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

PubMed

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

2016-01-01

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

The Development of a Web-Based Virtual Environment for Teaching Qualitative Analysis of Structures

ERIC Educational Resources Information Center

O'Dwyer, D. W.; Logan-Phelan, T. M.; O'Neill, E. A.

2007-01-01

The current paper describes the design and development of a qualitative analysis course and an interactive web-based teaching and assessment tool called VSE (virtual structural environment). The widespread reliance on structural analysis programs requires engineers to be able to verify computer output by carrying out qualitative analyses.…

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

PubMed

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

2015-02-21

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

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

PubMed

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

2018-04-20

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

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.

Web-based analysis and publication of flow cytometry experiments.

PubMed

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

2010-07-01

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

Web-Based Analysis and Publication of Flow Cytometry Experiments

PubMed Central

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

2014-01-01

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

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…

Web tools for predictive toxicology model building.

PubMed

Jeliazkova, Nina

2012-07-01

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

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/ .

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…

Web-based tools for modelling and analysis of multivariate data: California ozone pollution activity

PubMed Central

Dinov, Ivo D.; Christou, Nicolas

2014-01-01

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 and statistical inference on these data are presented. All components of this case study (data, tools, activity) are freely available online at: http://wiki.stat.ucla.edu/socr/index.php/SOCR_MotionCharts_CAOzoneData. Several types of exploratory (motion charts, box-and-whisker plots, spider charts) and quantitative (inference, regression, analysis of variance (ANOVA)) data analyses tools are demonstrated. Two specific human health related questions (temporal and geographic effects of ozone pollution) are discussed as motivational challenges. PMID:24465054

Web-based tools for modelling and analysis of multivariate data: California ozone pollution activity.

PubMed

Dinov, Ivo D; Christou, Nicolas

2011-09-01

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 and statistical inference on these data are presented. All components of this case study (data, tools, activity) are freely available online at: http://wiki.stat.ucla.edu/socr/index.php/SOCR_MotionCharts_CAOzoneData. Several types of exploratory (motion charts, box-and-whisker plots, spider charts) and quantitative (inference, regression, analysis of variance (ANOVA)) data analyses tools are demonstrated. Two specific human health related questions (temporal and geographic effects of ozone pollution) are discussed as motivational challenges.

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

RSAT 2018: regulatory sequence analysis tools 20th anniversary.

PubMed

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

2018-05-02

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

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.

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…

miTRATA: a web-based tool for microRNA Truncation and Tailing Analysis.

PubMed

Patel, Parth; Ramachandruni, S Deepthi; Kakrana, Atul; Nakano, Mayumi; Meyers, Blake C

2016-02-01

We describe miTRATA, the first web-based tool for microRNA Truncation and Tailing Analysis--the analysis of 3' modifications of microRNAs including the loss or gain of nucleotides relative to the canonical sequence. miTRATA is implemented in Python (version 3) and employs parallel processing modules to enhance its scalability when analyzing multiple small RNA (sRNA) sequencing datasets. It utilizes miRBase, currently version 21, as a source of known microRNAs for analysis. miTRATA notifies user(s) via email to download as well as visualize the results online. miTRATA's strengths lie in (i) its biologist-focused web interface, (ii) improved scalability via parallel processing and (iii) its uniqueness as a webtool to perform microRNA truncation and tailing analysis. miTRATA is developed in Python and PHP. It is available as a web-based application from https://wasabi.dbi.udel.edu/∼apps/ta/. meyers@dbi.udel.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB.

PubMed

Lagerstedt, Ingvar; Moore, William J; Patwardhan, Ardan; Sanz-García, Eduardo; Best, Christoph; Swedlow, Jason R; Kleywegt, Gerard J

2013-11-01

The Protein Data Bank in Europe (PDBe) has developed web-based tools for the visualisation and analysis of 3D electron microscopy (3DEM) structures in the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB). The tools include: (1) a volume viewer for 3D visualisation of maps, tomograms and models, (2) a slice viewer for inspecting 2D slices of tomographic reconstructions, and (3) visual analysis pages to facilitate analysis and validation of maps, tomograms and models. These tools were designed to help non-experts and experts alike to get some insight into the content and assess the quality of 3DEM structures in EMDB and PDB without the need to install specialised software or to download large amounts of data from these archives. The technical challenges encountered in developing these tools, as well as the more general considerations when making archived data available to the user community through a web interface, are discussed. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

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

PubMed

Zhou, Guangyan; Xia, Jianguo

2018-06-07

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

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

NASA Astrophysics Data System (ADS)

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

2006-12-01

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

RSAT: regulatory sequence analysis tools.

PubMed

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

2008-07-01

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

STRESSED SEBATES: A TRAIT-BASED EVALUATION OF CLIMATE RISKS TO ROCKFISHES OF THE NORTHEASTERN PACIFIC USING THE COASTAL BIOGEOGRAPHIC RISK ANALYSIS TOOL (CBRAT)

EPA Science Inventory

The EPA and USGS have developed a framework to evaluate the relative vulnerability of near-coastal species to impacts of climate change. This framework is implemented in a web-based tool, the Coastal Biogeographic Risk Analysis Tool (CBRAT). We evaluated the vulnerability of the ...

Stressed Sebastes: A Trait-Based Evaluation of Climate Risks to Rockfishes of the Northeastern Pacific Using the Coastal Biogeographic Risk Analysis Tool (CBRAT)

EPA Science Inventory

The EPA and USGS have developed a framework to evaluate the relative vulnerability of near-coastal species to impacts of climate change. This framework was implemented in a web-based tool, the Coastal Biogeographic Risk Analysis Tool (CBRAT). We evaluated the vulnerability of the...

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

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

WebArray: an online platform for microarray data analysis

PubMed Central

Xia, Xiaoqin; McClelland, Michael; Wang, Yipeng

2005-01-01

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

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

USGS Publications Warehouse

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

2009-01-01

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

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.

Statistics, Structures & Satisfied Customers: Using Web Log Data to Improve Site Performance.

ERIC Educational Resources Information Center

Peacock, Darren

This paper explores some of the ways in which the National Museum of Australia is using Web analysis tools to shape its future directions in the delivery of online services. In particular, it explores the potential of quantitative analysis, based on Web server log data, to convert these ephemeral traces of user experience into a strategic…

Web 2.0 Technologies for Effective Knowledge Management in Organizations: A Qualitative Analysis

ERIC Educational Resources Information Center

Nath, Anupam Kumar

2012-01-01

A new generation of Internet-based collaborative tools, commonly known as Web 2.0, has increased in popularity, availability, and power in the last few years (Kane and Fichman, 2009). Web 2.0 is a set of Internet-based applications that harness network effects by facilitating collaborative and participative computing (O'Reilly, 2006).…

Using Hi-FAME (High Feedback-Assessment-Multimedia-Environment) Instructional Model in WBI: A Case Study for Biology Teacher Education.

ERIC Educational Resources Information Center

Wang, Tzu-Hua; Wang, Wei-Lung; Wang, Kuo-Hua; Huang, Shih-Chieh

The study attempted to adapt two web tools, FFS system (Frontpage Feedback System) and WATA system (Web-based Assessment and Test Analysis System), to construct a Hi-FAME (High Feedback-Assessment-Multimedia-Environment) Model in WBI (Web-based Instruction) to facilitate pre-service teacher training. Participants were 30 junior pre-service…

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)

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

Participation, Retention, and Utilization of a Web-Based Chronic Disease Self-Management Intervention Among Older Adults.

PubMed

Portz, Jennifer Dickman; LaMendola, Walter F

2018-05-21

Web-based self-management (web-based SM) interventions provide a potential resource for older adults to engage in their own chronic disease management. The purpose of this study is to investigate the effect of age on participation, retention, and utilization of a web-based SM intervention. This study reports the results of a secondary data analysis of the effects of age in a randomized trial of a web-based diabetes SM intervention. Participation, reasons for nonenrollment, retention, reasons for disenrollment, and website utilization were examined by age using discriminant function, survival analysis, and multivariate analysis of variance as appropriate. Website utilization by all participants dropped after 6 months but did not vary significantly with age. Though older adults (>60 of age) were less likely to choose to participate (F = 57.20, p < 0.001), a slight majority of participants in the experiment (53%) were over 66 years of age. Enrolled older adults utilized website management tools at a rate equivalent to younger participants. At termination, they often reported the experiment as burdensome, but tended to stay in the study longer than younger participants. Web-based SM offers a feasible approach for older adults with chronic disease to engage in their health management, but it needs to be improved. Those older adults who passed the rigorous screens for this experiment and chose to participate may have been more likely than younger participants to utilize web-based SM intervention tools. They were more persistent in their use of the web-based SM to try to improve health outcomes and formed definitive opinions about its utility before termination.

Web-Based Virtual Laboratory for Food Analysis Course

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Family history assessment for colorectal cancer (CRC) risk analysis - comparison of diagram- and questionnaire-based web interfaces.

PubMed

Schultz, Michael; Seo, Steven Bohwan; Holt, Alec; Regenbrecht, Holger

2015-11-18

Colorectal cancer (CRC) has a high incidence, especially in New Zealand. The reasons for this are unknown. While most cancers develop sporadically, a positive family history, determined by the number and age at diagnosis of affected first and second degree relatives with CRC is one of the major factors, which may increase an individual's lifetime risk. Before a patient can be enrolled in a surveillance program a detailed assessment and documentation of the family history is important but time consuming and often inaccurate. The documentation is usually paper-based. Our aim was therefore to develop and validate the usability and efficacy of a web-based family history assessment tool for CRC suitable for the general population. The tool was also to calculate the risk and make a recommendation for surveillance. Two versions of an electronic assessment tool, diagram-based and questionnaire-based, were developed with the risk analysis and recommendations for surveillance based on the New Zealand Guidelines Group recommendations. Accuracy of our tool was tested prior to the study by comparing risk calculations based on family history by experienced gastroenterologists with the electronic assessment. The general public, visiting a local science fair were asked to use and comment on the usability of the two interfaces. Ninety people assessed and commented on the two interfaces. Both interfaces were effective in assessing the risk to develop CRC through their familial history for CRC. However, the questionnaire-based interface performed with significantly better satisfaction (p = 0.001) than the diagram-based interface. There was no difference in efficacy though. We conclude that a web-based questionnaire tool can assist in the accurate documentation and analysis of the family history relevant to determine the individual risk of CRC based on local guidelines. The calculator is now implemented and assessable through the web-page of a local charity for colorectal cancer awareness and integral part of the local general practitioners' e-referral system for colonic imaging.

Expert system for web based collaborative CAE

NASA Astrophysics Data System (ADS)

Hou, Liang; Lin, Zusheng

2006-11-01

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

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.

A Powerful, Cost Effective, Web Based Engineering Solution Supporting Conjunction Detection and Visual Analysis

NASA Astrophysics Data System (ADS)

Novak, Daniel M.; Biamonti, Davide; Gross, Jeremy; Milnes, Martin

2013-08-01

An innovative and visually appealing tool is presented for efficient all-vs-all conjunction analysis on a large catalogue of objects. The conjunction detection uses a nearest neighbour search algorithm, based on spatial binning and identification of pairs of objects in adjacent bins. This results in the fastest all vs all filtering the authors are aware of. The tool is constructed on a server-client architecture, where the server broadcasts to the client the conjunction data and ephemerides, while the client supports the user interface through a modern browser, without plug-in. In order to make the tool flexible and maintainable, Java software technologies were used on the server side, including Spring, Camel, ActiveMQ and CometD. The user interface and visualisation are based on the latest web technologies: HTML5, WebGL, THREE.js. Importance has been given on the ergonomics and visual appeal of the software. In fact certain design concepts have been borrowed from the gaming industry.

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.)…

GET SMARTE: DECISION TOOLS TO REVITALIZE BROWNFIELDS

EPA Science Inventory

SMARTe (Sustainable Management Approaches and Revitalization Tools-electronic) is an open-source, web-based, decision-support system for developing and evaluating future use scenarios for potentially contaminated sites (i.e., brownfields). It contains resources and analysis tools...

Using Web Maps to Analyze the Construction of Global Scale Cognitive Maps

ERIC Educational Resources Information Center

Pingel, Thomas J.

2018-01-01

Game-based Web sites and applications are changing the ways in which students learn the world map. In this study, a Web map-based digital learning tool was used as a study aid for a university-level geography course in order to examine the way in which global scale cognitive maps are constructed. A network analysis revealed that clicks were…

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

PubMed

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

2016-02-06

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

COMAN: a web server for comprehensive metatranscriptomics analysis.

PubMed

Ni, Yueqiong; Li, Jun; Panagiotou, Gianni

2016-08-11

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

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.…

GET SMARTE: DECISION TOOLS TO REVITALIZE COMMUNITIES (MAY 2006)

EPA Science Inventory

SMARTe (Sustainable Management Approaches and Revitalization Tools-electronic) is an open-source, web-based, decision-support system for developing and evaluating future use scenarios for potentially contaminated sites (i.e., brownfields). It contains resources and analysis tools...

Developing web-based data analysis tools for precision farming using R and Shiny

NASA Astrophysics Data System (ADS)

Jahanshiri, Ebrahim; Mohd Shariff, Abdul Rashid

2014-06-01

Technologies that are set to increase the productivity of agricultural practices require more and more data. Nevertheless, farming data is also being increasingly cheap to collect and maintain. Bulk of data that are collected by the sensors and samples need to be analysed in an efficient and transparent manner. Web technologies have long being used to develop applications that can assist the farmers and managers. However until recently, analysing the data in an online environment has not been an easy task especially in the eyes of data analysts. This barrier is now overcome by the availability of new application programming interfaces that can provide real-time web based data analysis. In this paper developing a prototype web based application for data analysis using new facilities in R statistical package and its web development facility, Shiny is explored. The pros and cons of this type of data analysis environment for precision farming are enumerated and future directions in web application development for agricultural data are discussed.

ADAM: analysis of discrete models of biological systems using computer algebra.

PubMed

Hinkelmann, Franziska; Brandon, Madison; Guang, Bonny; McNeill, Rustin; Blekherman, Grigoriy; Veliz-Cuba, Alan; Laubenbacher, Reinhard

2011-07-20

Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, to gain a better understanding of them. The computational complexity to analyze the complete dynamics of these models grows exponentially in the number of variables, which impedes working with complex models. There exist software tools to analyze discrete models, but they either lack the algorithmic functionality to analyze complex models deterministically or they are inaccessible to many users as they require understanding the underlying algorithm and implementation, do not have a graphical user interface, or are hard to install. Efficient analysis methods that are accessible to modelers and easy to use are needed. We propose a method for efficiently identifying attractors and introduce the web-based tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other analysis methods for discrete models. ADAM converts several discrete model types automatically into polynomial dynamical systems and analyzes their dynamics using tools from computer algebra. Specifically, we propose a method to identify attractors of a discrete model that is equivalent to solving a system of polynomial equations, a long-studied problem in computer algebra. Based on extensive experimentation with both discrete models arising in systems biology and randomly generated networks, we found that the algebraic algorithms presented in this manuscript are fast for systems with the structure maintained by most biological systems, namely sparseness and robustness. For a large set of published complex discrete models, ADAM identified the attractors in less than one second. Discrete modeling techniques are a useful tool for analyzing complex biological systems and there is a need in the biological community for accessible efficient analysis tools. ADAM provides analysis methods based on mathematical algorithms as a web-based tool for several different input formats, and it makes analysis of complex models accessible to a larger community, as it is platform independent as a web-service and does not require understanding of the underlying mathematics.

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

PubMed Central

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

2016-01-01

3Drefine is an interactive web server for consistent and computationally efficient protein structure refinement with the capability to perform web-based statistical and visual analysis. The 3Drefine refinement protocol utilizes iterative optimization of hydrogen bonding network combined with atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields for efficient protein structure refinement. The method has been extensively evaluated on blind CASP experiments as well as on large-scale and diverse benchmark datasets and exhibits consistent improvement over the initial structure in both global and local structural quality measures. The 3Drefine web server allows for convenient protein structure refinement through a text or file input submission, email notification, provided example submission and is freely available without any registration requirement. The server also provides comprehensive analysis of submissions through various energy and statistical feedback and interactive visualization of multiple refined models through the JSmol applet that is equipped with numerous protein model analysis tools. The web server has been extensively tested and used by many users. As a result, the 3Drefine web server conveniently provides a useful tool easily accessible to the community. The 3Drefine web server has been made publicly available at the URL: http://sysbio.rnet.missouri.edu/3Drefine/. PMID:27131371

GREAT: a web portal for Genome Regulatory Architecture Tools

PubMed Central

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

2016-01-01

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

OptoBase: A web platform for molecular optogenetics.

PubMed

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

2018-06-18

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

GAC: Gene Associations with Clinical, a web based application.

PubMed

Zhang, Xinyan; Rupji, Manali; Kowalski, Jeanne

2017-01-01

We present GAC, a shiny R based tool for interactive visualization of clinical associations based on high-dimensional data. The tool provides a web-based suite to perform supervised principal component analysis (SuperPC), an approach that uses both high-dimensional data, such as gene expression, combined with clinical data to infer clinical associations. We extended the approach to address binary outcomes, in addition to continuous and time-to-event data in our package, thereby increasing the use and flexibility of SuperPC.  Additionally, the tool provides an interactive visualization for summarizing results based on a forest plot for both binary and time-to-event data.  In summary, the GAC suite of tools provide a one stop shop for conducting statistical analysis to identify and visualize the association between a clinical outcome of interest and high-dimensional data types, such as genomic data. Our GAC package has been implemented in R and is available via http://shinygispa.winship.emory.edu/GAC/. The developmental repository is available at https://github.com/manalirupji/GAC.

Molecular beacon sequence design algorithm.

