma'ayan, Avi

2015-11-01

Gene set analysis of differential expression, which identifies collectively differentially expressed gene sets, has become an important tool for biology. The power of this approach lies in its reduction of the dimensionality of the statistical problem and its incorporation of biological interpretation by construction. Many approaches to gene set analysis have been proposed, but benchmarking their performance in the setting of real biological data is difficult due to the lack of a gold standard. In a previously published work we proposed a geometrical approach to differential expression which performed highly in benchmarking tests and compared well to the most popular methods of differential gene expression. As reported, this approach has a natural extension to gene set analysis which we call Principal Angle Enrichment Analysis (PAEA). PAEA employs dimensionality reduction and a multivariate approach for gene set enrichment analysis. However, the performance of this method has not been assessed nor its implementation as a web-based tool. Here we describe new benchmarking protocols for gene set analysis methods and find that PAEA performs highly. The PAEA method is implemented as a user-friendly web-based tool, which contains 70 gene set libraries and is freely available to the community.

Dynamic selection mechanism for quality of service aware web services

NASA Astrophysics Data System (ADS)

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

2010-02-01

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

Challenging Google, Microsoft Unveils a Search Tool for Scholarly Articles

ERIC Educational Resources Information Center

Carlson, Scott

2006-01-01

Microsoft has introduced a new search tool to help people find scholarly articles online. The service, which includes journal articles from prominent academic societies and publishers, puts Microsoft in direct competition with Google Scholar. The new free search tool, which should work on most Web browsers, is called Windows Live Academic Search…

Using Web Ontology Language to Integrate Heterogeneous Databases in the Neurosciences

PubMed Central

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

2006-01-01

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

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 ...

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

PubMed Central

2013-01-01

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

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

PubMed

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

2013-03-01

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

Cyberinfrastructure at IRIS: Challenges and Solutions Providing Integrated Data Access to EarthScope and Other Earth Science Data

NASA Astrophysics Data System (ADS)

Ahern, T. K.; Barga, R.; Casey, R.; Kamb, L.; Parastatidis, S.; Stromme, S.; Weertman, B. T.

2008-12-01

While mature methods of accessing seismic data from the IRIS DMC have existed for decades, the demands for improved interdisciplinary data integration call for new approaches. Talented software teams at the IRIS DMC, UNAVCO and the ICDP in Germany, have been developing web services for all EarthScope data including data from USArray, PBO and SAFOD. These web services are based upon SOAP and WSDL. The EarthScope Data Portal was the first external system to access data holdings from the IRIS DMC using Web Services. EarthScope will also draw more heavily upon products to aid in cross-disciplinary data reuse. A Product Management System called SPADE allows archive of and access to heterogeneous data products, presented as XML documents, at the IRIS DMC. Searchable metadata are extracted from the XML and enable powerful searches for products from EarthScope and other data sources. IRIS is teaming with the External Research Group at Microsoft Research to leverage a powerful Scientific Workflow Engine (Trident) and interact with the web services developed at centers such as IRIS to enable access to data services as well as computational services. We believe that this approach will allow web- based control of workflows and the invocation of computational services that transform data. This capability will greatly improve access to data across scientific disciplines. This presentation will review some of the traditional access tools as well as many of the newer approaches that use web services, scientific workflow to improve interdisciplinary data access.

Creative Commons: A New Tool for Schools

ERIC Educational Resources Information Center

Pitler, Howard

2006-01-01

Technology-savvy instructors often require students to create Web pages or videos, tasks that require finding materials such as images, music, or text on the Web, reusing them, and then republishing them in a technique that author Howard Pitler calls "remixing." However, this requires both the student and the instructor to deal with often thorny…

Preparing for the Real Web Generation

ERIC Educational Resources Information Center

Pence, Harry E.

2007-01-01

Some have called the current generation of college students the Web generation. They are wrong! The pace of technology change continues to quicken. The effects of globalization and social networking have not yet had their full impact. At best, the present students represent a transitional group. The tools we use define us, and the media revolution…

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…

Webpress: An Internet Outreach from NASA Dryden

NASA Technical Reports Server (NTRS)

Biezad, Daniel J.

1996-01-01

The Technology and Commercialization Office at NASA DRyden has developed many educational outreach programs for K-12 educators. This project concentrates on the internet portion of that effort, specifically focusing on the development of an internet tool for educators called Webpress. This tool will not only provide a user-friendly access to aeronautical topics and interesting individuals on the world wide web (web), but will also enable teachers to rapidly submit and display their own materials and links for use in the classroom.

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

PubMed

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

2012-02-01

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

Watershed Central: A New Gateway to Watershed Information

EPA Science Inventory

Many communities across the country struggle to find the right approaches, tools and data to in their watershed plans. EPA recently posted a new Web site called "Watershed Central, a “onestop" tool, to help watershed organizations and others find key resources to protect their ...

miRNAFold: a web server for fast miRNA precursor prediction in genomes.

PubMed

Tav, Christophe; Tempel, Sébastien; Poligny, Laurent; Tahi, Fariza

2016-07-08

Computational methods are required for prediction of non-coding RNAs (ncRNAs), which are involved in many biological processes, especially at post-transcriptional level. Among these ncRNAs, miRNAs have been largely studied and biologists need efficient and fast tools for their identification. In particular, ab initio methods are usually required when predicting novel miRNAs. Here we present a web server dedicated for miRNA precursors identification at a large scale in genomes. It is based on an algorithm called miRNAFold that allows predicting miRNA hairpin structures quickly with high sensitivity. miRNAFold is implemented as a web server with an intuitive and user-friendly interface, as well as a standalone version. The web server is freely available at: http://EvryRNA.ibisc.univ-evry.fr/miRNAFold. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model.

PubMed

Kawano, Shin; Watanabe, Tsutomu; Mizuguchi, Sohei; Araki, Norie; Katayama, Toshiaki; Yamaguchi, Atsuko

2014-07-01

TogoTable (http://togotable.dbcls.jp/) is a web tool that adds user-specified annotations to a table that a user uploads. Annotations are drawn from several biological databases that use the Resource Description Framework (RDF) data model. TogoTable uses database identifiers (IDs) in the table as a query key for searching. RDF data, which form a network called Linked Open Data (LOD), can be searched from SPARQL endpoints using a SPARQL query language. Because TogoTable uses RDF, it can integrate annotations from not only the reference database to which the IDs originally belong, but also externally linked databases via the LOD network. For example, annotations in the Protein Data Bank can be retrieved using GeneID through links provided by the UniProt RDF. Because RDF has been standardized by the World Wide Web Consortium, any database with annotations based on the RDF data model can be easily incorporated into this tool. We believe that TogoTable is a valuable Web tool, particularly for experimental biologists who need to process huge amounts of data such as high-throughput experimental output. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

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

NASA Astrophysics Data System (ADS)

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

2015-09-01

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

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

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

The Future of the Internet in Science

NASA Technical Reports Server (NTRS)

Guice, Jon; Duffy, Robert

2000-01-01

How are scientists going to make use of the Internet several years from now? This is a case study of a leading-edge experiment in building a 'virtual institute'-- using electronic communication tools to foster collaboration among geographically dispersed scientists. Our experience suggests: Scientists will want to use web-based document management systems. There will be a demand for Internet-enabled meeting support tools. While internet videoconferencing will have limited value for scientists, webcams will be in great demand as a tool for transmitting pictures of objects and settings, rather than "talking heads." and a significant share of scientists who do fieldwork will embrace mobile voice, data and video communication tools. The setting for these findings is a research consortium called the NASA Astrobiology Institute.

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

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

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

NASA Technical Reports Server (NTRS)

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

REopt Lite Web Tool

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

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

Using Web-Based Technologies and Tools in Future Choreographers' Training: British Experience

ERIC Educational Resources Information Center

Bidyuk, Dmytro

2016-01-01

In the paper the problem of using effective web-based technologies and tools in teaching choreography in British higher education institutions has been discussed. Researches on the usage of web-based technologies and tools for practical dance courses in choreographers' professional training at British higher education institutions by such British…

An Online Image Analysis Tool for Science Education

ERIC Educational Resources Information Center

Raeside, L.; Busschots, B.; Waddington, S.; Keating, J. G.

2008-01-01

This paper describes an online image analysis tool developed as part of an iterative, user-centered development of an online Virtual Learning Environment (VLE) called the Education through Virtual Experience (EVE) Portal. The VLE provides a Web portal through which schoolchildren and their teachers create scientific proposals, retrieve images and…

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.

Internet and World Wide Web-based tools for neuropathology practice and education.

PubMed

Fung, Kar-Ming; Tihan, Tarik

2009-04-01

The Internet and the World Wide Web (www) serve as a source of information and a communication network. Together they form a so-called web or network that allows for transmission and dissemination of information in unprecedented speed, volume and detail. This article presents an overview of the current status of neuropathology content on the www. As well as considering the Internet as a resource for neuropathology practice, education and research, we also address the issue of quality assurance when evaluating Internet and www content. Four major categories of websites (archival, broker, news and blog) are discussed and resources relevant to neuropathology of each type are highlighted. We believe that our report and similar attempts can provide an opportunity to discuss appropriate and effective use of the Internet by the neuropathology community.

Unveiling causal activity of complex networks

NASA Astrophysics Data System (ADS)

Williams-García, Rashid V.; Beggs, John M.; Ortiz, Gerardo

2017-07-01

We introduce a novel tool for analyzing complex network dynamics, allowing for cascades of causally-related events, which we call causal webs (c-webs), to be separated from other non-causally-related events. This tool shows that traditionally-conceived avalanches may contain mixtures of spatially-distinct but temporally-overlapping cascades of events, and dynamical disorder or noise. In contrast, c-webs separate these components, unveiling previously hidden features of the network and dynamics. We apply our method to mouse cortical data with resulting statistics which demonstrate for the first time that neuronal avalanches are not merely composed of causally-related events. The original version of this article was uploaded to the arXiv on March 17th, 2016 [1].

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.

ESAP plus: a web-based server for EST-SSR marker development.

PubMed

Ponyared, Piyarat; Ponsawat, Jiradej; Tongsima, Sissades; Seresangtakul, Pusadee; Akkasaeng, Chutipong; Tantisuwichwong, Nathpapat

2016-12-22

Simple sequence repeats (SSRs) have become widely used as molecular markers in plant genetic studies due to their abundance, high allelic variation at each locus and simplicity to analyze using conventional PCR amplification. To study plants with unknown genome sequence, SSR markers from Expressed Sequence Tags (ESTs), which can be obtained from the plant mRNA (converted to cDNA), must be utilized. With the advent of high-throughput sequencing technology, huge EST sequence data have been generated and are now accessible from many public databases. However, SSR marker identification from a large in-house or public EST collection requires a computational pipeline that makes use of several standard bioinformatic tools to design high quality EST-SSR primers. Some of these computational tools are not users friendly and must be tightly integrated with reference genomic databases. A web-based bioinformatic pipeline, called EST Analysis Pipeline Plus (ESAP Plus), was constructed for assisting researchers to develop SSR markers from a large EST collection. ESAP Plus incorporates several bioinformatic scripts and some useful standard software tools necessary for the four main procedures of EST-SSR marker development, namely 1) pre-processing, 2) clustering and assembly, 3) SSR mining and 4) SSR primer design. The proposed pipeline also provides two alternative steps for reducing EST redundancy and identifying SSR loci. Using public sugarcane ESTs, ESAP Plus automatically executed the aforementioned computational pipeline via a simple web user interface, which was implemented using standard PHP, HTML, CSS and Java scripts. With ESAP Plus, users can upload raw EST data and choose various filtering options and parameters to analyze each of the four main procedures through this web interface. All input EST data and their predicted SSR results will be stored in the ESAP Plus MySQL database. Users will be notified via e-mail when the automatic process is completed and they can download all the results through the web interface. ESAP Plus is a comprehensive and convenient web-based bioinformatic tool for SSR marker development. ESAP Plus offers all necessary EST-SSR development processes with various adjustable options that users can easily use to identify SSR markers from a large EST collection. With familiar web interface, users can upload the raw EST using the data submission page and visualize/download the corresponding EST-SSR information from within ESAP Plus. ESAP Plus can handle considerably large EST datasets. This EST-SSR discovery tool can be accessed directly from: http://gbp.kku.ac.th/esap_plus/ .

Towards elicitation of users requirements for hospital information system: from a care process modelling technique to a web based collaborative tool.

PubMed Central

Staccini, Pascal M.; Joubert, Michel; Quaranta, Jean-Francois; Fieschi, Marius

2002-01-01

Growing attention is being given to the use of process modeling methodology for user requirements elicitation. In the analysis phase of hospital information systems, the usefulness of care-process models has been investigated to evaluate the conceptual applicability and practical understandability by clinical staff and members of users teams. Nevertheless, there still remains a gap between users and analysts in their mutual ability to share conceptual views and vocabulary, keeping the meaning of clinical context while providing elements for analysis. One of the solutions for filling this gap is to consider the process model itself in the role of a hub as a centralized means of facilitating communication between team members. Starting with a robust and descriptive technique for process modeling called IDEF0/SADT, we refined the basic data model by extracting concepts from ISO 9000 process analysis and from enterprise ontology. We defined a web-based architecture to serve as a collaborative tool and implemented it using an object-oriented database. The prospects of such a tool are discussed notably regarding to its ability to generate data dictionaries and to be used as a navigation tool through the medium of hospital-wide documentation. PMID:12463921

Towards elicitation of users requirements for hospital information system: from a care process modelling technique to a web based collaborative tool.

PubMed

Staccini, Pascal M; Joubert, Michel; Quaranta, Jean-Francois; Fieschi, Marius

2002-01-01

Growing attention is being given to the use of process modeling methodology for user requirements elicitation. In the analysis phase of hospital information systems, the usefulness of care-process models has been investigated to evaluate the conceptual applicability and practical understandability by clinical staff and members of users teams. Nevertheless, there still remains a gap between users and analysts in their mutual ability to share conceptual views and vocabulary, keeping the meaning of clinical context while providing elements for analysis. One of the solutions for filling this gap is to consider the process model itself in the role of a hub as a centralized means of facilitating communication between team members. Starting with a robust and descriptive technique for process modeling called IDEF0/SADT, we refined the basic data model by extracting concepts from ISO 9000 process analysis and from enterprise ontology. We defined a web-based architecture to serve as a collaborative tool and implemented it using an object-oriented database. The prospects of such a tool are discussed notably regarding to its ability to generate data dictionaries and to be used as a navigation tool through the medium of hospital-wide documentation.

SieveSifter: a web-based tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials.

PubMed

Fiore-Gartland, Andrew; Kullman, Nicholas; deCamp, Allan C; Clenaghan, Graham; Yang, Wayne; Magaret, Craig A; Edlefsen, Paul T; Gilbert, Peter B

2017-08-01

Analysis of HIV-1 virions from participants infected in a randomized controlled preventive HIV-1 vaccine efficacy trial can help elucidate mechanisms of partial protection. By comparing the genetic sequence of viruses from vaccine and placebo recipients to the sequence of the vaccine itself, a technique called 'sieve analysis', one can identify functional specificities of vaccine-induced immune responses. We have created an interactive web-based visualization and data access tool for exploring the results of sieve analyses performed on four major preventive HIV-1 vaccine efficacy trials: (i) the HIV Vaccine Trial Network (HVTN) 502/Step trial, (ii) the RV144/Thai trial, (iii) the HVTN 503/Phambili trial and (iv) the HVTN 505 trial. The tool acts simultaneously as a platform for rapid reinterpretation of sieve effects and as a portal for organizing and sharing the viral sequence data. Access to these valuable datasets also enables the development of novel methodology for future sieve analyses. Visualization: http://sieve.fredhutch.org/viz . Source code: https://github.com/nkullman/SIEVE . Data API: http://sieve.fredhutch.org/data . agartlan@fredhutch.org. © The Author(s) 2017. Published by Oxford University Press.

GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies

PubMed Central

Zhang, Bing; Schmoyer, Denise; Kirov, Stefan; Snoddy, Jay

2004-01-01

Background Microarray and other high-throughput technologies are producing large sets of interesting genes that are difficult to analyze directly. Bioinformatics tools are needed to interpret the functional information in the gene sets. Results We have created a web-based tool for data analysis and data visualization for sets of genes called GOTree Machine (GOTM). This tool was originally intended to analyze sets of co-regulated genes identified from microarray analysis but is adaptable for use with other gene sets from other high-throughput analyses. GOTree Machine generates a GOTree, a tree-like structure to navigate the Gene Ontology Directed Acyclic Graph for input gene sets. This system provides user friendly data navigation and visualization. Statistical analysis helps users to identify the most important Gene Ontology categories for the input gene sets and suggests biological areas that warrant further study. GOTree Machine is available online at . Conclusion GOTree Machine has a broad application in functional genomic, proteomic and other high-throughput methods that generate large sets of interesting genes; its primary purpose is to help users sort for interesting patterns in gene sets. PMID:14975175

MetaSEEk: a content-based metasearch engine for images

NASA Astrophysics Data System (ADS)

Beigi, Mandis; Benitez, Ana B.; Chang, Shih-Fu

1997-12-01

Search engines are the most powerful resources for finding information on the rapidly expanding World Wide Web (WWW). Finding the desired search engines and learning how to use them, however, can be very time consuming. The integration of such search tools enables the users to access information across the world in a transparent and efficient manner. These systems are called meta-search engines. The recent emergence of visual information retrieval (VIR) search engines on the web is leading to the same efficiency problem. This paper describes and evaluates MetaSEEk, a content-based meta-search engine used for finding images on the Web based on their visual information. MetaSEEk is designed to intelligently select and interface with multiple on-line image search engines by ranking their performance for different classes of user queries. User feedback is also integrated in the ranking refinement. We compare MetaSEEk with a base line version of meta-search engine, which does not use the past performance of the different search engines in recommending target search engines for future queries.

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.

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.

CoVaCS: a consensus variant calling system.

PubMed

Chiara, Matteo; Gioiosa, Silvia; Chillemi, Giovanni; D'Antonio, Mattia; Flati, Tiziano; Picardi, Ernesto; Zambelli, Federico; Horner, David Stephen; Pesole, Graziano; Castrignanò, Tiziana

2018-02-05

The advent and ongoing development of next generation sequencing technologies (NGS) has led to a rapid increase in the rate of human genome re-sequencing data, paving the way for personalized genomics and precision medicine. The body of genome resequencing data is progressively increasing underlining the need for accurate and time-effective bioinformatics systems for genotyping - a crucial prerequisite for identification of candidate causal mutations in diagnostic screens. Here we present CoVaCS, a fully automated, highly accurate system with a web based graphical interface for genotyping and variant annotation. Extensive tests on a gold standard benchmark data-set -the NA12878 Illumina platinum genome- confirm that call-sets based on our consensus strategy are completely in line with those attained by similar command line based approaches, and far more accurate than call-sets from any individual tool. Importantly our system exhibits better sensitivity and higher specificity than equivalent commercial software. CoVaCS offers optimized pipelines integrating state of the art tools for variant calling and annotation for whole genome sequencing (WGS), whole-exome sequencing (WES) and target-gene sequencing (TGS) data. The system is currently hosted at Cineca, and offers the speed of a HPC computing facility, a crucial consideration when large numbers of samples must be analysed. Importantly, all the analyses are performed automatically allowing high reproducibility of the results. As such, we believe that CoVaCS can be a valuable tool for the analysis of human genome resequencing studies. CoVaCS is available at: https://bioinformatics.cineca.it/covacs .

ballaxy: web services for structural bioinformatics.

PubMed

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

2015-01-01

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

The iMeteo is a web-based weather visualization tool

NASA Astrophysics Data System (ADS)

Tuni San-Martín, Max; San-Martín, Daniel; Cofiño, Antonio S.

2010-05-01

iMeteo is a web-based weather visualization tool. Designed with an extensible J2EE architecture, it is capable of displaying information from heterogeneous data sources such as gridded data from numerical models (in NetCDF format) or databases of local predictions. All this information is presented in a user-friendly way, being able to choose the specific tool to display data (maps, graphs, information tables) and customize it to desired locations. *Modular Display System* Visualization of the data is achieved through a set of mini tools called widgets. A user can add them at will and arrange them around the screen easily with a drag and drop movement. They can be of various types and each can be configured separately, forming a really powerful and configurable system. The "Map" is the most complex widget, since it can show several variables simultaneously (either gridded or point-based) through a layered display. Other useful widgets are the the "Histogram", which generates a graph with the frequency characteristics of a variable and the "Timeline" which shows the time evolution of a variable at a given location in an interactive way. *Customization and security* Following the trends in web development, the user can easily customize the way data is displayed. Due to programming in client side with technologies like AJAX, the interaction with the application is similar to the desktop ones because there are rapid respone times. If a user is registered then he could also save his settings in the database, allowing access from any system with Internet access with his particular setup. There is particular emphasis on application security. The administrator can define a set of user profiles, which may have associated restrictions on access to certain data sources, geographic areas or time intervals.

ePORT, NASA's Computer Database Program for System Safety Risk Management Oversight (Electronic Project Online Risk Tool)

NASA Technical Reports Server (NTRS)

Johnson, Paul W.

2008-01-01

ePORT (electronic Project Online Risk Tool) provides a systematic approach to using an electronic database program to manage a program/project risk management processes. This presentation will briefly cover the standard risk management procedures, then thoroughly cover NASA's Risk Management tool called ePORT. This electronic Project Online Risk Tool (ePORT) is a web-based risk management program that provides a common framework to capture and manage risks, independent of a programs/projects size and budget. It is used to thoroughly cover the risk management paradigm providing standardized evaluation criterion for common management reporting, ePORT improves Product Line, Center and Corporate Management insight, simplifies program/project manager reporting, and maintains an archive of data for historical reference.

WebSat--a web software for microsatellite marker development.

PubMed

Martins, Wellington Santos; Lucas, Divino César Soares; Neves, Kelligton Fabricio de Souza; Bertioli, David John

2009-01-01

Simple sequence repeats (SSR), also known as microsatellites, have been extensively used as molecular markers due to their abundance and high degree of polymorphism. We have developed a simple to use web software, called WebSat, for microsatellite molecular marker prediction and development. WebSat is accessible through the Internet, requiring no program installation. Although a web solution, it makes use of Ajax techniques, providing a rich, responsive user interface. WebSat allows the submission of sequences, visualization of microsatellites and the design of primers suitable for their amplification. The program allows full control of parameters and the easy export of the resulting data, thus facilitating the development of microsatellite markers. The web tool may be accessed at http://purl.oclc.org/NET/websat/

ProGeRF: Proteome and Genome Repeat Finder Utilizing a Fast Parallel Hash Function

PubMed Central

Moraes, Walas Jhony Lopes; Rodrigues, Thiago de Souza; Bartholomeu, Daniella Castanheira

2015-01-01

Repetitive element sequences are adjacent, repeating patterns, also called motifs, and can be of different lengths; repetitions can involve their exact or approximate copies. They have been widely used as molecular markers in population biology. Given the sizes of sequenced genomes, various bioinformatics tools have been developed for the extraction of repetitive elements from DNA sequences. However, currently available tools do not provide options for identifying repetitive elements in the genome or proteome, displaying a user-friendly web interface, and performing-exhaustive searches. ProGeRF is a web site for extracting repetitive regions from genome and proteome sequences. It was designed to be efficient, fast, and accurate and primarily user-friendly web tool allowing many ways to view and analyse the results. ProGeRF (Proteome and Genome Repeat Finder) is freely available as a stand-alone program, from which the users can download the source code, and as a web tool. It was developed using the hash table approach to extract perfect and imperfect repetitive regions in a (multi)FASTA file, while allowing a linear time complexity. PMID:25811026

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.

tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers.

PubMed

Zheng, Ling-Ling; Xu, Wei-Lin; Liu, Shun; Sun, Wen-Ju; Li, Jun-Hao; Wu, Jie; Yang, Jian-Hua; Qu, Liang-Hu

2016-07-08

tRNA-derived small RNA fragments (tRFs) are one class of small non-coding RNAs derived from transfer RNAs (tRNAs). tRFs play important roles in cellular processes and are involved in multiple cancers. High-throughput small RNA (sRNA) sequencing experiments can detect all the cellular expressed sRNAs, including tRFs. However, distinguishing genuine tRFs from RNA fragments generated by random degradation remains a major challenge. In this study, we developed an integrated web-based computing system, tRF2Cancer, to accurately identify tRFs from sRNA deep-sequencing data and evaluate their expression in multiple cancers. The binomial test was introduced to evaluate whether reads from a small RNA-seq data set represent tRFs or degraded fragments. A classification method was then used to annotate the types of tRFs based on their sites of origin in pre-tRNA or mature tRNA. We applied the pipeline to analyze 10 991 data sets from 32 types of cancers and identified thousands of expressed tRFs. A tool called 'tRFinCancer' was developed to facilitate the users to inspect the expression of tRFs across different types of cancers. Another tool called 'tRFBrowser' shows both the sites of origin and the distribution of chemical modification sites in tRFs on their source tRNA. The tRF2Cancer web server is available at http://rna.sysu.edu.cn/tRFfinder/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

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.

Refining and validating a two-stage and web-based cancer risk assessment tool for village doctors in China.

PubMed

Shen, Xing-Rong; Chai, Jing; Feng, Rui; Liu, Tong-Zhu; Tong, Gui-Xian; Cheng, Jing; Li, Kai-Chun; Xie, Shao-Yu; Shi, Yong; Wang, De-Bin

2014-01-01

The big gap between efficacy of population level prevention and expectations due to heterogeneity and complexity of cancer etiologic factors calls for selective yet personalized interventions based on effective risk assessment. This paper documents our research protocol aimed at refining and validating a two-stage and web- based cancer risk assessment tool, from a tentative one in use by an ongoing project, capable of identifying individuals at elevated risk for one or more types of the 80% leading cancers in rural China with adequate sensitivity and specificity and featuring low cost, easy application and cultural and technical sensitivity for farmers and village doctors. The protocol adopted a modified population-based case control design using 72, 000 non-patients as controls, 2, 200 cancer patients as cases, and another 600 patients as cases for external validation. Factors taken into account comprised 8 domains including diet and nutrition, risk behaviors, family history, precancerous diseases, related medical procedures, exposure to environment hazards, mood and feelings, physical activities and anthropologic and biologic factors. Modeling stresses explored various methodologies like empirical analysis, logistic regression, neuro-network analysis, decision theory and both internal and external validation using concordance statistics, predictive values, etc..

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

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

Impact of a Temporary NRT Enhancement in a State Quitline and Web-Based Program.

PubMed

Cole, Sam; Suter, Casey; Nash, Chelsea; Pollard, Joseph

2018-06-01

To examine the impact of a nicotine replacement therapy (NRT) enhancement on quit outcomes. Observational study using an intent to treat as treated analysis. Not available. A total of 4022 Idaho tobacco users aged ≥18 years who received services from the Idaho Tobacco Quitline or Idaho's web-based program. One-call phone or web-based participants were sent a single 4- or 8-week NRT shipment. Multiple-call participants were sent NRT in a single 4-week shipment or two 4-week shipments (second shipment sent only to those completing a second coaching call). North American Quitline Consortium recommended Minimal Data Set items collected at registration and follow-up. Thirty-day point prevalence quit rates were assessed at 7-month follow-up. Multiple logistic regression models were used to examine the effects of program type and amount of NRT sent to participants while controlling for demographic and tobacco use characteristics. Abstinence rates were significantly higher among 8-week versus 4-week NRT recipients (42.5% vs 33.3%). The effect was only significant between multiple-call program participants who received both 4-week NRT shipments versus only the first of 2 possible 4-week shipments (51.1% vs 31.1%). Costs per quit were lowest among web-based participants who received 4 weeks of NRT (US$183 per quit) and highest among multiple-call participants who received only 1 of 2 possible NRT shipments (US$557 per quit). To better balance cost with clinical effectiveness, funders of state-based tobacco cessation services may want to consider (1) allowing tobacco users to choose between phone- and web-based programs while (2) limiting longer NRT benefits only to multiple-call program participants.

Capturing citation activity in three health sciences departments: a comparison study of Scopus and Web of Science.

PubMed

Sarkozy, Alexandra; Slyman, Alison; Wu, Wendy

2015-01-01

Scopus and Web of Science are the two major citation databases that collect and disseminate bibliometric statistics about research articles, journals, institutions, and individual authors. Liaison librarians are now regularly called upon to utilize these databases to assist faculty in finding citation activity on their published works for tenure and promotion, grant applications, and more. But questions about the accuracy, scope, and coverage of these tools deserve closer scrutiny. Discrepancies in citation capture led to a systematic study on how Scopus and Web of Science compared in a real-life situation encountered by liaisons: comparing three different disciplines at a medical school and nursing program. How many articles would each database retrieve for each faculty member using the author-searching tools provided? How many cited references for each faculty member would each tool generate? Results demonstrated troubling differences in publication and citation activity capture between Scopus and Web of Science. Implications for librarians are discussed.

GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects.

PubMed

Lee, Chi-Ching; Chen, Yi-Ping Phoebe; Yao, Tzu-Jung; Ma, Cheng-Yu; Lo, Wei-Cheng; Lyu, Ping-Chiang; Tang, Chuan Yi

2013-04-10

Sequencing of microbial genomes is important because of microbial-carrying antibiotic and pathogenetic activities. However, even with the help of new assembling software, finishing a whole genome is a time-consuming task. In most bacteria, pathogenetic or antibiotic genes are carried in genomic islands. Therefore, a quick genomic island (GI) prediction method is useful for ongoing sequencing genomes. In this work, we built a Web server called GI-POP (http://gipop.life.nthu.edu.tw) which integrates a sequence assembling tool, a functional annotation pipeline, and a high-performance GI predicting module, in a support vector machine (SVM)-based method called genomic island genomic profile scanning (GI-GPS). The draft genomes of the ongoing genome projects in contigs or scaffolds can be submitted to our Web server, and it provides the functional annotation and highly probable GI-predicting results. GI-POP is a comprehensive annotation Web server designed for ongoing genome project analysis. Researchers can perform annotation and obtain pre-analytic information include possible GIs, coding/non-coding sequences and functional analysis from their draft genomes. This pre-analytic system can provide useful information for finishing a genome sequencing project. Copyright © 2012 Elsevier B.V. All rights reserved.

Real-time access of large volume imagery through low-bandwidth links

NASA Astrophysics Data System (ADS)

Phillips, James; Grohs, Karl; Brower, Bernard; Kelly, Lawrence; Carlisle, Lewis; Pellechia, Matthew

2010-04-01

Providing current, time-sensitive imagery and geospatial information to deployed tactical military forces or first responders continues to be a challenge. This challenge is compounded through rapid increases in sensor collection volumes, both with larger arrays and higher temporal capture rates. Focusing on the needs of these military forces and first responders, ITT developed a system called AGILE (Advanced Geospatial Imagery Library Enterprise) Access as an innovative approach based on standard off-the-shelf techniques to solving this problem. The AGILE Access system is based on commercial software called Image Access Solutions (IAS) and incorporates standard JPEG 2000 processing. Our solution system is implemented in an accredited, deployable form, incorporating a suite of components, including an image database, a web-based search and discovery tool, and several software tools that act in concert to process, store, and disseminate imagery from airborne systems and commercial satellites. Currently, this solution is operational within the U.S. Government tactical infrastructure and supports disadvantaged imagery users in the field. This paper presents the features and benefits of this system to disadvantaged users as demonstrated in real-world operational environments.

Interpreting User's Choice of Technologies: A Quantitative Research on Choosing the Best Web-Based Communication Tools

ERIC Educational Resources Information Center

Adebiaye, Richmond

2010-01-01

The proliferation of web-based communication tools like email clients vis-a-vis Yahoo mail, Gmail, and Hotmail have led to new innovations in web-based communication. Email users benefit greatly from this technology, but lack of security of these tools can put users at risk of loss of privacy, including identity theft, corporate espionage, and…

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.

MAPI: towards the integrated exploitation of bioinformatics Web Services.

PubMed

Ramirez, Sergio; Karlsson, Johan; Trelles, Oswaldo

2011-10-27

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

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…

Web-based Tools for Educators: Outreach Activities of the Polar Radar for Ice Sheet Measurements (PRISM) Project

NASA Astrophysics Data System (ADS)

Braaten, D. A.; Holvoet, J. F.; Gogineni, S.