PubMed

Monroe, W Todd; Haselton, Frederick R

2003-01-01

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

SMARTe 2008

EPA Science Inventory

Sustainable Management Approaches and Revitalization Tools - electronic (SMARTe), is an open-source, web-based, decision support system for developing and evaluating future reuse scenarios for potentially contaminated land. SMARTe contains resources and analysis tools for all asp...

SMARTe 2011

EPA Science Inventory

Sustainable Management Approaches and Revitalization Tools - electronic (SMARTe), is an open-source, web-based, decisions support system for developing and evaluating future reuse scenarios for potentially contaminated land. SMARTe contains resources and analysis tools for all a...

EnviroAtlas Webinar

EPA Pesticide Factsheets

EnviroAtlas is a web-based decision support tool that combines maps, analysis tools, downloadable data and informational resources that states, tribes and communities can use to help inform policy and planning decisions impacting their surroundings.

SMARTE 2007

EPA Science Inventory

Sustainable Management Approaches and Revitalization Tools-electronic (SMARTe), is an open-source, web-based, decision support system for developing and evaluating future reuse scenarios for potentially contaminated land. SMARTe contains guidance and analysis tools for all aspect...

How Teachers Use and Manage Their Blogs? A Cluster Analysis of Teachers' Blogs in Taiwan

ERIC Educational Resources Information Center

Liu, Eric Zhi-Feng; Hou, Huei-Tse

2013-01-01

The development of Web 2.0 has ushered in a new set of web-based tools, including blogs. This study focused on how teachers use and manage their blogs. A sample of 165 teachers' blogs in Taiwan was analyzed by factor analysis, cluster analysis and qualitative content analysis. First, the teachers' blogs were analyzed according to six criteria…

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

PubMed

Baltasar Sánchez, Alicia; González-Sistal, Angel

2011-04-01

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

Analysis Tool Web Services from the EMBL-EBI.

PubMed

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

2013-07-01

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

Analysis Tool Web Services from the EMBL-EBI

PubMed Central

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

2013-01-01

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

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 ...

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

PubMed Central

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

2000-01-01

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

Providing web-based tools for time series access and analysis

NASA Astrophysics Data System (ADS)

Eberle, Jonas; Hüttich, Christian; Schmullius, Christiane

2014-05-01

Time series information is widely used in environmental change analyses and is also an essential information for stakeholders and governmental agencies. However, a challenging issue is the processing of raw data and the execution of time series analysis. In most cases, data has to be found, downloaded, processed and even converted in the correct data format prior to executing time series analysis tools. Data has to be prepared to use it in different existing software packages. Several packages like TIMESAT (Jönnson & Eklundh, 2004) for phenological studies, BFAST (Verbesselt et al., 2010) for breakpoint detection, and GreenBrown (Forkel et al., 2013) for trend calculations are provided as open-source software and can be executed from the command line. This is needed if data pre-processing and time series analysis is being automated. To bring both parts, automated data access and data analysis, together, a web-based system was developed to provide access to satellite based time series data and access to above mentioned analysis tools. Users of the web portal are able to specify a point or a polygon and an available dataset (e.g., Vegetation Indices and Land Surface Temperature datasets from NASA MODIS). The data is then being processed and provided as a time series CSV file. Afterwards the user can select an analysis tool that is being executed on the server. The final data (CSV, plot images, GeoTIFFs) is visualized in the web portal and can be downloaded for further usage. As a first use case, we built up a complimentary web-based system with NASA MODIS products for Germany and parts of Siberia based on the Earth Observation Monitor (www.earth-observation-monitor.net). The aim of this work is to make time series analysis with existing tools as easy as possible that users can focus on the interpretation of the results. References: Jönnson, P. and L. Eklundh (2004). TIMESAT - a program for analysing time-series of satellite sensor data. Computers and Geosciences 30, 833-845. Verbesselt, J., R. Hyndman, G. Newnham and D. Culvenor (2010). Detecting trend and seasonal changes in satellite image time series. Remote Sensing of Environment, 114, 106-115. DOI: 10.1016/j.rse.2009.08.014 Forkel, M., N. Carvalhais, J. Verbesselt, M. Mahecha, C. Neigh and M. Reichstein (2013). Trend Change Detection in NDVI Time Series: Effects of Inter-Annual Variability and Methodology. Remote Sensing 5, 2113-2144.

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.

Cytoscape: the network visualization tool for GenomeSpace workflows.

PubMed

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

2014-01-01

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

Cytoscape: the network visualization tool for GenomeSpace workflows

PubMed Central

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

2014-01-01

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

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…

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

PubMed

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

2017-02-01

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

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.

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

ERIC Educational Resources Information Center

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

2006-01-01

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

GREAT: a web portal for Genome Regulatory Architecture Tools.

PubMed

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

2016-07-08

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

CASAS: Cancer Survival Analysis Suite, a web based application

PubMed Central

Rupji, Manali; Zhang, Xinyan; Kowalski, Jeanne

2017-01-01

We present CASAS, a shiny R based tool for interactive survival analysis and visualization of results. The tool provides a web-based one stop shop to perform the following types of survival analysis:  quantile, landmark and competing risks, in addition to standard survival analysis.  The interface makes it easy to perform such survival analyses and obtain results using the interactive Kaplan-Meier and cumulative incidence plots.  Univariate analysis can be performed on one or several user specified variable(s) simultaneously, the results of which are displayed in a single table that includes log rank p-values and hazard ratios along with their significance. For several quantile survival analyses from multiple cancer types, a single summary grid is constructed. The CASAS package has been implemented in R and is available via http://shinygispa.winship.emory.edu/CASAS/. The developmental repository is available at https://github.com/manalirupji/CASAS/. PMID:28928946

CASAS: Cancer Survival Analysis Suite, a web based application.

PubMed

Rupji, Manali; Zhang, Xinyan; Kowalski, Jeanne

2017-01-01

We present CASAS, a shiny R based tool for interactive survival analysis and visualization of results. The tool provides a web-based one stop shop to perform the following types of survival analysis:  quantile, landmark and competing risks, in addition to standard survival analysis.  The interface makes it easy to perform such survival analyses and obtain results using the interactive Kaplan-Meier and cumulative incidence plots.  Univariate analysis can be performed on one or several user specified variable(s) simultaneously, the results of which are displayed in a single table that includes log rank p-values and hazard ratios along with their significance. For several quantile survival analyses from multiple cancer types, a single summary grid is constructed. The CASAS package has been implemented in R and is available via http://shinygispa.winship.emory.edu/CASAS/. The developmental repository is available at https://github.com/manalirupji/CASAS/.

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

PubMed

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

2016-07-08

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

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

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.

The EMBL-EBI bioinformatics web and programmatic tools framework.

PubMed

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

2015-07-01

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

Modeling potential Emerald Ash Borer spread through GIS/cell-based/gravity models with data bolstered by web-based inputs

Treesearch

Louis R. Iverson; Anantha M. Prasad; Davis Sydnor; Jonathan Bossenbroek; Mark W. Schwartz; Mark W. Schwartz

2006-01-01

We model the susceptibility and potential spread of the organism across the eastern United States and especially through Michigan and Ohio using Forest Inventory and Analysis (FIA) data. We are also developing a cell-based model for the potential spread of the organism. We have developed a web-based tool for public agencies and private individuals to enter the...

The Use of Web 2.0 Tools by Students in Learning and Leisure Contexts: A Study in a Portuguese Institution of Higher Education

ERIC Educational Resources Information Center

Costa, Carolina; Alvelos, Helena; Teixeira, Leonor

2016-01-01

This study analyses and compares the use of Web 2.0 tools by students in both learning and leisure contexts. Data were collected based on a questionnaire applied to 234 students from the University of Aveiro (Portugal) and the results were analysed by using descriptive analysis, paired samples t-tests, cluster analyses and Kruskal-Wallis tests.…

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.

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

PubMed

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

2017-09-12

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

Science Initiatives of the US Virtual Astronomical Observatory

NASA Astrophysics Data System (ADS)

Hanisch, R. J.

2012-09-01

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

A Secure Web Application Providing Public Access to High-Performance Data Intensive Scientific Resources - ScalaBLAST Web Application

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

Curtis, Darren S.; Peterson, Elena S.; Oehmen, Chris S.

2008-05-04

This work presents the ScalaBLAST Web Application (SWA), a web based application implemented using the PHP script language, MySQL DBMS, and Apache web server under a GNU/Linux platform. SWA is an application built as part of the Data Intensive Computer for Complex Biological Systems (DICCBS) project at the Pacific Northwest National Laboratory (PNNL). SWA delivers accelerated throughput of bioinformatics analysis via high-performance computing through a convenient, easy-to-use web interface. This approach greatly enhances emerging fields of study in biology such as ontology-based homology, and multiple whole genome comparisons which, in the absence of a tool like SWA, require a heroicmore » effort to overcome the computational bottleneck associated with genome analysis. The current version of SWA includes a user account management system, a web based user interface, and a backend process that generates the files necessary for the Internet scientific community to submit a ScalaBLAST parallel processing job on a dedicated cluster.« less

An overview of the web-based Google Earth coincident imaging tool

USGS Publications Warehouse

Chander, Gyanesh; Kilough, B.; Gowda, S.

2010-01-01

The Committee on Earth Observing Satellites (CEOS) Visualization Environment (COVE) tool is a browser-based application that leverages Google Earth web to display satellite sensor coverage areas. The analysis tool can also be used to identify near simultaneous surface observation locations for two or more satellites. The National Aeronautics and Space Administration (NASA) CEOS System Engineering Office (SEO) worked with the CEOS Working Group on Calibration and Validation (WGCV) to develop the COVE tool. The CEOS member organizations are currently operating and planning hundreds of Earth Observation (EO) satellites. Standard cross-comparison exercises between multiple sensors to compare near-simultaneous surface observations and to identify corresponding image pairs are time-consuming and labor-intensive. COVE is a suite of tools that have been developed to make such tasks easier.

GAC: Gene Associations with Clinical, a web based application

PubMed Central

Zhang, Xinyan; Rupji, Manali; Kowalski, Jeanne

2018-01-01

We present GAC, a shiny R based tool for interactive visualization of clinical associations based on high-dimensional data. The tool provides a web-based suite to perform supervised principal component analysis (SuperPC), an approach that uses both high-dimensional data, such as gene expression, combined with clinical data to infer clinical associations. We extended the approach to address binary outcomes, in addition to continuous and time-to-event data in our package, thereby increasing the use and flexibility of SuperPC.  Additionally, the tool provides an interactive visualization for summarizing results based on a forest plot for both binary and time-to-event data.  In summary, the GAC suite of tools provide a one stop shop for conducting statistical analysis to identify and visualize the association between a clinical outcome of interest and high-dimensional data types, such as genomic data. Our GAC package has been implemented in R and is available via http://shinygispa.winship.emory.edu/GAC/. The developmental repository is available at https://github.com/manalirupji/GAC. PMID:29263780

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…

The MetabolomeExpress Project: enabling web-based processing, analysis and transparent dissemination of GC/MS metabolomics datasets.

PubMed

Carroll, Adam J; Badger, Murray R; Harvey Millar, A

2010-07-14

Standardization of analytical approaches and reporting methods via community-wide collaboration can work synergistically with web-tool development to result in rapid community-driven expansion of online data repositories suitable for data mining and meta-analysis. In metabolomics, the inter-laboratory reproducibility of gas-chromatography/mass-spectrometry (GC/MS) makes it an obvious target for such development. While a number of web-tools offer access to datasets and/or tools for raw data processing and statistical analysis, none of these systems are currently set up to act as a public repository by easily accepting, processing and presenting publicly submitted GC/MS metabolomics datasets for public re-analysis. Here, we present MetabolomeExpress, a new File Transfer Protocol (FTP) server and web-tool for the online storage, processing, visualisation and statistical re-analysis of publicly submitted GC/MS metabolomics datasets. Users may search a quality-controlled database of metabolite response statistics from publicly submitted datasets by a number of parameters (eg. metabolite, species, organ/biofluid etc.). Users may also perform meta-analysis comparisons of multiple independent experiments or re-analyse public primary datasets via user-friendly tools for t-test, principal components analysis, hierarchical cluster analysis and correlation analysis. They may interact with chromatograms, mass spectra and peak detection results via an integrated raw data viewer. Researchers who register for a free account may upload (via FTP) their own data to the server for online processing via a novel raw data processing pipeline. MetabolomeExpress https://www.metabolome-express.org provides a new opportunity for the general metabolomics community to transparently present online the raw and processed GC/MS data underlying their metabolomics publications. Transparent sharing of these data will allow researchers to assess data quality and draw their own insights from published metabolomics datasets.

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

NASA Astrophysics Data System (ADS)

Huang, Xiaodong; Zhu, Yeping

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

SMARTE: HELPING COMMUNITIES OVERCOME OBSTACLES TO REVITALIZATION (04/23/07)

EPA Science Inventory

Sustainable Management Approaches and Revitalization Tools - electronic (SMARTe), is an open-source, web-based, decision support system for developing and evaluating future reuse scenarios for potentially contaminated land. SMARTe contains information and analysis tools for all a...

The Gamma-Ray Burst ToolSHED is Open for Business

NASA Astrophysics Data System (ADS)

Giblin, Timothy W.; Hakkila, Jon; Haglin, David J.; Roiger, Richard J.

2004-09-01

The GRB ToolSHED, a Gamma-Ray Burst SHell for Expeditions in Data-Mining, is now online and available via a web browser to all in the scientific community. The ToolSHED is an online web utility that contains pre-processed burst attributes of the BATSE catalog and a suite of induction-based machine learning and statistical tools for classification and cluster analysis. Users create their own login account and study burst properties within user-defined multi-dimensional parameter spaces. Although new GRB attributes are periodically added to the database for user selection, the ToolSHED has a feature that allows users to upload their own burst attributes (e.g. spectral parameters, etc.) so that additional parameter spaces can be explored. A data visualization feature using GNUplot and web-based IDL has also been implemented to provide interactive plotting of user-selected session output. In an era in which GRB observations and attributes are becoming increasingly more complex, a utility such as the GRB ToolSHED may play an important role in deciphering GRB classes and understanding intrinsic burst properties.

ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra

PubMed Central

2011-01-01

Background Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, to gain a better understanding of them. The computational complexity to analyze the complete dynamics of these models grows exponentially in the number of variables, which impedes working with complex models. There exist software tools to analyze discrete models, but they either lack the algorithmic functionality to analyze complex models deterministically or they are inaccessible to many users as they require understanding the underlying algorithm and implementation, do not have a graphical user interface, or are hard to install. Efficient analysis methods that are accessible to modelers and easy to use are needed. Results We propose a method for efficiently identifying attractors and introduce the web-based tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other analysis methods for discrete models. ADAM converts several discrete model types automatically into polynomial dynamical systems and analyzes their dynamics using tools from computer algebra. Specifically, we propose a method to identify attractors of a discrete model that is equivalent to solving a system of polynomial equations, a long-studied problem in computer algebra. Based on extensive experimentation with both discrete models arising in systems biology and randomly generated networks, we found that the algebraic algorithms presented in this manuscript are fast for systems with the structure maintained by most biological systems, namely sparseness and robustness. For a large set of published complex discrete models, ADAM identified the attractors in less than one second. Conclusions Discrete modeling techniques are a useful tool for analyzing complex biological systems and there is a need in the biological community for accessible efficient analysis tools. ADAM provides analysis methods based on mathematical algorithms as a web-based tool for several different input formats, and it makes analysis of complex models accessible to a larger community, as it is platform independent as a web-service and does not require understanding of the underlying mathematics. PMID:21774817

PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data.

PubMed

Hernández-de-Diego, Rafael; Tarazona, Sonia; Martínez-Mira, Carlos; Balzano-Nogueira, Leandro; Furió-Tarí, Pedro; Pappas, Georgios J; Conesa, Ana

2018-05-25

The increasing availability of multi-omic platforms poses new challenges to data analysis. Joint visualization of multi-omics data is instrumental in better understanding interconnections across molecular layers and in fully utilizing the multi-omic resources available to make biological discoveries. We present here PaintOmics 3, a web-based resource for the integrated visualization of multiple omic data types onto KEGG pathway diagrams. PaintOmics 3 combines server-end capabilities for data analysis with the potential of modern web resources for data visualization, providing researchers with a powerful framework for interactive exploration of their multi-omics information. Unlike other visualization tools, PaintOmics 3 covers a comprehensive pathway analysis workflow, including automatic feature name/identifier conversion, multi-layered feature matching, pathway enrichment, network analysis, interactive heatmaps, trend charts, and more. It accepts a wide variety of omic types, including transcriptomics, proteomics and metabolomics, as well as region-based approaches such as ATAC-seq or ChIP-seq data. The tool is freely available at www.paintomics.org.

MyGeoHub: A Collaborative Geospatial Research and Education Platform

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

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

PubMed

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

2017-06-01

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

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

PubMed Central

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

2017-01-01

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

On-Line Analysis of Southern FIA Data

Treesearch

Michael P. Spinney; Paul C. Van Deusen; Francis A. Roesch

2006-01-01

The Southern On-Line Estimator (SOLE) is a web-based FIA database analysis tool designed with an emphasis on modularity. The Java-based user interface is simple and intuitive to use and the R-based analysis engine is fast and stable. Each component of the program (data retrieval, statistical analysis and output) can be individually modified to accommodate major...

CNV-WebStore: online CNV analysis, storage and interpretation.

PubMed

Vandeweyer, Geert; Reyniers, Edwin; Wuyts, Wim; Rooms, Liesbeth; Kooy, R Frank

2011-01-05

Microarray technology allows the analysis of genomic aberrations at an ever increasing resolution, making functional interpretation of these vast amounts of data the main bottleneck in routine implementation of high resolution array platforms, and emphasising the need for a centralised and easy to use CNV data management and interpretation system. We present CNV-WebStore, an online platform to streamline the processing and downstream interpretation of microarray data in a clinical context, tailored towards but not limited to the Illumina BeadArray platform. Provided analysis tools include CNV analsyis, parent of origin and uniparental disomy detection. Interpretation tools include data visualisation, gene prioritisation, automated PubMed searching, linking data to several genome browsers and annotation of CNVs based on several public databases. Finally a module is provided for uniform reporting of results. CNV-WebStore is able to present copy number data in an intuitive way to both lab technicians and clinicians, making it a useful tool in daily clinical practice.

The Web Measurement Environment (WebME): A Tool for Combining and Modeling Distributed Data

NASA Technical Reports Server (NTRS)

Tesoriero, Roseanne; Zelkowitz, Marvin

1997-01-01

Many organizations have incorporated data collection into their software processes for the purpose of process improvement. However, in order to improve, interpreting the data is just as important as the collection of data. With the increased presence of the Internet and the ubiquity of the World Wide Web, the potential for software processes being distributed among several physically separated locations has also grown. Because project data may be stored in multiple locations and in differing formats, obtaining and interpreting data from this type of environment becomes even more complicated. The Web Measurement Environment (WebME), a Web-based data visualization tool, is being developed to facilitate the understanding of collected data in a distributed environment. The WebME system will permit the analysis of development data in distributed, heterogeneous environments. This paper provides an overview of the system and its capabilities.

Interactive metagenomic visualization in a Web browser.

PubMed

Ondov, Brian D; Bergman, Nicholas H; Phillippy, Adam M

2011-09-30

A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in assignments to these groups makes it important to consider both their hierarchical contexts and their prediction confidence. The current tools for visualizing metagenomic data, however, omit or distort quantitative hierarchical relationships and lack the facility for displaying secondary variables. Here we present Krona, a new visualization tool that allows intuitive exploration of relative abundances and confidences within the complex hierarchies of metagenomic classifications. Krona combines a variant of radial, space-filling displays with parametric coloring and interactive polar-coordinate zooming. The HTML5 and JavaScript implementation enables fully interactive charts that can be explored with any modern Web browser, without the need for installed software or plug-ins. This Web-based architecture also allows each chart to be an independent document, making them easy to share via e-mail or post to a standard Web server. To illustrate Krona's utility, we describe its application to various metagenomic data sets and its compatibility with popular metagenomic analysis tools. Krona is both a powerful metagenomic visualization tool and a demonstration of the potential of HTML5 for highly accessible bioinformatic visualizations. Its rich and interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages. Both the Krona rendering code and conversion tools are freely available under a BSD open-source license, and available from: http://krona.sourceforge.net.

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.

dbHiMo: a web-based epigenomics platform for histone-modifying enzymes

PubMed Central

Choi, Jaeyoung; Kim, Ki-Tae; Huh, Aram; Kwon, Seomun; Hong, Changyoung; Asiegbu, Fred O.; Jeon, Junhyun; Lee, Yong-Hwan

2015-01-01

Over the past two decades, epigenetics has evolved into a key concept for understanding regulation of gene expression. Among many epigenetic mechanisms, covalent modifications such as acetylation and methylation of lysine residues on core histones emerged as a major mechanism in epigenetic regulation. Here, we present the database for histone-modifying enzymes (dbHiMo; http://hme.riceblast.snu.ac.kr/) aimed at facilitating functional and comparative analysis of histone-modifying enzymes (HMEs). HMEs were identified by applying a search pipeline built upon profile hidden Markov model (HMM) to proteomes. The database incorporates 11 576 HMEs identified from 603 proteomes including 483 fungal, 32 plants and 51 metazoan species. The dbHiMo provides users with web-based personalized data browsing and analysis tools, supporting comparative and evolutionary genomics. With comprehensive data entries and associated web-based tools, our database will be a valuable resource for future epigenetics/epigenomics studies. Database URL: http://hme.riceblast.snu.ac.kr/ PMID:26055100

dbHiMo: a web-based epigenomics platform for histone-modifying enzymes.

PubMed

Choi, Jaeyoung; Kim, Ki-Tae; Huh, Aram; Kwon, Seomun; Hong, Changyoung; Asiegbu, Fred O; Jeon, Junhyun; Lee, Yong-Hwan

2015-01-01

Over the past two decades, epigenetics has evolved into a key concept for understanding regulation of gene expression. Among many epigenetic mechanisms, covalent modifications such as acetylation and methylation of lysine residues on core histones emerged as a major mechanism in epigenetic regulation. Here, we present the database for histone-modifying enzymes (dbHiMo; http://hme.riceblast.snu.ac.kr/) aimed at facilitating functional and comparative analysis of histone-modifying enzymes (HMEs). HMEs were identified by applying a search pipeline built upon profile hidden Markov model (HMM) to proteomes. The database incorporates 11,576 HMEs identified from 603 proteomes including 483 fungal, 32 plants and 51 metazoan species. The dbHiMo provides users with web-based personalized data browsing and analysis tools, supporting comparative and evolutionary genomics. With comprehensive data entries and associated web-based tools, our database will be a valuable resource for future epigenetics/epigenomics studies. © The Author(s) 2015. Published by Oxford University Press.

GET SMARTE: A DECISION SUPPORT SYSTEM TO REVITALIZE COMMUNITIES - CABERNET 2007

EPA Science Inventory

Sustainable Management Approaches and Revitalization Tools - electronic (SMARTe), is an open-source, web-based, decision support system for developing and evaluating future reuse scenarios for potentially contaminated land. SMARTe contains information and analysis tools for all a...

CoryneBase: Corynebacterium Genomic Resources and Analysis Tools at Your Fingertips

PubMed Central

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

2014-01-01

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

Towards a collaborative, global infrastructure for biodiversity assessment

PubMed Central

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

2007-01-01

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

Reads2Type: a web application for rapid microbial taxonomy identification.

PubMed

Saputra, Dhany; Rasmussen, Simon; Larsen, Mette V; Haddad, Nizar; Sperotto, Maria Maddalena; Aarestrup, Frank M; Lund, Ole; Sicheritz-Pontén, Thomas

2015-11-25

Identification of bacteria may be based on sequencing and molecular analysis of a specific locus such as 16S rRNA, or a set of loci such as in multilocus sequence typing. In the near future, healthcare institutions and routine diagnostic microbiology laboratories may need to sequence the entire genome of microbial isolates. Therefore we have developed Reads2Type, a web-based tool for taxonomy identification based on whole bacterial genome sequence data. Raw sequencing data provided by the user are mapped against a set of marker probes that are derived from currently available bacteria complete genomes. Using a dataset of 1003 whole genome sequenced bacteria from various sequencing platforms, Reads2Type was able to identify the species with 99.5 % accuracy and on the minutes time scale. In comparison with other tools, Reads2Type offers the advantage of not needing to transfer sequencing files, as the entire computational analysis is done on the computer of whom utilizes the web application. This also prevents data privacy issues to arise. The Reads2Type tool is available at http://www.cbs.dtu.dk/~dhany/reads2type.html.

Web-Based Instruction and Learning: Analysis and Needs Assessment

NASA Technical Reports Server (NTRS)

Grabowski, Barbara; McCarthy, Marianne; Koszalka, Tiffany

1998-01-01

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

BrucellaBase: Genome information resource.

PubMed

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

2016-09-01

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

CalFitter: a web server for analysis of protein thermal denaturation data.

PubMed

Mazurenko, Stanislav; Stourac, Jan; Kunka, Antonin; Nedeljkovic, Sava; Bednar, David; Prokop, Zbynek; Damborsky, Jiri

2018-05-14

Despite significant advances in the understanding of protein structure-function relationships, revealing protein folding pathways still poses a challenge due to a limited number of relevant experimental tools. Widely-used experimental techniques, such as calorimetry or spectroscopy, critically depend on a proper data analysis. Currently, there are only separate data analysis tools available for each type of experiment with a limited model selection. To address this problem, we have developed the CalFitter web server to be a unified platform for comprehensive data fitting and analysis of protein thermal denaturation data. The server allows simultaneous global data fitting using any combination of input data types and offers 12 protein unfolding pathway models for selection, including irreversible transitions often missing from other tools. The data fitting produces optimal parameter values, their confidence intervals, and statistical information to define unfolding pathways. The server provides an interactive and easy-to-use interface that allows users to directly analyse input datasets and simulate modelled output based on the model parameters. CalFitter web server is available free at https://loschmidt.chemi.muni.cz/calfitter/.

EpiHosp: A web-based visualization tool enabling the exploratory analysis of complications of implantable medical devices from a nationwide hospital database.

PubMed

Ficheur, Grégoire; Ferreira Careira, Lionel; Beuscart, Régis; Chazard, Emmanuel

2015-01-01

Administrative data can be used for the surveillance of the outcomes of implantable medical devices (IMDs). The objective of this work is to build a web-based tool allowing for an exploratory analysis of time-dependent events that may occur after the implementation of an IMD. This tool should enable a pharmacoepidemiologist to explore on the fly the relationship between a given IMD and a potential outcome. This tool mine the French nationwide database of inpatient stays from 2008 to 2013. The data are preprocessed in order to optimize the queries. A web tool is developed in PHP, MySQL and Javascript. The user selects one or a group of IMD from a tree, and can filter the results using years and hospital names. Four result pages describe the selected inpatient stays: (1) temporal and demographic description, (2) a description of the geographical location of the hospital, (3) a description of the geographical place of residence of the patient and (4) a table showing the rehospitalization reasons by decreasing order of frequency. Then, the user can select one readmission reason and display dynamically the probability of readmission by mean of a Kaplan-Meier curve with confidence intervals. This tool enables to dynamically monitor the occurrence of time-dependent complications of IMD.

Multi-tool accessibility assessment of government department websites:a case-study with JKGAD.

PubMed

Ismail, Abid; Kuppusamy, K S; Nengroo, Ab Shakoor

2017-08-02

Nature of being accessible to all categories of users is one of the primary factors for enabling the wider reach of the resources published through World Wide Web. The accessibility of websites has been analyzed through W3C guidelines with the help of various tools. This paper presents a multi-tool accessibility assessment of government department websites belonging to the Indian state of Jammu and Kashmir. A comparative analysis of six accessibility tools is also presented with 14 different parameters. The accessibility analysis tools used in this study for analysis are aChecker, Cynthia Says, Tenon, wave, Mauve, and Hera. These tools provide us the results of selected websites accessibility status on Web Content Accessibility Guidelines (WCAG) 1.0 and 2.0. It was found that there are variations in accessibility analysis results when using different accessibility metrics to measure the accessibility of websites. In addition to this, we have identified the guidelines which have frequently been violated. It was observed that there is a need for incorporating the accessibility component features among the selected websites. This paper presents a set of suggestions to improve the accessibility status of these sites so that the information and services provided by these sites shall reach a wider spectrum of audience without any barrier. Implications for rehabilitation The following points indicates that this case study of JKGAD websites comes under Rehabilitation focused on Visually Impaired users. Due to the universal nature of web, it should be accessible to all according to WCAG guidelines framed by World Wide Web Consortium. In this paper we have identified multiple accessibility barriers for persons with visual impairment while browsing the Jammu and Kashmir Government websites. Multi-tool analysis has been done to pin-point the potential barriers for persons with visually Impaired. Usability analysis has been performed to check whether these websites are suitable for persons with visual impairment. We provide some valuable suggestions which can be followed by developers and designers to minimize these potential accessibility barriers.Based on aforementioned key points, this article helps the persons with disability especially Visually Impaired Users to access the web resources better with the implementation of identified suggestions.

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

DTIC Science & Technology

2014-06-01

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

Cloud-based solution to identify statistically significant MS peaks differentiating sample categories.

PubMed

Ji, Jun; Ling, Jeffrey; Jiang, Helen; Wen, Qiaojun; Whitin, John C; Tian, Lu; Cohen, Harvey J; Ling, Xuefeng B

2013-03-23

Mass spectrometry (MS) has evolved to become the primary high throughput tool for proteomics based biomarker discovery. Until now, multiple challenges in protein MS data analysis remain: large-scale and complex data set management; MS peak identification, indexing; and high dimensional peak differential analysis with the concurrent statistical tests based false discovery rate (FDR). "Turnkey" solutions are needed for biomarker investigations to rapidly process MS data sets to identify statistically significant peaks for subsequent validation. Here we present an efficient and effective solution, which provides experimental biologists easy access to "cloud" computing capabilities to analyze MS data. The web portal can be accessed at http://transmed.stanford.edu/ssa/. Presented web application supplies large scale MS data online uploading and analysis with a simple user interface. This bioinformatic tool will facilitate the discovery of the potential protein biomarkers using MS.

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.

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

PubMed

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

2004-01-01

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

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

PubMed Central

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

2004-01-01

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

A web-based endodontic case difficulty assessment tool.

PubMed

Shah, P K; Chong, B S

2018-07-01

To develop a web-based tool to facilitate identification, evaluation and management of teeth requiring endodontic treatment. Following a literature search and thorough analysis of existing case difficulty assessment forms, the web-based tool was developed using an online survey builder (Qualtrics, Qualtrics Lab, UT, USA). Following feedback from a pilot study, it was refined and improved. A study was performed, using the updated version (EndoApp) on a cohort (n = 53) of dental professionals and dental students. The participants were e-mailed instructions detailing the assessment of five test cases using EndoApp, followed by completion of a structured feedback form. Analysis of the EndoApp responses was used to evaluate usage times, whereas the results of the feedback forms were used to assess user experience and relevance, other potential applications and comments on further improvement/s. The average usage time was 2 min 7 s; the average times needed for the last three (Cases 3-5) were significantly less than the preceding two (Cases 1 & 2) test cases. An overwhelming majority of participants expressed favourable views on user experience and relevance of the web-based case difficulty assessment tool. Only two participants (4%) were unlikely or very unlikely to use EndoApp again. The potential application of EndoApp as an 'educational tool' and for 'primary care triage' was deemed the most popular features and of greater importance than the secondary options of 'fee setting' and as a 'dento-legal justification tool'. Within the study limitations, owing to its ability to quantify the level of difficulty and provide guidance, EndoApp was considered user-friendly and helped facilitate endodontic case difficulty assessment. From the feedback, further improvements and the development of a Smartphone App version are in progress. EndoApp may facilitate treatment planning, improve treatment cost-effectiveness and reduce frequency of procedural errors by providing appropriate guidance on endodontic case management.

A Web-based environmental decision support system (WEDSS) for environmental planning and watershed management

NASA Astrophysics Data System (ADS)

Sugumaran, Ramanathan; Meyer, James C.; Davis, Jim

2004-10-01

Local governments often struggle to balance competing demands for residential, commercial and industrial development with imperatives to minimize environmental degradation. In order to effectively manage this development process on a sustainable basis, local planners and government agencies are increasingly seeking better tools and techniques. In this paper, we describe the development of a Web-Based Environmental Decision Support System (WEDSS), which helps to prioritize local watersheds in terms of environmental sensitivity using multiple criteria identified by planners and local government staff in the city of Columbia, and Boone County, Missouri. The development of the system involved three steps, the first was to establish the relevant environmental criteria and develop data layers for each criterion, then a spatial model was developed for analysis, and lastly a Web-based interface with analysis tools was developed using client-server technology. The WEDSS is an example of a way to run spatial models over the Web and represents a significant increase in capability over other WWW-based GIS applications that focus on database querying and map display. The WEDSS seeks to aid in the development of agreement regarding specific local areas deserving increased protection and the public policies to be pursued in minimizing the environmental impact of future development. The tool is also intended to assist ongoing public information and education efforts concerning watershed management and water quality issues for the City of Columbia, Missouri and adjacent developing areas within Boone County, Missouri.

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

PubMed

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

2008-07-01

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

On the Development of a Hospital-Patient Web-Based Communication Tool: A Case Study From Norway.

PubMed

Granja, Conceição; Dyb, Kari; Bolle, Stein Roald; Hartvigsen, Gunnar

2015-01-01

Surgery cancellations are undesirable in hospital settings as they increase costs, reduce productivity and efficiency, and directly affect the patient. The problem of elective surgery cancellations in a North Norwegian University Hospital is addressed. Based on a three-step methodology conducted at the hospital, the preoperative planning process was modeled taking into consideration the narratives from different health professions. From the analysis of the generated process models, it is concluded that in order to develop a useful patient centered web-based communication tool, it is necessary to fully understand how hospitals plan and organize surgeries today. Moreover, process reengineering is required to generate a standard process that can serve as a tool for health ICT designers to define the requirements for a robust and useful system.