2003-12-01

The Radar Systems and Remote Sensing Laboratory at the University of Kansas (KU) has implemented extensive outreach activities focusing on Polar Regions as part of the Polar Radar for Ice Sheet Measurements (PRISM) project. The PRISM project is developing advanced intelligent remote sensing technology that involves radar systems, an autonomous rover, and communications systems to measure detailed ice sheet characteristics, and to determine bed conditions (frozen or wet) below active ice sheets in both Greenland and Antarctica. These measurements will provide a better understanding of the response of polar ice sheets to global climate change and the resulting impact the ice sheets will have on sea level rise. Many of the research and technological development aspects of the PRISM project, such as robotics, radar systems, climate change and exploration of harsh environments, can kindle an excitement and interest in students about science and technology. These topics form the core of our K-12 education and training outreach initiatives, which are designed to capture the imagination of young students, and prompt them to consider an educational path that will lead them to scientific or engineering careers. The K-12 PRISM outreach initiatives are being developed and implemented in a collaboration with the Advanced Learning Technology Program (ALTec) of the High Plains Regional Technology in Education Consortium (HPR*TEC). ALTec is associated with the KU School of Education, and is a well-established educational research center that develops and hosts web tools to enable teachers nationwide to network, collaborate, and share resources with other teachers. An example of an innovative and successful web interface developed by ALTec is called TrackStar. Teachers can use TrackStar over the Web to develop interactive, resource-based lessons (called tracks) on-line for their students. Once developed, tracks are added to the TrackStar database and can be accessed and modified (if necessary) by teachers everywhere. The PRISM project has added a search engine for polar related tracks, and has developed numerous new tracks on robotics, polar exploration, and climate change under the guidance of a K-12 teacher advisory group. The PRISM project is also developing and hosting several other web-based lesson design tools and resources for K-12 educators and students on the PRISM project web page (http://www.ku-prism.org). These tools and resources include: i) "Polar Scientists and Explorers, Past and Present" covering the travels and/or unknown fate of polar explorers and scientists; ii) "Polar News" providing links to current news articles related to polar regions; iii) "Letter of Global Concern", which is a tool to help students draft a letter to a politician, government official, or business leader; iv) "Graphic Sleuth", which is an online utility that allows teachers to make lessons for student use; v) "Bears on Ice" for students in grades K - 6 that can follow the adventures of two stuffed bears that travel with scientists into polar regions; and vi) "K-12 Polar Resources," which provides teachers with images, information, TrackStar lessons, and a search engine designed to identify polar related lessons. In our presentation, we will describe and show examples of these tools and resources, and provide an assessment of their popularity with teachers nationwide.

Climate Model Diagnostic Analyzer

NASA Technical Reports Server (NTRS)

Lee, Seungwon; Pan, Lei; Zhai, Chengxing; Tang, Benyang; Kubar, Terry; Zhang, Zia; Wang, Wei

2015-01-01

The comprehensive and innovative evaluation of climate models with newly available global observations is critically needed for the improvement of climate model current-state representation and future-state predictability. A climate model diagnostic evaluation process requires physics-based multi-variable analyses that typically involve large-volume and heterogeneous datasets, making them both computation- and data-intensive. With an exploratory nature of climate data analyses and an explosive growth of datasets and service tools, scientists are struggling to keep track of their datasets, tools, and execution/study history, let alone sharing them with others. In response, we have developed a cloud-enabled, provenance-supported, web-service system called Climate Model Diagnostic Analyzer (CMDA). CMDA enables the physics-based, multivariable model performance evaluations and diagnoses through the comprehensive and synergistic use of multiple observational data, reanalysis data, and model outputs. At the same time, CMDA provides a crowd-sourcing space where scientists can organize their work efficiently and share their work with others. CMDA is empowered by many current state-of-the-art software packages in web service, provenance, and semantic search.

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…

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

PubMed

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

2011-04-01

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

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

PubMed Central

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

2007-01-01

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

WebSat ‐ A web software for microsatellite marker development

PubMed Central

Martins, Wellington Santos; Soares Lucas, Divino César; de Souza Neves, Kelligton Fabricio; Bertioli, David John

2009-01-01

Simple sequence repeats (SSR), also known as microsatellites, have been extensively used as molecular markers due to their abundance and high degree of polymorphism. We have developed a simple to use web software, called WebSat, for microsatellite molecular marker prediction and development. WebSat is accessible through the Internet, requiring no program installation. Although a web solution, it makes use of Ajax techniques, providing a rich, responsive user interface. WebSat allows the submission of sequences, visualization of microsatellites and the design of primers suitable for their amplification. The program allows full control of parameters and the easy export of the resulting data, thus facilitating the development of microsatellite markers. Availability The web tool may be accessed at http://purl.oclc.org/NET/websat/ PMID:19255650

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 ...

Filtering SPAM in P2PSIP Communities with Web of Trust

NASA Astrophysics Data System (ADS)

Heikkilä, Juho; Gurtov, Andrei

Spam is a dominant problem on email systems today. One of the reasons is the lack of infrastructure for security and trust. As Voice over IP (VoIP) communication becomes increasingly popular, proliferation of spam calls is only a matter of time. As SIP identity scheme is practically similar to email, those share the same threats. We utilized Host Identity Protocol (HIP) to provide basic security, such as end-to-end encryption. To provide call filtering, however, other tools are needed. In this paper, we suggest applying trust paths familiar from the PGP web of trust to prevent unwanted communication in P2PSIP communities.

Climate Model Diagnostic Analyzer Web Service System

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

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.

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.)

On transform coding tools under development for VP10

NASA Astrophysics Data System (ADS)

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

2016-09-01

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

Identification of immunoglobulins using Chou's pseudo amino acid composition with feature selection technique.

PubMed

Tang, Hua; Chen, Wei; Lin, Hao

2016-04-01

Immunoglobulins, also called antibodies, are a group of cell surface proteins which are produced by the immune system in response to the presence of a foreign substance (called antigen). They play key roles in many medical, diagnostic and biotechnological applications. Correct identification of immunoglobulins is crucial to the comprehension of humoral immune function. With the avalanche of protein sequences identified in postgenomic age, it is highly desirable to develop computational methods to timely identify immunoglobulins. In view of this, we designed a predictor called "IGPred" by formulating protein sequences with the pseudo amino acid composition into which nine physiochemical properties of amino acids were incorporated. Jackknife cross-validated results showed that 96.3% of immunoglobulins and 97.5% of non-immunoglobulins can be correctly predicted, indicating that IGPred holds very high potential to become a useful tool for antibody analysis. For the convenience of most experimental scientists, a web-server for IGPred was established at http://lin.uestc.edu.cn/server/IGPred. We believe that the web-server will become a powerful tool to study immunoglobulins and to guide related experimental validations.

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

VCS: Tool for Visualizing Copy Number Variation and Single Nucleotide Polymorphism.

PubMed

Kim, HyoYoung; Sung, Samsun; Cho, Seoae; Kim, Tae-Hun; Seo, Kangseok; Kim, Heebal

2014-12-01

Copy number variation (CNV) or single nucleotide phlyorphism (SNP) is useful genetic resource to aid in understanding complex phenotypes or deseases susceptibility. Although thousands of CNVs and SNPs are currently avaliable in the public databases, they are somewhat difficult to use for analyses without visualization tools. We developed a web-based tool called the VCS (visualization of CNV or SNP) to visualize the CNV or SNP detected. The VCS tool can assist to easily interpret a biological meaning from the numerical value of CNV and SNP. The VCS provides six visualization tools: i) the enrichment of genome contents in CNV; ii) the physical distribution of CNV or SNP on chromosomes; iii) the distribution of log2 ratio of CNVs with criteria of interested; iv) the number of CNV or SNP per binning unit; v) the distribution of homozygosity of SNP genotype; and vi) cytomap of genes within CNV or SNP region.

Interactive Visualization of Computational Fluid Dynamics using Mosaic

NASA Technical Reports Server (NTRS)

Clucas, Jean; Watson, Velvin; Chancellor, Marisa K. (Technical Monitor)

1994-01-01

The Web provides new Methods for accessing Information world-wide, but the current text-and-pictures approach neither utilizes all the Web's possibilities not provides for its limitations. While the inclusion of pictures and animations in a paper communicates more effectively than text alone, It Is essentially an extension of the concept of "publication." Also, as use of the Web increases putting images and animations online will quickly load even the "Information Superhighway." We need to find forms of communication that take advantage of the special nature of the Web. This paper presents one approach: the use of the Internet and the Mosaic interface for data sharing and collaborative analysis. We will describe (and In the presentation, demonstrate) our approach: using FAST (Flow Analysis Software Toolkit), a scientific visualization package, as a data viewer and interactive tool called from MOSAIC. Our intent is to stimulate the development of other tools that utilize the unique nature of electronic communication.

STITCHER 2.0: primer design for overlapping PCR applications

PubMed Central

O’Halloran, Damien M.; Uriagereka-Herburger, Isabel; Bode, Katrin

2017-01-01

Overlapping polymerase chain reaction (PCR) is a common technique used by researchers in very diverse fields that enables the user to ‘stitch’ individual pieces of DNA together. Previously, we have reported a web based tool called STITCHER that provides a platform for researchers to automate the design of primers for overlapping PCR applications. Here we present STITCHER 2.0, which represents a substantial update to STITCHER. STITCHER 2.0 is a newly designed web tool that automates the design of primers for overlapping PCR. Unlike STITCHER, STITCHER 2.0 considers diverse algorithmic parameters, and returns multiple result files that include a facility for the user to draw their own primers as well as comprehensive visual guides to the user’s input, output, and designed primers. These result files provide greater control and insight during experimental design and troubleshooting. STITCHER 2.0 is freely available to all users without signup or login requirements and can be accessed at the following webpage: www.ohalloranlab.net/STITCHER2.html. PMID:28358011

STITCHER 2.0: primer design for overlapping PCR applications.

PubMed

O'Halloran, Damien M; Uriagereka-Herburger, Isabel; Bode, Katrin

2017-03-30

Overlapping polymerase chain reaction (PCR) is a common technique used by researchers in very diverse fields that enables the user to 'stitch' individual pieces of DNA together. Previously, we have reported a web based tool called STITCHER that provides a platform for researchers to automate the design of primers for overlapping PCR applications. Here we present STITCHER 2.0, which represents a substantial update to STITCHER. STITCHER 2.0 is a newly designed web tool that automates the design of primers for overlapping PCR. Unlike STITCHER, STITCHER 2.0 considers diverse algorithmic parameters, and returns multiple result files that include a facility for the user to draw their own primers as well as comprehensive visual guides to the user's input, output, and designed primers. These result files provide greater control and insight during experimental design and troubleshooting. STITCHER 2.0 is freely available to all users without signup or login requirements and can be accessed at the following webpage: www.ohalloranlab.net/STITCHER2.html.

CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.

PubMed

Grissa, Ibtissem; Vergnaud, Gilles; Pourcel, Christine

2007-07-01

Clustered regularly interspaced short palindromic repeats (CRISPRs) constitute a particular family of tandem repeats found in a wide range of prokaryotic genomes (half of eubacteria and almost all archaea). They consist of a succession of highly conserved regions (DR) varying in size from 23 to 47 bp, separated by similarly sized unique sequences (spacer) of usually viral origin. A CRISPR cluster is flanked on one side by an AT-rich sequence called the leader and assumed to be a transcriptional promoter. Recent studies suggest that this structure represents a putative RNA-interference-based immune system. Here we describe CRISPRFinder, a web service offering tools to (i) detect CRISPRs including the shortest ones (one or two motifs); (ii) define DRs and extract spacers; (iii) get the flanking sequences to determine the leader; (iv) blast spacers against Genbank database and (v) check if the DR is found elsewhere in prokaryotic sequenced genomes. CRISPRFinder is freely accessible at http://crispr.u-psud.fr/Server/CRISPRfinder.php.

Extracting scientific articles from a large digital archive: BioStor and the Biodiversity Heritage Library.

PubMed

Page, Roderic D M

2011-05-23

The Biodiversity Heritage Library (BHL) is a large digital archive of legacy biological literature, comprising over 31 million pages scanned from books, monographs, and journals. During the digitisation process basic metadata about the scanned items is recorded, but not article-level metadata. Given that the article is the standard unit of citation, this makes it difficult to locate cited literature in BHL. Adding the ability to easily find articles in BHL would greatly enhance the value of the archive. A service was developed to locate articles in BHL based on matching article metadata to BHL metadata using approximate string matching, regular expressions, and string alignment. This article locating service is exposed as a standard OpenURL resolver on the BioStor web site http://biostor.org/openurl/. This resolver can be used on the web, or called by bibliographic tools that support OpenURL. BioStor provides tools for extracting, annotating, and visualising articles from the Biodiversity Heritage Library. BioStor is available from http://biostor.org/.

Creating a Pilot Educational Psychiatry Website: Opportunities, Barriers, and Next Steps.

PubMed

Torous, John; O'Connor, Ryan; Franzen, Jamie; Snow, Caitlin; Boland, Robert; Kitts, Robert

2015-11-05

While medical students and residents may be utilizing websites as online learning resources, medical trainees and educators now have the opportunity to create such educational websites and digital tools on their own. However, the process and theory of building educational websites for medical education have not yet been fully explored. To understand the opportunities, barriers, and process of creating a novel medical educational website. We created a pilot psychiatric educational website to better understand the options, opportunities, challenges, and processes involved in the creation of a psychiatric educational website. We sought to integrate visual and interactive Web design elements to underscore the potential of such Web technology. A pilot website (PsychOnCall) was created to demonstrate the potential of Web technology in medical and psychiatric education. Creating an educational website is now technically easier than ever before, and the primary challenge no longer is technology but rather the creation, validation, and maintenance of information for such websites as well as translating text-based didactics into visual and interactive tools. Medical educators can influence the design and implementation of online educational resources through creating their own websites and engaging medical students and residents in the process.

Creating a Pilot Educational Psychiatry Website: Opportunities, Barriers, and Next Steps

PubMed Central

O'Connor, Ryan; Franzen, Jamie; Snow, Caitlin; Boland, Robert; Kitts, Robert

2015-01-01

Background While medical students and residents may be utilizing websites as online learning resources, medical trainees and educators now have the opportunity to create such educational websites and digital tools on their own. However, the process and theory of building educational websites for medical education have not yet been fully explored. Objective To understand the opportunities, barriers, and process of creating a novel medical educational website. Methods We created a pilot psychiatric educational website to better understand the options, opportunities, challenges, and processes involved in the creation of a psychiatric educational website. We sought to integrate visual and interactive Web design elements to underscore the potential of such Web technology. Results A pilot website (PsychOnCall) was created to demonstrate the potential of Web technology in medical and psychiatric education. Conclusions Creating an educational website is now technically easier than ever before, and the primary challenge no longer is technology but rather the creation, validation, and maintenance of information for such websites as well as translating text-based didactics into visual and interactive tools. Medical educators can influence the design and implementation of online educational resources through creating their own websites and engaging medical students and residents in the process. PMID:27731837

Development and formative evaluation of a visual e-tool to help decision makers navigate the evidence around health financing.

PubMed

Skordis-Worrall, Jolene; Pulkki-Brännström, Anni-Maria; Utley, Martin; Kembhavi, Gayatri; Bricki, Nouria; Dutoit, Xavier; Rosato, Mikey; Pagel, Christina

2012-12-21

There are calls for low and middle income countries to develop robust health financing policies to increase service coverage. However, existing evidence around financing options is complex and often difficult for policy makers to access. To summarize the evidence on the impact of financing health systems and develop an e-tool to help decision makers navigate the findings. After reviewing the literature, we used thematic analysis to summarize the impact of 7 common health financing mechanisms on 5 common health system goals. Information on the relevance of each study to a user's context was provided by 11 country indicators. A Web-based e-tool was then developed to assist users in navigating the literature review. This tool was evaluated using feedback from early users, collected using an online survey and in-depth interviews with key informants. The e-tool provides graphical summaries that allow a user to assess the following parameters with a single snapshot: the number of relevant studies available in the literature, the heterogeneity of evidence, where key evidence is lacking, and how closely the evidence matches their own context. Users particularly liked the visual display and found navigating the tool intuitive. However there was concern that a lack of evidence on positive impact might be construed as evidence against a financing option and that the tool might over-simplify the available financing options. Complex evidence can be made more easily accessible and potentially more understandable using basic Web-based technology and innovative graphical representations that match findings to the users' goals and context.

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.

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.

Measuring engagement effectiveness in social media

NASA Astrophysics Data System (ADS)

Li, Lei; Sun, Tong; Peng, Wei; Li, Tao

2012-03-01

Social media is becoming increasingly prevalent with the advent of web 2.0 technologies. Popular social media websites, such as Twitter and Facebook, are attracting a gigantic number of online users to post and share information. An interesting phenomenon under this trend involves that more and more users share their experiences or issues with regard to a product, and then the product service agents use commercial social media listening and engagement tools (e.g. Radian6, Sysomos, etc.) to response to users' complaints or issues and help them tackle their problems. This is often called customer care in social media or social customer relationship management (CRM). However, all these existing commercial social media tools only provide an aggregated level of trends, patterns and sentiment analysis based on the keyword-centric brand relevant data, which have little insights for answering one of the key questions in social CRM system: how effective is our social customer care engagement? In this paper, we focus on addressing the problem of how to measure the effectiveness of engagement for service agents in customer care. Traditional CRM effectiveness measurements are defined under the scenario of the call center, where the effectiveness is mostly based on the duration time per call and/or number of answered calls per day. Different from customer care in a call center, we can obtain detailed conversations between agents and customers in social media, and therefore the effectiveness can be measured by analyzing the content of conversations and the sentiment of customers.

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.

Web-Based Teaching: The Beginning of the End for Universities?

ERIC Educational Resources Information Center

Wyatt, Ray

This paper describes a World Wide Web-based, generic, inter-disciplinary subject called computer-aided policymaking. It has been offered at Melbourne University (Australia) from the beginning of 2001. It has generated some salutary lessons in marketing and pedagogy, but overall it is concluded that Web-based teaching has a rosy future.…

Web-Based Quiz-Game-Like Formative Assessment: Development and Evaluation

ERIC Educational Resources Information Center

Wang, Tzu-Hua

2008-01-01

This research aims to develop a multiple-choice Web-based quiz-game-like formative assessment system, named GAM-WATA. The unique design of "Ask-Hint Strategy" turns the Web-based formative assessment into an online quiz game. "Ask-Hint Strategy" is composed of "Prune Strategy" and "Call-in Strategy".…

Development and Evaluation of Mechatronics Learning System in a Web-Based Environment

ERIC Educational Resources Information Center

Shyr, Wen-Jye

2011-01-01

The development of remote laboratory suitable for the reinforcement of undergraduate level teaching of mechatronics is important. For the reason, a Web-based mechatronics learning system, called the RECOLAB (REmote COntrol LABoratory), for remote learning in engineering education has been developed in this study. The web-based environment is an…

The Osseus platform: a prototype for advanced web-based distributed simulation

NASA Astrophysics Data System (ADS)

Franceschini, Derrick; Riecken, Mark

2016-05-01

Recent technological advances in web-based distributed computing and database technology have made possible a deeper and more transparent integration of some modeling and simulation applications. Despite these advances towards true integration of capabilities, disparate systems, architectures, and protocols will remain in the inventory for some time to come. These disparities present interoperability challenges for distributed modeling and simulation whether the application is training, experimentation, or analysis. Traditional approaches call for building gateways to bridge between disparate protocols and retaining interoperability specialists. Challenges in reconciling data models also persist. These challenges and their traditional mitigation approaches directly contribute to higher costs, schedule delays, and frustration for the end users. Osseus is a prototype software platform originally funded as a research project by the Defense Modeling & Simulation Coordination Office (DMSCO) to examine interoperability alternatives using modern, web-based technology and taking inspiration from the commercial sector. Osseus provides tools and services for nonexpert users to connect simulations, targeting the time and skillset needed to successfully connect disparate systems. The Osseus platform presents a web services interface to allow simulation applications to exchange data using modern techniques efficiently over Local or Wide Area Networks. Further, it provides Service Oriented Architecture capabilities such that finer granularity components such as individual models can contribute to simulation with minimal effort.

Electrophysiological signal analysis and visualization using Cloudwave for epilepsy clinical research.

PubMed

Jayapandian, Catherine P; Chen, Chien-Hung; Bozorgi, Alireza; Lhatoo, Samden D; Zhang, Guo-Qiang; Sahoo, Satya S

2013-01-01

Epilepsy is the most common serious neurological disorder affecting 50-60 million persons worldwide. Electrophysiological data recordings, such as electroencephalogram (EEG), are the gold standard for diagnosis and pre-surgical evaluation in epilepsy patients. The increasing trend towards multi-center clinical studies require signal visualization and analysis tools to support real time interaction with signal data in a collaborative environment, which cannot be supported by traditional desktop-based standalone applications. As part of the Prevention and Risk Identification of SUDEP Mortality (PRISM) project, we have developed a Web-based electrophysiology data visualization and analysis platform called Cloudwave using highly scalable open source cloud computing infrastructure. Cloudwave is integrated with the PRISM patient cohort identification tool called MEDCIS (Multi-modality Epilepsy Data Capture and Integration System). The Epilepsy and Seizure Ontology (EpSO) underpins both Cloudwave and MEDCIS to support query composition and result retrieval. Cloudwave is being used by clinicians and research staff at the University Hospital - Case Medical Center (UH-CMC) Epilepsy Monitoring Unit (EMU) and will be progressively deployed at four EMUs in the United States and the United Kingdomas part of the PRISM project.

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…

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.

Advancing Collaboration through Hydrologic Data and Model Sharing

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.; Castronova, A. M.; Miles, B.; Li, Z.; Morsy, M. M.

2015-12-01

HydroShare is an online, collaborative system for open sharing of hydrologic data, analytical tools, and models. It supports the sharing of and collaboration around "resources" which are defined primarily by standardized metadata, content data models for each resource type, and an overarching resource data model based on the Open Archives Initiative's Object Reuse and Exchange (OAI-ORE) standard and a hierarchical file packaging system called "BagIt". HydroShare expands the data sharing capability of the CUAHSI Hydrologic Information System by broadening the classes of data accommodated to include geospatial and multidimensional space-time datasets commonly used in hydrology. HydroShare also includes new capability for sharing models, model components, and analytical tools and will take advantage of emerging social media functionality to enhance information about and collaboration around hydrologic data and models. It also supports web services and server/cloud based computation operating on resources for the execution of hydrologic models and analysis and visualization of hydrologic data. HydroShare uses iRODS as a network file system for underlying storage of datasets and models. Collaboration is enabled by casting datasets and models as "social objects". Social functions include both private and public sharing, formation of collaborative groups of users, and value-added annotation of shared datasets and models. The HydroShare web interface and social media functions were developed using the Django web application framework coupled to iRODS. Data visualization and analysis is supported through the Tethys Platform web GIS software stack. Links to external systems are supported by RESTful web service interfaces to HydroShare's content. This presentation will introduce the HydroShare functionality developed to date and describe ongoing development of functionality to support collaboration and integration of data and models.

The Geogenomic Mutational Atlas of Pathogens (GoMAP) Web System

PubMed Central

Sargeant, David P.; Hedden, Michael W.; Deverasetty, Sandeep; Strong, Christy L.; Alaniz, Izua J.; Bartlett, Alexandria N.; Brandon, Nicholas R.; Brooks, Steven B.; Brown, Frederick A.; Bufi, Flaviona; Chakarova, Monika; David, Roxanne P.; Dobritch, Karlyn M.; Guerra, Horacio P.; Levit, Kelvy S.; Mathew, Kiran R.; Matti, Ray; Maza, Dorothea Q.; Mistry, Sabyasachy; Novakovic, Nemanja; Pomerantz, Austin; Rafalski, Timothy F.; Rathnayake, Viraj; Rezapour, Noura; Ross, Christian A.; Schooler, Steve G.; Songao, Sarah; Tuggle, Sean L.; Wing, Helen J.; Yousif, Sandy; Schiller, Martin R.

2014-01-01

We present a new approach for pathogen surveillance we call Geogenomics. Geogenomics examines the geographic distribution of the genomes of pathogens, with a particular emphasis on those mutations that give rise to drug resistance. We engineered a new web system called Geogenomic Mutational Atlas of Pathogens (GoMAP) that enables investigation of the global distribution of individual drug resistance mutations. As a test case we examined mutations associated with HIV resistance to FDA-approved antiretroviral drugs. GoMAP-HIV makes use of existing public drug resistance and HIV protein sequence data to examine the distribution of 872 drug resistance mutations in ∼502,000 sequences for many countries in the world. We also implemented a broadened classification scheme for HIV drug resistance mutations. Several patterns for geographic distributions of resistance mutations were identified by visual mining using this web tool. GoMAP-HIV is an open access web application available at http://www.bio-toolkit.com/GoMap/project/ PMID:24675726

The Geogenomic Mutational Atlas of Pathogens (GoMAP) web system.

PubMed

Sargeant, David P; Hedden, Michael W; Deverasetty, Sandeep; Strong, Christy L; Alaniz, Izua J; Bartlett, Alexandria N; Brandon, Nicholas R; Brooks, Steven B; Brown, Frederick A; Bufi, Flaviona; Chakarova, Monika; David, Roxanne P; Dobritch, Karlyn M; Guerra, Horacio P; Levit, Kelvy S; Mathew, Kiran R; Matti, Ray; Maza, Dorothea Q; Mistry, Sabyasachy; Novakovic, Nemanja; Pomerantz, Austin; Rafalski, Timothy F; Rathnayake, Viraj; Rezapour, Noura; Ross, Christian A; Schooler, Steve G; Songao, Sarah; Tuggle, Sean L; Wing, Helen J; Yousif, Sandy; Schiller, Martin R

2014-01-01

We present a new approach for pathogen surveillance we call Geogenomics. Geogenomics examines the geographic distribution of the genomes of pathogens, with a particular emphasis on those mutations that give rise to drug resistance. We engineered a new web system called Geogenomic Mutational Atlas of Pathogens (GoMAP) that enables investigation of the global distribution of individual drug resistance mutations. As a test case we examined mutations associated with HIV resistance to FDA-approved antiretroviral drugs. GoMAP-HIV makes use of existing public drug resistance and HIV protein sequence data to examine the distribution of 872 drug resistance mutations in ∼ 502,000 sequences for many countries in the world. We also implemented a broadened classification scheme for HIV drug resistance mutations. Several patterns for geographic distributions of resistance mutations were identified by visual mining using this web tool. GoMAP-HIV is an open access web application available at http://www.bio-toolkit.com/GoMap/project/

New approaches in assessing food intake in epidemiology.

PubMed

Conrad, Johanna; Koch, Stefanie A J; Nöthlings, Ute

2018-06-22

A promising direction for improving dietary intake measurement in epidemiologic studies is the combination of short-term and long-term dietary assessment methods using statistical methods. Thereby, web-based instruments are particularly interesting as their application offers several potential advantages such as self-administration and a shorter completion time. The objective of this review is to provide an overview of new web-based short-term instruments and to describe their features. A number of web-based short-term dietary assessment tools for application in different countries and age-groups have been developed so far. Particular attention should be paid to the underlying database and the search function of the tool. Moreover, web-based instruments can improve the estimation of portion sizes by offering several options to the user. Web-based dietary assessment methods are associated with lower costs and reduced burden for participants and researchers, and show a comparable validity with traditional instruments. When there is a need for a web-based tool researcher should consider the adaptation of existing tools rather than developing new instruments. The combination of short-term and long-term instruments seems more feasible with the use of new technology.

A Randomized Controlled Trial of COMPASS Web-Based and Face-to-Face Teacher Coaching in Autism

PubMed Central

Ruble, Lisa A.; McGrew, John H.; Toland, Michael D.; Dalrymple, Nancy J.; Jung, Lee Ann

2013-01-01

Objective Most children with autism rely on schools as their primary source of intervention, yet research has suggested that teachers rarely use evidence-based practices. To address the need for improved educational outcomes, a previously tested consultation intervention called the Collaborative Model for Promoting Competence and Success (COMPASS; Ruble, Dalrymple, & McGrew, 2010; Ruble, Dalrymple, & McGrew, 2012) was evaluated in a 2nd randomized controlled trial, with the addition of a web-based group. Method Forty-nine teacher–child dyads were randomized into 1 of 3 groups: (1) a placebo control (PBO) group, (2) COMPASS followed by face-to-face (FF) coaching sessions, and (3) COMPASS followed by web-based (WEB) coaching sessions. Three individualized goals (social, communication, and independence skills) were selected for intervention for each child. The primary outcome of independent ratings of child goal attainment and several process measures (e.g., consultant and teacher fidelity) were evaluated. Results Using an intent-to-treat approach, findings replicated earlier results with a very large effect size (d = 1.41) for the FF group and a large effect size (d = 1.12) for the WEB group relative to the PBO group. There were no differences in overall change across goal domains between the FF and WEB groups, suggesting the efficacy of videoconferencing technology. Conclusions COMPASS is effective and results in improved educational outcomes for young children with autism. Videoconferencing technology, as a scalable tool, has promise for facilitating access to autism specialists and bridging the research-to-practice gap. PMID:23438314

NASA GSFC Space Weather Center - Innovative Space Weather Dissemination: Web-Interfaces, Mobile Applications, and More

NASA Technical Reports Server (NTRS)

Maddox, Marlo; Zheng, Yihua; Rastaetter, Lutz; Taktakishvili, A.; Mays, M. L.; Kuznetsova, M.; Lee, Hyesook; Chulaki, Anna; Hesse, Michael; Mullinix, Richard;

vMon-mobile provides wireless connection to the electronic patient record

NASA Astrophysics Data System (ADS)

Oliveira, Pedro P., Jr.; Rebelo, Marina; Pilon, Paulo E.; Gutierrez, Marco A.; Tachinardi, Umberto

2002-05-01

This work presents the development of a set of tools to help doctors to continuously monitor critical patients. Real-time monitoring signals are displayed via a Web Based Electronic Patient Record (Web-EPR) developed at the Heart Institute. Any computer on the Hospital's Intranet can access the Web-EPR that will open a browser plug-in called vMon. Recently vMon was adapted to wireless mobile devices providing the same real-time visualization of vital signals of its desktop counterpart. The monitoring network communicates with the hospital network through a gateway using HL7 messages and has the ability to export waveforms in real time using the multicast protocol through an API library. A dedicated ActiveX component was built that establishes the streaming of the biomedical signals under monitoring and displays them on an Internet Explorer 5.x browser. The mobile version - called vMon-mobile - will parse the browser window and deliver it to a PDA device connected to a local area network. The result is a virtual monitor presenting real-time data on a mobile device. All parameters and signals acquired from the moment the patient is connected to the monitors are stored for a few days. The most clinically relevant information is added to patient's EPR.

Zooniverse - A Platform for Data-Driven Citizen Science

NASA Astrophysics Data System (ADS)

Smith, A.; Lintott, C.; Bamford, S.; Fortson, L.

2011-12-01

In July 2007 a team of astrophysicists created a web-based astronomy project called Galaxy Zoo in which members of the public were asked to classify galaxies from the Sloan Digital Sky Survey by their shape. Over the following year a community of more than 150,000 people classified each of the 1 million galaxies more than 50 times each. Four years later this community of 'citizen scientists' is more than 450,000 strong and is contributing their time and efforts to more than 10 Zooniverse projects each with its own science team and research case. With projects ranging from transcribing ancient greek texts (ancientlives.org) to lunar science (moonzoo.org) the challenges to the Zooniverse community have gone well beyond the relatively simple original Galaxy Zoo interface. Delivering a range of citizen science projects to a large web-based audience presents challenges on a number of fronts including interface design, data architecture/modelling and reduction techniques, web-infrastructure and software design. In this paper we will describe how the Zooniverse team (a collaboration of scientists, software developers and educators ) have developed tools and techniques to solve some of these issues.

ROSA: Resource-Oriented Service Management Schemes for Web of Things in a Smart Home.