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…

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

PubMed

Dwivedi, Bhakti; Kowalski, Jeanne

2018-01-01

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

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

PubMed Central

Dwivedi, Bhakti

2018-01-01

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

IsoWeb: A Bayesian Isotope Mixing Model for Diet Analysis of the Whole Food Web

PubMed Central

Kadoya, Taku; Osada, Yutaka; Takimoto, Gaku

2012-01-01

Quantitative description of food webs provides fundamental information for the understanding of population, community, and ecosystem dynamics. Recently, stable isotope mixing models have been widely used to quantify dietary proportions of different food resources to a focal consumer. Here we propose a novel mixing model (IsoWeb) that estimates diet proportions of all consumers in a food web based on stable isotope information. IsoWeb requires a topological description of a food web, and stable isotope signatures of all consumers and resources in the web. A merit of IsoWeb is that it takes into account variation in trophic enrichment factors among different consumer-resource links. Sensitivity analysis using realistic hypothetical food webs suggests that IsoWeb is applicable to a wide variety of food webs differing in the number of species, connectance, sample size, and data variability. Sensitivity analysis based on real topological webs showed that IsoWeb can allow for a certain level of topological uncertainty in target food webs, including erroneously assuming false links, omission of existent links and species, and trophic aggregation into trophospecies. Moreover, using an illustrative application to a real food web, we demonstrated that IsoWeb can compare the plausibility of different candidate topologies for a focal web. These results suggest that IsoWeb provides a powerful tool to analyze food-web structure from stable isotope data. We provide R and BUGS codes to aid efficient applications of IsoWeb. PMID:22848427

STATWIZ - AN ELECTRONIC STATISTICAL TOOL (ABSTRACT)

EPA Science Inventory

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

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

NASA Astrophysics Data System (ADS)

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

2015-03-01

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

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

NASA Astrophysics Data System (ADS)

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

2012-04-01

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

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

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…

Interactive metagenomic visualization in a Web browser

PubMed Central

2011-01-01

Background A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in assignments to these groups makes it important to consider both their hierarchical contexts and their prediction confidence. The current tools for visualizing metagenomic data, however, omit or distort quantitative hierarchical relationships and lack the facility for displaying secondary variables. Results Here we present Krona, a new visualization tool that allows intuitive exploration of relative abundances and confidences within the complex hierarchies of metagenomic classifications. Krona combines a variant of radial, space-filling displays with parametric coloring and interactive polar-coordinate zooming. The HTML5 and JavaScript implementation enables fully interactive charts that can be explored with any modern Web browser, without the need for installed software or plug-ins. This Web-based architecture also allows each chart to be an independent document, making them easy to share via e-mail or post to a standard Web server. To illustrate Krona's utility, we describe its application to various metagenomic data sets and its compatibility with popular metagenomic analysis tools. Conclusions Krona is both a powerful metagenomic visualization tool and a demonstration of the potential of HTML5 for highly accessible bioinformatic visualizations. Its rich and interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages. Both the Krona rendering code and conversion tools are freely available under a BSD open-source license, and available from: http://krona.sourceforge.net. PMID:21961884

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…

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.

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/.

Mars Trek: An Interactive Web Portal for Current and Future Missions to Mars

NASA Technical Reports Server (NTRS)

Law, E.; Day, B.

2017-01-01

NASA's Mars Trek (https://marstrek.jpl.nasa.gov) provides a web-based Portal and a suite of interactive visualization and analysis tools to enable mission planners, lunar scientists, and engineers to access mapped data products from past and current missions to Mars. During the past year, the capabilities and data served by Mars Trek have been significantly expanded beyond its original design as a public outreach tool. At the request of NASA's Science Mission Directorate and Human Exploration Operations Mission Directorate, Mars Trek's technology and capabilities are now being extended to support site selection and analysis activities for the first human missions to Mars.

Mars Trek: An Interactive Web Portal for Current and Future Missions to Mars

NASA Astrophysics Data System (ADS)

Law, E.; Day, B.

2017-09-01

NASA's Mars Trek (https://marstrek.jpl.nasa.gov) provides a web-based Portal and a suite of interactive visualization and analysis tools to enable mission planners, lunar scientists, and engineers to access mapped data products from past and current missions to Mars. During the past year, the capabilities and data served by Mars Trek have been significantly expanded beyond its original design as a public outreach tool. At the request of NASA's Science Mission Directorate and Human Exploration Operations Mission Directorate, Mars Trek's technology and capabilities are now being extended to support site selection and analysis activities for the first human missions to Mars.

Team Collaboration Software

NASA Technical Reports Server (NTRS)

Wang, Yeou-Fang; Schrock, Mitchell; Baldwin, John R.; Borden, Charles S.

2010-01-01

The Ground Resource Allocation and Planning Environment (GRAPE 1.0) is a Web-based, collaborative team environment based on the Microsoft SharePoint platform, which provides Deep Space Network (DSN) resource planners tools and services for sharing information and performing analysis.

Exploration of SWRL Rule Bases through Visualization, Paraphrasing, and Categorization of Rules

NASA Astrophysics Data System (ADS)

Hassanpour, Saeed; O'Connor, Martin J.; Das, Amar K.

Rule bases are increasingly being used as repositories of knowledge content on the Semantic Web. As the size and complexity of these rule bases increases, developers and end users need methods of rule abstraction to facilitate rule management. In this paper, we describe a rule abstraction method for Semantic Web Rule Language (SWRL) rules that is based on lexical analysis and a set of heuristics. Our method results in a tree data structure that we exploit in creating techniques to visualize, paraphrase, and categorize SWRL rules. We evaluate our approach by applying it to several biomedical ontologies that contain SWRL rules, and show how the results reveal rule patterns within the rule base. We have implemented our method as a plug-in tool for Protégé-OWL, the most widely used ontology modeling software for the Semantic Web. Our tool can allow users to rapidly explore content and patterns in SWRL rule bases, enabling their acquisition and management.

EAST: Developing an Electronic Assessment and Storage Tool.

ERIC Educational Resources Information Center

Edwards, Katherine I.; Fernandez, Eugenia; Milionis, Tracey M.; Williamson, David M.

2002-01-01

Describes the purpose, development, analysis, prototyping, and features of the Electronic Assessment and Storage Tool (EAST). The Web-based system aids curriculum assessment at Purdue School of Engineering and Technology at Indiana University Purdue University Indianapolis through the ability to easily store artifacts in electronic form, support…

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

ERIC Educational Resources Information Center

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

2016-01-01

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

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

PubMed

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

2016-07-08

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

A Web Application for Cotton Irrigation Management on The US Southern High Plains. Part I: Crop Yield Modeling and Profit Analysis

USDA-ARS?s Scientific Manuscript database

Irrigated cotton (Gossypium Hirsutum L.) production is a central part of west Texas agriculture that depends on the essentially non-renewable water resource of the Ogallala aquifer. Web-based decision support tools that estimate the profit effects of irrigation for cotton under varying lint price, p...

An online planning tool for designing terrace layouts

USDA-ARS?s Scientific Manuscript database

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

Web-Based Course Delivery and Administration Using Scheme.

ERIC Educational Resources Information Center

Salustri, Filippo A.

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

Web-Based Phylogenetic Assignment Tool for Analysis of Terminal Restriction Fragment Length Polymorphism Profiles of Microbial Communities

PubMed Central

Kent, Angela D.; Smith, Dan J.; Benson, Barbara J.; Triplett, Eric W.

2003-01-01

Culture-independent DNA fingerprints are commonly used to assess the diversity of a microbial community. However, relating species composition to community profiles produced by community fingerprint methods is not straightforward. Terminal restriction fragment length polymorphism (T-RFLP) is a community fingerprint method in which phylogenetic assignments may be inferred from the terminal restriction fragment (T-RF) sizes through the use of web-based resources that predict T-RF sizes for known bacteria. The process quickly becomes computationally intensive due to the need to analyze profiles produced by multiple restriction digests and the complexity of profiles generated by natural microbial communities. A web-based tool is described here that rapidly generates phylogenetic assignments from submitted community T-RFLP profiles based on a database of fragments produced by known 16S rRNA gene sequences. Users have the option of submitting a customized database generated from unpublished sequences or from a gene other than the 16S rRNA gene. This phylogenetic assignment tool allows users to employ T-RFLP to simultaneously analyze microbial community diversity and species composition. An analysis of the variability of bacterial species composition throughout the water column in a humic lake was carried out to demonstrate the functionality of the phylogenetic assignment tool. This method was validated by comparing the results generated by this program with results from a 16S rRNA gene clone library. PMID:14602639

Improving a web-based employability intervention for work-disabled employees: results of a pilot economic evaluation.

PubMed

Noben, Cindy; Evers, Silvia; Genabeek, Joost van; Nijhuis, Frans; de Rijk, Angelique

2017-04-01

Purpose The purpose of this study is to improve web-based employability interventions for employees with work-related health problems for both intervention content and study design by means of a pilot economic evaluation. Methods Uptake rate analysis for the intervention elements, cost effectiveness, cost utility and subgroup analyses were conducted to identify potential content-related intervention improvements. Differences in work ability and quality-adjusted life years and overall contribution of resource items to the total costs were assessed. These were used to guide study design improvements. Results Sixty-three participants were a-select allocated to either the intervention (n = 29) or the control (n = 34) group. Uptake regarding the intervention elements ranged between 3% and 70%. Cost-effectiveness and cost-utility analyses resulted in negative effects although higher total costs. Incremental effects were marginal (work ability -0.51; QALY -0.01). Conclusions The web-based tool to enhance employability among work disabled employees requires improvements regarding targeting and intensity; outcome measures selected and collection of cost data. With respect to the studies of disability and rehabilitation, the findings and methods presented in this pilot economic evaluation could guide the assessment of future assistive "e-health" technologies. IMPLICATIONS FOR REHABILITATION The methods presented in this pilot economic evaluation have large potentials to guide the assessment of future assistive e-health technologies addressing work-disabilities. The findings show that the web-based tool requires content related improvements with respect to targeting and intensity to enhance employability among work disabled employees. The findings show that the web-based tool would benefit from improvements related to the study design by more adequately selecting and collecting both outcome measures and cost data. The burden attributable to large-scale studies and implementation issues were prevented as the outcomes of the pilot economic evaluation did not support the implementation of the web-based tool.

Utility of a Web-based intervention for individuals with type 2 diabetes: the impact on physical activity levels and glycemic control.

PubMed

Kim, Chun-Ja; Kang, Duck-Hee

2006-01-01

Despite the numerous benefits of physical activity for patients with diabetes, most healthcare providers in busy clinical settings rarely find time to counsel their patients about it. A Web-based program for healthcare providers can be used as an effective counseling tool, when strategies are outlined for specific stages of readiness for physical activity. Seventy-three adults with type 2 diabetes were randomly assigned to Web-based intervention, printed-material intervention, or usual care. After 12 weeks, the effects of the interventions on physical activity, fasting blood sugar, and glycosylated hemoglobin were evaluated. Both Web-based and printed material intervention, compared with usual care, were effective in increasing physical activity (P < .001) and decreasing fasting blood sugar (P<.01) and glycosylated hemoglobin (P < .01). Post hoc analysis for change scores indicated significant differences between Web-based intervention and usual care and between printed material intervention and usual care, but not between web-based and printed material intervention. The findings of this study support the value of Web-based and printed material interventions in healthcare counseling. With increasing Web access, the effectiveness of Web-based programs offered directly to patients needs to be tested.

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

PubMed

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

2018-07-01

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

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.

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

PubMed

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

2011-11-29

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

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

PubMed Central

2011-01-01

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

Teaching bioinformatics and neuroinformatics by using free web-based tools.

PubMed

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

2010-01-01

This completely computer-based module's purpose is to introduce students to bioinformatics resources. We present an easy-to-adopt module that weaves together several important bioinformatic tools so students can grasp how these tools are used in answering research questions. Students integrate information gathered from websites dealing with anatomy (Mouse Brain Library), quantitative trait locus analysis (WebQTL from GeneNetwork), bioinformatics and gene expression analyses (University of California, Santa Cruz Genome Browser, National Center for Biotechnology Information's Entrez Gene, and the Allen Brain Atlas), and information resources (PubMed). Instructors can use these various websites in concert to teach genetics from the phenotypic level to the molecular level, aspects of neuroanatomy and histology, statistics, quantitative trait locus analysis, and molecular biology (including in situ hybridization and microarray analysis), and to introduce bioinformatic resources. Students use these resources to discover 1) the region(s) of chromosome(s) influencing the phenotypic trait, 2) a list of candidate genes-narrowed by expression data, 3) the in situ pattern of a given gene in the region of interest, 4) the nucleotide sequence of the candidate gene, and 5) articles describing the gene. Teaching materials such as a detailed student/instructor's manual, PowerPoints, sample exams, and links to free Web resources can be found at http://mdcune.psych.ucla.edu/modules/bioinformatics.

Faculty Recommendations for Web Tools: Implications for Course Management Systems

ERIC Educational Resources Information Center

Oliver, Kevin; Moore, John

2008-01-01

A gap analysis of web tools in Engineering was undertaken as one part of the Digital Library Network for Engineering and Technology (DLNET) grant funded by NSF (DUE-0085849). DLNET represents a Web portal and an online review process to archive quality knowledge objects in Engineering and Technology disciplines. The gap analysis coincided with the…

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

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.

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

PubMed Central

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

2008-01-01

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

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.)

Lars Lisell | NREL

Science.gov Websites

) Analysis of Web-Based Solar Photovoltaic Mapping Tools, NREL Conference Paper (2009) Solar Ready Building novel approach to solar rooftop optimization, NREL Conference Paper (2011) View all NREL publications

WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data.

PubMed

Devlin, Joseph C; Battaglia, Thomas; Blaser, Martin J; Ruggles, Kelly V

2018-06-25

Exploration of large data sets, such as shotgun metagenomic sequence or expression data, by biomedical experts and medical professionals remains as a major bottleneck in the scientific discovery process. Although tools for this purpose exist for 16S ribosomal RNA sequencing analysis, there is a growing but still insufficient number of user-friendly interactive visualization workflows for easy data exploration and figure generation. The development of such platforms for this purpose is necessary to accelerate and streamline microbiome laboratory research. We developed the Workflow Hub for Automated Metagenomic Exploration (WHAM!) as a web-based interactive tool capable of user-directed data visualization and statistical analysis of annotated shotgun metagenomic and metatranscriptomic data sets. WHAM! includes exploratory and hypothesis-based gene and taxa search modules for visualizing differences in microbial taxa and gene family expression across experimental groups, and for creating publication quality figures without the need for command line interface or in-house bioinformatics. WHAM! is an interactive and customizable tool for downstream metagenomic and metatranscriptomic analysis providing a user-friendly interface allowing for easy data exploration by microbiome and ecological experts to facilitate discovery in multi-dimensional and large-scale data sets.

Using Web Crawler Technology for Text Analysis of Geo-Events: A Case Study of the Huangyan Island Incident

NASA Astrophysics Data System (ADS)

Hu, H.; Ge, Y. J.

2013-11-01

With the social networking and network socialisation have brought more text information and social relationships into our daily lives, the question of whether big data can be fully used to study the phenomenon and discipline of natural sciences has prompted many specialists and scholars to innovate their research. Though politics were integrally involved in the hyperlinked word issues since 1990s, automatic assembly of different geospatial web and distributed geospatial information systems utilizing service chaining have explored and built recently, the information collection and data visualisation of geo-events have always faced the bottleneck of traditional manual analysis because of the sensibility, complexity, relativity, timeliness and unexpected characteristics of political events. Based on the framework of Heritrix and the analysis of web-based text, word frequency, sentiment tendency and dissemination path of the Huangyan Island incident is studied here by combining web crawler technology and the text analysis method. The results indicate that tag cloud, frequency map, attitudes pie, individual mention ratios and dissemination flow graph based on the data collection and processing not only highlight the subject and theme vocabularies of related topics but also certain issues and problems behind it. Being able to express the time-space relationship of text information and to disseminate the information regarding geo-events, the text analysis of network information based on focused web crawler technology can be a tool for understanding the formation and diffusion of web-based public opinions in political events.

A Web-Based Course Assessment Tool with Direct Mapping to Student Outcomes

ERIC Educational Resources Information Center

Ibrahim, Walid; Atif, Yacine; Shuaib, Khaled; Sampson, Demetrios

2015-01-01

The assessment of curriculum outcomes is an essential element for continuous academic improvement. However, the collection, aggregation and analysis of assessment data are notoriously complex and time-consuming processes. At the same time, only few developments of supporting electronic processes and tools for continuous academic program assessment…

EMBATTLED BIVALVES: BIOGEOGRAPHIC DISTRIBUTIONS AND ABUNDANCES FROM THE BEAUFORT SEA TO THE GULF OF CALIFORNIA

EPA Science Inventory

As part of an EPA/USGS project to predict the relative vulnerability of near-coastal species to climate change, we have synthesized in a web-based tool, the Coastal Biogeographic Risk Analysis Tool (CBRAT), the biogeographic distributions and abundances of bivalves, found in dept...

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.

Silicon photonics cloud (SiCloud)

NASA Astrophysics Data System (ADS)

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

2015-02-01

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

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

ERIC Educational Resources Information Center

Blummer, Barbara; Kenton, Jeffrey M.

2014-01-01

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

SCit: web tools for protein side chain conformation analysis.

PubMed

Gautier, R; Camproux, A-C; Tufféry, P

2004-07-01

SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the side chain conformations on the local backbone conformation, which is described using a structural alphabet that describes the conformation of fragments of four-residue length in a limited library of structural prototypes. Based on this concept, SCit uses sets of rotameric conformations dependent on the local backbone conformation of each protein for side chain positioning and the identification of side chains with unlikely conformations. The SCit web server is accessible at http://bioserv.rpbs.jussieu.fr/SCit.

Free Web-based personal health records: an analysis of functionality.

PubMed

Fernández-Alemán, José Luis; Seva-Llor, Carlos Luis; Toval, Ambrosio; Ouhbi, Sofia; Fernández-Luque, Luis

2013-12-01

This paper analyzes and assesses the functionality of free Web-based PHRs as regards health information, user actions and connection with other tools. A systematic literature review in Medline, ACM Digital Library, IEEE Digital Library and ScienceDirect was used to select 19 free Web-based PHRs from the 47 PHRs identified. The results show that none of the PHRs selected met 100% of the 28 functions presented in this paper. Two free Web-based PHRs target a particular public. Around 90 % of the PHRs identified allow users throughout the world to create their own profiles without any geographical restrictions. Only half of the PHRs selected provide physicians with user actions. Few PHRs can connect with other tools. There was considerable variability in the types of data included in free Web-based PHRs. Functionality may have implications for PHR use and adoption, particularly as regards patients with chronic illnesses or disabilities. Support for standard medical document formats and protocols are required to enable data to be exchanged with other stakeholders in the health care domain. The results of our study may assist users in selecting the PHR that best fits their needs, since no significant connection exists between the number of functions of the PHRs identified and their popularity.