PubMed

Liao, Chun-Feng; Chen, Peng-Yu

2017-09-21

A Pervasive-computing-enriched smart home environment, which contains many embedded and tiny intelligent devices and sensors coordinated by service management mechanisms, is capable of anticipating intentions of occupants and providing appropriate services accordingly. Although there are a wealth of research achievements in recent years, the degree of market acceptance is still low. The main reason is that most of the devices and services in such environments depend on particular platform or technology, making it hard to develop an application by composing the devices or services. Meanwhile, the concept of Web of Things (WoT) is becoming popular recently. Based on WoT, the developers can build applications based on popular web tools or technologies. Consequently, the objective of this paper is to propose a set of novel WoT-driven plug-and-play service management schemes for a smart home called Resource-Oriented Service Administration (ROSA). We have implemented an application prototype, and experiments are performed to show the effectiveness of the proposed approach. The results of this research can be a foundation for realizing the vision of "end user programmable smart environments".

Unraveling transcriptional control and cis-regulatory codes using the software suite GeneACT

PubMed Central

Cheung, Tom Hiu; Kwan, Yin Lam; Hamady, Micah; Liu, Xuedong

2006-01-01

Deciphering gene regulatory networks requires the systematic identification of functional cis-acting regulatory elements. We present a suite of web-based bioinformatics tools, called GeneACT , that can rapidly detect evolutionarily conserved transcription factor binding sites or microRNA target sites that are either unique or over-represented in differentially expressed genes from DNA microarray data. GeneACT provides graphic visualization and extraction of common regulatory sequence elements in the promoters and 3'-untranslated regions that are conserved across multiple mammalian species. PMID:17064417

ClimateWizard: A Framework and Easy-to-Use Web-Mapping Tool for Global, Regional, and Local Climate-Change Analysis

NASA Astrophysics Data System (ADS)

Girvetz, E. H.; Zganjar, C.; Raber, G. T.; Hoekstra, J.; Lawler, J. J.; Kareiva, P.

2008-12-01

Now that there is overwhelming evidence of global climate change, scientists, managers and planners (i.e. practitioners) need to assess the potential impacts of climate change on particular ecological systems, within specific geographic areas, and at spatial scales they care about, in order to make better land management, planning, and policy decisions. Unfortunately, this application of climate science to real world decisions and planning has proceeded too slowly because we lack tools for translating cutting-edge climate science and climate-model outputs into something managers and planners can work with at local or regional scales (CCSP 2008). To help increase the accessibility of climate information, we have developed a freely-available, easy-to-use, web-based climate-change analysis toolbox, called ClimateWizard, for assessing how climate has and is projected to change at specific geographic locations throughout the world. The ClimateWizard uses geographic information systems (GIS), web-services (SOAP/XML), statistical analysis platforms (e.g. R- project), and web-based mapping services (e.g. Google Earth/Maps, KML/GML) to provide a variety of different analyses (e.g. trends and departures) and outputs (e.g. maps, graphs, tables, GIS layers). Because ClimateWizard analyzes large climate datasets stored remotely on powerful computers, users of the tool do not need to have fast computers or expensive software, but simply need access to the internet. The analysis results are then provided to users in a Google Maps webpage tailored to the specific climate-change question being asked. The ClimateWizard is not a static product, but rather a framework to be built upon and modified to suit the purposes of specific scientific, management, and policy questions. For example, it can be expanded to include bioclimatic variables (e.g. evapotranspiration) and marine data (e.g. sea surface temperature), as well as improved future climate projections, and climate-change impact analyses involving hydrology, vegetation, wildfire, disease, and food security. By harnessing the power of computer and web- based technologies, the ClimateWizard puts local, regional, and global climate-change analyses in the hands of a wider array of managers, planners, and scientists.

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.

WebMeV | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

Web MeV (Multiple-experiment Viewer) is a web/cloud-based tool for genomic data analysis. Web MeV is being built to meet the challenge of exploring large public genomic data set with intuitive graphical interface providing access to state-of-the-art analytical tools.

Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models

PubMed Central

2014-01-01

Background Logos are commonly used in molecular biology to provide a compact graphical representation of the conservation pattern of a set of sequences. They render the information contained in sequence alignments or profile hidden Markov models by drawing a stack of letters for each position, where the height of the stack corresponds to the conservation at that position, and the height of each letter within a stack depends on the frequency of that letter at that position. Results We present a new tool and web server, called Skylign, which provides a unified framework for creating logos for both sequence alignments and profile hidden Markov models. In addition to static image files, Skylign creates a novel interactive logo plot for inclusion in web pages. These interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position. Conclusion Skylign is available as a website, a scriptable web service with a RESTful interface, and as a software package for download. Skylign’s interactive logos are easily incorporated into a web page with just a few lines of HTML markup. Skylign may be found at http://skylign.org. PMID:24410852

Semantic annotation of Web data applied to risk in food.

PubMed

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

2008-11-30

A preliminary step to risk in food assessment is the gathering of experimental data. In the framework of the Sym'Previus project (http://www.symprevius.org), a complete data integration system has been designed, grouping data provided by industrial partners and data extracted from papers published in the main scientific journals of the domain. Those data have been classified by means of a predefined vocabulary, called ontology. Our aim is to complement the database with data extracted from the Web. In the framework of the WebContent project (www.webcontent.fr), we have designed a semi-automatic acquisition tool, called @WEB, which retrieves scientific documents from the Web. During the @WEB process, data tables are extracted from the documents and then annotated with the ontology. We focus on the data tables as they contain, in general, a synthesis of data published in the documents. In this paper, we explain how the columns of the data tables are automatically annotated with data types of the ontology and how the relations represented by the table are recognised. We also give the results of our experimentation to assess the quality of such an annotation.

Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling

PubMed Central

Chang, Chun-Tien; Tsai, Chi-Neu; Tang, Chuan Yi; Chen, Chun-Houh; Lian, Jang-Hau; Hu, Chi-Yu; Tsai, Chia-Lung; Chao, Angel; Lai, Chyong-Huey; Wang, Tzu-Hao; Lee, Yun-Shien

2012-01-01

The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using the currently available Indelligent or ShiftDetector programs, which do not search reference sequences. However, the detection of other genomic variants remains a challenge due to the lack of appropriate tools for heterozygous base-calling fluorescence chromatogram data analysis. In this study, we developed a free web-based program, Mixed Sequence Reader (MSR), which can directly analyze heterozygous base-calling fluorescence chromatogram data in .abi file format using comparisons with reference sequences. The heterozygous sequences are identified as two distinct sequences and aligned with reference sequences. Our results showed that MSR may be used to (i) physically locate indel and STR sequences and determine STR copy number by searching NCBI reference sequences; (ii) predict combinations of microsatellite patterns using the Federal Bureau of Investigation Combined DNA Index System (CODIS); (iii) determine human papilloma virus (HPV) genotypes by searching current viral databases in cases of double infections; (iv) estimate the copy number of paralogous genes, such as β-defensin 4 (DEFB4) and its paralog HSPDP3. PMID:22778697

A randomized controlled study about the use of eHealth in the home health care of premature infants.

PubMed

Gund, Anna; Sjöqvist, Bengt Arne; Wigert, Helena; Hentz, Elisabet; Lindecrantz, Kaj; Bry, Kristina

2013-02-09

One area where the use of information and communication technology (ICT), or eHealth, could be developed is the home health care of premature infants. The aim of this randomized controlled study was to investigate whether the use of video conferencing or a web application improves parents' satisfaction in taking care of a premature infant at home and decreases the need of home visits. In addition, nurses' attitudes regarding the use of these tools were examined. Thirty-four families were randomized to one of three groups before their premature infant was discharged from the hospital to home health care: a control group receiving standard home health care (13 families); a web group receiving home health care supplemented with the use of a web application (12 families); a video group with home health care supplemented with video conferencing using Skype (9 families). Families and nursing staff answered questionnaires about the usefulness of ICT. In addition, semi-structured interviews were conducted with 16 families. All the parents in the web group found the web application easy to use. 83% of the families thought it was good to have access to their child's data through the application. All the families in the video group found Skype easy to use and were satisfied with the video calls. 88% of the families thought that video calls were better than ordinary phone calls. 33% of the families in the web group and 75% of those in the video group thought the need for home visits was decreased by the web application or Skype. 50% of the families in the web group and 100% of those in the video group thought the web application or the video calls had helped them feel more confident in caring for their child. Most of the nurses were motivated to use ICT but some were reluctant and avoided using the web application and video conferencing. The families were satisfied with both the web application and video conferencing. The families readily embraced the use of ICT, whereas motivating some of the nurses to accept and use ICT was a major challenge.

A randomized controlled study about the use of eHealth in the home health care of premature infants

PubMed Central

2013-01-01

Background One area where the use of information and communication technology (ICT), or eHealth, could be developed is the home health care of premature infants. The aim of this randomized controlled study was to investigate whether the use of video conferencing or a web application improves parents’ satisfaction in taking care of a premature infant at home and decreases the need of home visits. In addition, nurses’ attitudes regarding the use of these tools were examined. Method Thirty-four families were randomized to one of three groups before their premature infant was discharged from the hospital to home health care: a control group receiving standard home health care (13 families); a web group receiving home health care supplemented with the use of a web application (12 families); a video group with home health care supplemented with video conferencing using Skype (9 families). Families and nursing staff answered questionnaires about the usefulness of ICT. In addition, semi-structured interviews were conducted with 16 families. Results All the parents in the web group found the web application easy to use. 83% of the families thought it was good to have access to their child’s data through the application. All the families in the video group found Skype easy to use and were satisfied with the video calls. 88% of the families thought that video calls were better than ordinary phone calls. 33% of the families in the web group and 75% of those in the video group thought the need for home visits was decreased by the web application or Skype. 50% of the families in the web group and 100% of those in the video group thought the web application or the video calls had helped them feel more confident in caring for their child. Most of the nurses were motivated to use ICT but some were reluctant and avoided using the web application and video conferencing. Conclusion The families were satisfied with both the web application and video conferencing. The families readily embraced the use of ICT, whereas motivating some of the nurses to accept and use ICT was a major challenge. PMID:23394465

Web3DMol: interactive protein structure visualization based on WebGL.

PubMed

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

2017-07-03

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

TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets.

PubMed

Dang, Louis T; Tondl, Markus; Chiu, Man Ho H; Revote, Jerico; Paten, Benedict; Tano, Vincent; Tokolyi, Alex; Besse, Florence; Quaife-Ryan, Greg; Cumming, Helen; Drvodelic, Mark J; Eichenlaub, Michael P; Hallab, Jeannette C; Stolper, Julian S; Rossello, Fernando J; Bogoyevitch, Marie A; Jans, David A; Nim, Hieu T; Porrello, Enzo R; Hudson, James E; Ramialison, Mirana

2018-04-05

A strong focus of the post-genomic era is mining of the non-coding regulatory genome in order to unravel the function of regulatory elements that coordinate gene expression (Nat 489:57-74, 2012; Nat 507:462-70, 2014; Nat 507:455-61, 2014; Nat 518:317-30, 2015). Whole-genome approaches based on next-generation sequencing (NGS) have provided insight into the genomic location of regulatory elements throughout different cell types, organs and organisms. These technologies are now widespread and commonly used in laboratories from various fields of research. This highlights the need for fast and user-friendly software tools dedicated to extracting cis-regulatory information contained in these regulatory regions; for instance transcription factor binding site (TFBS) composition. Ideally, such tools should not require prior programming knowledge to ensure they are accessible for all users. We present TrawlerWeb, a web-based version of the Trawler_standalone tool (Nat Methods 4:563-5, 2007; Nat Protoc 5:323-34, 2010), to allow for the identification of enriched motifs in DNA sequences obtained from next-generation sequencing experiments in order to predict their TFBS composition. TrawlerWeb is designed for online queries with standard options common to web-based motif discovery tools. In addition, TrawlerWeb provides three unique new features: 1) TrawlerWeb allows the input of BED files directly generated from NGS experiments, 2) it automatically generates an input-matched biologically relevant background, and 3) it displays resulting conservation scores for each instance of the motif found in the input sequences, which assists the researcher in prioritising the motifs to validate experimentally. Finally, to date, this web-based version of Trawler_standalone remains the fastest online de novo motif discovery tool compared to other popular web-based software, while generating predictions with high accuracy. TrawlerWeb provides users with a fast, simple and easy-to-use web interface for de novo motif discovery. This will assist in rapidly analysing NGS datasets that are now being routinely generated. TrawlerWeb is freely available and accessible at: http://trawler.erc.monash.edu.au .

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).

Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking.

PubMed

McMurdie, Paul J; Holmes, Susan

2015-01-15

We have created a Shiny-based Web application, called Shiny-phyloseq, for dynamic interaction with microbiome data that runs on any modern Web browser and requires no programming, increasing the accessibility and decreasing the entrance requirement to using phyloseq and related R tools. Along with a data- and context-aware dynamic interface for exploring the effects of parameter and method choices, Shiny-phyloseq also records the complete user input and subsequent graphical results of a user's session, allowing the user to archive, share and reproduce the sequence of steps that created their result-without writing any new code themselves. Shiny-phyloseq is implemented entirely in the R language. It can be hosted/launched by any system with R installed, including Windows, Mac OS and most Linux distributions. Information technology administrators can also host Shiny--phyloseq from a remote server, in which case users need only have a Web browser installed. Shiny-phyloseq is provided free of charge under a GPL-3 open-source license through GitHub at http://joey711.github.io/shiny-phyloseq/. © The Author 2014. Published by Oxford University Press.

Biological data integration: wrapping data and tools.

PubMed

Lacroix, Zoé

2002-06-01

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

A life scientist's gateway to distributed data management and computing: the PathPort/ToolBus framework.

PubMed

Eckart, J Dana; Sobral, Bruno W S

2003-01-01

The emergent needs of the bioinformatics community challenge current information systems. The pace of biological data generation far outstrips Moore's Law. Therefore, a gap continues to widen between the capabilities to produce biological (molecular and cell) data sets and the capability to manage and analyze these data sets. As a result, Federal investments in large data set generation produces diminishing returns in terms of the community's capabilities of understanding biology and leveraging that understanding to make scientific and technological advances that improve society. We are building an open framework to address various data management issues including data and tool interoperability, nomenclature and data communication standardization, and database integration. PathPort, short for Pathogen Portal, employs a generic, web-services based framework to deal with some of the problems identified by the bioinformatics community. The motivating research goal of a scalable system to provide data management and analysis for key pathosystems, especially relating to molecular data, has resulted in a generic framework using two major components. On the server-side, we employ web-services. On the client-side, a Java application called ToolBus acts as a client-side "bus" for contacting data and tools and viewing results through a single, consistent user interface.

ICO amplicon NGS data analysis: a Web tool for variant detection in common high-risk hereditary cancer genes analyzed by amplicon GS Junior next-generation sequencing.

PubMed

Lopez-Doriga, Adriana; Feliubadaló, Lídia; Menéndez, Mireia; Lopez-Doriga, Sergio; Morón-Duran, Francisco D; del Valle, Jesús; Tornero, Eva; Montes, Eva; Cuesta, Raquel; Campos, Olga; Gómez, Carolina; Pineda, Marta; González, Sara; Moreno, Victor; Capellá, Gabriel; Lázaro, Conxi

2014-03-01

Next-generation sequencing (NGS) has revolutionized genomic research and is set to have a major impact on genetic diagnostics thanks to the advent of benchtop sequencers and flexible kits for targeted libraries. Among the main hurdles in NGS are the difficulty of performing bioinformatic analysis of the huge volume of data generated and the high number of false positive calls that could be obtained, depending on the NGS technology and the analysis pipeline. Here, we present the development of a free and user-friendly Web data analysis tool that detects and filters sequence variants, provides coverage information, and allows the user to customize some basic parameters. The tool has been developed to provide accurate genetic analysis of targeted sequencing of common high-risk hereditary cancer genes using amplicon libraries run in a GS Junior System. The Web resource is linked to our own mutation database, to assist in the clinical classification of identified variants. We believe that this tool will greatly facilitate the use of the NGS approach in routine laboratories.

Is there a "net generation" in veterinary medicine? A comparative study on the use of the Internet and Web 2.0 by students and the veterinary profession.

PubMed

Tenhaven, Christoph; Tipold, Andrea; Fischer, Martin R; Ehlers, Jan P

2013-01-01

Informal and formal lifelong learning is essential at university and in the workplace. Apart from classical learning techniques, Web 2.0 tools can be used. It is controversial whether there is a so-called net generation amongst people under 30. To test the hypothesis that a net generation among students and young veterinarians exists. An online survey of students and veterinarians was conducted in the German-speaking countries which was advertised via online media and traditional print media. 1780 people took part in the survey. Students and veterinarians have different usage patterns regarding social networks (91.9% vs. 69%) and IM (55.9% vs. 24.5%). All tools were predominantly used passively and in private, to a lesser extent also professionally and for studying. The use of Web 2.0 tools is useful, however, teaching information and media skills, preparing codes of conduct for the internet and verification of user generated content is essential.

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.

Gene calling and bacterial genome annotation with BG7.

PubMed

Tobes, Raquel; Pareja-Tobes, Pablo; Manrique, Marina; Pareja-Tobes, Eduardo; Kovach, Evdokim; Alekhin, Alexey; Pareja, Eduardo

2015-01-01

New massive sequencing technologies are providing many bacterial genome sequences from diverse taxa but a refined annotation of these genomes is crucial for obtaining scientific findings and new knowledge. Thus, bacterial genome annotation has emerged as a key point to investigate in bacteria. Any efficient tool designed specifically to annotate bacterial genomes sequenced with massively parallel technologies has to consider the specific features of bacterial genomes (absence of introns and scarcity of nonprotein-coding sequence) and of next-generation sequencing (NGS) technologies (presence of errors and not perfectly assembled genomes). These features make it convenient to focus on coding regions and, hence, on protein sequences that are the elements directly related with biological functions. In this chapter we describe how to annotate bacterial genomes with BG7, an open-source tool based on a protein-centered gene calling/annotation paradigm. BG7 is specifically designed for the annotation of bacterial genomes sequenced with NGS. This tool is sequence error tolerant maintaining their capabilities for the annotation of highly fragmented genomes or for annotating mixed sequences coming from several genomes (as those obtained through metagenomics samples). BG7 has been designed with scalability as a requirement, with a computing infrastructure completely based on cloud computing (Amazon Web Services).

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

Science 2.0: Communicating Science Creatively

ERIC Educational Resources Information Center

Smith, Ben; Mader, Jared

2017-01-01

This column shares web tools that support learning. The authors have been covering the International Society for Technology in Education (ISTE) standards in every issue since September 2016. This article examines the final standard, called Creative Communicator, which requires students to communicate effectively and creatively express themselves…

Paradigms, Citations, and Maps of Science: A Personal History.

ERIC Educational Resources Information Center

Small, Henry

2003-01-01

Discusses mapping science and Kuhn's theories of paradigms and scientific development. Highlights include cocitation clustering; bibliometric definition of a paradigm; specialty dynamics; pathways through science; a new Web tool called Essential Science Indicators (ESI) for studying the structure of science; and microrevolutions. (Author/LRW)

Wet Lab Accelerator: A Web-Based Application Democratizing Laboratory Automation for Synthetic Biology.

PubMed

Bates, Maxwell; Berliner, Aaron J; Lachoff, Joe; Jaschke, Paul R; Groban, Eli S

2017-01-20

Wet Lab Accelerator (WLA) is a cloud-based tool that allows a scientist to conduct biology via robotic control without the need for any programming knowledge. A drag and drop interface provides a convenient and user-friendly method of generating biological protocols. Graphically developed protocols are turned into programmatic instruction lists required to conduct experiments at the cloud laboratory Transcriptic. Prior to the development of WLA, biologists were required to write in a programming language called "Autoprotocol" in order to work with Transcriptic. WLA relies on a new abstraction layer we call "Omniprotocol" to convert the graphical experimental description into lower level Autoprotocol language, which then directs robots at Transcriptic. While WLA has only been tested at Transcriptic, the conversion of graphically laid out experimental steps into Autoprotocol is generic, allowing extension of WLA into other cloud laboratories in the future. WLA hopes to democratize biology by bringing automation to general biologists.

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…

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…

Aligning Web-Based Tools to the Research Process Cycle: A Resource for Collaborative Research Projects

ERIC Educational Resources Information Center

Price, Geoffrey P.; Wright, Vivian H.

2012-01-01

Using John Creswell's Research Process Cycle as a framework, this article describes various web-based collaborative technologies useful for enhancing the organization and efficiency of educational research. Visualization tools (Cacoo) assist researchers in identifying a research problem. Resource storage tools (Delicious, Mendeley, EasyBib)…

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…

Component Architectures and Web-Based Learning Environments

ERIC Educational Resources Information Center

Ferdig, Richard E.; Mishra, Punya; Zhao, Yong

2004-01-01

The Web has caught the attention of many educators as an efficient communication medium and content delivery system. But we feel there is another aspect of the Web that has not been given the attention it deserves. We call this aspect of the Web its "component architecture." Briefly it means that on the Web one can develop very complex…

VHBuild.com: A Web-Based System for Managing Knowledge in Projects.

ERIC Educational Resources Information Center

Li, Heng; Tang, Sandy; Man, K. F.; Love, Peter E. D.

2002-01-01

Describes an intelligent Web-based construction project management system called VHBuild.com which integrates project management, knowledge management, and artificial intelligence technologies. Highlights include an information flow model; time-cost optimization based on genetic algorithms; rule-based drawing interpretation; and a case-based…

QuadBase2: web server for multiplexed guanine quadruplex mining and visualization

PubMed Central

Dhapola, Parashar; Chowdhury, Shantanu

2016-01-01

DNA guanine quadruplexes or G4s are non-canonical DNA secondary structures which affect genomic processes like replication, transcription and recombination. G4s are computationally identified by specific nucleotide motifs which are also called putative G4 (PG4) motifs. Despite the general relevance of these structures, there is currently no tool available that can allow batch queries and genome-wide analysis of these motifs in a user-friendly interface. QuadBase2 (quadbase.igib.res.in) presents a completely reinvented web server version of previously published QuadBase database. QuadBase2 enables users to mine PG4 motifs in up to 178 eukaryotes through the EuQuad module. This module interfaces with Ensembl Compara database, to allow users mine PG4 motifs in the orthologues of genes of interest across eukaryotes. PG4 motifs can be mined across genes and their promoter sequences in 1719 prokaryotes through ProQuad module. This module includes a feature that allows genome-wide mining of PG4 motifs and their visualization as circular histograms. TetraplexFinder, the module for mining PG4 motifs in user-provided sequences is now capable of handling up to 20 MB of data. QuadBase2 is a comprehensive PG4 motif mining tool that further expands the configurations and algorithms for mining PG4 motifs in a user-friendly way. PMID:27185890

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)

WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets

PubMed Central

2014-01-01

Background Sharing sets of chemical data (e.g., chemical properties, docking scores, etc.) among collaborators with diverse skill sets is a common task in computer-aided drug design and medicinal chemistry. The ability to associate this data with images of the relevant molecular structures greatly facilitates scientific communication. There is a need for a simple, free, open-source program that can automatically export aggregated reports of entire chemical data sets to files viewable on any computer, regardless of the operating system and without requiring the installation of additional software. Results We here present a program called WebChem Viewer that automatically generates these types of highly portable reports. Furthermore, in designing WebChem Viewer we have also created a useful online web application for remotely generating molecular structures from SMILES strings. We encourage the direct use of this online application as well as its incorporation into other software packages. Conclusions With these features, WebChem Viewer enables interdisciplinary collaborations that require the sharing and visualization of small molecule structures and associated sets of heterogeneous chemical data. The program is released under the FreeBSD license and can be downloaded from http://nbcr.ucsd.edu/WebChemViewer. The associated web application (called “Smiley2png 1.0”) can be accessed through freely available web services provided by the National Biomedical Computation Resource at http://nbcr.ucsd.edu. PMID:24886360

The Joy of Playing with Oceanographic Data

NASA Astrophysics Data System (ADS)

Smith, A. T.; Xing, Z.; Armstrong, E. M.; Thompson, C. K.; Huang, T.

2013-12-01

The web is no longer just an after thought. It is no longer just a presentation layer filled with HTML, CSS, JavaScript, Frameworks, 3D, and more. It has become the medium of our communication. It is the database of all databases. It is the computing platform of all platforms. It has transformed the way we do science. Web service is the de facto method for communication between machines over the web. Representational State Transfer (REST) has standardized the way we architect services and their interfaces. In the Earth Science domain, we are familiar with tools and services such as Open-Source Project for Network Data Access Protocol (OPeNDAP), Thematic Realtime Environmental Distributed Data Services (THREDDS), and Live Access Server (LAS). We are also familiar with various data formats such as NetCDF3/4, HDF4/5, GRIB, TIFF, etc. One of the challenges for the Earth Science community is accessing information within these data. There are community-accepted readers that our users can download and install. However, the Application Programming Interface (API) between these readers is not standardized, which leads to non-portable applications. Webification (w10n) is an emerging technology, developed at the Jet Propulsion Laboratory, which exploits the hierarchical nature of a science data artifact to assign a URL to each element within the artifact. (e.g. a granule file). By embracing standards such as JSON, XML, and HTML5 and predictable URL, w10n provides a simple interface that enables tool-builders and researchers to develop portable tools/applications to interact with artifacts of various formats. The NASA Physical Oceanographic Distributed Active Archive Center (PO.DAAC) is the designated data center for observational products relevant to the physical state of the ocean. Over the past year PO.DAAC has been evaluating w10n technology by webifying its archive holdings to provide simplified access to oceanographic science artifacts and as a service to enable future tools and services development. In this talk, we will focus on a w10n-based system called Distributed Oceanographic Webification Service (DOWS) being developed at PO.DAAC to provide a newer and simpler method for working with observational data artifacts. As a continued effort at PO.DAAC to provide better tools and services to visualize our data, the talk will discuss the latest in web-based data visualization tools/frameworks (such as d3.js, Three.js, Leaflet.js, and more) and techniques for working with webified oceanographic science data in both a 2D and 3D web approach.

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.

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.

User Interface Requirements for Web-Based Integrated Care Pathways: Evidence from the Evaluation of an Online Care Pathway Investigation Tool.

PubMed

Balatsoukas, Panos; Williams, Richard; Davies, Colin; Ainsworth, John; Buchan, Iain

2015-11-01

Integrated care pathways (ICPs) define a chronological sequence of steps, most commonly diagnostic or treatment, to be followed in providing care for patients. Care pathways help to ensure quality standards are met and to reduce variation in practice. Although research on the computerisation of ICP progresses, there is still little knowledge on what are the requirements for designing user-friendly and usable electronic care pathways, or how users (normally health care professionals) interact with interfaces that support design, analysis and visualisation of ICPs. The purpose of the study reported in this paper was to address this gap by evaluating the usability of a novel web-based tool called COCPIT (Collaborative Online Care Pathway Investigation Tool). COCPIT supports the design, analysis and visualisation of ICPs at the population level. In order to address the aim of this study, an evaluation methodology was designed based on heuristic evaluations and a mixed method usability test. The results showed that modular visualisation and direct manipulation of information related to the design and analysis of ICPs is useful for engaging and stimulating users. However, designers should pay attention to issues related to the visibility of the system status and the match between the system and the real world, especially in relation to the display of statistical information about care pathways and the editing of clinical information within a care pathway. The paper concludes with recommendations for interface design.

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…

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;…

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…

Extracting scientific articles from a large digital archive: BioStor and the Biodiversity Heritage Library

PubMed Central

2011-01-01

Background The Biodiversity Heritage Library (BHL) is a large digital archive of legacy biological literature, comprising over 31 million pages scanned from books, monographs, and journals. During the digitisation process basic metadata about the scanned items is recorded, but not article-level metadata. Given that the article is the standard unit of citation, this makes it difficult to locate cited literature in BHL. Adding the ability to easily find articles in BHL would greatly enhance the value of the archive. Description A service was developed to locate articles in BHL based on matching article metadata to BHL metadata using approximate string matching, regular expressions, and string alignment. This article locating service is exposed as a standard OpenURL resolver on the BioStor web site http://biostor.org/openurl/. This resolver can be used on the web, or called by bibliographic tools that support OpenURL. Conclusions BioStor provides tools for extracting, annotating, and visualising articles from the Biodiversity Heritage Library. BioStor is available from http://biostor.org/. PMID:21605356

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…

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.

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.

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 VO-Dance web application at the IA2 data center

NASA Astrophysics Data System (ADS)

Molinaro, Marco; Knapic, Cristina; Smareglia, Riccardo

2012-09-01

Italian center for Astronomical Archives (IA2, http://ia2.oats.inaf.it) is a national infrastructure project of the Italian National Institute for Astrophysics (Istituto Nazionale di AstroFisica, INAF) that provides services for the astronomical community. Besides data hosting for the Large Binocular Telescope (LBT) Corporation, the Galileo National Telescope (Telescopio Nazionale Galileo, TNG) Consortium and other telescopes and instruments, IA2 offers proprietary and public data access through user portals (both developed and mirrored) and deploys resources complying the Virtual Observatory (VO) standards. Archiving systems and web interfaces are developed to be extremely flexible about adding new instruments from other telescopes. VO resources publishing, along with data access portals, implements the International Virtual Observatory Alliance (IVOA) protocols providing astronomers with new ways of analyzing data. Given the large variety of data flavours and IVOA standards, the need for tools to easily accomplish data ingestion and data publishing arises. This paper describes the VO-Dance tool, that IA2 started developing to address VO resources publishing in a dynamical way from already existent database tables or views. The tool consists in a Java web application, potentially DBMS and platform independent, that stores internally the services' metadata and information, exposes restful endpoints to accept VO queries for these services and dynamically translates calls to these endpoints to SQL queries coherent with the published table or view. In response to the call VO-Dance translates back the database answer in a VO compliant way.

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,…

Designing Crop Simulation Web Service with Service Oriented Architecture Principle

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Cold Calling and Web Postings: Do They Improve Students' Preparation and Learning in Statistics?

ERIC Educational Resources Information Center

Levy, Dan

2014-01-01

Getting students to prepare well for class is a common challenge faced by instructors all over the world. This study investigates the effects that two frequently used techniques to increase student preparation--web postings and cold calling--have on student outcomes. The study is based on two experiments and a qualitative study conducted in a…

TAPIR, a web server for the prediction of plant microRNA targets, including target mimics.

PubMed

Bonnet, Eric; He, Ying; Billiau, Kenny; Van de Peer, Yves

2010-06-15

We present a new web server called TAPIR, designed for the prediction of plant microRNA targets. The server offers the possibility to search for plant miRNA targets using a fast and a precise algorithm. The precise option is much slower but guarantees to find less perfectly paired miRNA-target duplexes. Furthermore, the precise option allows the prediction of target mimics, which are characterized by a miRNA-target duplex having a large loop, making them undetectable by traditional tools. The TAPIR web server can be accessed at: http://bioinformatics.psb.ugent.be/webtools/tapir. Supplementary data are available at Bioinformatics online.

Using Collaborative Simulation Modeling to Develop a Web-Based Tool to Support Policy-Level Decision Making About Breast Cancer Screening Initiation Age

PubMed Central

Burnside, Elizabeth S.; Lee, Sandra J.; Bennette, Carrie; Near, Aimee M.; Alagoz, Oguzhan; Huang, Hui; van den Broek, Jeroen J.; Kim, Joo Yeon; Ergun, Mehmet A.; van Ravesteyn, Nicolien T.; Stout, Natasha K.; de Koning, Harry J.; Mandelblatt, Jeanne S.

2017-01-01

Background There are no publicly available tools designed specifically to assist policy makers to make informed decisions about the optimal ages of breast cancer screening initiation for different populations of US women. Objective To use three established simulation models to develop a web-based tool called Mammo OUTPuT. Methods The simulation models use the 1970 US birth cohort and common parameters for incidence, digital screening performance, and treatment effects. Outcomes include breast cancers diagnosed, breast cancer deaths averted, breast cancer mortality reduction, false-positive mammograms, benign biopsies, and overdiagnosis. The Mammo OUTPuT tool displays these outcomes for combinations of age at screening initiation (every year from 40 to 49), annual versus biennial interval, lifetime versus 10-year horizon, and breast density, compared to waiting to start biennial screening at age 50 and continuing to 74. The tool was piloted by decision makers (n = 16) who completed surveys. Results The tool demonstrates that benefits in the 40s increase linearly with earlier initiation age, without a specific threshold age. Likewise, the harms of screening increase monotonically with earlier ages of initiation in the 40s. The tool also shows users how the balance of benefits and harms varies with breast density. Surveys revealed that 100% of users (16/16) liked the appearance of the site; 94% (15/16) found the tool helpful; and 94% (15/16) would recommend the tool to a colleague. Conclusions This tool synthesizes a representative subset of the most current CISNET (Cancer Intervention and Surveillance Modeling Network) simulation model outcomes to provide policy makers with quantitative data on the benefits and harms of screening women in the 40s. Ultimate decisions will depend on program goals, the population served, and informed judgments about the weight of benefits and harms. PMID:29376135

Oceans 2.0: a Data Management Infrastructure as a Platform

NASA Astrophysics Data System (ADS)

Pirenne, B.; Guillemot, E.