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.

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.

Addressing and Presenting Quality of Satellite Data via Web-Based Services

NASA Technical Reports Server (NTRS)

Leptoukh, Gregory; Lynnes, C.; Ahmad, S.; Fox, P.; Zednik, S.; West, P.

2011-01-01

With the recent attention to climate change and proliferation of remote-sensing data utilization, climate model and various environmental monitoring and protection applications have begun to increasingly rely on satellite measurements. Research application users seek good quality satellite data, with uncertainties and biases provided for each data point. However, different communities address remote sensing quality issues rather inconsistently and differently. We describe our attempt to systematically characterize, capture, and provision quality and uncertainty information as it applies to the NASA MODIS Aerosol Optical Depth data product. In particular, we note the semantic differences in quality/bias/uncertainty at the pixel, granule, product, and record levels. We outline various factors contributing to uncertainty or error budget; errors. Web-based science analysis and processing tools allow users to access, analyze, and generate visualizations of data while alleviating users from having directly managing complex data processing operations. These tools provide value by streamlining the data analysis process, but usually shield users from details of the data processing steps, algorithm assumptions, caveats, etc. Correct interpretation of the final analysis requires user understanding of how data has been generated and processed and what potential biases, anomalies, or errors may have been introduced. By providing services that leverage data lineage provenance and domain-expertise, expert systems can be built to aid the user in understanding data sources, processing, and the suitability for use of products generated by the tools. We describe our experiences developing a semantic, provenance-aware, expert-knowledge advisory system applied to NASA Giovanni web-based Earth science data analysis tool as part of the ESTO AIST-funded Multi-sensor Data Synergy Advisor project.

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.

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.

The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis

PubMed Central

Rampp, Markus; Soddemann, Thomas; Lederer, Hermann

2006-01-01

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

The BioExtract Server: a web-based bioinformatic workflow platform

PubMed Central

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

2011-01-01

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

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

PubMed

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

2015-01-01

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

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.

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.

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

PubMed

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

2018-04-15

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

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

PubMed Central

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

2018-01-01

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

mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences

PubMed Central

Lee, Hwan Young; Song, Injee; Ha, Eunho; Cho, Sung-Bae; Yang, Woo Ick; Shin, Kyoung-Jin

2008-01-01

Background For the past few years, scientific controversy has surrounded the large number of errors in forensic and literature mitochondrial DNA (mtDNA) data. However, recent research has shown that using mtDNA phylogeny and referring to known mtDNA haplotypes can be useful for checking the quality of sequence data. Results We developed a Web-based bioinformatics resource "mtDNAmanager" that offers a convenient interface supporting the management and quality analysis of mtDNA sequence data. The mtDNAmanager performs computations on mtDNA control-region sequences to estimate the most-probable mtDNA haplogroups and retrieves similar sequences from a selected database. By the phased designation of the most-probable haplogroups (both expected and estimated haplogroups), mtDNAmanager enables users to systematically detect errors whilst allowing for confirmation of the presence of clear key diagnostic mutations and accompanying mutations. The query tools of mtDNAmanager also facilitate database screening with two options of "match" and "include the queried nucleotide polymorphism". In addition, mtDNAmanager provides Web interfaces for users to manage and analyse their own data in batch mode. Conclusion The mtDNAmanager will provide systematic routines for mtDNA sequence data management and analysis via easily accessible Web interfaces, and thus should be very useful for population, medical and forensic studies that employ mtDNA analysis. mtDNAmanager can be accessed at . PMID:19014619

NeisseriaBase: a specialised Neisseria genomic resource and analysis platform.

PubMed

Zheng, Wenning; Mutha, Naresh V R; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah; Choo, Siew Woh

2016-01-01

Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my.

NeisseriaBase: a specialised Neisseria genomic resource and analysis platform

PubMed Central

Zheng, Wenning; Mutha, Naresh V.R.; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S.; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah

2016-01-01

Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my. PMID:27017950

A web application for cotton irrigation management on the U.S. southern high plains. Part I: Crop yield modeling and profit analysis

USDA-ARS?s Scientific Manuscript database

Irrigated cotton (Gossypium Hirsutum L.) production is a central part of west Texas agriculture that depends on the essentially non-renewable water resource of the Ogallala aquifer. Web-based decision support tools that estimate the profit effects of irrigation for cotton under varying lint price, p...

GenePattern | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

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

AstrodyToolsWeb an e-Science project in Astrodynamics and Celestial Mechanics fields

NASA Astrophysics Data System (ADS)

López, R.; San-Juan, J. F.

2013-05-01

Astrodynamics Web Tools, AstrodyToolsWeb (http://tastrody.unirioja.es), is an ongoing collaborative Web Tools computing infrastructure project which has been specially designed to support scientific computation. AstrodyToolsWeb provides project collaborators with all the technical and human facilities in order to wrap, manage, and use specialized noncommercial software tools in Astrodynamics and Celestial Mechanics fields, with the aim of optimizing the use of resources, both human and material. However, this project is open to collaboration from the whole scientific community in order to create a library of useful tools and their corresponding theoretical backgrounds. AstrodyToolsWeb offers a user-friendly web interface in order to choose applications, introduce data, and select appropriate constraints in an intuitive and easy way for the user. After that, the application is executed in real time, whenever possible; then the critical information about program behavior (errors and logs) and output, including the postprocessing and interpretation of its results (graphical representation of data, statistical analysis or whatever manipulation therein), are shown via the same web interface or can be downloaded to the user's computer.

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

PubMed

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

2015-02-20

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

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

PubMed Central

Linn, Shai; Rafaeli, Sheizaf

2015-01-01

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

Web-based Visual Analytics for Extreme Scale Climate Science

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

Steed, Chad A; Evans, Katherine J; Harney, John F

In this paper, we introduce a Web-based visual analytics framework for democratizing advanced visualization and analysis capabilities pertinent to large-scale earth system simulations. We address significant limitations of present climate data analysis tools such as tightly coupled dependencies, ineffi- cient data movements, complex user interfaces, and static visualizations. Our Web-based visual analytics framework removes critical barriers to the widespread accessibility and adoption of advanced scientific techniques. Using distributed connections to back-end diagnostics, we minimize data movements and leverage HPC platforms. We also mitigate system dependency issues by employing a RESTful interface. Our framework embraces the visual analytics paradigm via newmore » visual navigation techniques for hierarchical parameter spaces, multi-scale representations, and interactive spatio-temporal data mining methods that retain details. Although generalizable to other science domains, the current work focuses on improving exploratory analysis of large-scale Community Land Model (CLM) and Community Atmosphere Model (CAM) simulations.« less

Metadyn View: Fast web-based viewer of free energy surfaces calculated by metadynamics

NASA Astrophysics Data System (ADS)

Hošek, Petr; Spiwok, Vojtěch

2016-01-01

Metadynamics is a highly successful enhanced sampling technique for simulation of molecular processes and prediction of their free energy surfaces. An in-depth analysis of data obtained by this method is as important as the simulation itself. Although there are several tools to compute free energy surfaces from metadynamics data, they usually lack user friendliness and a build-in visualization part. Here we introduce Metadyn View as a fast and user friendly viewer of bias potential/free energy surfaces calculated by metadynamics in Plumed package. It is based on modern web technologies including HTML5, JavaScript and Cascade Style Sheets (CSS). It can be used by visiting the web site and uploading a HILLS file. It calculates the bias potential/free energy surface on the client-side, so it can run online or offline without necessity to install additional web engines. Moreover, it includes tools for measurement of free energies and free energy differences and data/image export.

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…

Analysis of semantic search within the domains of uncertainty: using Keyword Effectiveness Indexing as an evaluation tool.

PubMed

Lorence, Daniel; Abraham, Joanna

2006-01-01

Medical and health-related searches pose a special case of risk when using the web as an information resource. Uninsured consumers, lacking access to a trained provider, will often rely on information from the internet for self-diagnosis and treatment. In areas where treatments are uncertain or controversial, most consumers lack the knowledge to make an informed decision. This exploratory technology assessment examines the use of Keyword Effectiveness Indexing (KEI) analysis as a potential tool for profiling information search and keyword retrieval patterns. Results demonstrate that the KEI methodology can be useful in identifying e-health search patterns, but is limited by semantic or text-based web environments.

Surging Seas Risk Finder: A Simple Search-Based Web Tool for Local Sea Level Rise Projections, Coastal Flood Risk Forecasts, and Inundation Exposure Analysis

NASA Astrophysics Data System (ADS)

Strauss, B.; Dodson, D.; Kulp, S. A.; Rizza, D. H.

2016-12-01

Surging Seas Risk Finder (riskfinder.org) is an online tool for accessing extensive local projections and analysis of sea level rise; coastal floods; and land, populations, contamination sources, and infrastructure and other assets that may be exposed to inundation. Risk Finder was first published in 2013 for Florida, New York and New Jersey, expanding to all states in the contiguous U.S. by 2016, when a major new version of the tool was released with a completely new interface. The revised tool was informed by hundreds of survey responses from and conversations with planners, local officials and other coastal stakeholders, plus consideration of modern best practices for responsive web design and user interfaces, and social science-based principles for science communication. Overarching design principles include simplicity and ease of navigation, leading to a landing page with Google-like sparsity and focus on search, and to an architecture based on search, so that each coastal zip code, city, county, state or other place type has its own webpage gathering all relevant analysis in modular, scrollable units. Millions of users have visited the Surging Seas suite of tools to date, and downloaded thousands of files, for stated purposes ranging from planning to business to education to personal decisions; and from institutions ranging from local to federal government agencies, to businesses, to NGOs, and to academia.

A Knowledge Portal and Collaboration Environment for the Earth Sciences

NASA Astrophysics Data System (ADS)

D'Agnese, F. A.

2008-12-01

Earth Knowledge is developing a web-based 'Knowledge Portal and Collaboration Environment' that will serve as the information-technology-based foundation of a modular Internet-based Earth-Systems Monitoring, Analysis, and Management Tool. This 'Knowledge Portal' is essentially a 'mash- up' of web-based and client-based tools and services that support on-line collaboration, community discussion, and broad public dissemination of earth and environmental science information in a wide-area distributed network. In contrast to specialized knowledge-management or geographic-information systems developed for long- term and incremental scientific analysis, this system will exploit familiar software tools using industry standard protocols, formats, and APIs to discover, process, fuse, and visualize existing environmental datasets using Google Earth and Google Maps. An early form of these tools and services is being used by Earth Knowledge to facilitate the investigations and conversations of scientists, resource managers, and citizen-stakeholders addressing water resource sustainability issues in the Great Basin region of the desert southwestern United States. These ongoing projects will serve as use cases for the further development of this information-technology infrastructure. This 'Knowledge Portal' will accelerate the deployment of Earth- system data and information into an operational knowledge management system that may be used by decision-makers concerned with stewardship of water resources in the American Desert Southwest.

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.

Development of a Web-based resident profiling tool to support training in practice-based learning and improvement.

PubMed

Lyman, Jason A; Schorling, John; Nadkarni, Mohan; May, Natalie; Scully, Ken; Voss, John

2008-04-01

Multiple factors are driving residency programs to explicitly address practice-based learning and improvement (PBLI), yet few information systems exist to facilitate such training. We developed, implemented, and evaluated a Web-based tool that provides Internal Medicine residents at the University of Virginia Health System with population-based reports about their ambulatory clinical experiences. Residents use Systems and Practice Analysis for Resident Competencies (SPARC) to identify potential areas for practice improvement. Thirty-three (65%) of 51 residents completed a survey assessing SPARC's usefulness, with 94% agreeing that it was a useful educational tool. Twenty-six residents (51%) completed a before-after study indicating increased agreement (5-point Likert scale, with 5=strongly agree) with statements regarding confidence in ability to access population-based data about chronic disease management (mean [SD] 2.5 [1.2] vs. 4.5 [0.5], p < .001, sign test) and information comparing their practice style to that of their peers (2.2 [1.2] vs. 4.6 [0.5], p < .001).

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.

Growing Reading Fluency: Engaging Readers with Technology and Text

ERIC Educational Resources Information Center

Parenti, Melissa A.; Chen, Xiaojun

2015-01-01

The presence of technology in K-12 classrooms continues to increase. With the onset of these technological advances, a refined lens for analysis of the effectiveness of these tools is required. Web based tools necessitate a synthesis of Technological, Pedagogical and Content knowledge. Moreover, the use of technology should support the content and…

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

EPA Science Inventory

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

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

NASA Astrophysics Data System (ADS)

Netzel, P.; Stepinski, T.

2012-12-01

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

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.

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

PubMed Central

Porollo, Aleksey; Meller, Jaroslaw

2010-01-01

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

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

PubMed Central

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

2017-01-01

Background Patients with chronic conditions require ongoing care which not only necessitates support from health care providers outside appointments but also self-management. Web-based tools for text-based patient-provider communication, such as secure messaging, allow for sharing of contextual information and personal narrative in a simple accessible medium, empowering patients and enabling their providers to address emerging care needs. Objective The objectives of this study were to (1) conduct a systematic search of the published literature and the Internet for Web-based tools for text-based communication between patients and providers; (2) map tool characteristics, their intended use, contexts in which they were used, and by whom; (3) describe the nature of their evaluation; and (4) understand the terminology used to describe the tools. Methods We conducted a scoping review using the MEDLINE (Medical Literature Analysis and Retrieval System Online) and EMBASE (Excerpta Medica Database) databases. We summarized information on the characteristics of the tools (structure, functions, and communication paradigm), intended use, context and users, evaluation (study design and outcomes), and terminology. We performed a parallel search of the Internet to compare with tools identified in the published literature. Results We identified 54 papers describing 47 unique tools from 13 countries studied in the context of 68 chronic health conditions. The majority of tools (77%, 36/47) had functions in addition to communication (eg, viewable care plan, symptom diary, or tracker). Eight tools (17%, 8/47) were described as allowing patients to communicate with the team or multiple health care providers. Most of the tools were intended to support communication regarding symptom reporting (49%, 23/47), and lifestyle or behavior modification (36%, 17/47). The type of health care providers who used tools to communicate with patients were predominantly allied health professionals of various disciplines (30%, 14/47), nurses (23%, 11/47), and physicians (19%, 9/47), among others. Over half (52%, 25/48) of the tools were evaluated in randomized controlled trials, and 23 tools (48%, 23/48) were evaluated in nonrandomized studies. Terminology of tools varied by intervention type and functionality and did not consistently reflect a theme of communication. The majority of tools found in the Internet search were patient portals from 6 developers; none were found among published articles. Conclusions Web-based tools for text-based patient-provider communication were identified from a wide variety of clinical contexts and with varied functionality. Tools were most prevalent in contexts where intended use was self-management. Few tools for team-based communication were found, but this may become increasingly important as chronic disease care becomes more interdisciplinary. PMID:29079552

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

PubMed

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

2017-10-27

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

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

NASA Astrophysics Data System (ADS)

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

2017-07-01

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

MS Data Miner: a web-based software tool to analyze, compare, and share mass spectrometry protein identifications.

PubMed

Dyrlund, Thomas F; Poulsen, Ebbe T; Scavenius, Carsten; Sanggaard, Kristian W; Enghild, Jan J

2012-09-01

Data processing and analysis of proteomics data are challenging and time consuming. In this paper, we present MS Data Miner (MDM) (http://sourceforge.net/p/msdataminer), a freely available web-based software solution aimed at minimizing the time required for the analysis, validation, data comparison, and presentation of data files generated in MS software, including Mascot (Matrix Science), Mascot Distiller (Matrix Science), and ProteinPilot (AB Sciex). The program was developed to significantly decrease the time required to process large proteomic data sets for publication. This open sourced system includes a spectra validation system and an automatic screenshot generation tool for Mascot-assigned spectra. In addition, a Gene Ontology term analysis function and a tool for generating comparative Excel data reports are included. We illustrate the benefits of MDM during a proteomics study comprised of more than 200 LC-MS/MS analyses recorded on an AB Sciex TripleTOF 5600, identifying more than 3000 unique proteins and 3.5 million peptides. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

dada - a web-based 2D detector analysis tool

NASA Astrophysics Data System (ADS)

Osterhoff, Markus

2017-06-01

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

Microbial Genome Analysis and Comparisons: Web-based Protocols and Resources

USDA-ARS?s Scientific Manuscript database

Fully annotated genome sequences of many microorganisms are publicly available as a resource. However, in-depth analysis of these genomes using specialized tools is required to derive meaningful information. We describe here the utility of three powerful publicly available genome databases and ana...

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

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

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

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.

Web-based platform for collaborative medical imaging research

NASA Astrophysics Data System (ADS)

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

2015-03-01

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

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

PubMed

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

2016-07-01

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

Web-Based Analysis for Student-Generated Complex Genetic Profiles

ERIC Educational Resources Information Center

Kass, David H.; LaRoe, Robert

2007-01-01

A simple, rapid method for generating complex genetic profiles using Alu-based markers was recently developed for students primarily at the undergraduate level to learn more about forensics and paternity analysis. On the basis of the Cold Spring Harbor Allele Server, which provides an excellent tool for analyzing a single Alu variant, we present a…

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 .

SCit: web tools for protein side chain conformation analysis

PubMed Central

Gautier, R.; Camproux, A.-C.; Tufféry, P.

2004-01-01

SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the side chain conformations on the local backbone conformation, which is described using a structural alphabet that describes the conformation of fragments of four-residue length in a limited library of structural prototypes. Based on this concept, SCit uses sets of rotameric conformations dependent on the local backbone conformation of each protein for side chain positioning and the identification of side chains with unlikely conformations. The SCit web server is accessible at http://bioserv.rpbs.jussieu.fr/SCit. PMID:15215438

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).

Impact of a web-based tool (WebCONSORT) to improve the reporting of randomised trials: results of a randomised controlled trial.

PubMed

Hopewell, Sally; Boutron, Isabelle; Altman, Douglas G; Barbour, Ginny; Moher, David; Montori, Victor; Schriger, David; Cook, Jonathan; Gerry, Stephen; Omar, Omar; Dutton, Peter; Roberts, Corran; Frangou, Eleni; Clifton, Lei; Chiocchia, Virginia; Rombach, Ines; Wartolowska, Karolina; Ravaud, Philippe

2016-11-28

The CONSORT Statement is an evidence-informed guideline for reporting randomised controlled trials. A number of extensions have been developed that specify additional information to report for more complex trials. The aim of this study was to evaluate the impact of using a simple web-based tool (WebCONSORT, which incorporates a number of different CONSORT extensions) on the completeness of reporting of randomised trials published in biomedical publications. We conducted a parallel group randomised trial. Journals which endorsed the CONSORT Statement (i.e. referred to it in the Instruction to Authors) but do not actively implement it (i.e. require authors to submit a completed CONSORT checklist) were invited to participate. Authors of randomised trials were requested by the editor to use the web-based tool at the manuscript revision stage. Authors registering to use the tool were randomised (centralised computer generated) to WebCONSORT or control. In the WebCONSORT group, they had access to a tool allowing them to combine the different CONSORT extensions relevant to their trial and generate a customised checklist and flow diagram that they must submit to the editor. In the control group, authors had only access to a CONSORT flow diagram generator. Authors, journal editors, and outcome assessors were blinded to the allocation. The primary outcome was the proportion of CONSORT items (main and extensions) reported in each article post revision. A total of 46 journals actively recruited authors into the trial (25 March 2013 to 22 September 2015); 324 author manuscripts were randomised (WebCONSORT n = 166; control n = 158), of which 197 were reports of randomised trials (n = 94; n = 103). Over a third (39%; n = 127) of registered manuscripts were excluded from the analysis, mainly because the reported study was not a randomised trial. Of those included in the analysis, the most common CONSORT extensions selected were non-pharmacologic (n = 43; n = 50), pragmatic (n = 20; n = 16) and cluster (n = 10; n = 9). In a quarter of manuscripts, authors either wrongly selected an extension or failed to select the right extension when registering their manuscript on the WebCONSORT study site. Overall, there was no important difference in the overall mean score between WebCONSORT (mean score 0.51) and control (0.47) in the proportion of CONSORT and CONSORT extension items reported pertaining to a given study (mean difference, 0.04; 95% CI -0.02 to 0.10). This study failed to show a beneficial effect of a customised web-based CONSORT checklist to help authors prepare more complete trial reports. However, the exclusion of a large number of inappropriately registered manuscripts meant we had less precision than anticipated to detect a difference. Better education is needed, earlier in the publication process, for both authors and journal editorial staff on when and how to implement CONSORT and, in particular, CONSORT-related extensions. ClinicalTrials.gov: NCT01891448 [registered 24 May 2013].

Small numbers, disclosure risk, security, and reliability issues in Web-based data query systems.

PubMed

Rudolph, Barbara A; Shah, Gulzar H; Love, Denise

2006-01-01

This article describes the process for developing consensus guidelines and tools for releasing public health data via the Web and highlights approaches leading agencies have taken to balance disclosure risk with public dissemination of reliable health statistics. An agency's choice of statistical methods for improving the reliability of released data for Web-based query systems is based upon a number of factors, including query system design (dynamic analysis vs preaggregated data and tables), population size, cell size, data use, and how data will be supplied to users. The article also describes those efforts that are necessary to reduce the risk of disclosure of an individual's protected health information.

ProstateAnalyzer: Web-based medical application for the management of prostate cancer using multiparametric MR imaging.

PubMed

Mata, Christian; Walker, Paul M; Oliver, Arnau; Brunotte, François; Martí, Joan; Lalande, Alain

2016-01-01

In this paper, we present ProstateAnalyzer, a new web-based medical tool for prostate cancer diagnosis. ProstateAnalyzer allows the visualization and analysis of magnetic resonance images (MRI) in a single framework. ProstateAnalyzer recovers the data from a PACS server and displays all the associated MRI images in the same framework, usually consisting of 3D T2-weighted imaging for anatomy, dynamic contrast-enhanced MRI for perfusion, diffusion-weighted imaging in the form of an apparent diffusion coefficient (ADC) map and MR Spectroscopy. ProstateAnalyzer allows annotating regions of interest in a sequence and propagates them to the others. From a representative case, the results using the four visualization platforms are fully detailed, showing the interaction among them. The tool has been implemented as a Java-based applet application to facilitate the portability of the tool to the different computer architectures and software and allowing the possibility to work remotely via the web. ProstateAnalyzer enables experts to manage prostate cancer patient data set more efficiently. The tool allows delineating annotations by experts and displays all the required information for use in diagnosis. According to the current European Society of Urogenital Radiology guidelines, it also includes the PI-RADS structured reporting scheme.

Tox21 Enricher: Web-based Chemical/Biological Functional Annotation Analysis Tool Based on Tox21 Toxicity Screening Platform.

PubMed

Hur, Junguk; Danes, Larson; Hsieh, Jui-Hua; McGregor, Brett; Krout, Dakota; Auerbach, Scott

2018-05-01

The US Toxicology Testing in the 21st Century (Tox21) program was established to develop more efficient and human-relevant toxicity assessment methods. The Tox21 program screens >10,000 chemicals using quantitative high-throughput screening (qHTS) of assays that measure effects on toxicity pathways. To date, more than 70 assays have yielded >12 million concentration-response curves. The patterns of activity across assays can be used to define similarity between chemicals. Assuming chemicals with similar activity profiles have similar toxicological properties, we may infer toxicological properties based on its neighbourhood. One approach to inference is chemical/biological annotation enrichment analysis. Here, we present Tox21 Enricher, a web-based chemical annotation enrichment tool for the Tox21 toxicity screening platform. Tox21 Enricher identifies over-represented chemical/biological annotations among lists of chemicals (neighbourhoods), facilitating the identification of the toxicological properties and mechanisms in the chemical set. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

PubMed Central

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

2006-01-01

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

A smartphone-based platform to test the performance of wireless mobile networks and preliminary findings

NASA Astrophysics Data System (ADS)

Geng, Xinli; Xu, Hao; Qin, Xiaowei

2016-10-01

During the last several years, the amount of wireless network traffic data increased fast and relative technologies evolved rapidly. In order to improve the performance and Quality of Experience (QoE) of wireless network services, the analysis of field network data and existing delivery mechanisms comes to be a promising research topic. In order to achieve this goal, a smartphone based platform named Monitor and Diagnosis of Mobile Applications (MDMA) was developed to collect field data. Based on this tool, the web browsing service of High Speed Downlink Packet Access (HSDPA) network was tested. The top 200 popular websites in China were selected and loaded on smartphone for thousands times automatically. Communication packets between the smartphone and the cell station were captured for various scenarios (e.g. residential area, urban roads, bus station etc.) in the selected city. A cross-layer database was constructed to support the off-line analysis. Based on the results of client-side experiments and analysis, the usability of proposed portable tool was verified. The preliminary findings and results for existing web browsing service were also presented.

ISAAC - InterSpecies Analysing Application using Containers.

PubMed

Baier, Herbert; Schultz, Jörg

2014-01-15

Information about genes, transcripts and proteins is spread over a wide variety of databases. Different tools have been developed using these databases to identify biological signals in gene lists from large scale analysis. Mostly, they search for enrichments of specific features. But, these tools do not allow an explorative walk through different views and to change the gene lists according to newly upcoming stories. To fill this niche, we have developed ISAAC, the InterSpecies Analysing Application using Containers. The central idea of this web based tool is to enable the analysis of sets of genes, transcripts and proteins under different biological viewpoints and to interactively modify these sets at any point of the analysis. Detailed history and snapshot information allows tracing each action. Furthermore, one can easily switch back to previous states and perform new analyses. Currently, sets can be viewed in the context of genomes, protein functions, protein interactions, pathways, regulation, diseases and drugs. Additionally, users can switch between species with an automatic, orthology based translation of existing gene sets. As todays research usually is performed in larger teams and consortia, ISAAC provides group based functionalities. Here, sets as well as results of analyses can be exchanged between members of groups. ISAAC fills the gap between primary databases and tools for the analysis of large gene lists. With its highly modular, JavaEE based design, the implementation of new modules is straight forward. Furthermore, ISAAC comes with an extensive web-based administration interface including tools for the integration of third party data. Thus, a local installation is easily feasible. In summary, ISAAC is tailor made for highly explorative interactive analyses of gene, transcript and protein sets in a collaborative environment.

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.

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

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

PubMed

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

2017-05-04

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

RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation.

PubMed

Li, Ying; Shi, Xiaohu; Liang, Yanchun; Xie, Juan; Zhang, Yu; Ma, Qin

2017-01-21

RNAs have been found to carry diverse functionalities in nature. Inferring the similarity between two given RNAs is a fundamental step to understand and interpret their functional relationship. The majority of functional RNAs show conserved secondary structures, rather than sequence conservation. Those algorithms relying on sequence-based features usually have limitations in their prediction performance. Hence, integrating RNA structure features is very critical for RNA analysis. Existing algorithms mainly fall into two categories: alignment-based and alignment-free. The alignment-free algorithms of RNA comparison usually have lower time complexity than alignment-based algorithms. An alignment-free RNA comparison algorithm was proposed, in which novel numerical representations RNA-TVcurve (triple vector curve representation) of RNA sequence and corresponding secondary structure features are provided. Then a multi-scale similarity score of two given RNAs was designed based on wavelet decomposition of their numerical representation. In support of RNA mutation and phylogenetic analysis, a web server (RNA-TVcurve) was designed based on this alignment-free RNA comparison algorithm. It provides three functional modules: 1) visualization of numerical representation of RNA secondary structure; 2) detection of single-point mutation based on secondary structure; and 3) comparison of pairwise and multiple RNA secondary structures. The inputs of the web server require RNA primary sequences, while corresponding secondary structures are optional. For the primary sequences alone, the web server can compute the secondary structures using free energy minimization algorithm in terms of RNAfold tool from Vienna RNA package. RNA-TVcurve is the first integrated web server, based on an alignment-free method, to deliver a suite of RNA analysis functions, including visualization, mutation analysis and multiple RNAs structure comparison. The comparison results with two popular RNA comparison tools, RNApdist and RNAdistance, showcased that RNA-TVcurve can efficiently capture subtle relationships among RNAs for mutation detection and non-coding RNA classification. All the relevant results were shown in an intuitive graphical manner, and can be freely downloaded from this server. RNA-TVcurve, along with test examples and detailed documents, are available at: http://ml.jlu.edu.cn/tvcurve/ .

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

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

PubMed

Kovanci, Gökhan; Ghaffar, Mehmood; Sommer, Björn

2016-12-21

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

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

PubMed

Kovanci, Gökhan; Ghaffar, Mehmood; Sommer, Björn

2016-10-01

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

SpirPep: an in silico digestion-based platform to assist bioactive peptides discovery from a genome-wide database.

PubMed

Anekthanakul, Krittima; Hongsthong, Apiradee; Senachak, Jittisak; Ruengjitchatchawalya, Marasri

2018-04-20

Bioactive peptides, including biological sources-derived peptides with different biological activities, are protein fragments that influence the functions or conditions of organisms, in particular humans and animals. Conventional methods of identifying bioactive peptides are time-consuming and costly. To quicken the processes, several bioinformatics tools are recently used to facilitate screening of the potential peptides prior their activity assessment in vitro and/or in vivo. In this study, we developed an efficient computational method, SpirPep, which offers many advantages over the currently available tools. The SpirPep web application tool is a one-stop analysis and visualization facility to assist bioactive peptide discovery. The tool is equipped with 15 customized enzymes and 1-3 miscleavage options, which allows in silico digestion of protein sequences encoded by protein-coding genes from single, multiple, or genome-wide scaling, and then directly classifies the peptides by bioactivity using an in-house database that contains bioactive peptides collected from 13 public databases. With this tool, the resulting peptides are categorized by each selected enzyme, and shown in a tabular format where the peptide sequences can be tracked back to their original proteins. The developed tool and webpages are coded in PHP and HTML with CSS/JavaScript. Moreover, the tool allows protein-peptide alignment visualization by Generic Genome Browser (GBrowse) to display the region and details of the proteins and peptides within each parameter, while considering digestion design for the desirable bioactivity. SpirPep is efficient; it takes less than 20 min to digest 3000 proteins (751,860 amino acids) with 15 enzymes and three miscleavages for each enzyme, and only a few seconds for single enzyme digestion. Obviously, the tool identified more bioactive peptides than that of the benchmarked tool; an example of validated pentapeptide (FLPIL) from LC-MS/MS was demonstrated. The web and database server are available at http://spirpepapp.sbi.kmutt.ac.th . SpirPep, a web-based bioactive peptide discovery application, is an in silico-based tool with an overview of the results. The platform is a one-stop analysis and visualization facility; and offers advantages over the currently available tools. This tool may be useful for further bioactivity analysis and the quantitative discovery of desirable peptides.

Solar System Treks: Interactive Web Portals or STEM, Exploration and Beyond

NASA Astrophysics Data System (ADS)

Law, E.; Day, B. H.; Viotti, M.

2017-12-01

NASA's Solar System Treks project produces a suite of online visualization and analysis tools for lunar and planetary mapping and modeling. These portals offer great benefits for education and public outreach, providing access to data from a wide range of instruments aboard a variety of past and current missions. As a component of NASA's STEM Activation Infrastructure, they are available as resources for NASA STEM programs, and to the greater STEM community. As new missions are planned to a variety of planetary bodies, these tools facilitate public understanding of the missions and engage the public in the process of identifying and selecting where these missions will land. There are currently three web portals in the program: Moon Trek (https://moontrek.jpl.nasa.gov), Mars Trek (https://marstrek.jpl.nasa.gov), and Vesta Trek (https://vestatrek.jpl.nasa.gov). A new release of Mars Trek includes new tools and data products focusing on human landing site selection. Backed by evidence-based cognitive and computer science findings, an additional version is available for educational and public audiences in support of earning along novice-to-expert pathways, enabling authentic, real-world interaction with planetary data. Portals for additional planetary bodies are planned. As web-based toolsets, the portals do not require users to purchase or install any software beyond current web browsers. The portals provide analysis tools for measurement and study of planetary terrain. They allow data to be layered and adjusted to optimize visualization. Visualizations are easily stored and shared. The portals provide 3D visualization and give users the ability to mark terrain for generation of STL/OBJ files that can be directed to 3D printers. Such 3D prints are valuable tools in museums, public exhibits, and classrooms - especially for the visually impaired. The program supports additional clients, web services, and APIs facilitating dissemination of planetary data to external applications and venues. NASA challenges and hackathons also provide members of the software development community opportunities to participate in tool development and leverage data from the portals.

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.

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

PubMed

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

2012-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

Lamprey: tracking users on the World Wide Web.

PubMed

Felciano, R M; Altman, R B

1996-01-01

Tracking individual web sessions provides valuable information about user behavior. This information can be used for general purpose evaluation of web-based user interfaces to biomedical information systems. To this end, we have developed Lamprey, a tool for doing quantitative and qualitative analysis of Web-based user interfaces. Lamprey can be used from any conforming browser, and does not require modification of server or client software. By rerouting WWW navigation through a centralized filter, Lamprey collects the sequence and timing of hyperlinks used by individual users to move through the web. Instead of providing marginal statistics, it retains the full information required to recreate a user session. We have built Lamprey as a standard Common Gateway Interface (CGI) that works with all standard WWW browsers and servers. In this paper, we describe Lamprey and provide a short demonstration of this approach for evaluating web usage patterns.

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…

WebGL and web audio software lightweight components for multimedia education

NASA Astrophysics Data System (ADS)

Chang, Xin; Yuksel, Kivanc; Skarbek, Władysław

2017-08-01

The paper presents the results of our recent work on development of contemporary computing platform DC2 for multimedia education usingWebGL andWeb Audio { the W3C standards. Using literate programming paradigm the WEBSA educational tools were developed. It offers for a user (student), the access to expandable collection of WEBGL Shaders and web Audio scripts. The unique feature of DC2 is the option of literate programming, offered for both, the author and the reader in order to improve interactivity to lightweightWebGL andWeb Audio components. For instance users can define: source audio nodes including synthetic sources, destination audio nodes, and nodes for audio processing such as: sound wave shaping, spectral band filtering, convolution based modification, etc. In case of WebGL beside of classic graphics effects based on mesh and fractal definitions, the novel image processing analysis by shaders is offered like nonlinear filtering, histogram of gradients, and Bayesian classifiers.

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…

A web-based tool for groundwater mapping and drought analysis

NASA Astrophysics Data System (ADS)

Christensen, S.; Burns, M.; Jones, N.; Strassberg, G.