2012-04-01

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

Translation of SNOMED CT - strategies and description of a pilot project.

PubMed

Klein, Gunnar O; Chen, Rong

2009-01-01

The translation and localization of SNOMED CT (Systematized Nomenclature of Medicine - Clinical Terms) have been initiated in a few countries. In Sweden, we conducted the first evaluation of this terminology in a project called REFTERM in which we also developed a software tool which could handle a large scale translation with a number of translators and reviewers in a web-based environment. The system makes use of existing authorized English-Swedish translations of medical terminologies such as ICD-10. The paper discusses possible strategies for a national project to translate and adapt this terminology.

Design and evaluation of web-based image transmission and display with different protocols

NASA Astrophysics Data System (ADS)

Tan, Bin; Chen, Kuangyi; Zheng, Xichuan; Zhang, Jianguo

2011-03-01

There are many Web-based image accessing technologies used in medical imaging area, such as component-based (ActiveX Control) thick client Web display, Zerofootprint thin client Web viewer (or called server side processing Web viewer), Flash Rich Internet Application(RIA) ,or HTML5 based Web display. Different Web display methods have different peformance in different network environment. In this presenation, we give an evaluation on two developed Web based image display systems. The first one is used for thin client Web display. It works between a PACS Web server with WADO interface and thin client. The PACS Web server provides JPEG format images to HTML pages. The second one is for thick client Web display. It works between a PACS Web server with WADO interface and thick client running in browsers containing ActiveX control, Flash RIA program or HTML5 scripts. The PACS Web server provides native DICOM format images or JPIP stream for theses clients.

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…

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…

Telecommunications Relay Service

MedlinePlus

... used with an existing voice telephone and a computer or other Web-enabled device without requiring any ... based TRS call. The user may use a computer or other web-enabled device to communicate with ...

Architecture for biomedical multimedia information delivery on the World Wide Web

NASA Astrophysics Data System (ADS)

Long, L. Rodney; Goh, Gin-Hua; Neve, Leif; Thoma, George R.

1997-10-01

Research engineers at the National Library of Medicine are building a prototype system for the delivery of multimedia biomedical information on the World Wide Web. This paper discuses the architecture and design considerations for the system, which will be used initially to make images and text from the third National Health and Nutrition Examination Survey (NHANES) publicly available. We categorized our analysis as follows: (1) fundamental software tools: we analyzed trade-offs among use of conventional HTML/CGI, X Window Broadway, and Java; (2) image delivery: we examined the use of unconventional TCP transmission methods; (3) database manager and database design: we discuss the capabilities and planned use of the Informix object-relational database manager and the planned schema for the HNANES database; (4) storage requirements for our Sun server; (5) user interface considerations; (6) the compatibility of the system with other standard research and analysis tools; (7) image display: we discuss considerations for consistent image display for end users. Finally, we discuss the scalability of the system in terms of incorporating larger or more databases of similar data, and the extendibility of the system for supporting content-based retrieval of biomedical images. The system prototype is called the Web-based Medical Information Retrieval System. An early version was built as a Java applet and tested on Unix, PC, and Macintosh platforms. This prototype used the MiniSQL database manager to do text queries on a small database of records of participants in the second NHANES survey. The full records and associated x-ray images were retrievable and displayable on a standard Web browser. A second version has now been built, also a Java applet, using the MySQL database manager.

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.

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,…

Cloud-based MOTIFSIM: Detecting Similarity in Large DNA Motif Data Sets.

PubMed

Tran, Ngoc Tam L; Huang, Chun-Hsi

2017-05-01

We developed the cloud-based MOTIFSIM on Amazon Web Services (AWS) cloud. The tool is an extended version from our web-based tool version 2.0, which was developed based on a novel algorithm for detecting similarity in multiple DNA motif data sets. This cloud-based version further allows researchers to exploit the computing resources available from AWS to detect similarity in multiple large-scale DNA motif data sets resulting from the next-generation sequencing technology. The tool is highly scalable with expandable AWS.

iCOSSY: An Online Tool for Context-Specific Subnetwork Discovery from Gene Expression Data

PubMed Central

Saha, Ashis; Jeon, Minji; Tan, Aik Choon; Kang, Jaewoo

2015-01-01

Pathway analyses help reveal underlying molecular mechanisms of complex biological phenotypes. Biologists tend to perform multiple pathway analyses on the same dataset, as there is no single answer. It is often inefficient for them to implement and/or install all the algorithms by themselves. Online tools can help the community in this regard. Here we present an online gene expression analytical tool called iCOSSY which implements a novel pathway-based COntext-specific Subnetwork discoverY (COSSY) algorithm. iCOSSY also includes a few modifications of COSSY to increase its reliability and interpretability. Users can upload their gene expression datasets, and discover important subnetworks of closely interacting molecules to differentiate between two phenotypes (context). They can also interactively visualize the resulting subnetworks. iCOSSY is a web server that finds subnetworks that are differentially expressed in two phenotypes. Users can visualize the subnetworks to understand the biology of the difference. PMID:26147457

A web-based resource for promoting equity in midwifery education and training: Towards meaningful diversity and inclusion.

PubMed

Effland, Kristin J; Hays, Karen

2018-06-01

Increasing the midwifery workforce requires that aspiring midwives complete education and training, but structural racism and microaggressions impact the lives of underrepresented midwifery students and apprentices, adding stressors and disparities to the usual demanding educational challenges. In order to be resilient, students rely on preceptors, faculty, administrators and institutions to promote equity. Equity-focused learning environments improve student experiences and success rates, and better prepare all students to provide culturally humble and sensitive care to diverse childbearing persons and other essential competencies outlined by the International Confederation of Midwives. The comprehensive web-based resource, www.equitymidwifery.org, is designed to support midwifery educators in promoting equity and social justice in midwifery education and training. The website highlights examples and provides tools including original webinar content and encourages visitors to attend virtual strategy and collaboration calls. It offers a model of continuous professional development that is easily accessible. Copyright © 2018 Elsevier Ltd. All rights reserved.

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.

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.

ROSA: Resource-Oriented Service Management Schemes for Web of Things in a Smart Home

PubMed Central

Chen, Peng-Yu

2017-01-01

A Pervasive-computing-enriched smart home environment, which contains many embedded and tiny intelligent devices and sensors coordinated by service management mechanisms, is capable of anticipating intentions of occupants and providing appropriate services accordingly. Although there are a wealth of research achievements in recent years, the degree of market acceptance is still low. The main reason is that most of the devices and services in such environments depend on particular platform or technology, making it hard to develop an application by composing the devices or services. Meanwhile, the concept of Web of Things (WoT) is becoming popular recently. Based on WoT, the developers can build applications based on popular web tools or technologies. Consequently, the objective of this paper is to propose a set of novel WoT-driven plug-and-play service management schemes for a smart home called Resource-Oriented Service Administration (ROSA). We have implemented an application prototype, and experiments are performed to show the effectiveness of the proposed approach. The results of this research can be a foundation for realizing the vision of “end user programmable smart environments”. PMID:28934159

MAPI: a software framework for distributed biomedical applications

PubMed Central

2013-01-01

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

Myria: Scalable Analytics as a Service

NASA Astrophysics Data System (ADS)

Howe, B.; Halperin, D.; Whitaker, A.

2014-12-01

At the UW eScience Institute, we're working to empower non-experts, especially in the sciences, to write and use data-parallel algorithms. To this end, we are building Myria, a web-based platform for scalable analytics and data-parallel programming. Myria's internal model of computation is the relational algebra extended with iteration, such that every program is inherently data-parallel, just as every query in a database is inherently data-parallel. But unlike databases, iteration is a first class concept, allowing us to express machine learning tasks, graph traversal tasks, and more. Programs can be expressed in a number of languages and can be executed on a number of execution environments, but we emphasize a particular language called MyriaL that supports both imperative and declarative styles and a particular execution engine called MyriaX that uses an in-memory column-oriented representation and asynchronous iteration. We deliver Myria over the web as a service, providing an editor, performance analysis tools, and catalog browsing features in a single environment. We find that this web-based "delivery vector" is critical in reaching non-experts: they are insulated from irrelevant effort technical work associated with installation, configuration, and resource management. The MyriaX backend, one of several execution runtimes we support, is a main-memory, column-oriented, RDBMS-on-the-worker system that supports cyclic data flows as a first-class citizen and has been shown to outperform competitive systems on 100-machine cluster sizes. I will describe the Myria system, give a demo, and present some new results in large-scale oceanographic microbiology.

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

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...

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

Is there a “net generation” in veterinary medicine? A comparative study on the use of the Internet and Web 2.0 by students and the veterinary profession

PubMed Central

Tenhaven, Christoph; Tipold, Andrea; Fischer, Martin R.; Ehlers, Jan P.

2013-01-01

Introduction: Informal and formal lifelong learning is essential at university and in the workplace. Apart from classical learning techniques, Web 2.0 tools can be used. It is controversial whether there is a so-called net generation amongst people under 30. Aims: To test the hypothesis that a net generation among students and young veterinarians exists. Methods: An online survey of students and veterinarians was conducted in the German-speaking countries which was advertised via online media and traditional print media. Results: 1780 people took part in the survey. Students and veterinarians have different usage patterns regarding social networks (91.9% vs. 69%) and IM (55.9% vs. 24.5%). All tools were predominantly used passively and in private, to a lesser extent also professionally and for studying. Outlook: The use of Web 2.0 tools is useful, however, teaching information and media skills, preparing codes of conduct for the internet and verification of user generated content is essential. PMID:23467682

SporeWeb: an interactive journey through the complete sporulation cycle of Bacillus subtilis.

PubMed

Eijlander, Robyn T; de Jong, Anne; Krawczyk, Antonina O; Holsappel, Siger; Kuipers, Oscar P

2014-01-01

Bacterial spores are a continuous problem for both food-based and health-related industries. Decades of scientific research dedicated towards understanding molecular and gene regulatory aspects of sporulation, spore germination and spore properties have resulted in a wealth of data and information. To facilitate obtaining a complete overview as well as new insights concerning this complex and tightly regulated process, we have developed a database-driven knowledge platform called SporeWeb (http://sporeweb.molgenrug.nl) that focuses on gene regulatory networks during sporulation in the Gram-positive bacterium Bacillus subtilis. Dynamic features allow the user to navigate through all stages of sporulation with review-like descriptions, schematic overviews on transcriptional regulation and detailed information on all regulators and the genes under their control. The Web site supports data acquisition on sporulation genes and their expression, regulon network interactions and direct links to other knowledge platforms or relevant literature. The information found on SporeWeb (including figures and tables) can and will be updated as new information becomes available in the literature. In this way, SporeWeb offers a novel, convenient and timely reference, an information source and a data acquisition tool that will aid in the general understanding of the dynamics of the complete sporulation cycle.

Teaching the principles of health management to first year veterinary students.

PubMed

Duffield, Todd; Lissemore, Kerry; Sandals, David

2003-01-01

A course called Health Management 1 was created as part of a new DVM curriculum at the Ontario Veterinary College. This full year course was designed to introduce students to basic concepts of health management, integrating the disciplines of epidemiology, ethology, and public health in the context of selected animal industries. The course was comprised of 60 lecture hours and four two-hour laboratories. A common definition of health management, incorporating five principles, was used throughout the course, in order to reinforce the concepts and to maintain continuity between lecture blocks. Unlike in the years prior to the introduction of the new curriculum, epidemiology was presented as a tool of health management rather than as a separate discipline. To supplement the lecture and laboratory material, a Web-based resource was created and the students were required to review the appropriate section prior to each lecture block. Small quizzes, consisting of 10 questions each within WebCT, were used to stimulate self-directed learning. Overall, the course was well received by the students. The Web resources combined with the WebCT quizzes proved to be an effective method of stimulating students to prepare for lecture.

webPOISONCONTROL: can poison control be automated?

PubMed

Litovitz, Toby; Benson, Blaine E; Smolinske, Susan

2016-08-01

A free webPOISONCONTROL app allows the public to determine the appropriate triage of poison ingestions without calling poison control. If accepted and safe, this alternative expands access to reliable poison control services to those who prefer the Internet over the telephone. This study assesses feasibility, safety, and user-acceptance of automated online triage of asymptomatic, nonsuicidal poison ingestion cases. The user provides substance name, amount, age, and weight in an automated online tool or downloadable app, and is given a specific triage recommendation to stay home, go to the emergency department, or call poison control for further guidance. Safety was determined by assessing outcomes of consecutive home-triaged cases with follow-up and by confirming the correct application of algorithms. Case completion times and user perceptions of speed and ease of use were measures of user-acceptance. Of 9256 cases, 73.3% were triaged to home, 2.1% to an emergency department, and 24.5% directed to call poison control. Children younger than 6 years were involved in 75.2% of cases. Automated follow-up was done in 31.2% of home-triaged cases; 82.3% of these had no effect. No major or fatal outcomes were reported. More than 91% of survey respondents found the tool quick and easy to use. Median case completion time was 4.1 minutes. webPOISONCONTROL augments traditional poison control services by providing automated, accurate online access to case-specific triage and first aid guidance for poison ingestions. It is safe, quick, and easy to use. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Outcomes and Utilization of a Low Intensity Workplace Weight Loss Program

PubMed Central

Carpenter, Kelly M.; Lovejoy, Jennifer C.; Lange, Jane M.; Hapgood, Jenny E.; Zbikowski, Susan M.

2014-01-01

Obesity is related to high health care costs and lost productivity in the workplace. Employers are increasingly sponsoring weight loss and wellness programs to ameliorate these costs. We evaluated weight loss outcomes, treatment utilization, and health behavior change in a low intensity phone- and web-based, employer-sponsored weight loss program. The intervention included three proactive counseling phone calls with a registered dietician and a behavioral health coach as well as a comprehensive website. At six months, one third of those who responded to the follow-up survey had lost a clinically significant amount of weight (≥5% of body weight). Clinically significant weight loss was predicted by the use of both the counseling calls and the website. When examining specific features of the web site, the weight tracking tool was the most predictive of weight loss. Health behavior changes such as eating more fruits and vegetables, increasing physical activity, and reducing stress were all predictive of clinically significant weight loss. Although limited by the low follow-up rate, this evaluation suggests that even low intensity weight loss programs can lead to clinical weight loss for a significant number of participants. PMID:24688791

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…

STOP-IT: Windows executable software for the stop-signal paradigm.

PubMed

Verbruggen, Frederick; Logan, Gordon D; Stevens, Michaël A

2008-05-01

The stop-signal paradigm is a useful tool for the investigation of response inhibition. In this paradigm, subjects are instructed to respond as fast as possible to a stimulus unless a stop signal is presented after a variable delay. However, programming the stop-signal task is typically considered to be difficult. To overcome this issue, we present software called STOP-IT, for running the stop-signal task, as well as an additional analyzing program called ANALYZE-IT. The main advantage of both programs is that they are a precompiled executable, and for basic use there is no need for additional programming. STOP-IT and ANALYZE-IT are completely based on free software, are distributed under the GNU General Public License, and are available at the personal Web sites of the first two authors or at expsy.ugent.be/tscope/stop.html.

A Brief Introduction to Web-Based Note Capture

ERIC Educational Resources Information Center

Ovadia, Steven

2012-01-01

While physical notebooks and locally saved electronic files are certainly helpful, there are a number of web-based solutions that might be useful to someone conducting research online, or looking to hold their notes in a web-based environment. The main advantage of a web-based note capture tool is that one is able to access it from just about…

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…

a Web-Based Interactive Tool for Multi-Resolution 3d Models of a Maya Archaeological Site

NASA Astrophysics Data System (ADS)

Agugiaro, G.; Remondino, F.; Girardi, G.; von Schwerin, J.; Richards-Rissetto, H.; De Amicis, R.

2011-09-01

Continuous technological advances in surveying, computing and digital-content delivery are strongly contributing to a change in the way Cultural Heritage is "perceived": new tools and methodologies for documentation, reconstruction and research are being created to assist not only scholars, but also to reach more potential users (e.g. students and tourists) willing to access more detailed information about art history and archaeology. 3D computer-simulated models, sometimes set in virtual landscapes, offer for example the chance to explore possible hypothetical reconstructions, while on-line GIS resources can help interactive analyses of relationships and change over space and time. While for some research purposes a traditional 2D approach may suffice, this is not the case for more complex analyses concerning spatial and temporal features of architecture, like for example the relationship of architecture and landscape, visibility studies etc. The project aims therefore at creating a tool, called "QueryArch3D" tool, which enables the web-based visualisation and queries of an interactive, multi-resolution 3D model in the framework of Cultural Heritage. More specifically, a complete Maya archaeological site, located in Copan (Honduras), has been chosen as case study to test and demonstrate the platform's capabilities. Much of the site has been surveyed and modelled at different levels of detail (LoD) and the geometric model has been semantically segmented and integrated with attribute data gathered from several external data sources. The paper describes the characteristics of the research work, along with its implementation issues and the initial results of the developed prototype.

Vocabulary Learning on Learner-Created Content by Using Web 2.0 Tools

ERIC Educational Resources Information Center

Eren, Omer

2015-01-01

The present research examined the use of Web 2.0 tools to improve students' vocabulary knowledge at the School of Foreign Languages, Gaziantep University. Current studies in literature mostly deal with descriptions of students' attitudes towards the reasons for the use of web-based platforms. However, integrating usual classroom environment with…

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…

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…

If You Build It, They Will Scan: Oxford University's Exploration of Community Collections

ERIC Educational Resources Information Center

Lee, Stuart D.; Lindsay, Kate

2009-01-01

Traditional large digitization projects demand massive resources from the central unit (library, museum, or university) that has acquired funding for them. Another model, enabled by easy access to cameras, scanners, and web tools, calls for public contributions to community collections of artifacts. In 2009, the University of Oxford ran a…

Generic Service Integration in Adaptive Learning Experiences Using IMS Learning Design

ERIC Educational Resources Information Center

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

2011-01-01

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

ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data.

PubMed

Gonzalez, Sergio; Clavijo, Bernardo; Rivarola, Máximo; Moreno, Patricio; Fernandez, Paula; Dopazo, Joaquín; Paniego, Norma

2017-02-22

In the last years, applications based on massively parallelized RNA sequencing (RNA-seq) have become valuable approaches for studying non-model species, e.g., without a fully sequenced genome. RNA-seq is a useful tool for detecting novel transcripts and genetic variations and for evaluating differential gene expression by digital measurements. The large and complex datasets resulting from functional genomic experiments represent a challenge in data processing, management, and analysis. This problem is especially significant for small research groups working with non-model species. We developed a web-based application, called ATGC transcriptomics, with a flexible and adaptable interface that allows users to work with new generation sequencing (NGS) transcriptomic analysis results using an ontology-driven database. This new application simplifies data exploration, visualization, and integration for a better comprehension of the results. ATGC transcriptomics provides access to non-expert computer users and small research groups to a scalable storage option and simple data integration, including database administration and management. The software is freely available under the terms of GNU public license at http://atgcinta.sourceforge.net .

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…

SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies

PubMed Central

2013-01-01

Background Surrogate variable analysis (SVA) is a powerful method to identify, estimate, and utilize the components of gene expression heterogeneity due to unknown and/or unmeasured technical, genetic, environmental, or demographic factors. These sources of heterogeneity are common in gene expression studies, and failing to incorporate them into the analysis can obscure results. Using SVA increases the biological accuracy and reproducibility of gene expression studies by identifying these sources of heterogeneity and correctly accounting for them in the analysis. Results Here we have developed a web application called SVAw (Surrogate variable analysis Web app) that provides a user friendly interface for SVA analyses of genome-wide expression studies. The software has been developed based on open source bioconductor SVA package. In our software, we have extended the SVA program functionality in three aspects: (i) the SVAw performs a fully automated and user friendly analysis workflow; (ii) It calculates probe/gene Statistics for both pre and post SVA analysis and provides a table of results for the regression of gene expression on the primary variable of interest before and after correcting for surrogate variables; and (iii) it generates a comprehensive report file, including graphical comparison of the outcome for the user. Conclusions SVAw is a web server freely accessible solution for the surrogate variant analysis of high-throughput datasets and facilitates removing all unwanted and unknown sources of variation. It is freely available for use at http://psychiatry.igm.jhmi.edu/sva. The executable packages for both web and standalone application and the instruction for installation can be downloaded from our web site. PMID:23497726

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.

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.

Implementing a low-cost web-based clinical trial management system for community studies: a case study.

PubMed

Geyer, John; Myers, Kathleen; Vander Stoep, Ann; McCarty, Carolyn; Palmer, Nancy; DeSalvo, Amy

2011-10-01

Clinical trials with multiple intervention locations and a single research coordinating center can be logistically difficult to implement. Increasingly, web-based systems are used to provide clinical trial support with many commercial, open source, and proprietary systems in use. New web-based tools are available which can be customized without programming expertise to deliver web-based clinical trial management and data collection functions. To demonstrate the feasibility of utilizing low-cost configurable applications to create a customized web-based data collection and study management system for a five intervention site randomized clinical trial establishing the efficacy of providing evidence-based treatment via teleconferencing to children with attention-deficit hyperactivity disorder. The sites are small communities that would not usually be included in traditional randomized trials. A major goal was to develop database that participants could access from computers in their home communities for direct data entry. Discussed is the selection process leading to the identification and utilization of a cost-effective and user-friendly set of tools capable of customization for data collection and study management tasks. An online assessment collection application, template-based web portal creation application, and web-accessible Access 2007 database were selected and customized to provide the following features: schedule appointments, administer and monitor online secure assessments, issue subject incentives, and securely transmit electronic documents between sites. Each tool was configured by users with limited programming expertise. As of June 2011, the system has successfully been used with 125 participants in 5 communities, who have completed 536 sets of assessment questionnaires, 8 community therapists, and 11 research staff at the research coordinating center. Total automation of processes is not possible with the current set of tools as each is loosely affiliated, creating some inefficiency. This system is best suited to investigations with a single data source e.g., psychosocial questionnaires. New web-based applications can be used by investigators with limited programming experience to implement user-friendly, efficient, and cost-effective tools for multi-site clinical trials with small distant communities. Such systems allow the inclusion in research of populations that are not usually involved in clinical trials.

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.

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.

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

PubMed Central

Metsalu, Tauno; Vilo, Jaak

2015-01-01

The Principal Component Analysis (PCA) is a widely used method of reducing the dimensionality of high-dimensional data, often followed by visualizing two of the components on the scatterplot. Although widely used, the method is lacking an easy-to-use web interface that scientists with little programming skills could use to make plots of their own data. The same applies to creating heatmaps: it is possible to add conditional formatting for Excel cells to show colored heatmaps, but for more advanced features such as clustering and experimental annotations, more sophisticated analysis tools have to be used. We present a web tool called ClustVis that aims to have an intuitive user interface. Users can upload data from a simple delimited text file that can be created in a spreadsheet program. It is possible to modify data processing methods and the final appearance of the PCA and heatmap plots by using drop-down menus, text boxes, sliders etc. Appropriate defaults are given to reduce the time needed by the user to specify input parameters. As an output, users can download PCA plot and heatmap in one of the preferred file formats. This web server is freely available at http://biit.cs.ut.ee/clustvis/. PMID:25969447

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."

Finding, Browsing and Getting Data Easily Using SPDF Web Services

NASA Technical Reports Server (NTRS)

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

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

Speakeasy Studio and Cafe: Information Literacy, Web-based Library Instruction, and Technology.

ERIC Educational Resources Information Center

Jacobs, Mark

2001-01-01

Discussion of academic library instruction and information literacy focuses on a Web-based program developed at Washington State University called Speakeasy Studio and Cafe that is used for bibliographic instruction. Highlights include the research process; asking the right question; and adapting to students' differing learning styles. (LRW)

EVA: An Interactive Web-Based Collaborative Learning Environment

ERIC Educational Resources Information Center

Sheremetov, Leonid; Arenas, Adolfo Guzman

2002-01-01

In this paper, a Web-based learning environment developed within the project called Virtual Learning Spaces (EVA, in Spanish) is described. The environment is composed of knowledge, collaboration, consulting and experimentation spaces as a collection of agents and conventional software components working over the knowledge domains. All user…

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

NASA Astrophysics Data System (ADS)

Kim, Guehee; Suzuki, Yoshio; Teshima, Naoya

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

Web-Based Video-Coaching to Assist an Automated Computer-Tailored Physical Activity Intervention for Inactive Adults: A Randomized Controlled Trial.

PubMed

Alley, Stephanie; Jennings, Cally; Plotnikoff, Ronald C; Vandelanotte, Corneel

2016-08-12

Web-based physical activity interventions that apply computer tailoring have shown to improve engagement and behavioral outcomes but provide limited accountability and social support for participants. It is unknown how video calls with a behavioral expert in a Web-based intervention will be received and whether they improve the effectiveness of computer-tailored advice. The purpose of this study was to determine the feasibility and effectiveness of brief video-based coaching in addition to fully automated computer-tailored advice in a Web-based physical activity intervention for inactive adults. Participants were assigned to one of the three groups: (1) tailoring + video-coaching where participants received an 8-week computer-tailored Web-based physical activity intervention ("My Activity Coach") including 4 10-minute coaching sessions with a behavioral expert using a Web-based video-calling program (eg, Skype; n=52); (2) tailoring-only where participants received the same intervention without the coaching sessions (n=54); and (3) a waitlist control group (n=45). Demographics were measured at baseline, intervention satisfaction at week 9, and physical activity at baseline, week 9, and 6 months by Web-based self-report surveys. Feasibility was analyzed by comparing intervention groups on retention, adherence, engagement, and satisfaction using t tests and chi-square tests. Effectiveness was assessed using linear mixed models to compare physical activity changes between groups. A total of 23 tailoring + video-coaching participants, 30 tailoring-only participants, and 30 control participants completed the postintervention survey (83/151, 55.0% retention). A low percentage of tailoring + video-coaching completers participated in the coaching calls (11/23, 48%). However, the majority of those who participated in the video calls were satisfied with them (5/8, 71%) and had improved intervention adherence (9/11, 82% completed 3 or 4 modules vs 18/42, 43%, P=.01) and engagement (110 minutes spent on the website vs 78 minutes, P=.02) compared with other participants. There were no overall retention, adherence, engagement, and satisfaction differences between tailoring + video-coaching and tailoring-only participants. At 9 weeks, physical activity increased from baseline to postintervention in all groups (tailoring + video-coaching: +150 minutes/week; tailoring only: +123 minutes/week; waitlist control: +34 minutes/week). The increase was significantly higher in the tailoring + video-coaching group compared with the control group (P=.01). No significant difference was found between intervention groups and no significant between-group differences were found for physical activity change at 6 months. Only small improvements were observed when video-coaching was added to computer-tailored advice in a Web-based physical activity intervention. However, combined Web-based video-coaching and computer-tailored advice was effective in comparison with a control group. More research is needed to determine whether Web-based coaching is more effective than stand-alone computer-tailored advice. Australian New Zealand Clinical Trials Registry (ACTRN): 12614000339651; http://www.anzctr.org.au/TrialSearch.aspx?searchTxt=ACTRN12614000339651+&isBasic=True (Archived by WebCite at http://www.webcitation.org/6jTnOv0Ld).

Web-Based Video-Coaching to Assist an Automated Computer-Tailored Physical Activity Intervention for Inactive Adults: A Randomized Controlled Trial

PubMed Central

Jennings, Cally; Plotnikoff, Ronald C; Vandelanotte, Corneel

2016-01-01

Background Web-based physical activity interventions that apply computer tailoring have shown to improve engagement and behavioral outcomes but provide limited accountability and social support for participants. It is unknown how video calls with a behavioral expert in a Web-based intervention will be received and whether they improve the effectiveness of computer-tailored advice. Objective The purpose of this study was to determine the feasibility and effectiveness of brief video-based coaching in addition to fully automated computer-tailored advice in a Web-based physical activity intervention for inactive adults. Methods Participants were assigned to one of the three groups: (1) tailoring + video-coaching where participants received an 8-week computer-tailored Web-based physical activity intervention (“My Activity Coach”) including 4 10-minute coaching sessions with a behavioral expert using a Web-based video-calling program (eg, Skype; n=52); (2) tailoring-only where participants received the same intervention without the coaching sessions (n=54); and (3) a waitlist control group (n=45). Demographics were measured at baseline, intervention satisfaction at week 9, and physical activity at baseline, week 9, and 6 months by Web-based self-report surveys. Feasibility was analyzed by comparing intervention groups on retention, adherence, engagement, and satisfaction using t tests and chi-square tests. Effectiveness was assessed using linear mixed models to compare physical activity changes between groups. Results A total of 23 tailoring + video-coaching participants, 30 tailoring-only participants, and 30 control participants completed the postintervention survey (83/151, 55.0% retention). A low percentage of tailoring + video-coaching completers participated in the coaching calls (11/23, 48%). However, the majority of those who participated in the video calls were satisfied with them (5/8, 71%) and had improved intervention adherence (9/11, 82% completed 3 or 4 modules vs 18/42, 43%, P=.01) and engagement (110 minutes spent on the website vs 78 minutes, P=.02) compared with other participants. There were no overall retention, adherence, engagement, and satisfaction differences between tailoring + video-coaching and tailoring-only participants. At 9 weeks, physical activity increased from baseline to postintervention in all groups (tailoring + video-coaching: +150 minutes/week; tailoring only: +123 minutes/week; waitlist control: +34 minutes/week). The increase was significantly higher in the tailoring + video-coaching group compared with the control group (P=.01). No significant difference was found between intervention groups and no significant between-group differences were found for physical activity change at 6 months. Conclusions Only small improvements were observed when video-coaching was added to computer-tailored advice in a Web-based physical activity intervention. However, combined Web-based video-coaching and computer-tailored advice was effective in comparison with a control group. More research is needed to determine whether Web-based coaching is more effective than stand-alone computer-tailored advice. Trial Registration Australian New Zealand Clinical Trials Registry (ACTRN): 12614000339651; http://www.anzctr.org.au/TrialSearch.aspx?searchTxt=ACTRN12614000339651+&isBasic=True (Archived by WebCite at http://www.webcitation.org/6jTnOv0Ld) PMID:27520283

Big data analytics in immunology: a knowledge-based approach.

PubMed

Zhang, Guang Lan; Sun, Jing; Chitkushev, Lou; Brusic, Vladimir

2014-01-01

With the vast amount of immunological data available, immunology research is entering the big data era. These data vary in granularity, quality, and complexity and are stored in various formats, including publications, technical reports, and databases. The challenge is to make the transition from data to actionable knowledge and wisdom and bridge the knowledge gap and application gap. We report a knowledge-based approach based on a framework called KB-builder that facilitates data mining by enabling fast development and deployment of web-accessible immunological data knowledge warehouses. Immunological knowledge discovery relies heavily on both the availability of accurate, up-to-date, and well-organized data and the proper analytics tools. We propose the use of knowledge-based approaches by developing knowledgebases combining well-annotated data with specialized analytical tools and integrating them into analytical workflow. A set of well-defined workflow types with rich summarization and visualization capacity facilitates the transformation from data to critical information and knowledge. By using KB-builder, we enabled streamlining of normally time-consuming processes of database development. The knowledgebases built using KB-builder will speed up rational vaccine design by providing accurate and well-annotated data coupled with tailored computational analysis tools and workflow.