2012-12-01

In 2011-2012, the state of Texas saw the worst one-year drought on record. Fluctuations in gravity measured by GRACE satellites indicate that as much as 100 cubic kilometers of water was lost during this period. Much of this came from reservoirs and shallow soil moisture, but a significant amount came from aquifers. In response to this crisis, a Texas Drought Technology Steering Committee (TDTSC) consisting of academics and water managers was formed to develop new tools and strategies to assist the state in monitoring, predicting, and responding to drought events. In this presentation, we describe one of the tools that was developed as part of this effort. When analyzing the impact of drought on groundwater levels, it is fairly common to examine time series data at selected monitoring wells. However, accurately assessing impacts and trends requires both spatial and temporal analysis involving the development of detailed water level maps at various scales. Creating such maps in a flexible and rapid fashion is critical for effective drought analysis, but can be challenging due to the massive amounts of data involved and the processing required to generate such maps. Furthermore, wells are typically not sampled at the same points in time, and so developing a water table map for a particular date requires both spatial and temporal interpolation of water elevations. To address this challenge, a Cloud-based water level mapping system was developed for the state of Texas. The system is based on the Texas Water Development Board (TWDB) groundwater database, but can be adapted to use other databases as well. The system involves a set of ArcGIS workflows running on a server with a web-based front end and a Google Earth plug-in. A temporal interpolation geoprocessing tool was developed to estimate the piezometric heads for all wells in a given region at a specific date using a regression analysis. This interpolation tool is coupled with other geoprocessing tools to filter data and interpolate point elevations spatially to produce water level, drawdown, and depth to groundwater maps. The web interface allows for users to generate these maps at locations and times of interest. A sequence of maps can be generated over a period of time and animated to visualize how water levels are changing. The time series regression analysis can also be used to do short-term predictions of future water levels.

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…

State Analysis Database Tool

NASA Technical Reports Server (NTRS)

Rasmussen, Robert; Bennett, Matthew

2006-01-01

The State Analysis Database Tool software establishes a productive environment for collaboration among software and system engineers engaged in the development of complex interacting systems. The tool embodies State Analysis, a model-based system engineering methodology founded on a state-based control architecture (see figure). A state represents a momentary condition of an evolving system, and a model may describe how a state evolves and is affected by other states. The State Analysis methodology is a process for capturing system and software requirements in the form of explicit models and states, and defining goal-based operational plans consistent with the models. Requirements, models, and operational concerns have traditionally been documented in a variety of system engineering artifacts that address different aspects of a mission s lifecycle. In State Analysis, requirements, models, and operations information are State Analysis artifacts that are consistent and stored in a State Analysis Database. The tool includes a back-end database, a multi-platform front-end client, and Web-based administrative functions. The tool is structured to prompt an engineer to follow the State Analysis methodology, to encourage state discovery and model description, and to make software requirements and operations plans consistent with model descriptions.

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)

SMARTE TUTORIAL CD

EPA Science Inventory

SMARTe is a web-based decision support tool intended to help revitalization practitioners find information, perform data analysis, communicate, and evaluate future reuse options for a site or area. A tutorial was developed to help users navigate SMARTe. This tutorial is approxima...

LENS: web-based lens for enrichment and network studies of human proteins

PubMed Central

2015-01-01

Background Network analysis is a common approach for the study of genetic view of diseases and biological pathways. Typically, when a set of genes are identified to be of interest in relation to a disease, say through a genome wide association study (GWAS) or a different gene expression study, these genes are typically analyzed in the context of their protein-protein interaction (PPI) networks. Further analysis is carried out to compute the enrichment of known pathways and disease-associations in the network. Having tools for such analysis at the fingertips of biologists without the requirement for computer programming or curation of data would accelerate the characterization of genes of interest. Currently available tools do not integrate network and enrichment analysis and their visualizations, and most of them present results in formats not most conducive to human cognition. Results We developed the tool Lens for Enrichment and Network Studies of human proteins (LENS) that performs network and pathway and diseases enrichment analyses on genes of interest to users. The tool creates a visualization of the network, provides easy to read statistics on network connectivity, and displays Venn diagrams with statistical significance values of the network's association with drugs, diseases, pathways, and GWASs. We used the tool to analyze gene sets related to craniofacial development, autism, and schizophrenia. Conclusion LENS is a web-based tool that does not require and download or plugins to use. The tool is free and does not require login for use, and is available at http://severus.dbmi.pitt.edu/LENS. PMID:26680011

A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis

PubMed Central

Guardia, Gabriela D. A.; Pires, Luís Ferreira; Vêncio, Ricardo Z. N.; Malmegrim, Kelen C. R.; de Farias, Cléver R. G.

2015-01-01

Gene expression studies are generally performed through multi-step analysis processes, which require the integrated use of a number of analysis tools. In order to facilitate tool/data integration, an increasing number of analysis tools have been developed as or adapted to semantic web services. In recent years, some approaches have been defined for the development and semantic annotation of web services created from legacy software tools, but these approaches still present many limitations. In addition, to the best of our knowledge, no suitable approach has been defined for the functional genomics domain. Therefore, this paper aims at defining an integrated methodology for the implementation of RESTful semantic web services created from gene expression analysis tools and the semantic annotation of such services. We have applied our methodology to the development of a number of services to support the analysis of different types of gene expression data, including microarray and RNASeq. All developed services are publicly available in the Gene Expression Analysis Services (GEAS) Repository at http://dcm.ffclrp.usp.br/lssb/geas. Additionally, we have used a number of the developed services to create different integrated analysis scenarios to reproduce parts of two gene expression studies documented in the literature. The first study involves the analysis of one-color microarray data obtained from multiple sclerosis patients and healthy donors. The second study comprises the analysis of RNA-Seq data obtained from melanoma cells to investigate the role of the remodeller BRG1 in the proliferation and morphology of these cells. Our methodology provides concrete guidelines and technical details in order to facilitate the systematic development of semantic web services. Moreover, it encourages the development and reuse of these services for the creation of semantically integrated solutions for gene expression analysis. PMID:26207740

A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis.

PubMed

Guardia, Gabriela D A; Pires, Luís Ferreira; Vêncio, Ricardo Z N; Malmegrim, Kelen C R; de Farias, Cléver R G

2015-01-01

Gene expression studies are generally performed through multi-step analysis processes, which require the integrated use of a number of analysis tools. In order to facilitate tool/data integration, an increasing number of analysis tools have been developed as or adapted to semantic web services. In recent years, some approaches have been defined for the development and semantic annotation of web services created from legacy software tools, but these approaches still present many limitations. In addition, to the best of our knowledge, no suitable approach has been defined for the functional genomics domain. Therefore, this paper aims at defining an integrated methodology for the implementation of RESTful semantic web services created from gene expression analysis tools and the semantic annotation of such services. We have applied our methodology to the development of a number of services to support the analysis of different types of gene expression data, including microarray and RNASeq. All developed services are publicly available in the Gene Expression Analysis Services (GEAS) Repository at http://dcm.ffclrp.usp.br/lssb/geas. Additionally, we have used a number of the developed services to create different integrated analysis scenarios to reproduce parts of two gene expression studies documented in the literature. The first study involves the analysis of one-color microarray data obtained from multiple sclerosis patients and healthy donors. The second study comprises the analysis of RNA-Seq data obtained from melanoma cells to investigate the role of the remodeller BRG1 in the proliferation and morphology of these cells. Our methodology provides concrete guidelines and technical details in order to facilitate the systematic development of semantic web services. Moreover, it encourages the development and reuse of these services for the creation of semantically integrated solutions for gene expression analysis.

EasyFRAP-web: a web-based tool for the analysis of fluorescence recovery after photobleaching data.

PubMed

Koulouras, Grigorios; Panagopoulos, Andreas; Rapsomaniki, Maria A; Giakoumakis, Nickolaos N; Taraviras, Stavros; Lygerou, Zoi

2018-06-13

Understanding protein dynamics is crucial in order to elucidate protein function and interactions. Advances in modern microscopy facilitate the exploration of the mobility of fluorescently tagged proteins within living cells. Fluorescence recovery after photobleaching (FRAP) is an increasingly popular functional live-cell imaging technique which enables the study of the dynamic properties of proteins at a single-cell level. As an increasing number of labs generate FRAP datasets, there is a need for fast, interactive and user-friendly applications that analyze the resulting data. Here we present easyFRAP-web, a web application that simplifies the qualitative and quantitative analysis of FRAP datasets. EasyFRAP-web permits quick analysis of FRAP datasets through an intuitive web interface with interconnected analysis steps (experimental data assessment, different types of normalization and estimation of curve-derived quantitative parameters). In addition, easyFRAP-web provides dynamic and interactive data visualization and data and figure export for further analysis after every step. We test easyFRAP-web by analyzing FRAP datasets capturing the mobility of the cell cycle regulator Cdt2 in the presence and absence of DNA damage in cultured cells. We show that easyFRAP-web yields results consistent with previous studies and highlights cell-to-cell heterogeneity in the estimated kinetic parameters. EasyFRAP-web is platform-independent and is freely accessible at: https://easyfrap.vmnet.upatras.gr/.

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

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.

Hydrogen Financial Analysis Scenario Tool (H2FAST) Documentation

Science.gov Websites

for the web and spreadsheet versions of H2FAST. H2FAST Web Tool User's Manual H2FAST Spreadsheet Tool User's Manual (DRAFT) Technical Support Send questions or feedback about H2FAST to H2FAST@nrel.gov. Home

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.

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.

Bioinformatic tools for inferring functional information from plant microarray data: tools for the first steps.

PubMed

Page, Grier P; Coulibaly, Issa

2008-01-01

Microarrays are a very powerful tool for quantifying the amount of RNA in samples; however, their ability to query essentially every gene in a genome, which can number in the tens of thousands, presents analytical and interpretative problems. As a result, a variety of software and web-based tools have been developed to help with these issues. This article highlights and reviews some of the tools for the first steps in the analysis of a microarray study. We have tried for a balance between free and commercial systems. We have organized the tools by topics including image processing tools (Section 2), power analysis tools (Section 3), image analysis tools (Section 4), database tools (Section 5), databases of functional information (Section 6), annotation tools (Section 7), statistical and data mining tools (Section 8), and dissemination tools (Section 9).

miRNAtools: Advanced Training Using the miRNA Web of Knowledge.

PubMed

Stępień, Ewa Ł; Costa, Marina C; Enguita, Francisco J

2018-02-16

Micro-RNAs (miRNAs) are small non-coding RNAs that act as negative regulators of the genomic output. Their intrinsic importance within cell biology and human disease is well known. Their mechanism of action based on the base pairing binding to their cognate targets have helped the development not only of many computer applications for the prediction of miRNA target recognition but also of specific applications for functional assessment and analysis. Learning about miRNA function requires practical training in the use of specific computer and web-based applications that are complementary to wet-lab studies. In order to guide the learning process about miRNAs, we have created miRNAtools (http://mirnatools.eu), a web repository of miRNA tools and tutorials. This article compiles tools with which miRNAs and their regulatory action can be analyzed and that function to collect and organize information dispersed on the web. The miRNAtools website contains a collection of tutorials that can be used by students and tutors engaged in advanced training courses. The tutorials engage in analyses of the functions of selected miRNAs, starting with their nomenclature and genomic localization and finishing with their involvement in specific cellular functions.

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…

SurvExpress: an online biomarker validation tool and database for cancer gene expression data using survival analysis.

PubMed

Aguirre-Gamboa, Raul; Gomez-Rueda, Hugo; Martínez-Ledesma, Emmanuel; Martínez-Torteya, Antonio; Chacolla-Huaringa, Rafael; Rodriguez-Barrientos, Alberto; Tamez-Peña, José G; Treviño, Victor

2013-01-01

Validation of multi-gene biomarkers for clinical outcomes is one of the most important issues for cancer prognosis. An important source of information for virtual validation is the high number of available cancer datasets. Nevertheless, assessing the prognostic performance of a gene expression signature along datasets is a difficult task for Biologists and Physicians and also time-consuming for Statisticians and Bioinformaticians. Therefore, to facilitate performance comparisons and validations of survival biomarkers for cancer outcomes, we developed SurvExpress, a cancer-wide gene expression database with clinical outcomes and a web-based tool that provides survival analysis and risk assessment of cancer datasets. The main input of SurvExpress is only the biomarker gene list. We generated a cancer database collecting more than 20,000 samples and 130 datasets with censored clinical information covering tumors over 20 tissues. We implemented a web interface to perform biomarker validation and comparisons in this database, where a multivariate survival analysis can be accomplished in about one minute. We show the utility and simplicity of SurvExpress in two biomarker applications for breast and lung cancer. Compared to other tools, SurvExpress is the largest, most versatile, and quickest free tool available. SurvExpress web can be accessed in http://bioinformatica.mty.itesm.mx/SurvExpress (a tutorial is included). The website was implemented in JSP, JavaScript, MySQL, and R.

SurvExpress: An Online Biomarker Validation Tool and Database for Cancer Gene Expression Data Using Survival Analysis

PubMed Central

Aguirre-Gamboa, Raul; Gomez-Rueda, Hugo; Martínez-Ledesma, Emmanuel; Martínez-Torteya, Antonio; Chacolla-Huaringa, Rafael; Rodriguez-Barrientos, Alberto; Tamez-Peña, José G.; Treviño, Victor

2013-01-01

Validation of multi-gene biomarkers for clinical outcomes is one of the most important issues for cancer prognosis. An important source of information for virtual validation is the high number of available cancer datasets. Nevertheless, assessing the prognostic performance of a gene expression signature along datasets is a difficult task for Biologists and Physicians and also time-consuming for Statisticians and Bioinformaticians. Therefore, to facilitate performance comparisons and validations of survival biomarkers for cancer outcomes, we developed SurvExpress, a cancer-wide gene expression database with clinical outcomes and a web-based tool that provides survival analysis and risk assessment of cancer datasets. The main input of SurvExpress is only the biomarker gene list. We generated a cancer database collecting more than 20,000 samples and 130 datasets with censored clinical information covering tumors over 20 tissues. We implemented a web interface to perform biomarker validation and comparisons in this database, where a multivariate survival analysis can be accomplished in about one minute. We show the utility and simplicity of SurvExpress in two biomarker applications for breast and lung cancer. Compared to other tools, SurvExpress is the largest, most versatile, and quickest free tool available. SurvExpress web can be accessed in http://bioinformatica.mty.itesm.mx/SurvExpress (a tutorial is included). The website was implemented in JSP, JavaScript, MySQL, and R. PMID:24066126

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

PubMed

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

2014-12-01

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

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…

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…

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

PubMed Central

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

2017-01-01

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

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.

GlycoExtractor: a web-based interface for high throughput processing of HPLC-glycan data.

PubMed

Artemenko, Natalia V; Campbell, Matthew P; Rudd, Pauline M

2010-04-05

Recently, an automated high-throughput HPLC platform has been developed that can be used to fully sequence and quantify low concentrations of N-linked sugars released from glycoproteins, supported by an experimental database (GlycoBase) and analytical tools (autoGU). However, commercial packages that support the operation of HPLC instruments and data storage lack platforms for the extraction of large volumes of data. The lack of resources and agreed formats in glycomics is now a major limiting factor that restricts the development of bioinformatic tools and automated workflows for high-throughput HPLC data analysis. GlycoExtractor is a web-based tool that interfaces with a commercial HPLC database/software solution to facilitate the extraction of large volumes of processed glycan profile data (peak number, peak areas, and glucose unit values). The tool allows the user to export a series of sample sets to a set of file formats (XML, JSON, and CSV) rather than a collection of disconnected files. This approach not only reduces the amount of manual refinement required to export data into a suitable format for data analysis but also opens the field to new approaches for high-throughput data interpretation and storage, including biomarker discovery and validation and monitoring of online bioprocessing conditions for next generation biotherapeutics.

Development of a Web-based Resident Profiling Tool to Support Training in Practice-based Learning and Improvement

PubMed Central

Schorling, John; Nadkarni, Mohan; May, Natalie; Scully, Ken; Voss, John

2008-01-01

Multiple factors are driving residency programs to explicitly address practice-based learning and improvement (PBLI), yet few information systems exist to facilitate such training. We developed, implemented, and evaluated a Web-based tool that provides Internal Medicine residents at the University of Virginia Health System with population-based reports about their ambulatory clinical experiences. Residents use Systems and Practice Analysis for Resident Competencies (SPARC) to identify potential areas for practice improvement. Thirty-three (65%) of 51 residents completed a survey assessing SPARC’s usefulness, with 94% agreeing that it was a useful educational tool. Twenty-six residents (51%) completed a before–after study indicating increased agreement (5-point Likert scale, with 5=strongly agree) with statements regarding confidence in ability to access population-based data about chronic disease management (mean [SD] 2.5 [1.2] vs. 4.5 [0.5], p < .001, sign test) and information comparing their practice style to that of their peers (2.2 [1.2] vs. 4.6 [0.5], p < .001). PMID:18373150

CABS-fold: Server for the de novo and consensus-based prediction of protein structure.

PubMed

Blaszczyk, Maciej; Jamroz, Michal; Kmiecik, Sebastian; Kolinski, Andrzej

2013-07-01

The CABS-fold web server provides tools for protein structure prediction from sequence only (de novo modeling) and also using alternative templates (consensus modeling). The web server is based on the CABS modeling procedures ranked in previous Critical Assessment of techniques for protein Structure Prediction competitions as one of the leading approaches for de novo and template-based modeling. Except for template data, fragmentary distance restraints can also be incorporated into the modeling process. The web server output is a coarse-grained trajectory of generated conformations, its Jmol representation and predicted models in all-atom resolution (together with accompanying analysis). CABS-fold can be freely accessed at http://biocomp.chem.uw.edu.pl/CABSfold.