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…

Web-Based Mathematics Progress Monitoring in Second Grade

ERIC Educational Resources Information Center

Salaschek, Martin; Souvignier, Elmar

2014-01-01

We examined a web-based mathematics progress monitoring tool for second graders. The tool monitors the learning progress of two competences, number sense and computation. A total of 414 students from 19 classrooms in Germany were checked every 3 weeks from fall to spring. Correlational analyses indicate that alternate-form reliability was adequate…

Designing and Evaluating an Interactive Multimedia Web-Based Simulation for Developing Nurses’ Competencies in Acute Nursing Care: Randomized Controlled Trial

PubMed Central

Wong, Lai Fun; Chan, Sally Wai-Chi; Ho, Jasmine Tze Yin; Mordiffi, Siti Zubaidah; Ang, Sophia Bee Leng; Goh, Poh Sun; Ang, Emily Neo Kim

2015-01-01

Background Web-based learning is becoming an increasingly important instructional tool in nursing education. Multimedia advancements offer the potential for creating authentic nursing activities for developing nursing competency in clinical practice. Objective This study aims to describe the design, development, and evaluation of an interactive multimedia Web-based simulation for developing nurses’ competencies in acute nursing care. Methods Authentic nursing activities were developed in a Web-based simulation using a variety of instructional strategies including animation video, multimedia instructional material, virtual patients, and online quizzes. A randomized controlled study was conducted on 67 registered nurses who were recruited from the general ward units of an acute care tertiary hospital. Following a baseline evaluation of all participants’ clinical performance in a simulated clinical setting, the experimental group received 3 hours of Web-based simulation and completed a survey to evaluate their perceptions of the program. All participants were re-tested for their clinical performances using a validated tool. Results The clinical performance posttest scores of the experimental group improved significantly (P<.001) from the pretest scores after the Web-based simulation. In addition, compared to the control group, the experimental group had significantly higher clinical performance posttest scores (P<.001) after controlling the pretest scores. The participants from the experimental group were satisfied with their learning experience and gave positive ratings for the quality of the Web-based simulation. Themes emerging from the comments about the most valuable aspects of the Web-based simulation include relevance to practice, instructional strategies, and fostering problem solving. Conclusions Engaging in authentic nursing activities using interactive multimedia Web-based simulation can enhance nurses’ competencies in acute care. Web-based simulations provide a promising educational tool in institutions where large groups of nurses need to be trained in acute nursing care and accessibility to repetitive training is essential for achieving long-term retention of clinical competency. PMID:25583029

Designing and evaluating an interactive multimedia Web-based simulation for developing nurses' competencies in acute nursing care: randomized controlled trial.

PubMed

Liaw, Sok Ying; Wong, Lai Fun; Chan, Sally Wai-Chi; Ho, Jasmine Tze Yin; Mordiffi, Siti Zubaidah; Ang, Sophia Bee Leng; Goh, Poh Sun; Ang, Emily Neo Kim

2015-01-12

Web-based learning is becoming an increasingly important instructional tool in nursing education. Multimedia advancements offer the potential for creating authentic nursing activities for developing nursing competency in clinical practice. This study aims to describe the design, development, and evaluation of an interactive multimedia Web-based simulation for developing nurses' competencies in acute nursing care. Authentic nursing activities were developed in a Web-based simulation using a variety of instructional strategies including animation video, multimedia instructional material, virtual patients, and online quizzes. A randomized controlled study was conducted on 67 registered nurses who were recruited from the general ward units of an acute care tertiary hospital. Following a baseline evaluation of all participants' clinical performance in a simulated clinical setting, the experimental group received 3 hours of Web-based simulation and completed a survey to evaluate their perceptions of the program. All participants were re-tested for their clinical performances using a validated tool. The clinical performance posttest scores of the experimental group improved significantly (P<.001) from the pretest scores after the Web-based simulation. In addition, compared to the control group, the experimental group had significantly higher clinical performance posttest scores (P<.001) after controlling the pretest scores. The participants from the experimental group were satisfied with their learning experience and gave positive ratings for the quality of the Web-based simulation. Themes emerging from the comments about the most valuable aspects of the Web-based simulation include relevance to practice, instructional strategies, and fostering problem solving. Engaging in authentic nursing activities using interactive multimedia Web-based simulation can enhance nurses' competencies in acute care. Web-based simulations provide a promising educational tool in institutions where large groups of nurses need to be trained in acute nursing care and accessibility to repetitive training is essential for achieving long-term retention of clinical competency.

Microbe-ID: an open source toolbox for microbial genotyping and species identification.

PubMed

Tabima, Javier F; Everhart, Sydney E; Larsen, Meredith M; Weisberg, Alexandra J; Kamvar, Zhian N; Tancos, Matthew A; Smart, Christine D; Chang, Jeff H; Grünwald, Niklaus J

2016-01-01

Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org) and provided a working implementation for the genus Phytophthora (phytophthora-id.org). In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID.

The Effectiveness of Web-Based Learning Environment: A Case Study of Public Universities in Kenya

ERIC Educational Resources Information Center

Kirui, Paul A.; Mutai, Sheila J.

2010-01-01

Web mining is emerging in many aspects of e-learning, aiming at improving online learning and teaching processes and making them more transparent and effective. Researchers using Web mining tools and techniques are challenged to learn more about the online students' reshaping online courses and educational websites, and create tools for…

The Knowledge of Web 2.0 by Library and Information Science Academics

ERIC Educational Resources Information Center

Al-Daihani, Sultan

2009-01-01

This research paper reports the results of a Web-based survey designed to explore the attitude of Library and Information Science (LIS) academics to Web 2.0. It investigates their familiarity with Web 2.0 concepts, tools and services and applications as these relate to LIS education, and the barriers to their use. A Web-based questionnaire was…

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

PubMed Central

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

2013-01-01

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

WebCHECK: The Website Evaluation Instrument

ERIC Educational Resources Information Center

Small, Ruth V.; Arnone, Marilyn P.

2014-01-01

Just as with print resources, as the number of Web-based resources continues to soar, the need to evaluate them has become a critical information skill for both children and adults. This is particularly true for schools where librarians often are called on to recommend Web resources to classroom teachers, parents, and students, and to support…

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

PubMed

van Griensven, A; Vanrolleghem, P A

2006-01-01

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

Designing a Web-Based Science Learning Environment for Model-Based Collaborative Inquiry

ERIC Educational Resources Information Center

Sun, Daner; Looi, Chee-Kit

2013-01-01

The paper traces a research process in the design and development of a science learning environment called WiMVT (web-based inquirer with modeling and visualization technology). The WiMVT system is designed to help secondary school students build a sophisticated understanding of scientific conceptions, and the science inquiry process, as well as…

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.

Engineering Laboratory Instruction in Virtual Environment--"eLIVE"

ERIC Educational Resources Information Center

Chaturvedi, Sushil; Prabhakaran, Ramamurthy; Yoon, Jaewan; Abdel-Salam, Tarek

2011-01-01

A novel application of web-based virtual laboratories to prepare students for physical experiments is explored in some detail. The pedagogy of supplementing physical laboratory with web-based virtual laboratories is implemented by developing a web-based tool, designated in this work as "eLIVE", an acronym for Engineering Laboratory…

Web-Based Surveys Facilitate Undergraduate Research and Knowledge

ERIC Educational Resources Information Center

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

2008-01-01

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

Emerging Instructional Technologies: Exploring the Extent of Faculty Use of Web 2.0 Tools at a Midwestern Community College

ERIC Educational Resources Information Center

Daher, Tareq; Lazarevic, Bojan

2014-01-01

The purpose of this research is to provide insight into the several aspects of instructional use of emerging web-based technologies. The study first explores the extent of Web 2.0 technology integration into face-to-face classroom activities. In this phase, the main focus of research interests was on the types and dynamics of Web 2.0 tools used by…

Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data

PubMed Central

Fernandez, Nicolas F.; Gundersen, Gregory W.; Rahman, Adeeb; Grimes, Mark L.; Rikova, Klarisa; Hornbeck, Peter; Ma’ayan, Avi

2017-01-01

Most tools developed to visualize hierarchically clustered heatmaps generate static images. Clustergrammer is a web-based visualization tool with interactive features such as: zooming, panning, filtering, reordering, sharing, performing enrichment analysis, and providing dynamic gene annotations. Clustergrammer can be used to generate shareable interactive visualizations by uploading a data table to a web-site, or by embedding Clustergrammer in Jupyter Notebooks. The Clustergrammer core libraries can also be used as a toolkit by developers to generate visualizations within their own applications. Clustergrammer is demonstrated using gene expression data from the cancer cell line encyclopedia (CCLE), original post-translational modification data collected from lung cancer cells lines by a mass spectrometry approach, and original cytometry by time of flight (CyTOF) single-cell proteomics data from blood. Clustergrammer enables producing interactive web based visualizations for the analysis of diverse biological data. PMID:28994825

ODMedit: uniform semantic annotation for data integration in medicine based on a public metadata repository.

PubMed

Dugas, Martin; Meidt, Alexandra; Neuhaus, Philipp; Storck, Michael; Varghese, Julian

2016-06-01

The volume and complexity of patient data - especially in personalised medicine - is steadily increasing, both regarding clinical data and genomic profiles: Typically more than 1,000 items (e.g., laboratory values, vital signs, diagnostic tests etc.) are collected per patient in clinical trials. In oncology hundreds of mutations can potentially be detected for each patient by genomic profiling. Therefore data integration from multiple sources constitutes a key challenge for medical research and healthcare. Semantic annotation of data elements can facilitate to identify matching data elements in different sources and thereby supports data integration. Millions of different annotations are required due to the semantic richness of patient data. These annotations should be uniform, i.e., two matching data elements shall contain the same annotations. However, large terminologies like SNOMED CT or UMLS don't provide uniform coding. It is proposed to develop semantic annotations of medical data elements based on a large-scale public metadata repository. To achieve uniform codes, semantic annotations shall be re-used if a matching data element is available in the metadata repository. A web-based tool called ODMedit ( https://odmeditor.uni-muenster.de/ ) was developed to create data models with uniform semantic annotations. It contains ~800,000 terms with semantic annotations which were derived from ~5,800 models from the portal of medical data models (MDM). The tool was successfully applied to manually annotate 22 forms with 292 data items from CDISC and to update 1,495 data models of the MDM portal. Uniform manual semantic annotation of data models is feasible in principle, but requires a large-scale collaborative effort due to the semantic richness of patient data. A web-based tool for these annotations is available, which is linked to a public metadata repository.

Technology Integration in Science Classrooms: Framework, Principles, and Examples

ERIC Educational Resources Information Center

Kim, Minchi C.; Freemyer, Sarah

2011-01-01

A great number of technologies and tools have been developed to support science learning and teaching. However, science teachers and researchers point out numerous challenges to implementing such tools in science classrooms. For instance, guidelines, lesson plans, Web links, and tools teachers can easily find through Web-based search engines often…

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

PubMed

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

2014-01-01

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

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

PubMed Central

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

2014-01-01

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

indCAPS: A tool for designing screening primers for CRISPR/Cas9 mutagenesis events.

PubMed

Hodgens, Charles; Nimchuk, Zachary L; Kieber, Joseph J

2017-01-01

Genetic manipulation of organisms using CRISPR/Cas9 technology generally produces small insertions/deletions (indels) that can be difficult to detect. Here, we describe a technique to easily and rapidly identify such indels. Sequence-identified mutations that alter a restriction enzyme recognition site can be readily distinguished from wild-type alleles using a cleaved amplified polymorphic sequence (CAPS) technique. If a restriction site is created or altered by the mutation such that only one allele contains the restriction site, a polymerase chain reaction (PCR) followed by a restriction digest can be used to distinguish the two alleles. However, in the case of most CRISPR-induced alleles, no such restriction sites are present in the target sequences. In this case, a derived CAPS (dCAPS) approach can be used in which mismatches are purposefully introduced in the oligonucleotide primers to create a restriction site in one, but not both, of the amplified templates. Web-based tools exist to aid dCAPS primer design, but when supplied sequences that include indels, the current tools often fail to suggest appropriate primers. Here, we report the development of a Python-based, species-agnostic web tool, called indCAPS, suitable for the design of PCR primers used in dCAPS assays that is compatible with indels. This tool should have wide utility for screening editing events following CRISPR/Cas9 mutagenesis as well as for identifying specific editing events in a pool of CRISPR-mediated mutagenesis events. This tool was field-tested in a CRISPR mutagenesis experiment targeting a cytokinin receptor (AHK3) in Arabidopsis thaliana. The tool suggested primers that successfully distinguished between wild-type and edited alleles of a target locus and facilitated the isolation of two novel ahk3 null alleles. Users can access indCAPS and design PCR primers to employ dCAPS to identify CRISPR/Cas9 alleles at http://indcaps.kieber.cloudapps.unc.edu/.

A Large-scale Dissemination and Implementation Model for Evidence-based Treatment and Continuing Care

PubMed Central

Garner, Bryan R.; Smith, Jane Ellen; Meyers, Robert J.; Godley, Mark D.

2010-01-01

Multiple evidence-based treatments for adolescents with substance use disorders are available; however, the diffusion of these treatments in practice remains minimal. A dissemination and implementation model incorporating research-based training components for simultaneous implementation across 33 dispersed sites and over 200 clinical staff is described. Key elements for the diffusion of the Adolescent Community Reinforcement Approach and Assertive Continuing Care were: (a) three years of funding to support local implementation; (b) comprehensive training, including a 3.5 day workshop, bi-weekly coaching calls, and ongoing performance feedback facilitated by a web tool; (c) a clinician certification process; (d) a supervisor certification process to promote long-term sustainability; and (e) random fidelity reviews after certification. Process data are summarized for 167 clinicians and 64 supervisors. PMID:21547241

Visualization of CDA laboratory reports and long term trends as a possible EHR application for patients and physicians.

PubMed

Obenaus, Manuel; Burgsteiner, Harald

2014-01-01

To increase the patient's acceptance of electronic health records and understanding for their laboratory findings a web application was developed which presents all parameters and possible deviations of standard values in a clear way and visualizes the time based trend of all recorded parameters graphically. Documents corresponding to the Clinical document architecture (CDA) R2 laboratory reports standard and a rapid prototyping framework called Groovy on Grails were used. This work shows, that it is possible to create a useful, standards based tool for patients and physicians with comparatively few resources - an application that could be in similar form a part of an electronic Health Record (EHR) system like the Austrian electronic Health Record (ELGA).

Acquiring geographical data with web harvesting

NASA Astrophysics Data System (ADS)

Dramowicz, K.

2016-04-01

Many websites contain very attractive and up to date geographical information. This information can be extracted, stored, analyzed and mapped using web harvesting techniques. Poorly organized data from websites are transformed with web harvesting into a more structured format, which can be stored in a database and analyzed. Almost 25% of web traffic is related to web harvesting, mostly while using search engines. This paper presents how to harvest geographic information from web documents using the free tool called the Beautiful Soup, one of the most commonly used Python libraries for pulling data from HTML and XML files. It is a relatively easy task to process one static HTML table. The more challenging task is to extract and save information from tables located in multiple and poorly organized websites. Legal and ethical aspects of web harvesting are discussed as well. The paper demonstrates two case studies. The first one shows how to extract various types of information about the Good Country Index from the multiple web pages, load it into one attribute table and map the results. The second case study shows how script tools and GIS can be used to extract information from one hundred thirty six websites about Nova Scotia wines. In a little more than three minutes a database containing one hundred and six liquor stores selling these wines is created. Then the availability and spatial distribution of various types of wines (by grape types, by wineries, and by liquor stores) are mapped and analyzed.

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

PubMed

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

2013-01-01

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

HC Forum®: a web site based on an international human cytogenetic database

PubMed Central

Cohen, Olivier; Mermet, Marie-Ange; Demongeot, Jacques

2001-01-01

Familial structural rearrangements of chromosomes represent a factor of malformation risk that could vary over a large range, making genetic counseling difficult. However, they also represent a powerful tool for increasing knowledge of the genome, particularly by studying breakpoints and viable imbalances of the genome. We have developed a collaborative database that now includes data on more than 4100 families, from which we have developed a web site called HC Forum® (http://HCForum.imag.fr). It offers geneticists assistance in diagnosis and in genetic counseling by assessing the malformation risk with statistical models. For researchers, interactive interfaces exhibit the distribution of chromosomal breakpoints and of the genome regions observed at birth in trisomy or in monosomy. Dedicated tools including an interactive pedigree allow electronic submission of data, which will be anonymously shown in a forum for discussions. After validation, data are definitively registered in the database with the email of the sender, allowing direct location of biological material. Thus HC Forum® constitutes a link between diagnosis laboratories and genome research centers, and after 1 year, more than 700 users from about 40 different countries already exist. PMID:11125121

Component Technology for High-Performance Scientific Simulation Software

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

Epperly, T; Kohn, S; Kumfert, G

2000-11-09

We are developing scientific software component technology to manage the complexity of modem, parallel simulation software and increase the interoperability and re-use of scientific software packages. In this paper, we describe a language interoperability tool named Babel that enables the creation and distribution of language-independent software libraries using interface definition language (IDL) techniques. We have created a scientific IDL that focuses on the unique interface description needs of scientific codes, such as complex numbers, dense multidimensional arrays, complicated data types, and parallelism. Preliminary results indicate that in addition to language interoperability, this approach provides useful tools for thinking about themore » design of modem object-oriented scientific software libraries. Finally, we also describe a web-based component repository called Alexandria that facilitates the distribution, documentation, and re-use of scientific components and libraries.« less

Web 2.0 Reflective Inquiry: A Transformative Literacy Teacher Education Tool

ERIC Educational Resources Information Center

Stevens, Elizabeth Years

2013-01-01

The author describes a graduate class she teaches called Perspectives on Literacy and Technology, whose first goal is to provide a space for teachers enrolled in a literacy education MS program to reflect on current theory and research related to digital technologies and literacy. A secondary goal is to foster their use of "cutting-edge"…

An Unexpected Ally: Using Microsoft's SharePoint to Create a Departmental Intranet

ERIC Educational Resources Information Center

Dahl, David

2010-01-01

In September 2008, the Albert S. Cook Library at Towson University implemented an intranet to support the various functions of the library's Reference Department. This intranet is called the RefPortal. After exploring open source options and other Web 2.0 tools, the department (under the guidance of the library technology coordinator) chose…

ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences.

PubMed

Lee, Imchang; Chalita, Mauricio; Ha, Sung-Min; Na, Seong-In; Yoon, Seok-Hwan; Chun, Jongsik

2017-06-01

Thanks to the recent advancement of DNA sequencing technology, the cost and time of prokaryotic genome sequencing have been dramatically decreased. It has repeatedly been reported that genome sequencing using high-throughput next-generation sequencing is prone to contaminations due to its high depth of sequencing coverage. Although a few bioinformatics tools are available to detect potential contaminations, these have inherited limitations as they only use protein-coding genes. Here we introduce a new algorithm, called ContEst16S, to detect potential contaminations using 16S rRNA genes from genome assemblies. We screened 69 745 prokaryotic genomes from the NCBI Assembly Database using ContEst16S and found that 594 were contaminated by bacteria, human and plants. Of the predicted contaminated genomes, 8 % were not predicted by the existing protein-coding gene-based tool, implying that both methods can be complementary in the detection of contaminations. A web-based service of the algorithm is available at www.ezbiocloud.net/tools/contest16s.

Handling Internet-Based Health Information: Improving Health Information Web Site Literacy Among Undergraduate Nursing Students.

PubMed

Wang, Weiwen; Sun, Ran; Mulvehill, Alice M; Gilson, Courtney C; Huang, Linda L

2017-02-01

Patient care problems arise when health care consumers and professionals find health information on the Internet because that information is often inaccurate. To mitigate this problem, nurses can develop Web literacy and share that skill with health care consumers. This study evaluated a Web-literacy intervention for undergraduate nursing students to find reliable Web-based health information. A pre- and postsurvey queried undergraduate nursing students in an informatics course; the intervention comprised lecture, in-class practice, and assignments about health Web site evaluation tools. Data were analyzed using Wilcoxon and ANOVA signed-rank tests. Pre-intervention, 75.9% of participants reported using Web sites to obtain health information. Postintervention, 87.9% displayed confidence in using an evaluation tool. Both the ability to critique health Web sites (p = .005) and confidence in finding reliable Internet-based health information (p = .058) increased. Web-literacy education guides nursing students to find, evaluate, and use reliable Web sites, which improves their ability to deliver safer patient care. [J Nurs Educ. 2017;56(2):110-114.]. Copyright 2017, SLACK Incorporated.

Teaching with technology: free Web resources for teaching and learning.

PubMed

Wink, Diane M; Smith-Stoner, Marilyn

2011-01-01

In this bimonthly series, the department editor examines how nurse educators can use Internet and Web-based computer technologies such as search, communication, collaborative writing tools; social networking, and social bookmarking sites; virtual worlds; and Web-based teaching and learning programs. In this article, the department editor and her coauthor describe free Web-based resources that can be used to support teaching and learning.

Phone and Web-Based Tobacco Cessation Treatment: Real-World Utilization Patterns and Outcomes for 11,000 Tobacco Users

PubMed Central

Hapgood, Jenny; Smucker Barnwell, Sara; McAfee, Tim

2008-01-01

Background Phone-based tobacco cessation programs have been proven effective and widely adopted. Web-based solutions exist; however, the evidence base is not yet well established. Many cessation treatments are commercially available, but few integrate the phone and Web for delivery and no published studies exist for integrated programs. Objective This paper describes a comprehensive integrated phone/Web tobacco cessation program and the characteristics, experience, and outcomes of smokers enrolled in this program from a real-world evaluation. Methods We tracked program utilization (calls completed, Web log-ins), quit status, satisfaction, and demographics of 11,143 participants who enrolled in the Free & Clear Quit For Life Program between May 2006 and October 2007. All participants received up to five proactive phone counseling sessions with Quit Coaches, unlimited access to an interactive website, up to 20 tailored emails, printed Quit Guides, and cessation medication information. The program was designed to encourage use of all program components rather than asking participants to choose which components they wanted to use while quitting. Results We found that participants tended to use phone services more than Web services. On average, participants completed 2-2.5 counseling calls and logged in to the online program 1-2 times. Women were more adherent to the overall program; women utilized Web and phone services significantly (P = .003) more than men. Older smokers (> 26 years) and moderate smokers (15-20 cigarettes/day) utilized services more (P < .001) than younger (< 26 years) and light or heavy smokers. Satisfaction with services was high (92% to 95%) and varied somewhat with Web utilization. Thirty-day quit rates at the 6-month follow-up were 41% using responder analysis and 21% using intent-to-treat analysis. Web utilization was significantly associated with increased call completion and tobacco abstinence rates at the 6-month follow-up evaluation. Conclusions This paper expands our understanding of a real-world treatment program combining two mediums, phone and Web. Greater adherence to the program, as defined by using both the phone and Web components, is associated with higher quit rates. This study has implications for reaching and treating tobacco users with an integrated phone/Web program and offers evidence regarding the effectiveness of integrated cessation programs. PMID:19017583

Factors Influencing the Use of Cognitive Tools in Web-Based Learning Environments: A Case Study

ERIC Educational Resources Information Center

Ozcelik, Erol; Yildirim, Soner

2005-01-01

High demands on learners in Web-based learning environments and constraints of the human cognitive system cause disorientation and cognitive overload. These problems could be inhibited if appropriate cognitive tools are provided to support learners' cognitive processes. The purpose of this study was to explore the factors influencing the use of…

Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS): A web-based tool for addressing the challenges of cross-species extrapolation of chemical toxicity

EPA Science Inventory

Conservation of a molecular target across species can be used as a line-of-evidence to predict the likelihood of chemical susceptibility. The web-based Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool was developed to simplify, streamline, and quantitat...

WaveNet: A Web-Based Metocean Data Access, Processing and Analysis Tool; Part 5 - WW3 Database

DTIC Science & Technology

2015-02-01

Program ( CDIP ); and Part 4 for the Great Lakes Observing System/Coastal Forecasting System (GLOS/GLCFS). Using step-by-step instructions, this Part 5...Demirbilek, Z., L. Lin, and D. Wilson. 2014a. WaveNet: A web-based metocean data access, processing, and analysis tool; part 3– CDIP database

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...

Virtual Reality Simulations and Animations in a Web-Based Interactive Manufacturing Engineering Module

ERIC Educational Resources Information Center

Ong, S. K.; Mannan, M. A.

2004-01-01

This paper presents a web-based interactive teaching package that provides a comprehensive and conducive yet dynamic and interactive environment for a module on automated machine tools in the Manufacturing Division at the National University of Singapore. The use of Internet technologies in this teaching tool makes it possible to conjure…

Spatial Visualization Learning in Engineering: Traditional Methods vs. a Web-Based Tool

ERIC Educational Resources Information Center

Pedrosa, Carlos Melgosa; Barbero, Basilio Ramos; Miguel, Arturo Román

2014-01-01

This study compares an interactive learning manager for graphic engineering to develop spatial vision (ILMAGE_SV) to traditional methods. ILMAGE_SV is an asynchronous web-based learning tool that allows the manipulation of objects with a 3D viewer, self-evaluation, and continuous assessment. In addition, student learning may be monitored, which…

Web accessibility and open source software.

PubMed

Obrenović, Zeljko

2009-07-01

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

An interactive, web-based tool for learning anatomic landmarks.

PubMed

Hallgren, Richard C; Parkhurst, Perrin E; Monson, Carol L; Crewe, Nancy M

2002-03-01

To evaluate the effectiveness of a Web-based interactive teaching tool that uses self-assessment exercises with real-time feedback to aid students' learning in a gross anatomy class. A total of 107 of 124 first-year medical students at one school were enrolled in the study. Students were divided into three groups: Group 1 (n = 63) received introductory material and activated their Web-based accounts; Group 2 (n = 44) received introductory material but did not activate their Web-based accounts; and Group 3 (n = 17) were not enrolled in the study and received no introductory material. Students in Group 1 had access to a graphic showing the locations of anatomic landmarks, a drill exercise, and a self-evaluation exercise. Students' ability to identify the anatomic landmarks on a 30-question midterm and a 30-question final exam were compared among the groups. The mean scores of students in Group 1 (midterm = 28.5, final = 28.1) were significantly higher than were the mean scores of students in Group 2 (midterm = 26.8, p <.001; final = 26.9, p <.017) and Group 3 (midterm = 24.8, p <.001; final = 26.4, p <.007). The Web-based tool was effective in improving students' scores on anatomic landmark exams. Future studies will determine whether the tool aids students in identifying structures located in three-dimensional space within regions such as the cranium and the abdominal cavity.

Evaluating a Web-Based Video Corpus through an Analysis of User Interactions

ERIC Educational Resources Information Center

Caws, Catherine G.

2013-01-01

As shown by several studies, successful integration of technology in language learning requires a holistic approach in order to scientifically understand what learners do when working with web-based technology (cf. Raby, 2007). Additionally, a growing body of research in computer assisted language learning (CALL) evaluation, design and…

Feasibility testing of a web-based symptom self-management system for persons living with HIV.

PubMed

Schnall, Rebecca; Wantland, Dean; Velez, Olivia; Cato, Kenrick; Jia, Haomiao

2014-01-01

The purpose of this study was to explore the feasibility of using a Web-based tool to provide tailored symptom management strategies for persons living with HIV (PLWH) and to estimate the effect size of the tool for future studies. Testing the components of the Web-based system was done by incorporating a repeated-measures design measuring the outcomes of symptom frequency and intensity, use of symptom management strategies, and engagement with health care providers. We recruited 42 PLWH; participants were enrolled in the study for 12 weeks and were asked to use the system and complete the questionnaires every 2 weeks. Our results showed that participants who used the strategies were more likely to have a decrease in symptom frequency and intensity. Findings from this feasibility study provide preliminary evidence for the use of a Web-based HIV symptom management tool with self-management strategies for individuals living with HIV infection. Copyright © 2014 Association of Nurses in AIDS Care. Published by Elsevier Inc. All rights reserved.

Sequence History Update Tool

NASA Technical Reports Server (NTRS)

Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

2008-01-01

The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

Comparison of a Web-Based Teaching Tool and Traditional Didactic Learning for In Vitro Fertilization Patients: A Preliminary Randomized Controlled Trial.

PubMed

Vause, Tannys Dawn Reiko; Allison, David J; Vause, Tricia; Tekok-Kilic, Ayda; Ditor, David S; Min, Jason K

2018-05-01

The objective of this prospective RCT was to compare the efficacy of a web-based teaching tool to traditional didactic teaching in IVF patients. Forty women undergoing their first IVF cycle were randomly allocated to an interactive web-based teaching session or a nurse-led didactic teaching session. The primary outcome measure was participant knowledge regarding the IVF process, risks, and logistics assessed before and after the respective teaching session. Secondary outcomes included patient stress, assessed before and after the respective teaching session, and patient satisfaction, assessed following the respective teaching session and on the day of embryo transfer (following implementation of the teaching protocol). Both groups demonstrated similar and significant improvements in knowledge and stress after exposure to their respective teaching sessions. The web-based group was significantly more satisfied than the didactic teaching group. Web-based teaching was also shown to be equally effective for participants of high versus low income and education status for knowledge, stress, and satisfaction. This study provides preliminary support for the use of web-based teaching as an equally effective tool for increasing knowledge and reducing stress compared to traditional didactic teaching in IVF patients, with the added benefit of increased patient satisfaction. Copyright © 2018 Society of Obstetricians and Gynaecologists of Canada. Published by Elsevier Inc. All rights reserved.

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.

Scaling Up: From Web-Enhanced Courses to a Web-Enhanced Curriculum

ERIC Educational Resources Information Center

Wood, Robert E.

2004-01-01

In the past decade, the most important technological innovation in higher education has been the enhancement of academic courses with Web-based information and tools. Given the success and popularity of numerous Web-based innovations, the author and two colleagues wondered whether the benefits of technology use could be scaled up from the course…

WebQuest on Conic Sections as a Learning Tool for Prospective Teachers

ERIC Educational Resources Information Center

Kurtulus, Aytac; Ada, Tuba

2012-01-01

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

A Java tool for dynamic web-based 3D visualization of anatomy and overlapping gene or protein expression patterns.

PubMed

Gerth, Victor E; Vize, Peter D

2005-04-01

The Gene Expression Viewer is a web-launched three-dimensional visualization tool, tailored to compare surface reconstructions of multi-channel image volumes generated by confocal microscopy or micro-CT.

The PubChem chemical structure sketcher

PubMed Central

2009-01-01

PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects. PMID:20298522

FwWebViewPlus: integration of web technologies into WinCC OA based Human-Machine Interfaces at CERN

NASA Astrophysics Data System (ADS)

Golonka, Piotr; Fabian, Wojciech; Gonzalez-Berges, Manuel; Jasiun, Piotr; Varela-Rodriguez, Fernando

2014-06-01

The rapid growth in popularity of web applications gives rise to a plethora of reusable graphical components, such as Google Chart Tools and JQuery Sparklines, implemented in JavaScript and run inside a web browser. In the paper we describe the tool that allows for seamless integration of web-based widgets into WinCC Open Architecture, the SCADA system used commonly at CERN to build complex Human-Machine Interfaces. Reuse of widely available widget libraries and pushing the development efforts to a higher abstraction layer based on a scripting language allow for significant reduction in maintenance of the code in multi-platform environments compared to those currently used in C++ visualization plugins. Adequately designed interfaces allow for rapid integration of new web widgets into WinCC OA. At the same time, the mechanisms familiar to HMI developers are preserved, making the use of new widgets "native". Perspectives for further integration between the realms of WinCC OA and Web development are also discussed.

Web-Based Instruction: A Guide for Libraries, Third Edition

ERIC Educational Resources Information Center

Smith, Susan Sharpless

2010-01-01

Expanding on the popular, practical how-to guide for public, academic, school, and special libraries, technology expert Susan Sharpless Smith offers library instructors the confidence to take Web-based instruction into their own hands. Smith has thoroughly updated "Web-Based Instruction: A Guide for Libraries" to include new tools and trends,…

Exploring the Relationship between Self-Regulated Vocabulary Learning and Web-Based Collaboration

ERIC Educational Resources Information Center

Liu, Sarah Hsueh-Jui; Lan, Yu-Ju; Ho, Cloudia Ya-Yu

2014-01-01

Collaborative learning has placed an emphasis on co-constructing knowledge by sharing and negotiating meaning for problem-solving activities, and this cannot be accomplished without governing the self-regulatory processes of students. This study employed a Web-based tool, Google Docs, to determine the effects of Web-based collaboration on…

A Study of Multimedia Annotation of Web-Based Materials

ERIC Educational Resources Information Center

Hwang, Wu-Yuin; Wang, Chin-Yu; Sharples, Mike

2007-01-01

Web-based learning has become an important way to enhance learning and teaching, offering many learning opportunities. A limitation of current Web-based learning is the restricted ability of students to personalize and annotate the learning materials. Providing personalized tools and analyzing some types of learning behavior, such as students'…

Executing SADI services in Galaxy.

PubMed

Aranguren, Mikel Egaña; González, Alejandro Rodríguez; Wilkinson, Mark D

2014-01-01

In recent years Galaxy has become a popular workflow management system in bioinformatics, due to its ease of installation, use and extension. The availability of Semantic Web-oriented tools in Galaxy, however, is limited. This is also the case for Semantic Web Services such as those provided by the SADI project, i.e. services that consume and produce RDF. Here we present SADI-Galaxy, a tool generator that deploys selected SADI Services as typical Galaxy tools. SADI-Galaxy is a Galaxy tool generator: through SADI-Galaxy, any SADI-compliant service becomes a Galaxy tool that can participate in other out-standing features of Galaxy such as data storage, history, workflow creation, and publication. Galaxy can also be used to execute and combine SADI services as it does with other Galaxy tools. Finally, we have semi-automated the packing and unpacking of data into RDF such that other Galaxy tools can easily be combined with SADI services, plugging the rich SADI Semantic Web Service environment into the popular Galaxy ecosystem. SADI-Galaxy bridges the gap between Galaxy, an easy to use but "static" workflow system with a wide user-base, and SADI, a sophisticated, semantic, discovery-based framework for Web Services, thus benefiting both user communities.

Increasing the availability and usability of terrestrial ecology data through geospatial Web services and visualization tools (Invited)

NASA Astrophysics Data System (ADS)

Santhana Vannan, S.; Cook, R. B.; Wilson, B. E.; Wei, Y.

2010-12-01

Terrestrial ecology data sets are produced from diverse data sources such as model output, field data collection, laboratory analysis and remote sensing observation. These data sets can be created, distributed, and consumed in diverse ways as well. However, this diversity can hinder the usability of the data, and limit data users’ abilities to validate and reuse data for science and application purposes. Geospatial web services, such as those described in this paper, are an important means of reducing this burden. Terrestrial ecology researchers generally create the data sets in diverse file formats, with file and data structures tailored to the specific needs of their project, possibly as tabular data, geospatial images, or documentation in a report. Data centers may reformat the data to an archive-stable format and distribute the data sets through one or more protocols, such as FTP, email, and WWW. Because of the diverse data preparation, delivery, and usage patterns, users have to invest time and resources to bring the data into the format and structure most useful for their analysis. This time-consuming data preparation process shifts valuable resources from data analysis to data assembly. To address these issues, the ORNL DAAC, a NASA-sponsored terrestrial ecology data center, has utilized geospatial Web service technology, such as Open Geospatial Consortium (OGC) Web Map Service (WMS) and OGC Web Coverage Service (WCS) standards, to increase the usability and availability of terrestrial ecology data sets. Data sets are standardized into non-proprietary file formats and distributed through OGC Web Service standards. OGC Web services allow the ORNL DAAC to store data sets in a single format and distribute them in multiple ways and formats. Registering the OGC Web services through search catalogues and other spatial data tools allows for publicizing the data sets and makes them more available across the Internet. The ORNL DAAC has also created a Web-based graphical user interface called Spatial Data Access Tool (SDAT) that utilizes OGC Web services standards and allows data distribution and consumption for users not familiar with OGC standards. SDAT also allows for users to visualize the data set prior to download. Google Earth visualizations of the data set are also provided through SDAT. The use of OGC Web service standards at the ORNL DAAC has enabled an increase in data consumption. In one case, a data set had ~10 fold increase in download through OGC Web service in comparison to the conventional FTP and WWW method of access. The increase in download suggests that users are not only finding the data sets they need but also able to consume them readily in the format they need.

The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows

PubMed Central

O'Connor, Brian D.; Yuen, Denis; Chung, Vincent; Duncan, Andrew G.; Liu, Xiang Kun; Patricia, Janice; Paten, Benedict; Stein, Lincoln; Ferretti, Vincent

2017-01-01

As genomic datasets continue to grow, the feasibility of downloading data to a local organization and running analysis on a traditional compute environment is becoming increasingly problematic. Current large-scale projects, such as the ICGC PanCancer Analysis of Whole Genomes (PCAWG), the Data Platform for the U.S. Precision Medicine Initiative, and the NIH Big Data to Knowledge Center for Translational Genomics, are using cloud-based infrastructure to both host and perform analysis across large data sets. In PCAWG, over 5,800 whole human genomes were aligned and variant called across 14 cloud and HPC environments; the processed data was then made available on the cloud for further analysis and sharing. If run locally, an operation at this scale would have monopolized a typical academic data centre for many months, and would have presented major challenges for data storage and distribution. However, this scale is increasingly typical for genomics projects and necessitates a rethink of how analytical tools are packaged and moved to the data. For PCAWG, we embraced the use of highly portable Docker images for encapsulating and sharing complex alignment and variant calling workflows across highly variable environments. While successful, this endeavor revealed a limitation in Docker containers, namely the lack of a standardized way to describe and execute the tools encapsulated inside the container. As a result, we created the Dockstore ( https://dockstore.org), a project that brings together Docker images with standardized, machine-readable ways of describing and running the tools contained within. This service greatly improves the sharing and reuse of genomics tools and promotes interoperability with similar projects through emerging web service standards developed by the Global Alliance for Genomics and Health (GA4GH). PMID:28344774

The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows.

PubMed

O'Connor, Brian D; Yuen, Denis; Chung, Vincent; Duncan, Andrew G; Liu, Xiang Kun; Patricia, Janice; Paten, Benedict; Stein, Lincoln; Ferretti, Vincent

2017-01-01

As genomic datasets continue to grow, the feasibility of downloading data to a local organization and running analysis on a traditional compute environment is becoming increasingly problematic. Current large-scale projects, such as the ICGC PanCancer Analysis of Whole Genomes (PCAWG), the Data Platform for the U.S. Precision Medicine Initiative, and the NIH Big Data to Knowledge Center for Translational Genomics, are using cloud-based infrastructure to both host and perform analysis across large data sets. In PCAWG, over 5,800 whole human genomes were aligned and variant called across 14 cloud and HPC environments; the processed data was then made available on the cloud for further analysis and sharing. If run locally, an operation at this scale would have monopolized a typical academic data centre for many months, and would have presented major challenges for data storage and distribution. However, this scale is increasingly typical for genomics projects and necessitates a rethink of how analytical tools are packaged and moved to the data. For PCAWG, we embraced the use of highly portable Docker images for encapsulating and sharing complex alignment and variant calling workflows across highly variable environments. While successful, this endeavor revealed a limitation in Docker containers, namely the lack of a standardized way to describe and execute the tools encapsulated inside the container. As a result, we created the Dockstore ( https://dockstore.org), a project that brings together Docker images with standardized, machine-readable ways of describing and running the tools contained within. This service greatly improves the sharing and reuse of genomics tools and promotes interoperability with similar projects through emerging web service standards developed by the Global Alliance for Genomics and Health (GA4GH).

UnCover on the Web: search hints and applications in library environments.

PubMed

Galpern, N F; Albert, K M

1997-01-01

Among the huge maze of resources available on the Internet, UnCoverWeb stands out as a valuable tool for medical libraries. This up-to-date, free-access, multidisciplinary database of periodical references is searched through an easy-to-learn graphical user interface that is a welcome improvement over the telnet version. This article reviews the basic and advanced search techniques for UnCoverWeb, as well as providing information on the document delivery functions and table of contents alerting service called Reveal. UnCover's currency is evaluated and compared with other current awareness resources. System deficiencies are discussed, with the conclusion that although UnCoverWeb lacks the sophisticated features of many commercial database search services, it is nonetheless a useful addition to the repertoire of information sources available in a library.

Translation, cross-cultural adaptation and validation of the Diabetes Empowerment Scale – Short Form

PubMed Central

Chaves, Fernanda Figueredo; Reis, Ilka Afonso; Pagano, Adriana Silvina; Torres, Heloísa de Carvalho

2017-01-01

ABSTRACT OBJECTIVE To translate, cross-culturally adapt and validate the Diabetes Empowerment Scale – Short Form for assessment of psychosocial self-efficacy in diabetes care within the Brazilian cultural context. METHODS Assessment of the instrument’s conceptual equivalence, as well as its translation and cross-cultural adaptation were performed following international standards. The Expert Committee’s assessment of the translated version was conducted through a web questionnaire developed and applied via the web tool e-Surv. The cross-culturally adapted version was used for the pre-test, which was carried out via phone call in a group of eleven health care service users diagnosed with type 2 diabetes mellitus. The pre-test results were examined by a group of experts, composed by health care consultants, applied linguists and statisticians, aiming at an adequate version of the instrument, which was subsequently used for test and retest in a sample of 100 users diagnosed with type 2 diabetes mellitus via phone call, their answers being recorded by the web tool e-Surv. Internal consistency and reproducibility of analysis were carried out within the statistical programming environment R. RESULTS Face and content validity were attained and the Brazilian Portuguese version, entitled Escala de Autoeficácia em Diabetes – Versão Curta, was established. The scale had acceptable internal consistency with Cronbach’s alpha of 0.634 (95%CI 0.494– 0.737), while the correlation of the total score in the two periods was considered moderate (0.47). The intraclass correlation coefficient was 0.50. CONCLUSIONS The translated and cross-culturally adapted version of the instrument to spoken Brazilian Portuguese was considered valid and reliable to be used for assessment within the Brazilian population diagnosed with type 2 diabetes mellitus. The use of a web tool (e-Surv) for recording the Expert Committee responses as well as the responses in the validation tests proved to be a reliable, safe and innovative method. PMID:28355337

Self-Monitoring Symptoms in Glaucoma: A Feasibility Study of a Web-Based Diary Tool

PubMed Central

McDonald, Leanne; Glen, Fiona C.; Taylor, Deanna J.

2017-01-01

Purpose. Glaucoma patients annually spend only a few hours in an eye clinic but spend more than 5000 waking hours engaged in everything else. We propose that patients could self-monitor changes in visual symptoms providing valuable between clinic information; we test the hypothesis that this is feasible using a web-based diary tool. Methods. Ten glaucoma patients with a range of visual field loss took part in an eight-week pilot study. After completing a series of baseline tests, volunteers were prompted to monitor symptoms every three days and complete a diary about their vision during daily life using a bespoke web-based diary tool. Response to an end of a study questionnaire about the usefulness of the exercise was a main outcome measure. Results. Eight of the 10 patients rated the monitoring scheme to be “valuable” or “very valuable.” Completion rate to items was excellent (96%). Themes from a qualitative synthesis of the diary entries related to behavioural aspects of glaucoma. One patient concluded that a constant focus on monitoring symptoms led to negative feelings. Conclusions. A web-based diary tool for monitoring self-reported glaucoma symptoms is practically feasible. The tool must be carefully designed to ensure participants are benefitting, and it is not increasing anxiety. PMID:28546876

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

PubMed

Veloso, Mário

2014-09-01

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

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.

Simulation Platform: a cloud-based online simulation environment.

PubMed

Yamazaki, Tadashi; Ikeno, Hidetoshi; Okumura, Yoshihiro; Satoh, Shunji; Kamiyama, Yoshimi; Hirata, Yutaka; Inagaki, Keiichiro; Ishihara, Akito; Kannon, Takayuki; Usui, Shiro

2011-09-01

For multi-scale and multi-modal neural modeling, it is needed to handle multiple neural models described at different levels seamlessly. Database technology will become more important for these studies, specifically for downloading and handling the neural models seamlessly and effortlessly. To date, conventional neuroinformatics databases have solely been designed to archive model files, but the databases should provide a chance for users to validate the models before downloading them. In this paper, we report our on-going project to develop a cloud-based web service for online simulation called "Simulation Platform". Simulation Platform is a cloud of virtual machines running GNU/Linux. On a virtual machine, various software including developer tools such as compilers and libraries, popular neural simulators such as GENESIS, NEURON and NEST, and scientific software such as Gnuplot, R and Octave, are pre-installed. When a user posts a request, a virtual machine is assigned to the user, and the simulation starts on that machine. The user remotely accesses to the machine through a web browser and carries out the simulation, without the need to install any software but a web browser on the user's own computer. Therefore, Simulation Platform is expected to eliminate impediments to handle multiple neural models that require multiple software. Copyright © 2011 Elsevier Ltd. All rights reserved.

Reprint of: Simulation Platform: a cloud-based online simulation environment.

PubMed

Yamazaki, Tadashi; Ikeno, Hidetoshi; Okumura, Yoshihiro; Satoh, Shunji; Kamiyama, Yoshimi; Hirata, Yutaka; Inagaki, Keiichiro; Ishihara, Akito; Kannon, Takayuki; Usui, Shiro

2011-11-01

For multi-scale and multi-modal neural modeling, it is needed to handle multiple neural models described at different levels seamlessly. Database technology will become more important for these studies, specifically for downloading and handling the neural models seamlessly and effortlessly. To date, conventional neuroinformatics databases have solely been designed to archive model files, but the databases should provide a chance for users to validate the models before downloading them. In this paper, we report our on-going project to develop a cloud-based web service for online simulation called "Simulation Platform". Simulation Platform is a cloud of virtual machines running GNU/Linux. On a virtual machine, various software including developer tools such as compilers and libraries, popular neural simulators such as GENESIS, NEURON and NEST, and scientific software such as Gnuplot, R and Octave, are pre-installed. When a user posts a request, a virtual machine is assigned to the user, and the simulation starts on that machine. The user remotely accesses to the machine through a web browser and carries out the simulation, without the need to install any software but a web browser on the user's own computer. Therefore, Simulation Platform is expected to eliminate impediments to handle multiple neural models that require multiple software. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

PubMed

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

2012-05-01

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

eCDRweb User Guide–Primary Support

EPA Pesticide Factsheets

This document presents the user guide for the Office of Pollution Prevention and Toxics’ (OPPT) e-CDR web tool. E-CDRweb is the electronic, web-based tool provided by the Environmental Protection Agency (EPA) for the submission of Chemical Data Reporting (CDR) information. This document is the user guide for the Primary Support user of the e-CDRweb tool.

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…

eCDRweb User Guide–Secondary Support

EPA Pesticide Factsheets

This document presents the user guide for the Office of Pollution Prevention and Toxics’ (OPPT) e-CDR web tool. E-CDRweb is the electronic, web-based tool provided by the Environmental Protection Agency (EPA) for the submission of Chemical Data Reporting (CDR) information. This document is the user guide for the Secondary Support user of the e-CDRweb tool.

76 FR 17933 - Infrastructure Protection Data Call Survey

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-31

... Survey AGENCY: National Protection and Programs Directorate, DHS. ACTION: 60-Day Notice and request for... mission, IP requests opinions and information in a survey from IP Data Call participants regarding the IP Data Call process and the web-based application used to collect the CIKR data. The survey data...

DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes

PubMed Central

Sebestyén, Endre; Nagy, Tibor; Suhai, Sándor; Barta, Endre

2009-01-01

Background The comparative genomic analysis of a large number of orthologous promoter regions of the chordate and plant genes from the DoOP databases shows thousands of conserved motifs. Most of these motifs differ from any known transcription factor binding site (TFBS). To identify common conserved motifs, we need a specific tool to be able to search amongst them. Since conserved motifs from the DoOP databases are linked to genes, the result of such a search can give a list of genes that are potentially regulated by the same transcription factor(s). Results We have developed a new tool called DoOPSearch for the analysis of the conserved motifs in the promoter regions of chordate or plant genes. We used the orthologous promoters of the DoOP database to extract thousands of conserved motifs from different taxonomic groups. The advantage of this approach is that different sets of conserved motifs might be found depending on how broad the taxonomic coverage of the underlying orthologous promoter sequence collection is (consider e.g. primates vs. mammals or Brassicaceae vs. Viridiplantae). The DoOPSearch tool allows the users to search these motif collections or the promoter regions of DoOP with user supplied query sequences or any of the conserved motifs from the DoOP database. To find overrepresented gene ontologies, the gene lists obtained can be analysed further using a modified version of the GeneMerge program. Conclusion We present here a comparative genomics based promoter analysis tool. Our system is based on a unique collection of conserved promoter motifs characteristic of different taxonomic groups. We offer both a command line and a web-based tool for searching in these motif collections using user specified queries. These can be either short promoter sequences or consensus sequences of known transcription factor binding sites. The GeneMerge analysis of the search results allows the user to identify statistically overrepresented Gene Ontology terms that might provide a clue on the function of the motifs and genes. PMID:19534755

MySQL/PHP web database applications for IPAC proposal submission

NASA Astrophysics Data System (ADS)

Crane, Megan K.; Storrie-Lombardi, Lisa J.; Silbermann, Nancy A.; Rebull, Luisa M.

2008-07-01

The Infrared Processing and Analysis Center (IPAC) is NASA's multi-mission center of expertise for long-wavelength astrophysics. Proposals for various IPAC missions and programs are ingested via MySQL/PHP web database applications. Proposers use web forms to enter coversheet information and upload PDF files related to the proposal. Upon proposal submission, a unique directory is created on the webserver into which all of the uploaded files are placed. The coversheet information is converted into a PDF file using a PHP extension called FPDF. The files are concatenated into one PDF file using the command-line tool pdftk and then forwarded to the review committee. This work was performed at the California Institute of Technology under contract to the National Aeronautics and Space Administration.

Development of Continuing Nursing Education Offerings for the World Wide Web.

ERIC Educational Resources Information Center

Billings, Diane M.; Rowles, Connie J.

2001-01-01

Describes steps for web-based continuing education courses in terms of planning (strategic plan, website development, resource team, marketing plan), implementing (course design, web-based tools, copyright and intellectual property), and evaluating (pilot test, formative/summative evaluation, continuous quality improvement). (Contains 16…

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

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

Two Screens and an Ocean: Collaborating across Continents and Cultures with Web-Based Tools

ERIC Educational Resources Information Center

Frydenberg, Mark; Andone, Diana

2010-01-01

This paper describes the implementation and results of a cross-cultural pairing between college students in the United States and Romania who worked together over the period of one month to create a multimedia presentation that shared their learning about topics of multimedia and culture. Students could use any web-based collaboration tools of…

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...

Fostering Self-Efficacy through Time Management in an Online Learning Environment

ERIC Educational Resources Information Center

Terry, Krista P.; Doolittle, Peter E.

2008-01-01

In this study, we investigated the use of a web-based tool designed to influence levels of student self-efficacy by engaging participants in a time management strategy. On a daily basis for 16 days, a total of 64 undergraduate and graduate students engaged in the web-based time management tool in which students set goals regarding how they planned…

Mining Student Data Captured from a Web-Based Tutoring Tool: Initial Exploration and Results

ERIC Educational Resources Information Center

Merceron, Agathe; Yacef, Kalina

2004-01-01

In this article we describe the initial investigations that we have conducted on student data collected from a web-based tutoring tool. We have used some data mining techniques such as association rule and symbolic data analysis, as well as traditional SQL queries to gain further insight on the students' learning and deduce information to improve…

w4CSeq: software and web application to analyze 4C-seq data.

PubMed

Cai, Mingyang; Gao, Fan; Lu, Wange; Wang, Kai

2016-11-01

Circularized Chromosome Conformation Capture followed by deep sequencing (4C-Seq) is a powerful technique to identify genome-wide partners interacting with a pre-specified genomic locus. Here, we present a computational and statistical approach to analyze 4C-Seq data generated from both enzyme digestion and sonication fragmentation-based methods. We implemented a command line software tool and a web interface called w4CSeq, which takes in the raw 4C sequencing data (FASTQ files) as input, performs automated statistical analysis and presents results in a user-friendly manner. Besides providing users with the list of candidate interacting sites/regions, w4CSeq generates figures showing genome-wide distribution of interacting regions, and sketches the enrichment of key features such as TSSs, TTSs, CpG sites and DNA replication timing around 4C sites. Users can establish their own web server by downloading source codes at https://github.com/WGLab/w4CSeq Additionally, a demo web server is available at http://w4cseq.wglab.org CONTACT: kaiwang@usc.edu or wangelu@usc.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

X-train: teaching professionals remotely.

PubMed

Santerre, Charles R

2005-05-01

Increased popularity of the Internet, along with the development of new software applications have dramatically improved our ability to create and deliver online continuing education trainings to professionals in the areas of nutrition and food safety. In addition, these technological advances permit effective and affordable measurement of training outcomes, i.e., changes in knowledge, attitude, and behavior, that result from these educational efforts. Impact assessment of engagement programs is becoming increasing important for demonstrating the value of training activities to stakeholders. A novel software program, called X-Train, takes advantage of technological advances (databases, computer graphics, Web-based interfaces, and network speed) for delivering high-quality trainings to teachers and health care professionals. X-Train automatically collects outcome data, and generates and sends certificates of completion and communicates with participants through electronic messages. X-Train can be used as a collaborative tool whereby experts from various academic institutions are brought together to develop Web-based trainings. Finally, X-Train uses a unique approach that encourages cooperative extension specialists and educators to promote these educational opportunities within their state or county.

Creation of a Web-Based GIS Server and Custom Geoprocessing Tools for Enhanced Hydrologic Applications

NASA Astrophysics Data System (ADS)

Welton, B.; Chouinard, K.; Sultan, M.; Becker, D.; Milewski, A.; Becker, R.

2010-12-01

Rising populations in the arid and semi arid parts of the World are increasing the demand for fresh water supplies worldwide. Many data sets needed for assessment of hydrologic applications across vast regions of the world are expensive, unpublished, difficult to obtain, or at varying scales which complicates their use. Fortunately, this situation is changing with the development of global remote sensing datasets and web-based platforms such as GIS Server. GIS provides a cost effective vehicle for comparing, analyzing, and querying a variety of spatial datasets as geographically referenced layers. We have recently constructed a web-based GIS, that incorporates all relevant geological, geochemical, geophysical, and remote sensing data sets that were readily used to identify reservoir types and potential well locations on local and regional scales in various tectonic settings including: (1) extensional environment (Red Sea rift), (2) transcurrent fault system (Najd Fault in the Arabian-Nubian Shield), and (3) compressional environments (Himalayas). The web-based GIS could also be used to detect spatial and temporal trends in precipitation, recharge, and runoff in large watersheds on local, regional, and continental scales. These applications were enabled through the construction of a web-based ArcGIS Server with Google Map’s interface and the development of customized geoprocessing tools. ArcGIS Server provides out-of-the-box setups that are generic in nature. This platform includes all of the standard web based GIS tools (e.g. pan, zoom, identify, search, data querying, and measurement). In addition to the standard suite of tools provided by ArcGIS Server an additional set of advanced data manipulation and display tools was also developed to allow for a more complete and customizable view of the area of interest. The most notable addition to the standard GIS Server tools is the custom on-demand geoprocessing tools (e.g., graph, statistical functions, custom raster creation, profile, TRMM). The generation of a wide range of derivative maps (e.g., buffer zone, contour map, graphs, temporal rainfall distribution maps) from various map layers (e.g., geologic maps, geophysics, satellite images) allows for more user flexibility. The use of these tools along with Google Map’s API which enables the website user to utilize high quality GeoEye 2 images provide by Google in conjunction with our data, creates a more complete image of the area being observed and allows for custom derivative maps to be created in the field and viewed immediately on the web, processes that were restricted to offline databases.

The Role of Web-Based Simulations in Technology Education

ERIC Educational Resources Information Center

Page, Tom

2009-01-01

This paper discusses the theoretical underpinning and main aspects of the development and application of the web-orientation agent (WOA) and presents preliminary results concerning its use in university studies. The web-orientation agent (WOA) is a software based tool which produces an interactive learning environment offering support and guidance…

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

PubMed

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

2015-08-28

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

Computational algorithm to evaluate product disassembly cost index

NASA Astrophysics Data System (ADS)

Zeid, Ibrahim; Gupta, Surendra M.

2002-02-01

Environmentally conscious manufacturing is an important paradigm in today's engineering practice. Disassembly is a crucial factor in implementing this paradigm. Disassembly allows the reuse and recycling of parts and products that reach their death after their life cycle ends. There are many questions that must be answered before a disassembly decision can be reached. The most important question is economical. The cost of disassembly versus the cost of scrapping a product is always considered. This paper develops a computational tool that allows decision-makers to calculate the disassembly cost of a product. The tool makes it simple to perform 'what if' scenarios fairly quickly. The tool is Web based and has two main parts. The front-end part is a Web page and runs on the client side in a Web browser, while the back-end part is a disassembly engine (servlet) that has disassembly knowledge and costing algorithms and runs on the server side. The tool is based on the client/server model that is pervasively utilized throughout the World Wide Web. An example is used to demonstrate the implementation and capabilities of the tool.

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…

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

ERIC Educational Resources Information Center

Wang, Wei-Tsong; Wang, Chun-Chieh

2009-01-01

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

Efficacy of a Web-Based, Tailored, Alcohol Prevention/Intervention Program for College Students: Initial Findings

ERIC Educational Resources Information Center

Bingham, C. Raymond; Barretto, Andrea Ippel; Walton, Maureen A.; Bryant, Christopher M.; Shope, Jean T.; Raghunathan, Trivellore E.

2010-01-01

Objective: Reduce college student at-risk drinking (ARD) using a Web-based brief motivational alcohol prevention/intervention called "Michigan Prevention and Alcohol Safety for Students" (M-PASS). Participants: Participants included 1,137 randomly sampled first-year college students, including 59% female, 80% white, and averaged age 18.1…

Listening Strategy Use and Influential Factors in Web-Based Computer Assisted Language Learning

ERIC Educational Resources Information Center

Chen, L.; Zhang, R.; Liu, C.

2014-01-01

This study investigates second and foreign language (L2) learners' listening strategy use and factors that influence their strategy use in a Web-based computer assisted language learning (CALL) system. A strategy inventory, a factor questionnaire and a standardized listening test were used to collect data from a group of 82 Chinese students…

Toward a Web Based Environment for Evaluation and Design of Pedagogical Hypermedia

ERIC Educational Resources Information Center

Trigano, Philippe C.; Pacurar-Giacomini, Ecaterina

2004-01-01

We are working on a method, called CEPIAH. We propose a web based system used to help teachers to design multimedia documents and to evaluate their prototypes. Our current research objectives are to create a methodology to sustain the educational hypermedia design and evaluation. A module is used to evaluate multimedia software applied in…

Use of Interactive Web-Based Exercises for English as a Foreign Language Learning: Learners' Perceptions

ERIC Educational Resources Information Center

Wang, Yen-Hui

2014-01-01

The study investigated the learner perceptions of a CALL component in a blended language learning context. 52 Taiwanese college students attended instructional classroom sessions and did weekly online assignments in the form of interactive web-based exercises over one semester. Their learning performance was measured by means of two computer-based…

Efficacy of a Web-Based, Tailored, Alcohol Prevention/Intervention Program for College Students: 3-Month Follow-Up

ERIC Educational Resources Information Center

Bingham, C. Raymond; Barretto, Andrea Ippel; Walton, Maureen A.; Bryant, Christopher M.; Shope, Jean T.; Raghunathan, Trivellore E.

2011-01-01

This study presents the results of an efficacy evaluation of a web-based brief motivational alcohol prevention/intervention program called "Michigan Prevention and Alcohol Safety for Students" (M-PASS). Four on-line sessions providing individually-tailored feedback were delivered to first-year college students over 9 weeks. Non- and…

Highly Relevant Mentoring (HRM) as a Faculty Development Model for Web-Based Instruction

ERIC Educational Resources Information Center

Carter, Lorraine; Salyers, Vincent; Page, Aroha; Williams, Lynda; Albl, Liz; Hofsink, Clarence

2012-01-01

This paper describes a faculty development model called the highly relevant mentoring (HRM) model; the model includes a framework as well as some practical strategies for meeting the professional development needs of faculty who teach web-based courses. The paper further emphasizes the need for faculty and administrative buy-in for HRM and…

Web-Based Text Structure Strategy Instruction Improves Seventh Graders' Content Area Reading Comprehension

ERIC Educational Resources Information Center

Wijekumar, Kausalai; Meyer, Bonnie J. F.; Lei, Puiwa

2017-01-01

Reading comprehension in the content areas is a challenge for many middle grade students. Text structure-based instruction has yielded positive outcomes in reading comprehension at all grade levels in small and large studies. The text structure strategy delivered via the web, called Intelligent Tutoring System for the Text Structure Strategy…

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…

Collaborative writing: Tools and tips.

PubMed

Eapen, Bell Raj

2007-01-01

Majority of technical writing is done by groups of experts and various web based applications have made this collaboration easy. Email exchange of word processor documents with tracked changes used to be the standard technique for collaborative writing. However web based tools like Google docs and Spreadsheets have made the process fast and efficient. Various versioning tools and synchronous editors are available for those who need additional functionality. Having a group leader who decides the scheduling, communication and conflict resolving protocols is important for successful collaboration.

NeuronDepot: keeping your colleagues in sync by combining modern cloud storage services, the local file system, and simple web applications

PubMed Central

Rautenberg, Philipp L.; Kumaraswamy, Ajayrama; Tejero-Cantero, Alvaro; Doblander, Christoph; Norouzian, Mohammad R.; Kai, Kazuki; Jacobsen, Hans-Arno; Ai, Hiroyuki; Wachtler, Thomas; Ikeno, Hidetoshi

2014-01-01

Neuroscience today deals with a “data deluge” derived from the availability of high-throughput sensors of brain structure and brain activity, and increased computational resources for detailed simulations with complex output. We report here (1) a novel approach to data sharing between collaborating scientists that brings together file system tools and cloud technologies, (2) a service implementing this approach, called NeuronDepot, and (3) an example application of the service to a complex use case in the neurosciences. The main drivers for our approach are to facilitate collaborations with a transparent, automated data flow that shields scientists from having to learn new tools or data structuring paradigms. Using NeuronDepot is simple: one-time data assignment from the originator and cloud based syncing—thus making experimental and modeling data available across the collaboration with minimum overhead. Since data sharing is cloud based, our approach opens up the possibility of using new software developments and hardware scalabitliy which are associated with elastic cloud computing. We provide an implementation that relies on existing synchronization services and is usable from all devices via a reactive web interface. We are motivating our solution by solving the practical problems of the GinJang project, a collaboration of three universities across eight time zones with a complex workflow encompassing data from electrophysiological recordings, imaging, morphological reconstructions, and simulations. PMID:24971059

NeuronDepot: keeping your colleagues in sync by combining modern cloud storage services, the local file system, and simple web applications.

PubMed

Rautenberg, Philipp L; Kumaraswamy, Ajayrama; Tejero-Cantero, Alvaro; Doblander, Christoph; Norouzian, Mohammad R; Kai, Kazuki; Jacobsen, Hans-Arno; Ai, Hiroyuki; Wachtler, Thomas; Ikeno, Hidetoshi

2014-01-01

Neuroscience today deals with a "data deluge" derived from the availability of high-throughput sensors of brain structure and brain activity, and increased computational resources for detailed simulations with complex output. We report here (1) a novel approach to data sharing between collaborating scientists that brings together file system tools and cloud technologies, (2) a service implementing this approach, called NeuronDepot, and (3) an example application of the service to a complex use case in the neurosciences. The main drivers for our approach are to facilitate collaborations with a transparent, automated data flow that shields scientists from having to learn new tools or data structuring paradigms. Using NeuronDepot is simple: one-time data assignment from the originator and cloud based syncing-thus making experimental and modeling data available across the collaboration with minimum overhead. Since data sharing is cloud based, our approach opens up the possibility of using new software developments and hardware scalabitliy which are associated with elastic cloud computing. We provide an implementation that relies on existing synchronization services and is usable from all devices via a reactive web interface. We are motivating our solution by solving the practical problems of the GinJang project, a collaboration of three universities across eight time zones with a complex workflow encompassing data from electrophysiological recordings, imaging, morphological reconstructions, and simulations.

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

NASA Astrophysics Data System (ADS)

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

2017-03-01

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

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data.

PubMed

Ambrosini, Giovanna; Dreos, René; Kumar, Sunil; Bucher, Philipp

2016-11-18

ChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friendly tools for access, visualization and itegrative analysis of such data. Here we present the ChIP-Seq command line tools and web server, implementing basic algorithms for ChIP-seq data analysis starting with a read alignment file. The tools are optimized for memory-efficiency and speed thus allowing for processing of large data volumes on inexpensive hardware. The web interface provides access to a large database of public data. The ChIP-Seq tools have a modular and interoperable design in that the output from one application can serve as input to another one. Complex and innovative tasks can thus be achieved by running several tools in a cascade. The various ChIP-Seq command line tools and web services either complement or compare favorably to related bioinformatics resources in terms of computational efficiency, ease of access to public data and interoperability with other web-based tools. The ChIP-Seq server is accessible at http://ccg.vital-it.ch/chipseq/ .

Web Audio/Video Streaming Tool

NASA Technical Reports Server (NTRS)

Guruvadoo, Eranna K.

2003-01-01

In order to promote NASA-wide educational outreach program to educate and inform the public of space exploration, NASA, at Kennedy Space Center, is seeking efficient ways to add more contents to the web by streaming audio/video files. This project proposes a high level overview of a framework for the creation, management, and scheduling of audio/video assets over the web. To support short-term goals, the prototype of a web-based tool is designed and demonstrated to automate the process of streaming audio/video files. The tool provides web-enabled users interfaces to manage video assets, create publishable schedules of video assets for streaming, and schedule the streaming events. These operations are performed on user-defined and system-derived metadata of audio/video assets stored in a relational database while the assets reside on separate repository. The prototype tool is designed using ColdFusion 5.0.

Usability testing of ANSWER: a web-based methotrexate decision aid for patients with rheumatoid arthritis

PubMed Central

2013-01-01

Background Decision aids are evidence-based tools designed to inform people of the potential benefit and harm of treatment options, clarify their preferences and provide a shared decision-making structure for discussion at a clinic visit. For patients with rheumatoid arthritis (RA) who are considering methotrexate, we have developed a web-based patient decision aid called the ANSWER (Animated, Self-serve, Web-based Research Tool). This study aimed to: 1) assess the usability of the ANSWER prototype; 2) identify strengths and limitations of the ANSWER from the patient’s perspective. Methods The ANSWER prototype consisted of: 1) six animated patient stories and narrated information on the evidence of methotrexate for RA; 2) interactive questionnaires to clarify patients’ treatment preferences. Eligible participants for the usability test were patients with RA who had been prescribed methotrexate. They were asked to verbalize their thoughts (i.e., think aloud) while using the ANSWER, and to complete the System Usability Scale (SUS) to assess overall usability (range = 0-100; higher = more user friendly). Participants were audiotaped and observed, and field notes were taken. The testing continued until no new modifiable issues were found. We used descriptive statistics to summarize participant characteristics and the SUS scores. Content analysis was used to identified usability issues and navigation problems. Results 15 patients participated in the usability testing. The majority were aged 50 or over and were university/college graduates (n = 8, 53.4%). On average they took 56 minutes (SD = 34.8) to complete the tool. The mean SUS score was 81.2 (SD = 13.5). Content analysis of audiotapes and field notes revealed four categories of modifiable usability issues: 1) information delivery (i.e., clarity of the information and presentation style); 2) navigation control (i.e., difficulties in recognizing and using the navigation control buttons); 3) layout (i.e., position of the videos, text, diagrams and navigation buttons); 4) aesthetic (i.e., the colour, look and feel of the online tool). Conclusions Although the SUS score indicated high usability before and after major modification, findings from the think-aloud sessions illustrated areas that required further refinement. Our results highlight the importance of formative evaluation in usability testing. PMID:24289731

Usability testing of ANSWER: a web-based methotrexate decision aid for patients with rheumatoid arthritis.

PubMed

Li, Linda C; Adam, Paul M; Townsend, Anne F; Lacaille, Diane; Yousefi, Charlene; Stacey, Dawn; Gromala, Diane; Shaw, Chris D; Tugwell, Peter; Backman, Catherine L

2013-12-01

Decision aids are evidence-based tools designed to inform people of the potential benefit and harm of treatment options, clarify their preferences and provide a shared decision-making structure for discussion at a clinic visit. For patients with rheumatoid arthritis (RA) who are considering methotrexate, we have developed a web-based patient decision aid called the ANSWER (Animated, Self-serve, Web-based Research Tool). This study aimed to: 1) assess the usability of the ANSWER prototype; 2) identify strengths and limitations of the ANSWER from the patient's perspective. The ANSWER prototype consisted of: 1) six animated patient stories and narrated information on the evidence of methotrexate for RA; 2) interactive questionnaires to clarify patients' treatment preferences. Eligible participants for the usability test were patients with RA who had been prescribed methotrexate. They were asked to verbalize their thoughts (i.e., think aloud) while using the ANSWER, and to complete the System Usability Scale (SUS) to assess overall usability (range = 0-100; higher = more user friendly). Participants were audiotaped and observed, and field notes were taken. The testing continued until no new modifiable issues were found. We used descriptive statistics to summarize participant characteristics and the SUS scores. Content analysis was used to identified usability issues and navigation problems. 15 patients participated in the usability testing. The majority were aged 50 or over and were university/college graduates (n = 8, 53.4%). On average they took 56 minutes (SD = 34.8) to complete the tool. The mean SUS score was 81.2 (SD = 13.5). Content analysis of audiotapes and field notes revealed four categories of modifiable usability issues: 1) information delivery (i.e., clarity of the information and presentation style); 2) navigation control (i.e., difficulties in recognizing and using the navigation control buttons); 3) layout (i.e., position of the videos, text, diagrams and navigation buttons); 4) aesthetic (i.e., the colour, look and feel of the online tool). Although the SUS score indicated high usability before and after major modification, findings from the think-aloud sessions illustrated areas that required further refinement. Our results highlight the importance of formative evaluation in usability testing.

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

NASA Technical Reports Server (NTRS)

Heinrichs, W.; Smith, J.

1999-01-01

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

Reading the Writing on the Graffiti Wall: The World Wide Web and Training.

ERIC Educational Resources Information Center

Jones, Charles M.

This paper examines the benefits to be derived from networked computer-based instruction (CBI) and discusses the potential of the World Wide Web (WWW) as an effective tool in employee training. Methods of utilizing the WWW as a training tool and communication tool are explored. The discussion is divided into the following sections: (1) "WWW and…

e-CDRweb User Guide – Secondary Authorized Official

EPA Pesticide Factsheets

This document presents the user guide for the Office of Pollution Prevention and Toxics’ (OPPT) e-CDRweb tool. E-CDRweb is the electronic, web-based tool provided by the Environmental Protection Agency (EPA) for the submission of Chemical Data Reporting (CDR) information. This document is the user guide for the Secondary Authorized Official (AO) user of the e-CDR web tool.

CHOPPI: A Web Tool for the Analysis of Immunogenicity Risk from Host Cell Proteins in CHO-Based Protein Production

PubMed Central

Bailey-Kellogg, Chris; Gutiérrez, Andres H; Moise, Leonard; Terry, Frances; Martin, William D; De Groot, Anne S

2014-01-01

Despite high quality standards and continual process improvements in manufacturing, host cell protein (HCP) process impurities remain a substantial risk for biological products. Even at low levels, residual HCPs can induce a detrimental immune response compromising the safety and efficacy of a biologic. Consequently, advanced-stage clinical trials have been cancelled due to the identification of antibodies against HCPs. To enable earlier and rapid assessment of the risks in Chinese Hamster Ovary (CHO)-based protein production of residual CHO protein impurities (CHOPs), we have developed a web tool called CHOPPI, for CHO Protein Predicted Immunogenicity. CHOPPI integrates information regarding the possible presence of CHOPs (expression and secretion) with characterizations of their immunogenicity (T cell epitope count and density, and relative conservation with human counterparts). CHOPPI can generate a report for a specified CHO protein (e.g., identified from proteomics or immunoassays) or characterize an entire specified subset of the CHO genome (e.g., filtered based on confidence in transcription and similarity to human proteins). The ability to analyze potential CHOPs at a genomic scale provides a baseline to evaluate relative risk. We show here that CHOPPI can identify clear differences in immunogenicity risk among previously validated CHOPs, as well as identify additional “risky” CHO proteins that may be expressed during production and induce a detrimental immune response upon delivery. We conclude that CHOPPI is a powerful tool that provides a valuable computational complement to existing experimental approaches for CHOP risk assessment and can focus experimental efforts in the most important directions. Biotechnol. Bioeng. 2014;111: 2170–2182. PMID:24888712

Telehealth weight management intervention for adults with physical disabilities: a randomized controlled trial.

PubMed

Rimmer, James H; Wang, Edward; Pellegrini, Christine A; Lullo, Carolyn; Gerber, Ben S

2013-12-01

Weight reduction programs are not generally designed or adapted for people with physical disabilities. This study examined the effect of a 9-months remote, telephone-based weight management program for people with physical disabilities using a Web-based system (Personalized Online Weight and Exercise Response System [POWERS]). A total of 102 participants (mean ± SD age, 46.5 ± 12.7 yrs; body mass index, 32.0 ± 5.8 kg/m(2)) with a physical disability (spinal cord injury, multiple sclerosis, spina bifida, cerebral palsy, stroke, or lupus) were randomized to one of three conditions: physical activity only (POWERS), physical activity plus nutrition (POWERS(plus)), and control. The POWERS group received a physical activity tool kit and regular coaching telephone calls. The POWERS(plus) group received an intervention identical to that of the POWERS group plus nutritional information. The control group received the physical activity tool kit and self-guided health promotion resources at the completion of the trial but no coaching. Postintervention differences in body weight were found between the groups. There was a significant group × time interaction (P < 0.01) in postintervention body weight, with both the POWERS and POWERS(plus) groups demonstrating greater reduction in body weight compared with the control group (POWERS: -2.1 ± 5.5 kg, -2.4 ± -5.9%; POWERS(plus): -0.5 ± 5.0 kg, -0.6 ± 4.3%; control: +2.6 ± 5.3 kg, 3.1 ± 7.4%). A low-cost telephone intervention supported with a Web-based remote coaching tool (POWERS) can be an effective strategy for assisting overweight adults with physical disabilities in maintaining or reducing their body weight.

An intelligent tool for activity data collection.

PubMed

Sarkar, A M Jehad

2011-01-01

Activity recognition systems using simple and ubiquitous sensors require a large variety of real-world sensor data for not only evaluating their performance but also training the systems for better functioning. However, a tremendous amount of effort is required to setup an environment for collecting such data. For example, expertise and resources are needed to design and install the sensors, controllers, network components, and middleware just to perform basic data collections. It is therefore desirable to have a data collection method that is inexpensive, flexible, user-friendly, and capable of providing large and diverse activity datasets. In this paper, we propose an intelligent activity data collection tool which has the ability to provide such datasets inexpensively without physically deploying the testbeds. It can be used as an inexpensive and alternative technique to collect human activity data. The tool provides a set of web interfaces to create a web-based activity data collection environment. It also provides a web-based experience sampling tool to take the user's activity input. The tool generates an activity log using its activity knowledge and the user-given inputs. The activity knowledge is mined from the web. We have performed two experiments to validate the tool's performance in producing reliable datasets.

Teaching a Foreign Language to Deaf People via Vodcasting & Web 2.0 Tools

NASA Astrophysics Data System (ADS)

Drigas, Athanasios; Vrettaros, John; Tagoulis, Alexandors; Kouremenos, Dimitris

This paper presents the design and development of an e-learning course in teaching deaf people in a foreign language, whose first language is the sign language. The course is based in e-material, vodcasting and web 2.0 tools such as social networking and blog The course has been designed especially for deaf people and it is exploring the possibilities that e-learning material vodcasting and web 2.0 tools can offer to enhance the learning process and achieve more effective learning results.

Do We Really Know how Much it Costs to Construct High Performance Buildings?

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

Livingston, Olga V.; Dillon, Heather E.; Halverson, Mark A.

2012-08-31

Understanding the cost of energy efficient construction is critical to decision makers in building design, code development, and energy analysis. How much does it cost to upgrade from R-13 to R-19 in a building wall? How much do low-e windows really cost? Can we put a dollar figure on commissioning? Answers to these questions have a fuzzy nature, based on educated guesses and industry lore. The response depends on location, perspective, bulk buying, and hand waving. This paper explores the development of a web tool intended to serve as a publicly available repository of building component costs. In 2011 themore » U.S. Department of Energy (DOE) funded the launch of a web tool called the Building Component Cost Community (BC3), dedicated to publishing building component costs from documented sources, actively gathering verifiable cost data from the users, and collecting feedback from a wide range of participants on the quality of the posted cost data. The updated BC3 database, available at http://bc3.pnnl.gov, went live on April 30, 2012. BC3 serves as the ultimate source of the energy-related component costs for DOE’s residential code development activities, including cost-effectiveness analyses. The paper discusses BC3 objectives, structure, functionality and the current content of the database. It aims to facilitate a dialog about the lack of verifiable transparent cost data, as well as introduce a web tool that helps to address the problem. The questions posed above will also be addressed by this paper, but they have to be resolved by the user community by providing feedback and cost data to the BC3 database, thus increasing transparency and removing information asymmetry.« less

Experimental evaluation of the impact of packet capturing tools for web services.

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

Choe, Yung Ryn; Mohapatra, Prasant; Chuah, Chen-Nee

Network measurement is a discipline that provides the techniques to collect data that are fundamental to many branches of computer science. While many capturing tools and comparisons have made available in the literature and elsewhere, the impact of these packet capturing tools on existing processes have not been thoroughly studied. While not a concern for collection methods in which dedicated servers are used, many usage scenarios of packet capturing now requires the packet capturing tool to run concurrently with operational processes. In this work we perform experimental evaluations of the performance impact that packet capturing process have on web-based services;more » in particular, we observe the impact on web servers. We find that packet capturing processes indeed impact the performance of web servers, but on a multi-core system the impact varies depending on whether the packet capturing and web hosting processes are co-located or not. In addition, the architecture and behavior of the web server and process scheduling is coupled with the behavior of the packet capturing process, which in turn also affect the web server's performance.« less

Accessibility, usability, and usefulness of a Web-based clinical decision support tool to enhance provider-patient communication around Self-management TO Prevent (STOP) Stroke.

PubMed

Anderson, Jane A; Godwin, Kyler M; Saleem, Jason J; Russell, Scott; Robinson, Joshua J; Kimmel, Barbara

2014-12-01

This article reports redesign strategies identified to create a Web-based user-interface for the Self-management TO Prevent (STOP) Stroke Tool. Members of a Stroke Quality Improvement Network (N = 12) viewed a visualization video of a proposed prototype and provided feedback on implementation barriers/facilitators. Stroke-care providers (N = 10) tested the Web-based prototype in think-aloud sessions of simulated clinic visits. Participants' dialogues were coded into themes. Access to comprehensive information and the automated features/systematized processes were the primary accessibility and usability facilitator themes. The need for training, time to complete the tool, and computer-centric care were identified as possible usability barriers. Patient accountability, reminders for best practice, goal-focused care, and communication/counseling themes indicate that the STOP Stroke Tool supports the paradigm of patient-centered care. The STOP Stroke Tool was found to prompt clinicians on secondary stroke-prevention clinical-practice guidelines, facilitate comprehensive documentation of evidence-based care, and support clinicians in providing patient-centered care through the shared decision-making process that occurred while using the action-planning/goal-setting feature of the tool. © The Author(s) 2013.

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

PubMed

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

2015-06-02

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

Perceived Benefits and Attitudes of Student Teachers to Web-Quest as a Motivating, Creative and Inquiry-Based Learning Tool in Education

ERIC Educational Resources Information Center

Aina, Samuel Ayobami; Sofowora, Alaba Olaniyi

2013-01-01

This study discussed how the Department of Teacher Education, University of Ibadan utilized Web-Quest as a motivating and creative tool to teach a compulsory and large pre-service teachers' Course (TEE 304) The study also investigated the attitude and perception of pre-service teachers to the use of Web-Quest. The results showed that the sample…

WebScope: A New Tool for Fusion Data Analysis and Visualization

NASA Astrophysics Data System (ADS)

Yang, Fei; Dang, Ningning; Xiao, Bingjia

2010-04-01

A visualization tool was developed through a web browser based on Java applets embedded into HTML pages, in order to provide a world access to the EAST experimental data. It can display data from various trees in different servers in a single panel. With WebScope, it is easier to make a comparison between different data sources and perform a simple calculation over different data sources.

Microbe-ID: an open source toolbox for microbial genotyping and species identification

PubMed Central

Tabima, Javier F.; Everhart, Sydney E.; Larsen, Meredith M.; Weisberg, Alexandra J.; Kamvar, Zhian N.; Tancos, Matthew A.; Smart, Christine D.; Chang, Jeff H.

2016-01-01

Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org) and provided a working implementation for the genus Phytophthora (phytophthora-id.org). In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID. PMID:27602267

The East London glaucoma prediction score: web-based validation of glaucoma risk screening tool

PubMed Central

Stephen, Cook; Benjamin, Longo-Mbenza

2013-01-01

AIM It is difficult for Optometrists and General Practitioners to know which patients are at risk. The East London glaucoma prediction score (ELGPS) is a web based risk calculator that has been developed to determine Glaucoma risk at the time of screening. Multiple risk factors that are available in a low tech environment are assessed to provide a risk assessment. This is extremely useful in settings where access to specialist care is difficult. Use of the calculator is educational. It is a free web based service. Data capture is user specific. METHOD The scoring system is a web based questionnaire that captures and subsequently calculates the relative risk for the presence of Glaucoma at the time of screening. Three categories of patient are described: Unlikely to have Glaucoma; Glaucoma Suspect and Glaucoma. A case review methodology of patients with known diagnosis is employed to validate the calculator risk assessment. RESULTS Data from the patient records of 400 patients with an established diagnosis has been captured and used to validate the screening tool. The website reports that the calculated diagnosis correlates with the actual diagnosis 82% of the time. Biostatistics analysis showed: Sensitivity = 88%; Positive predictive value = 97%; Specificity = 75%. CONCLUSION Analysis of the first 400 patients validates the web based screening tool as being a good method of screening for the at risk population. The validation is ongoing. The web based format will allow a more widespread recruitment for different geographic, population and personnel variables. PMID:23550097

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

PubMed Central

Paley, Suzanne M.; Krummenacker, Markus; Latendresse, Mario; Dale, Joseph M.; Lee, Thomas J.; Kaipa, Pallavi; Gilham, Fred; Spaulding, Aaron; Popescu, Liviu; Altman, Tomer; Paulsen, Ian; Keseler, Ingrid M.; Caspi, Ron

2010-01-01

Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc integrates the evolving understanding of the genes, proteins, metabolic network and regulatory network of an organism. This article provides an overview of Pathway Tools capabilities. The software performs multiple computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers and prediction of operons. It enables interactive editing of PGDBs by DB curators. It supports web publishing of PGDBs, and provides a large number of query and visualization tools. The software also supports comparative analyses of PGDBs, and provides several systems biology analyses of PGDBs including reachability analysis of metabolic networks, and interactive tracing of metabolites through a metabolic network. More than 800 PGDBs have been created using Pathway Tools by scientists around the world, many of which are curated DBs for important model organisms. Those PGDBs can be exchanged using a peer-to-peer DB sharing system called the PGDB Registry. PMID:19955237

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…

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

PubMed Central

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

2013-01-01

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

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.

A World Wide Web-based antimicrobial stewardship program improves efficiency, communication, and user satisfaction and reduces cost in a tertiary care pediatric medical center.

PubMed

Agwu, Allison L; Lee, Carlton K K; Jain, Sanjay K; Murray, Kara L; Topolski, Jason; Miller, Robert E; Townsend, Timothy; Lehmann, Christoph U

2008-09-15

Antimicrobial stewardship programs aim to reduce inappropriate hospital antimicrobial use. At the Johns Hopkins Children's Medical and Surgical Center (Baltimore, MD), we implemented a World Wide Web-based antimicrobial restriction program to address problems with the existing restriction program. A user survey identified opportunities for improvement of an existing antimicrobial restriction program and resulted in subsequent design, implementation, and evaluation of a World Wide Web-based antimicrobial restriction program at a 175-bed, tertiary care pediatric teaching hospital. The program provided automated clinical decision support, facilitated approval, and enhanced real-time communication among prescribers, pharmacists, and pediatric infectious diseases fellows. Approval status, duration, and rationale; missing request notifications; and expiring approvals were stored in a database that is accessible via a secure Intranet site. Before and after implementation of the program, user satisfaction, reports of missed and/or delayed doses, antimicrobial dispensing times, and cost were evaluated. After implementation of the program, there was a $370,069 reduction in projected annual cost associated with restricted antimicrobial use and an 11.6% reduction in the number of dispensed doses. User satisfaction increased from 22% to 68% and from 13% to 69% among prescribers and pharmacists, respectively. There were 21% and 32% reductions in the number of prescriber reports of missed and delayed doses, respectively, and there was a 37% reduction in the number of pharmacist reports of delayed approvals; measured dispensing times were unchanged (P = .24). In addition, 40% fewer restricted antimicrobial-related phone calls were noted by the pharmacy. The World Wide Web-based antimicrobial approval program led to improved communication, more-efficient antimicrobial administration, increased user satisfaction, and significant cost savings. Integrated tools, such as this World Wide Web-based antimicrobial approval program, will effectively enhance antimicrobial stewardship programs.

READY: a web-based geographical information system for enhanced flood resilience through raising awareness in citizens

NASA Astrophysics Data System (ADS)

Albano, R.; Sole, A.; Adamowski, J.

2015-02-01

As evidenced by the EU Floods Directive (2007/60/EC), flood management strategies in Europe have undergone a shift in focus in recent years. The goal of flood prevention using structural measures has been replaced by an emphasis on the management of flood risks using non-structural measures. One implication of this is that it is no longer public authorities alone who take responsibility for flood management. A broader range of stakeholders, who may experience the negative effects of flooding, also take on responsibility to protect themselves. Therefore, it is vital that information concerning flood risks are conveyed to those who may be affected in order to facilitate the self-protection of citizens. Experience shows that even where efforts have been made to communicate flood risks, problems persist. There is a need for the development of new tools, which are able to rapidly disseminate flood risk information to the general public. To be useful, these tools must be able to present information relevant to the location of the user. Moreover, the content and design of the tool need to be adjusted to laypeople's needs. Dissemination and communication influences both people's access to and understanding of natural risk information. Such a tool could be a useful aid to effective management of flood risks. To address this gap, a Web-based Geographical Information System, (WebGIS), has been developed through the collaborative efforts of a group of scientists, hazard and risk analysts and managers, GIS analysts, system developers and communication designers. This tool, called "READY: Risk, Extreme Events, Adaptation, Defend Yourself", aims to enhance the general public knowledge of flood risk, making them more capable of responding appropriately during a flood event. The READY WebGIS has allowed for the visualization and easy querying of a complex hazard and risk database thanks to a high degree of interactivity and its easily readable maps. In this way, READY has enabled fast exploration of alternative flood scenarios or past calamitous events. Combined also with a system of graphic symbols designed ad hoc for communication of self-protection behaviors, it is believed READY could lead to an increase in citizen participation, informed discussion and consensus building. The platform has been developed for a site-specific application, i.e. the Basilicata Region, Italy, has been selected as pilot application area. The goal of the prototype is to raise citizen awareness of flood risks, and to build social capacity and enhanced resilience to flood events.

READY: a web-based geographical information system for enhanced flood resilience through raising awareness in citizens

NASA Astrophysics Data System (ADS)

Albano, R.; Sole, A.; Adamowski, J.

2015-07-01

As evidenced by the EU Floods Directive (2007/60/EC), flood management strategies in Europe have undergone a shift in focus in recent years. The goal of flood prevention using structural measures has been replaced by an emphasis on the management of flood risks using non-structural measures. One implication of this is that public authorities alone not only take responsibility for flood management. A broader range of stakeholders, who may personally experience the negative effects of flooding, also take on responsibility for protecting themselves. Therefore, it is vital that information concerning flood risks is conveyed to those who may be affected in order to facilitate the self-protection of citizens. Experience shows that problems persist even where efforts have been made to communicate flood risks. There is a need for the development of new tools that are able to rapidly disseminate flood-risk information to the general public. To be useful these tools must be able to present information relevant to the location of the user. Moreover, the content and design of the tool need to be adjusted to laypeople's needs. Dissemination and communication influence both people's access to and understanding of natural risk information. Such a tool could be a useful aid to effective management of flood risks. To address this gap, a web-based geographical information system (WebGIS) has been developed through the collaborative efforts of a group of scientists, hazard and risk analysts and managers, GIS analysts, system developers and communication designers. This tool, called "READY: Risk, Extreme Events, Adaptation, Defend Yourself", aims to enhance the general public knowledge of flood risk, making citizens more capable of responding appropriately during a flood event. The READY WebGIS has allowed for the visualization and easy querying of a complex hazard and risk database thanks to a high degree of interactivity and easily read maps. In this way, READY has enabled fast exploration of alternative flood scenarios or past calamitous events. Combined also with a system of graphic symbols designed ad hoc for communication of self-protection behaviours, it is believed READY could lead to an increase in citizen participation, informed discussion and consensus building. The platform has been developed for a site-specific application: the Basilicata region, Italy, has been selected as pilot application area. The goal of the prototype is to raise citizen awareness of flood risks and to build social capacity and enhanced resilience to flood events.

A web-based intervention for elementary school teachers of students with attention-deficit/hyperactivity disorder (ADHD).

PubMed

Barnett, Brittany; Corkum, Penny; Elik, Nezihe

2012-05-01

The goal of the present study was to determine whether a web-based medium is an effective tool for supporting knowledge, attitude, and behavior change in teachers of elementary school children with attention-deficit/hyperactivity disorder (ADHD). Nineteen teachers from Nova Scotia, Canada completed a 7-week intervention that consisted of presentations, web links, and discussion board activities related to different aspects of ADHD. Teachers' knowledge positively changed from pre- to post-intervention (p = .03), as did teachers' attitudes related to perceived control in their classrooms (p = .001) and competence in teaching (p < .0001). The study demonstrated that a web-based medium is a useful tool for knowledge creation and translation and has potential as a means of providing professional development to teachers about ADHD.

MycoCosm, an Integrated Fungal Genomics Resource

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

Shabalov, Igor; Grigoriev, Igor

2012-03-16

MycoCosm is a web-based interactive fungal genomics resource, which was first released in March 2010, in response to an urgent call from the fungal community for integration of all fungal genomes and analytical tools in one place (Pan-fungal data resources meeting, Feb 21-22, 2010, Alexandria, VA). MycoCosm integrates genomics data and analysis tools to navigate through over 100 fungal genomes sequenced at JGI and elsewhere. This resource allows users to explore fungal genomes in the context of both genome-centric analysis and comparative genomics, and promotes user community participation in data submission, annotation and analysis. MycoCosm has over 4500 unique visitors/monthmore » or 35000+ visitors/year as well as hundreds of registered users contributing their data and expertise to this resource. Its scalable architecture allows significant expansion of the data expected from JGI Fungal Genomics Program, its users, and integration with external resources used by fungal community.« less

An effective automatic procedure for testing parameter identifiability of HIV/AIDS models.

PubMed

Saccomani, Maria Pia

2011-08-01

Realistic HIV models tend to be rather complex and many recent models proposed in the literature could not yet be analyzed by traditional identifiability testing techniques. In this paper, we check a priori global identifiability of some of these nonlinear HIV models taken from the recent literature, by using a differential algebra algorithm based on previous work of the author. The algorithm is implemented in a software tool, called DAISY (Differential Algebra for Identifiability of SYstems), which has been recently released (DAISY is freely available on the web site http://www.dei.unipd.it/~pia/ ). The software can be used to automatically check global identifiability of (linear and) nonlinear models described by polynomial or rational differential equations, thus providing a general and reliable tool to test global identifiability of several HIV models proposed in the literature. It can be used by researchers with a minimum of mathematical background.

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters

PubMed Central

Ono, Keiichiro; Demchak, Barry; Ideker, Trey

2014-01-01

In this paper we present new data export modules for Cytoscape 3 that can generate network files for Cytoscape.js and D3.js. Cytoscape.js exporter is implemented as a core feature of Cytoscape 3, and D3.js exporter is available as a Cytoscape 3 app. These modules enable users to seamlessly export network and table data sets generated in Cytoscape to popular JavaScript library readable formats. In addition, we implemented template web applications for browser-based interactive network visualization that can be used as basis for complex data visualization applications for bioinformatics research. Example web applications created with these tools demonstrate how Cytoscape works in modern data visualization workflows built with traditional desktop tools and emerging web-based technologies. This interactivity enables researchers more flexibility than with static images, thereby greatly improving the quality of insights researchers can gain from them. PMID:25520778

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters.

PubMed

Ono, Keiichiro; Demchak, Barry; Ideker, Trey

2014-01-01

In this paper we present new data export modules for Cytoscape 3 that can generate network files for Cytoscape.js and D3.js. Cytoscape.js exporter is implemented as a core feature of Cytoscape 3, and D3.js exporter is available as a Cytoscape 3 app. These modules enable users to seamlessly export network and table data sets generated in Cytoscape to popular JavaScript library readable formats. In addition, we implemented template web applications for browser-based interactive network visualization that can be used as basis for complex data visualization applications for bioinformatics research. Example web applications created with these tools demonstrate how Cytoscape works in modern data visualization workflows built with traditional desktop tools and emerging web-based technologies. This interactivity enables researchers more flexibility than with static images, thereby greatly improving the quality of insights researchers can gain from them.

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…

A World-Wide Net of Solar Radio Spectrometers: e-CALLISTO

NASA Astrophysics Data System (ADS)

Benz, A. O.; Monstein, C.; Meyer, H.; Manoharan, P. K.; Ramesh, R.; Altyntsev, A.; Lara, A.; Paez, J.; Cho, K.-S.

2009-04-01

Radio spectrometers of the CALLISTO type to observe solar flares have been distributed to nine locations around the globe. The instruments observe automatically, their data is collected every day via internet and stored in a central data base. A public web-interface exists through which data can be browsed and retrieved. The nine instruments form a network called e-CALLISTO. It is still growing in the number of stations, as redundancy is desirable for full 24 h coverage of the solar radio emission in the meter and low decimeter band. The e-CALLISTO system has already proven to be a valuable new tool for monitoring solar activity and for space weather research.

Economics: A Discriminant Analysis of Students' Perceptions of Web-Based Learning.

ERIC Educational Resources Information Center

Usip, Ebenge E.; Bee, Richard H.

1998-01-01

Users and nonusers of Web-based instruction (WBI) in an undergraduate statistics classes at Youngstown State University were surveyed. Users concluded that distance learning via the Web was a good method of obtaining general information and useful tool in improving their academic performance. Nonusers thought the university should provide…

QUEST: An Assessment Tool for Web-Based Learning.

ERIC Educational Resources Information Center

Choren, Ricardo; Blois, Marcelo; Fuks, Hugo

In 1997, the Software Engineering Laboratory at Pontifical Catholic University of Rio de Janeiro (Brazil) implemented the first version of AulaNet (TM) a World Wide Web-based educational environment. Some of the teaching staff will use this environment in 1998 to offer regular term disciplines through the Web. This paper introduces Quest, a tool…

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…

DiAs Web Monitoring: A Real-Time Remote Monitoring System Designed for Artificial Pancreas Outpatient Trials

PubMed Central

Place, Jérôme; Robert, Antoine; Brahim, Najib Ben; Patrick, Keith-Hynes; Farret, Anne; Marie-Josée, Pelletier; Buckingham, Bruce; Breton, Marc; Kovatchev, Boris; Renard, Eric

2013-01-01

Background Developments in an artificial pancreas (AP) for patients with type 1 diabetes have allowed a move toward performing outpatient clinical trials. “Home-like” environment implies specific protocol and system adaptations among which the introduction of remote monitoring is meaningful. We present a novel tool allowing multiple patients to monitor AP use in home-like settings. Methods We investigated existing systems, performed interviews of experienced clinical teams, listed required features, and drew several mockups of the user interface. The resulting application was tested on the bench before it was used in three outpatient studies representing 3480 h of remote monitoring. Results Our tool, called DiAs Web Monitoring (DWM), is a web-based application that ensures reception, storage, and display of data sent by AP systems. Continuous glucose monitoring (CGM) and insulin delivery data are presented in a colored chart to facilitate reading and interpretation. Several subjects can be monitored simultaneously on the same screen, and alerts are triggered to help detect events such as hypoglycemia or CGM failures. In the third trial, DWM received approximately 460 data per subject per hour: 77% for log messages, 5% for CGM data. More than 97% of transmissions were achieved in less than 5 min. Conclusions Transition from a hospital setting to home-like conditions requires specific AP supervision to which remote monitoring systems can contribute valuably. DiAs Web Monitoring worked properly when tested in our outpatient studies. It could facilitate subject monitoring and even accelerate medical and technical assessment of the AP. It should now be adapted for long-term studies with an enhanced notification feature. J Diabetes Sci Technol 2013;7(6):1427–1435 PMID:24351169

DiAs web monitoring: a real-time remote monitoring system designed for artificial pancreas outpatient trials.

PubMed

Place, Jérôme; Robert, Antoine; Ben Brahim, Najib; Keith-Hynes, Patrick; Farret, Anne; Pelletier, Marie-Josée; Buckingham, Bruce; Breton, Marc; Kovatchev, Boris; Renard, Eric

2013-11-01

Developments in an artificial pancreas (AP) for patients with type 1 diabetes have allowed a move toward performing outpatient clinical trials. "Home-like" environment implies specific protocol and system adaptations among which the introduction of remote monitoring is meaningful. We present a novel tool allowing multiple patients to monitor AP use in home-like settings. We investigated existing systems, performed interviews of experienced clinical teams, listed required features, and drew several mockups of the user interface. The resulting application was tested on the bench before it was used in three outpatient studies representing 3480 h of remote monitoring. Our tool, called DiAs Web Monitoring (DWM), is a web-based application that ensures reception, storage, and display of data sent by AP systems. Continuous glucose monitoring (CGM) and insulin delivery data are presented in a colored chart to facilitate reading and interpretation. Several subjects can be monitored simultaneously on the same screen, and alerts are triggered to help detect events such as hypoglycemia or CGM failures. In the third trial, DWM received approximately 460 data per subject per hour: 77% for log messages, 5% for CGM data. More than 97% of transmissions were achieved in less than 5 min. Transition from a hospital setting to home-like conditions requires specific AP supervision to which remote monitoring systems can contribute valuably. DiAs Web Monitoring worked properly when tested in our outpatient studies. It could facilitate subject monitoring and even accelerate medical and technical assessment of the AP. It should now be adapted for long-term studies with an enhanced notification feature. © 2013 Diabetes Technology Society.

[EEQ in clinical embryology: a starting program].

PubMed

Boyer, Pierre; Brugnon, Florence; Levy, Rachel; Pfeffer, Jérôme; Siest, Jean-Pascal

2014-01-01

Every laboratory including those working in assisted reproductive technologies have to be accredited EN ISO 15189 before 2020. This standardisation includes an external quality evaluation (EQE). In order to work out an EQE tool, we used images extracted from our own database developed during daily practice. We achieved an easily online tool called: "EEQ en embryologie clinique", developed on Biologie prospective web site with ART French biologists Association (Blefco) expertise in evaluation of early human embryonic stages. In 2013, 38 ART laboratories participate to the first program with more than 90% of appropriates results. The present article aims at describing this tool and discussing its limits.

Document Exploration and Automatic Knowledge Extraction for Unstructured Biomedical Text

NASA Astrophysics Data System (ADS)

Chu, S.; Totaro, G.; Doshi, N.; Thapar, S.; Mattmann, C. A.; Ramirez, P.

2015-12-01

We describe our work on building a web-browser based document reader with built-in exploration tool and automatic concept extraction of medical entities for biomedical text. Vast amounts of biomedical information are offered in unstructured text form through scientific publications and R&D reports. Utilizing text mining can help us to mine information and extract relevant knowledge from a plethora of biomedical text. The ability to employ such technologies to aid researchers in coping with information overload is greatly desirable. In recent years, there has been an increased interest in automatic biomedical concept extraction [1, 2] and intelligent PDF reader tools with the ability to search on content and find related articles [3]. Such reader tools are typically desktop applications and are limited to specific platforms. Our goal is to provide researchers with a simple tool to aid them in finding, reading, and exploring documents. Thus, we propose a web-based document explorer, which we called Shangri-Docs, which combines a document reader with automatic concept extraction and highlighting of relevant terms. Shangri-Docsalso provides the ability to evaluate a wide variety of document formats (e.g. PDF, Words, PPT, text, etc.) and to exploit the linked nature of the Web and personal content by performing searches on content from public sites (e.g. Wikipedia, PubMed) and private cataloged databases simultaneously. Shangri-Docsutilizes Apache cTAKES (clinical Text Analysis and Knowledge Extraction System) [4] and Unified Medical Language System (UMLS) to automatically identify and highlight terms and concepts, such as specific symptoms, diseases, drugs, and anatomical sites, mentioned in the text. cTAKES was originally designed specially to extract information from clinical medical records. Our investigation leads us to extend the automatic knowledge extraction process of cTAKES for biomedical research domain by improving the ontology guided information extraction process. We will describe our experience and implementation of our system and share lessons learned from our development. We will also discuss ways in which this could be adapted to other science fields. [1] Funk et al., 2014. [2] Kang et al., 2014. [3] Utopia Documents, http://utopiadocs.com [4] Apache cTAKES, http://ctakes.apache.org

The Adversarial Route Analysis Tool: A Web Application

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

Casson, William H. Jr.

2012-08-02

The Adversarial Route Analysis Tool is a type of Google maps for adversaries. It's a web-based Geospatial application similar to Google Maps. It helps the U.S. government plan operations that predict where an adversary might be. It's easily accessible and maintainble and it's simple to use without much training.

What Do Faculty Want?

ERIC Educational Resources Information Center

Chizmar, John F.; Williams, David B.

2001-01-01

Uses classroom experience and data from a faculty survey to explore what faculty want from instructional technology. Presents several assertions, such as "faculty want instructional technology driven by pedagogical goals" and "faculty desire Web-based tools designed for a specific pedagogical task as opposed to a Swiss-Army-knife Web tool designed…

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…

Design and Evaluation of a Web-Based Symptom Monitoring Tool for Heart Failure.

PubMed

Wakefield, Bonnie J; Alexander, Gregory; Dohrmann, Mary; Richardson, James

2017-05-01

Heart failure is a chronic condition where symptom recognition and between-visit communication with providers are critical. Patients are encouraged to track disease-specific data, such as weight and shortness of breath. Use of a Web-based tool that facilitates data display in graph form may help patients recognize exacerbations and more easily communicate out-of-range data to clinicians. The purposes of this study were to (1) design a Web-based tool to facilitate symptom monitoring and symptom recognition in patients with chronic heart failure and (2) conduct a usability evaluation of the Web site. Patient participants generally had a positive view of the Web site and indicated it would support recording their health status and communicating with their doctors. Clinician participants generally had a positive view of the Web site and indicated it would be a potentially useful adjunct to electronic health delivery systems. Participants expressed a need to incorporate decision support within the site and wanted to add other data, for example, blood pressure, and have the ability to adjust font size. A few expressed concerns about data privacy and security. Technologies require careful design and testing to ensure they are useful, usable, and safe for patients and do not add to the burden of busy providers.

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

PubMed

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

2015-01-01

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

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

PubMed Central

2015-01-01

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

CONSORT-EHEALTH: Improving and Standardizing Evaluation Reports of Web-based and Mobile Health Interventions

PubMed Central

2011-01-01

Background Web-based and mobile health interventions (also called “Internet interventions” or "eHealth/mHealth interventions") are tools or treatments, typically behaviorally based, that are operationalized and transformed for delivery via the Internet or mobile platforms. These include electronic tools for patients, informal caregivers, healthy consumers, and health care providers. The Consolidated Standards of Reporting Trials (CONSORT) statement was developed to improve the suboptimal reporting of randomized controlled trials (RCTs). While the CONSORT statement can be applied to provide broad guidance on how eHealth and mHealth trials should be reported, RCTs of web-based interventions pose very specific issues and challenges, in particular related to reporting sufficient details of the intervention to allow replication and theory-building. Objective To develop a checklist, dubbed CONSORT-EHEALTH (Consolidated Standards of Reporting Trials of Electronic and Mobile HEalth Applications and onLine TeleHealth), as an extension of the CONSORT statement that provides guidance for authors of eHealth and mHealth interventions. Methods A literature review was conducted, followed by a survey among eHealth experts and a workshop. Results A checklist instrument was constructed as an extension of the CONSORT statement. The instrument has been adopted by the Journal of Medical Internet Research (JMIR) and authors of eHealth RCTs are required to submit an electronic checklist explaining how they addressed each subitem. Conclusions CONSORT-EHEALTH has the potential to improve reporting and provides a basis for evaluating the validity and applicability of eHealth trials. Subitems describing how the intervention should be reported can also be used for non-RCT evaluation reports. As part of the development process, an evaluation component is essential; therefore, feedback from authors will be solicited, and a before-after study will evaluate whether reporting has been improved. PMID:22209829

Minimizing Barriers in Learning for On-Call Radiology Residents-End-to-End Web-Based Resident Feedback System.

PubMed

Choi, Hailey H; Clark, Jennifer; Jay, Ann K; Filice, Ross W

2018-02-01

Feedback is an essential part of medical training, where trainees are provided with information regarding their performance and further directions for improvement. In diagnostic radiology, feedback entails a detailed review of the differences between the residents' preliminary interpretation and the attendings' final interpretation of imaging studies. While the on-call experience of independently interpreting complex cases is important to resident education, the more traditional synchronous "read-out" or joint review is impossible due to multiple constraints. Without an efficient method to compare reports, grade discrepancies, convey salient teaching points, and view images, valuable lessons in image interpretation and report construction are lost. We developed a streamlined web-based system, including report comparison and image viewing, to minimize barriers in asynchronous communication between attending radiologists and on-call residents. Our system provides real-time, end-to-end delivery of case-specific and user-specific feedback in a streamlined, easy-to-view format. We assessed quality improvement subjectively through surveys and objectively through participation metrics. Our web-based feedback system improved user satisfaction for both attending and resident radiologists, and increased attending participation, particularly with regards to cases where substantive discrepancies were identified.

Immediate Dissemination of Student Discoveries to a Model Organism Database Enhances Classroom-Based Research Experiences

PubMed Central

Wiley, Emily A.; Stover, Nicholas A.

2014-01-01

Use of inquiry-based research modules in the classroom has soared over recent years, largely in response to national calls for teaching that provides experience with scientific processes and methodologies. To increase the visibility of in-class studies among interested researchers and to strengthen their impact on student learning, we have extended the typical model of inquiry-based labs to include a means for targeted dissemination of student-generated discoveries. This initiative required: 1) creating a set of research-based lab activities with the potential to yield results that a particular scientific community would find useful and 2) developing a means for immediate sharing of student-generated results. Working toward these goals, we designed guides for course-based research aimed to fulfill the need for functional annotation of the Tetrahymena thermophila genome, and developed an interactive Web database that links directly to the official Tetrahymena Genome Database for immediate, targeted dissemination of student discoveries. This combination of research via the course modules and the opportunity for students to immediately “publish” their novel results on a Web database actively used by outside scientists culminated in a motivational tool that enhanced students’ efforts to engage the scientific process and pursue additional research opportunities beyond the course. PMID:24591511

Immediate dissemination of student discoveries to a model organism database enhances classroom-based research experiences.

PubMed

Wiley, Emily A; Stover, Nicholas A

2014-01-01

Use of inquiry-based research modules in the classroom has soared over recent years, largely in response to national calls for teaching that provides experience with scientific processes and methodologies. To increase the visibility of in-class studies among interested researchers and to strengthen their impact on student learning, we have extended the typical model of inquiry-based labs to include a means for targeted dissemination of student-generated discoveries. This initiative required: 1) creating a set of research-based lab activities with the potential to yield results that a particular scientific community would find useful and 2) developing a means for immediate sharing of student-generated results. Working toward these goals, we designed guides for course-based research aimed to fulfill the need for functional annotation of the Tetrahymena thermophila genome, and developed an interactive Web database that links directly to the official Tetrahymena Genome Database for immediate, targeted dissemination of student discoveries. This combination of research via the course modules and the opportunity for students to immediately "publish" their novel results on a Web database actively used by outside scientists culminated in a motivational tool that enhanced students' efforts to engage the scientific process and pursue additional research opportunities beyond the course.

The open research system: a web-based metadata and data repository for collaborative research

Treesearch

Charles M. Schweik; Alexander Stepanov; J. Morgan Grove

2005-01-01

Beginning in 1999, a web-based metadata and data repository we call the "open research system" (ORS) was designed and built to assist geographically distributed scientific research teams. The purpose of this innovation was to promote the open sharing of data within and across organizational lines and across geographic distances. As the use of the system...

Creating Project CREATE: Lessons Learned and Best Practices for Developing Web-Based Resources for Public Health Practitioners

ERIC Educational Resources Information Center

McGladrey, Margaret; Noar, Seth; Crosby, Richard; Young, April; Webb, Elizabeth

2012-01-01

Background: This paper discusses the Rural Center for AIDS/STD Prevention's effort to develop a web-based service called Project CREATE that responds to a need for targeted health promotion materials expressed by directors of HIV/STD prevention services in predominately rural states. Purpose: Project CREATE allows users to select customized…

Service-based analysis of biological pathways

PubMed Central

Zheng, George; Bouguettaya, Athman

2009-01-01

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

A Comprehensive Web-Based Patient Information Environment

DTIC Science & Technology

2001-10-25

hospitals. Keywords - I. INTRODUCTION This paper describes a comprehensive, web-enabled, patient - centric medical information system called PiRiLiS...clinically focused. The system was found to reduce time for medical administration. The ability to view the entire patient record at anytime, anywhere in...Abstract- The paper describes a new type of medical information environment which is fully web-enabled. The system can handle any type medical

Comparison of Physics Frameworks for WebGL-Based Game Engine

NASA Astrophysics Data System (ADS)

Yogya, Resa; Kosala, Raymond

2014-03-01

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

AWARE: Adaptive Software Monitoring and Dynamic Reconfiguration for Critical Infrastructure Protection

DTIC Science & Technology

2015-04-29

in which we applied these adaptation patterns to an adaptive news web server intended to tolerate extremely heavy, unexpected loads. To address...collection of existing models used as benchmarks for OO-based refactoring and an existing web -based repository called REMODD to provide users with model...invariant properties. Specifically, we developed Avida- MDE (based on the Avida digital evolution platform) to support the automatic generation of software

SU-E-T-29: A Web Application for GPU-Based Monte Carlo IMRT/VMAT QA with Delivered Dose Verification

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

Folkerts, M; University of California, San Diego, La Jolla, CA; Graves, Y

Purpose: To enable an existing web application for GPU-based Monte Carlo (MC) 3D dosimetry quality assurance (QA) to compute “delivered dose” from linac logfile data. Methods: We added significant features to an IMRT/VMAT QA web application which is based on existing technologies (HTML5, Python, and Django). This tool interfaces with python, c-code libraries, and command line-based GPU applications to perform a MC-based IMRT/VMAT QA. The web app automates many complicated aspects of interfacing clinical DICOM and logfile data with cutting-edge GPU software to run a MC dose calculation. The resultant web app is powerful, easy to use, and is ablemore » to re-compute both plan dose (from DICOM data) and delivered dose (from logfile data). Both dynalog and trajectorylog file formats are supported. Users upload zipped DICOM RP, CT, and RD data and set the expected statistic uncertainty for the MC dose calculation. A 3D gamma index map, 3D dose distribution, gamma histogram, dosimetric statistics, and DVH curves are displayed to the user. Additional the user may upload the delivery logfile data from the linac to compute a 'delivered dose' calculation and corresponding gamma tests. A comprehensive PDF QA report summarizing the results can also be downloaded. Results: We successfully improved a web app for a GPU-based QA tool that consists of logfile parcing, fluence map generation, CT image processing, GPU based MC dose calculation, gamma index calculation, and DVH calculation. The result is an IMRT and VMAT QA tool that conducts an independent dose calculation for a given treatment plan and delivery log file. The system takes both DICOM data and logfile data to compute plan dose and delivered dose respectively. Conclusion: We sucessfully improved a GPU-based MC QA tool to allow for logfile dose calculation. The high efficiency and accessibility will greatly facilitate IMRT and VMAT QA.« less

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

PubMed

Bui, Thanh Quang; Pham, Hai Minh

2016-01-01

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

An Analysis of the Elements of Collaboration Associated with Top Collaborative Tools

DTIC Science & Technology

2010-03-01

lets you access your e-mail, calendar, and files from any web browser anywhere in the world. Web based www.hotoffice.com Noodle Vialect’s (parent...www.taroby.org Yuuguu Yuuguu is an instant screen sharing, web conferencing, remote support, desktop remote control and messaging tool. Client...Office, Noodle , Novlet, Revizr, Taroby, and Yuuguu) received all seven NS ratings (see Table 20 below). The overall ratings for the major elements

Using Maps in Web Analytics to Evaluate the Impact of Web-Based Extension Programs

ERIC Educational Resources Information Center

Veregin, Howard

2015-01-01

Maps can be a valuable addition to the Web analytics toolbox for Extension programs that use the Web to disseminate information. Extension professionals use Web analytics tools to evaluate program impacts. Maps add a unique perspective through visualization and analysis of geographic patterns and their relationships to other variables. Maps can…

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

PubMed

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

2009-10-01

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

A journey to Semantic Web query federation in the life sciences

PubMed Central

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

2009-01-01

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

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

PubMed

O'Connell, Timothy; Chang, Debra

2012-01-01

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

SequenceCEROSENE: a computational method and web server to visualize spatial residue neighborhoods at the sequence level.

PubMed

Heinke, Florian; Bittrich, Sebastian; Kaiser, Florian; Labudde, Dirk

2016-01-01

To understand the molecular function of biopolymers, studying their structural characteristics is of central importance. Graphics programs are often utilized to conceive these properties, but with the increasing number of available structures in databases or structure models produced by automated modeling frameworks this process requires assistance from tools that allow automated structure visualization. In this paper a web server and its underlying method for generating graphical sequence representations of molecular structures is presented. The method, called SequenceCEROSENE (color encoding of residues obtained by spatial neighborhood embedding), retrieves the sequence of each amino acid or nucleotide chain in a given structure and produces a color coding for each residue based on three-dimensional structure information. From this, color-highlighted sequences are obtained, where residue coloring represent three-dimensional residue locations in the structure. This color encoding thus provides a one-dimensional representation, from which spatial interactions, proximity and relations between residues or entire chains can be deduced quickly and solely from color similarity. Furthermore, additional heteroatoms and chemical compounds bound to the structure, like ligands or coenzymes, are processed and reported as well. To provide free access to SequenceCEROSENE, a web server has been implemented that allows generating color codings for structures deposited in the Protein Data Bank or structure models uploaded by the user. Besides retrieving visualizations in popular graphic formats, underlying raw data can be downloaded as well. In addition, the server provides user interactivity with generated visualizations and the three-dimensional structure in question. Color encoded sequences generated by SequenceCEROSENE can aid to quickly perceive the general characteristics of a structure of interest (or entire sets of complexes), thus supporting the researcher in the initial phase of structure-based studies. In this respect, the web server can be a valuable tool, as users are allowed to process multiple structures, quickly switch between results, and interact with generated visualizations in an intuitive manner. The SequenceCEROSENE web server is available at https://biosciences.hs-mittweida.de/seqcerosene.

Metadata-Driven SOA-Based Application for Facilitation of Real-Time Data Warehousing

NASA Astrophysics Data System (ADS)

Pintar, Damir; Vranić, Mihaela; Skočir, Zoran

Service-oriented architecture (SOA) has already been widely recognized as an effective paradigm for achieving integration of diverse information systems. SOA-based applications can cross boundaries of platforms, operation systems and proprietary data standards, commonly through the usage of Web Services technology. On the other side, metadata is also commonly referred to as a potential integration tool given the fact that standardized metadata objects can provide useful information about specifics of unknown information systems with which one has interest in communicating with, using an approach commonly called "model-based integration". This paper presents the result of research regarding possible synergy between those two integration facilitators. This is accomplished with a vertical example of a metadata-driven SOA-based business process that provides ETL (Extraction, Transformation and Loading) and metadata services to a data warehousing system in need of a real-time ETL support.

Use of email and telephone prompts to increase self-monitoring in a Web-based intervention: randomized controlled trial.

PubMed

Greaney, Mary L; Sprunck-Harrild, Kim; Bennett, Gary G; Puleo, Elaine; Haines, Jess; Viswanath, K Vish; Emmons, Karen M

2012-07-27

Self-monitoring is a key behavior change mechanism associated with sustained health behavior change. Although Web-based interventions can offer user-friendly approaches for self-monitoring, engagement with these tools is suboptimal. Increased use could encourage, promote, and sustain behavior change. To determine whether email prompts or email plus telephone prompts increase self-monitoring of behaviors on a website created for a multiple cancer risk reduction program. We recruited and enrolled participants (N = 100) in a Web-based intervention during a primary care well visit at an urban primary care health center. The frequency of daily self-monitoring was tracked on the study website. Participants who tracked at least one behavior 3 or more times during week 1 were classified as meeting the tracking threshold and were assigned to the observation-only group (OO, n = 14). This group was followed but did not receive prompts. Participants who did not meet the threshold during week 1 were randomly assigned to one of 2 prompting conditions: automated assistance (AA, n = 36) or automated assistance + calls (AAC, n = 50). During prompting periods (weeks 2-3), participants in the AA and AAC conditions received daily automated emails that encouraged tracking and two tailored self-monitoring reports (end of week 2, end of week 3) that provided feedback on tracking frequency. Individuals in the AAC condition also received two technical assistance calls from trained study staff. Frequency of self-monitoring was tracked from week 2 through week 17. Self-monitoring rates increased in both intervention conditions during prompting and declined when prompting ceased. Over the 16 weeks of observation, there was a significant between-group difference in the percentage who met the self-monitoring threshold each week, with better maintenance in the AAC than in the AA condition (P < .001). Self-monitoring rates were greater in the OO group than in either the AA or AAC condition (P < .001). Prompting can increase self-monitoring rates. The decrease in self-monitoring after the promoting period suggests that additional reminder prompts would be useful. The use of technical assistance calls appeared to have a greater effect in promoting self-monitoring at a therapeutic threshold than email reminders and the tailored self-monitoring reports alone. ClinicalTrials.gov NCT01415492; http://clinicaltrials.gov/ct2/show/NCT01415492 (Archived by WebCite at http://www.webcitation.org/68LOXOMe2).

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

PubMed

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

2016-12-01

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

Gene Ontology-Based Analysis of Zebrafish Omics Data Using the Web Tool Comparative Gene Ontology.

PubMed

Ebrahimie, Esmaeil; Fruzangohar, Mario; Moussavi Nik, Seyyed Hani; Newman, Morgan

2017-10-01

Gene Ontology (GO) analysis is a powerful tool in systems biology, which uses a defined nomenclature to annotate genes/proteins within three categories: "Molecular Function," "Biological Process," and "Cellular Component." GO analysis can assist in revealing functional mechanisms underlying observed patterns in transcriptomic, genomic, and proteomic data. The already extensive and increasing use of zebrafish for modeling genetic and other diseases highlights the need to develop a GO analytical tool for this organism. The web tool Comparative GO was originally developed for GO analysis of bacterial data in 2013 ( www.comparativego.com ). We have now upgraded and elaborated this web tool for analysis of zebrafish genetic data using GOs and annotations from the Gene Ontology Consortium.

Assessing the Success Rate of Students Using a Learning Management System Together with a Collaborative Tool in Web-Based Teaching of Programming Languages

ERIC Educational Resources Information Center

Cavus, Nadire; Ibrahim, Dogan

2007-01-01

The development of collaborative studies in learning has led to a renewed interest in the field of Web-based education. In this experimental study a highly interactive and collaborative virtual teaching environment has been created by supporting Moodle LMS with collaborative learning tool GREWPtool. The aim of this experimental study has been to…

Development and Evaluation of a Web Map Mind Tool Environment with the Theory of Spatial Thinking and Project-Based Learning Strategy

ERIC Educational Resources Information Center

Hou, Huei-Tse; Yu, Tsai-Fang; Wu, Yi-Xuan; Sung, Yao-Ting; Chang, Kuo-En

2016-01-01

The theory of spatial thinking is relevant to the learning and teaching of many academic domains. One promising method to facilitate learners' higher-order thinking is to utilize a web map mind tool to assist learners in applying spatial thinking to cooperative problem solving. In this study, an environment is designed based on the theory of…

Continuous Improvement of Team Assignments: Using a Web-based Tool and the Plan-Do-Check-Act Cycle in Design and Redesign

ERIC Educational Resources Information Center

Morgan, Shona D.; Stewart, Alice C.

2017-01-01

The purpose of this brief is twofold. First, it describes a useful template for business instructors to improve teamwork assignment design and efficacy; and second, it provides an example of how to use data collected and analyzed from a Web-based tool, Comprehensive Assessment of Team Member Effectiveness (CATME). Though CATME has been the subject…

A Reflective E-Learning Journey from the Dawn of CALL to Web 2.0 Intercultural Communicative Competence (ICC)

ERIC Educational Resources Information Center

Orsini-Jones, Marina

2015-01-01

The author reflects on how she has used technology as a language teacher since the mid-1980s. She describes the evolution of technology in language learning pre- and Internet tools, from "blended learning" to social media. She concludes with the telecollaboration projects she has been recently working on and the issues they have found…

Faculty Usage of Social Media and Mobile Devices: Analysis of Advantages and Concerns

ERIC Educational Resources Information Center

Roebuck, Deborah Britt; Siha, Samia; Bell, Reginald L.

2013-01-01

This study seeks to understand the perceptions of professors using social media (also called Web 2.0 tools) in the classroom, what kinds of mobile devices are used to access the social media used, and what drives individuals to use them. In addition, it seeks to identify the advantages and concerns faculty has with the use of social media for…

Tools for Administration of a UNIX-Based Network

NASA Technical Reports Server (NTRS)

LeClaire, Stephen; Farrar, Edward

2004-01-01

Several computer programs have been developed to enable efficient administration of a large, heterogeneous, UNIX-based computing and communication network that includes a variety of computers connected to a variety of subnetworks. One program provides secure software tools for administrators to create, modify, lock, and delete accounts of specific users. This program also provides tools for users to change their UNIX passwords and log-in shells. These tools check for errors. Another program comprises a client and a server component that, together, provide a secure mechanism to create, modify, and query quota levels on a network file system (NFS) mounted by use of the VERITAS File SystemJ software. The client software resides on an internal secure computer with a secure Web interface; one can gain access to the client software from any authorized computer capable of running web-browser software. The server software resides on a UNIX computer configured with the VERITAS software system. Directories where VERITAS quotas are applied are NFS-mounted. Another program is a Web-based, client/server Internet Protocol (IP) address tool that facilitates maintenance lookup of information about IP addresses for a network of computers.

77 FR 28786 - Disaster Assistance; Crisis Counseling Regular Program; Amendment to Regulation

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-16

... individuals can call the National Suicide Prevention Lifeline at 1-800-273-TALK or via the Web at http://www.suicidepreventionlifeline.org . Callers are routed to a suicide prevention call center near them based on the area code from...

SeqMule: automated pipeline for analysis of human exome/genome sequencing data.

PubMed

Guo, Yunfei; Ding, Xiaolei; Shen, Yufeng; Lyon, Gholson J; Wang, Kai

2015-09-18

Next-generation sequencing (NGS) technology has greatly helped us identify disease-contributory variants for Mendelian diseases. However, users are often faced with issues such as software compatibility, complicated configuration, and no access to high-performance computing facility. Discrepancies exist among aligners and variant callers. We developed a computational pipeline, SeqMule, to perform automated variant calling from NGS data on human genomes and exomes. SeqMule integrates computational-cluster-free parallelization capability built on top of the variant callers, and facilitates normalization/intersection of variant calls to generate consensus set with high confidence. SeqMule integrates 5 alignment tools, 5 variant calling algorithms and accepts various combinations all by one-line command, therefore allowing highly flexible yet fully automated variant calling. In a modern machine (2 Intel Xeon X5650 CPUs, 48 GB memory), when fast turn-around is needed, SeqMule generates annotated VCF files in a day from a 30X whole-genome sequencing data set; when more accurate calling is needed, SeqMule generates consensus call set that improves over single callers, as measured by both Mendelian error rate and consistency. SeqMule supports Sun Grid Engine for parallel processing, offers turn-key solution for deployment on Amazon Web Services, allows quality check, Mendelian error check, consistency evaluation, HTML-based reports. SeqMule is available at http://seqmule.openbioinformatics.org.

Revel8or: Model Driven Capacity Planning Tool Suite

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

Zhu, Liming; Liu, Yan; Bui, Ngoc B.

2007-05-31

Designing complex multi-tier applications that must meet strict performance requirements is a challenging software engineering problem. Ideally, the application architect could derive accurate performance predictions early in the project life-cycle, leveraging initial application design-level models and a description of the target software and hardware platforms. To this end, we have developed a capacity planning tool suite for component-based applications, called Revel8tor. The tool adheres to the model driven development paradigm and supports benchmarking and performance prediction for J2EE, .Net and Web services platforms. The suite is composed of three different tools: MDAPerf, MDABench and DSLBench. MDAPerf allows annotation of designmore » diagrams and derives performance analysis models. MDABench allows a customized benchmark application to be modeled in the UML 2.0 Testing Profile and automatically generates a deployable application, with measurement automatically conducted. DSLBench allows the same benchmark modeling and generation to be conducted using a simple performance engineering Domain Specific Language (DSL) in Microsoft Visual Studio. DSLBench integrates with Visual Studio and reuses its load testing infrastructure. Together, the tool suite can assist capacity planning across platforms in an automated fashion.« less

Data in the Classroom: New Tools for Engaging Students with Data

NASA Astrophysics Data System (ADS)

Dean, A.; Pisut, D.

2017-12-01

The ability to understand and analyze data effectively can increase students ability to understand current and historical global change. Since 2009, NOAA Data in the Classroom Project has been offering formal education resources and tools aimed at helping teachers to build data and environmental literacy in their classrooms. Currently, NOAA is modernizing its Data in the Classroom resources using a web application within Esri's web-based GIS platform, Story Maps. Story Maps have been used for a wide variety of purposes, including teaching and instruction, for more than a decade. This technology can help to engage students in a story, like El Niño, while harnessing the power of data - using maps, data visualizations and data query tools. The aim is to create an effective education tool that allows students access to user-friendly, relevant data sets from NOAA, ultimately providing the opportunity to explore dynamic Earth processes and understand the impact of environmental events on a regional or global scale. This presentation will include demonstrations of the recently launched web-based curricular modules, highlighting the Esri web technology used to build and distribute each module and the interactive data tools that are unique to this project.

Map-IT! A Web-Based GIS Tool for Watershed Science Education.

ERIC Educational Resources Information Center

Curtis, David H.; Hewes, Christopher M.; Lossau, Matthew J.

This paper describes the development of a prototypic, Web-accessible GIS solution for K-12 science education and citizen-based watershed monitoring. The server side consists of ArcView IMS running on an NT workstation. The client is built around MapCafe. The client interface, which runs through a standard Web browser, supports standard MapCafe…

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

PubMed

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

2016-08-19

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

A Web-Based Learning Support System for Inquiry-Based Learning

NASA Astrophysics Data System (ADS)

Kim, Dong Won; Yao, Jingtao

The emergence of the Internet and Web technology makes it possible to implement the ideals of inquiry-based learning, in which students seek truth, information, or knowledge by questioning. Web-based learning support systems can provide a good framework for inquiry-based learning. This article presents a study on a Web-based learning support system called Online Treasure Hunt. The Web-based learning support system mainly consists of a teaching support subsystem, a learning support subsystem, and a treasure hunt game. The teaching support subsystem allows instructors to design their own inquiry-based learning environments. The learning support subsystem supports students' inquiry activities. The treasure hunt game enables students to investigate new knowledge, develop ideas, and review their findings. Online Treasure Hunt complies with a treasure hunt model. The treasure hunt model formalizes a general treasure hunt game to contain the learning strategies of inquiry-based learning. This Web-based learning support system empowered with the online-learning game and founded on the sound learning strategies furnishes students with the interactive and collaborative student-centered learning environment.

Teaching Tectonics to Undergraduates with Web GIS

NASA Astrophysics Data System (ADS)

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

2013-12-01

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