CABS-fold: server for the de novo and consensus-based prediction of protein structure

PubMed Central

Blaszczyk, Maciej; Jamroz, Michal; Kmiecik, Sebastian; Kolinski, Andrzej

2013-01-01

The CABS-fold web server provides tools for protein structure prediction from sequence only (de novo modeling) and also using alternative templates (consensus modeling). The web server is based on the CABS modeling procedures ranked in previous Critical Assessment of techniques for protein Structure Prediction competitions as one of the leading approaches for de novo and template-based modeling. Except for template data, fragmentary distance restraints can also be incorporated into the modeling process. The web server output is a coarse-grained trajectory of generated conformations, its Jmol representation and predicted models in all-atom resolution (together with accompanying analysis). CABS-fold can be freely accessed at http://biocomp.chem.uw.edu.pl/CABSfold. PMID:23748950

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

ERIC Educational Resources Information Center

May, Madeth; George, Sebastien; Prevot, Patrick

2011-01-01

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

Antigen Receptor Galaxy: A User-Friendly, Web-Based Tool for Analysis and Visualization of T and B Cell Receptor Repertoire Data

PubMed Central

IJspeert, Hanna; van Schouwenburg, Pauline A.; van Zessen, David; Pico-Knijnenburg, Ingrid

2017-01-01

Antigen Receptor Galaxy (ARGalaxy) is a Web-based tool for analyses and visualization of TCR and BCR sequencing data of 13 species. ARGalaxy consists of four parts: the demultiplex tool, the international ImMunoGeneTics information system (IMGT) concatenate tool, the immune repertoire pipeline, and the somatic hypermutation (SHM) and class switch recombination (CSR) pipeline. Together they allow the analysis of all different aspects of the immune repertoire. All pipelines can be run independently or combined, depending on the available data and the question of interest. The demultiplex tool allows data trimming and demultiplexing, whereas with the concatenate tool multiple IMGT/HighV-QUEST output files can be merged into a single file. The immune repertoire pipeline is an extended version of our previously published ImmunoGlobulin Galaxy (IGGalaxy) virtual machine that was developed to visualize V(D)J gene usage. It allows analysis of both BCR and TCR rearrangements, visualizes CDR3 characteristics (length and amino acid usage) and junction characteristics, and calculates the diversity of the immune repertoire. Finally, ARGalaxy includes the newly developed SHM and CSR pipeline to analyze SHM and/or CSR in BCR rearrangements. It analyzes the frequency and patterns of SHM, Ag selection (including BASELINe), clonality (Change-O), and CSR. The functionality of the ARGalaxy tool is illustrated in several clinical examples of patients with primary immunodeficiencies. In conclusion, ARGalaxy is a novel tool for the analysis of the complete immune repertoire, which is applicable to many patient groups with disturbances in the immune repertoire such as autoimmune diseases, allergy, and leukemia, but it can also be used to address basic research questions in repertoire formation and selection. PMID:28416602

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.

Hydrologic analysis for selection and placement of conservation practices at the watershed scale

NASA Astrophysics Data System (ADS)

Wilson, C.; Brooks, E. S.; Boll, J.

2012-12-01

When a water body is exceeding water quality standards and a Total Maximum Daily Load has been established, conservation practices in the watershed are able to reduce point and non-point source pollution. Hydrological analysis is needed to place conservation practices in the most hydrologically sensitive areas. The selection and placement of conservation practices, however, is challenging in ungauged watersheds with little or no data for the hydrological analysis. The objective of this research is to perform a hydrological analysis for mitigation of erosion and total phosphorus in a mixed land use watershed, and to select and place the conservation practices in the most sensitive areas. The study area is the Hangman Creek watershed in Idaho and Washington State, upstream of Long Lake (WA) reservoir, east of Spokane, WA. While the pollutant of concern is total phosphorus (TP), reductions in TP were translated to total suspended solids or reductions in nonpoint source erosion and sediment delivery to streams. Hydrological characterization was done with a simple web-based tool, which runs the Water Erosion Prediction Project (WEPP) model for representative land types in the watersheds, where a land type is defined as a unique combination of soil type, slope configuration, land use and management, and climate. The web-based tool used site-specific spatial and temporal data on land use, soil physical parameters, slope, and climate derived from readily available data sources and provided information on potential pollutant pathways (i.e. erosion, runoff, lateral flow, and percolation). Multiple land types representative in the watershed were ordered from most effective to least effective, and displayed spatially using GIS. The methodology for the Hangman Creek watershed was validated in the nearby Paradise Creek watershed that has long-term stream discharge and monitoring as well as land use data. Output from the web-based tool shows the potential reductions for different tillage practices, buffer strips, streamside management, and conversion to the conservation reserve program in the watershed. The output also includes the relationship between land area where conservation practices are placed and the potential reduction in pollution, showing the diminished returns on investment as less sensitive areas are being treated. This application of a simple web-based tool and the use of a physically-based erosion model (i.e. WEPP) illustrates that quantitative, spatial and temporal analysis of changes in pollutant loading and site-specific recommendations of conservation practices can be made in ungauged watersheds.

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.

A web-based information system for management and analysis of patient data after refractive eye surgery.

PubMed

Zuberbuhler, Bruno; Galloway, Peter; Reddy, Aravind; Saldana, Manuel; Gale, Richard

2007-12-01

The aim was to develop a software tool for refractive surgeons using a standard user-friendly web-based interface, providing the user with a secure environment to protect large volumes of patient data. The software application was named "Internet-based refractive analysis" (IBRA), and was programmed with the computer languages PHP, HTML and JavaScript, attached to the opensource MySQL database. IBRA facilitated internationally accepted presentation methods including the stability chart, the predictability chart and the safety chart; it was able to perform vector analysis for the course of a single patient or for group data. With the integrated nomogram calculation, treatment could be customised to reduce the postoperative refractive error. Multicenter functions permitted quality-control comparisons between different surgeons and laser units.

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...

web-based interactive data processing: application to stable isotope metrology.

PubMed

Verkouteren, R M; Lee, J N

2001-08-01

To address a fundamental need in stable isotope metrology, the National Institute of Standards and Technology (NIST) has established a web-based interactive data-processing system accessible through a common gateway interface (CGI) program on the internet site http://www. nist.gov/widps-co2. This is the first application of a web-based tool that improves the measurement traceability afforded by a series of NIST standard materials. Specifically, this tool promotes the proper usage of isotope reference materials (RMs) and improves the quality of reported data from extensive measurement networks. Through the International Atomic Energy Agency (IAEA), we have defined standard procedures for stable isotope measurement and data-processing, and have determined and applied consistent reference values for selected NIST and IAEA isotope RMs. Measurement data of samples and RMs are entered into specified fields on the web-based form. These data are submitted through the CGI program on a NIST Web server, where appropriate calculations are performed and results returned to the client. Several international laboratories have independently verified the accuracy of the procedures and algorithm for measurements of naturally occurring carbon-13 and oxygen-18 abundances and slightly enriched compositions up to approximately 150% relative to natural abundances. To conserve the use of the NIST RMs, users may determine value assignments for a secondary standard to be used in routine analysis. Users may also wish to validate proprietary algorithms embedded in their laboratory instrumentation, or specify the values of fundamental variables that are usually fixed in reduction algorithms to see the effect on the calculations. The results returned from the web-based tool are limited in quality only by the measurements themselves, and further value may be realized through the normalization function. When combined with stringent measurement protocols, two- to threefold improvements have been realized in the reproducibility of carbon-13 and oxygen-18 determinations across laboratories.

Earth Exploration Toolbook Workshops: Helping Teachers and Students Analyze Web-based Scientific Data

NASA Astrophysics Data System (ADS)

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

2007-12-01

One of the challenges faced by Earth science teachers, particularly in K-12 settings, is that of connecting scientific research to classroom experiences. Helping teachers and students analyze Web-based scientific data is one way to bring scientific research to the classroom. The Earth Exploration Toolbook (EET) was developed as an online resource to accomplish precisely that. The EET consists of chapters containing step-by-step instructions for accessing Web-based scientific data and for using a software analysis tool to explore issues or concepts in science, technology, and mathematics. For example, in one EET chapter, users download Earthquake data from the USGS and bring it into a geographic information system (GIS), analyzing factors affecting the distribution of earthquakes. The goal of the EET Workshops project is to provide professional development that enables teachers to incorporate Web-based scientific data and analysis tools in ways that meet their curricular needs. In the EET Workshops project, Earth science teachers participate in a pair of workshops that are conducted in a combined teleconference and Web-conference format. In the first workshop, the EET Data Analysis Workshop, participants are introduced to the National Science Digital Library (NSDL) and the Digital Library for Earth System Education (DLESE). They also walk through an Earth Exploration Toolbook (EET) chapter and discuss ways to use Earth science datasets and tools with their students. In a follow-up second workshop, the EET Implementation Workshop, teachers share how they used these materials in the classroom by describing the projects and activities that they carried out with students. The EET Workshops project offers unique and effective professional development. Participants work at their own Internet-connected computers, and dial into a toll-free group teleconference for step-by-step facilitation and interaction. They also receive support via Elluminate, a Web-conferencing software program. The software allows participants to see the facilitator's computer as the analysis techniques of an EET chapter are demonstrated. If needed, the facilitator can also view individual participant's computers, assisting with technical difficulties. In addition, it enables a large number of end users, often widely distributed, to engage in interactive, real-time instruction. In this presentation, we will describe the elements of an EET Workshop pair, highlighting the capabilities and use of Elluminate. We will share lessons learned through several years of conducting this type of professional development. We will also share findings from survey data gathered from teachers who have participated in our workshops.

WaveNet: A Web-Based Metocean Data Access, Processing, and Analysis Tool. Part 3 - CDIP Database

DTIC Science & Technology

2014-06-01

and Analysis Tool; Part 3 – CDIP Database by Zeki Demirbilek, Lihwa Lin, and Derek Wilson PURPOSE: This Coastal and Hydraulics Engineering...Technical Note (CHETN) describes coupling of the Coastal Data Information Program ( CDIP ) database to WaveNet, the first module of MetOcnDat (Meteorological...provides a step-by-step procedure to access, process, and analyze wave and wind data from the CDIP database. BACKGROUND: WaveNet addresses a basic

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.

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

PubMed

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

2018-05-25

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

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

Computational Tools and Facilities for the Next-Generation Analysis and Design Environment

NASA Technical Reports Server (NTRS)

Noor, Ahmed K. (Compiler); Malone, John B. (Compiler)

1997-01-01

This document contains presentations from the joint UVA/NASA Workshop on Computational Tools and Facilities for the Next-Generation Analysis and Design Environment held at the Virginia Consortium of Engineering and Science Universities in Hampton, Virginia on September 17-18, 1996. The presentations focused on the computational tools and facilities for analysis and design of engineering systems, including, real-time simulations, immersive systems, collaborative engineering environment, Web-based tools and interactive media for technical training. Workshop attendees represented NASA, commercial software developers, the aerospace industry, government labs, and academia. The workshop objectives were to assess the level of maturity of a number of computational tools and facilities and their potential for application to the next-generation integrated design environment.

Measuring participant rurality in Web-based interventions.

PubMed

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

2007-08-31

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

An efficient scheme for automatic web pages categorization using the support vector machine

NASA Astrophysics Data System (ADS)

Bhalla, Vinod Kumar; Kumar, Neeraj

2016-07-01

In the past few years, with an evolution of the Internet and related technologies, the number of the Internet users grows exponentially. These users demand access to relevant web pages from the Internet within fraction of seconds. To achieve this goal, there is a requirement of an efficient categorization of web page contents. Manual categorization of these billions of web pages to achieve high accuracy is a challenging task. Most of the existing techniques reported in the literature are semi-automatic. Using these techniques, higher level of accuracy cannot be achieved. To achieve these goals, this paper proposes an automatic web pages categorization into the domain category. The proposed scheme is based on the identification of specific and relevant features of the web pages. In the proposed scheme, first extraction and evaluation of features are done followed by filtering the feature set for categorization of domain web pages. A feature extraction tool based on the HTML document object model of the web page is developed in the proposed scheme. Feature extraction and weight assignment are based on the collection of domain-specific keyword list developed by considering various domain pages. Moreover, the keyword list is reduced on the basis of ids of keywords in keyword list. Also, stemming of keywords and tag text is done to achieve a higher accuracy. An extensive feature set is generated to develop a robust classification technique. The proposed scheme was evaluated using a machine learning method in combination with feature extraction and statistical analysis using support vector machine kernel as the classification tool. The results obtained confirm the effectiveness of the proposed scheme in terms of its accuracy in different categories of web pages.

Tools for Economic Analysis of Patient Management Interventions in Heart Failure Cost-Effectiveness Model: A Web-based program designed to evaluate the cost-effectiveness of disease management programs in heart failure.

PubMed

Reed, Shelby D; Neilson, Matthew P; Gardner, Matthew; Li, Yanhong; Briggs, Andrew H; Polsky, Daniel E; Graham, Felicia L; Bowers, Margaret T; Paul, Sara C; Granger, Bradi B; Schulman, Kevin A; Whellan, David J; Riegel, Barbara; Levy, Wayne C

2015-11-01

Heart failure disease management programs can influence medical resource use and quality-adjusted survival. Because projecting long-term costs and survival is challenging, a consistent and valid approach to extrapolating short-term outcomes would be valuable. We developed the Tools for Economic Analysis of Patient Management Interventions in Heart Failure Cost-Effectiveness Model, a Web-based simulation tool designed to integrate data on demographic, clinical, and laboratory characteristics; use of evidence-based medications; and costs to generate predicted outcomes. Survival projections are based on a modified Seattle Heart Failure Model. Projections of resource use and quality of life are modeled using relationships with time-varying Seattle Heart Failure Model scores. The model can be used to evaluate parallel-group and single-cohort study designs and hypothetical programs. Simulations consist of 10,000 pairs of virtual cohorts used to generate estimates of resource use, costs, survival, and incremental cost-effectiveness ratios from user inputs. The model demonstrated acceptable internal and external validity in replicating resource use, costs, and survival estimates from 3 clinical trials. Simulations to evaluate the cost-effectiveness of heart failure disease management programs across 3 scenarios demonstrate how the model can be used to design a program in which short-term improvements in functioning and use of evidence-based treatments are sufficient to demonstrate good long-term value to the health care system. The Tools for Economic Analysis of Patient Management Interventions in Heart Failure Cost-Effectiveness Model provides researchers and providers with a tool for conducting long-term cost-effectiveness analyses of disease management programs in heart failure. Copyright © 2015 Elsevier Inc. All rights reserved.

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…

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

PubMed Central

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

2013-01-01

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

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

PubMed

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

2013-01-01

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

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…

Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples.

PubMed

Díaz-Gay, Marcos; Vila-Casadesús, Maria; Franch-Expósito, Sebastià; Hernández-Illán, Eva; Lozano, Juan José; Castellví-Bel, Sergi

2018-06-14

Mutational signatures have been proved as a valuable pattern in somatic genomics, mainly regarding cancer, with a potential application as a biomarker in clinical practice. Up to now, several bioinformatic packages to address this topic have been developed in different languages/platforms. MutationalPatterns has arisen as the most efficient tool for the comparison with the signatures currently reported in the Catalogue of Somatic Mutations in Cancer (COSMIC) database. However, the analysis of mutational signatures is nowadays restricted to a small community of bioinformatic experts. In this work we present Mutational Signatures in Cancer (MuSiCa), a new web tool based on MutationalPatterns and built using the Shiny framework in R language. By means of a simple interface suited to non-specialized researchers, it provides a comprehensive analysis of the somatic mutational status of the supplied cancer samples. It permits characterizing the profile and burden of mutations, as well as quantifying COSMIC-reported mutational signatures. It also allows classifying samples according to the above signature contributions. MuSiCa is a helpful web application to characterize mutational signatures in cancer samples. It is accessible online at http://bioinfo.ciberehd.org/GPtoCRC/en/tools.html and source code is freely available at https://github.com/marcos-diazg/musica .

Stable-isotope analysis: a neglected tool for placing parasites in food webs.

PubMed

Sabadel, A J M; Stumbo, A D; MacLeod, C D

2018-02-28

Parasites are often overlooked in the construction of food webs, despite their ubiquitous presence in almost every type of ecosystem. Researchers who do recognize their importance often struggle to include parasites using classical food-web theory, mainly due to the parasites' multiple hosts and life stages. A novel approach using compound-specific stable-isotope analysis promises to provide considerable insight into the energetic exchanges of parasite and host, which may solve some of the issues inherent in incorporating parasites using a classical approach. Understanding the role of parasites within food webs, and tracing the associated biomass transfers, are crucial to constructing new models that will expand our knowledge of food webs. This mini-review focuses on stable-isotope studies published in the past decade, and introduces compound-specific stable-isotope analysis as a powerful, but underutilized, newly developed tool that may answer many unresolved questions regarding the role of parasites in food webs.

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...

The Human Transcript Database: A Catalogue of Full Length cDNA Inserts

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

Bouckk John; Michael McLeod; Kim Worley

1999-09-10

The BCM Search Launcher provided improved access to web-based sequence analysis services during the granting period and beyond. The Search Launcher web site grouped analysis procedures by function and provided default parameters that provided reasonable search results for most applications. For instance, most queries were automatically masked for repeat sequences prior to sequence database searches to avoid spurious matches. In addition to the web-based access and arrangements that were made using the functions easier, the BCM Search Launcher provided unique value-added applications like the BEAUTY sequence database search tool that combined information about protein domains and sequence database search resultsmore » to give an enhanced, more complete picture of the reliability and relative value of the information reported. This enhanced search tool made evaluating search results more straight-forward and consistent. Some of the favorite features of the web site are the sequence utilities and the batch client functionality that allows processing of multiple samples from the command line interface. One measure of the success of the BCM Search Launcher is the number of sites that have adopted the models first developed on the site. The graphic display on the BLAST search from the NCBI web site is one such outgrowth, as is the display of protein domain search results within BLAST search results, and the design of the Biology Workbench application. The logs of usage and comments from users confirm the great utility of this resource.« less

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,…

Application of ESE Data and Tools to Air Quality Management: Services for Helping the Air Quality Community use ESE Data (SHAirED)

NASA Technical Reports Server (NTRS)

Falke, Stefan; Husar, Rudolf

2011-01-01

The goal of this REASoN applications and technology project is to deliver and use Earth Science Enterprise (ESE) data and tools in support of air quality management. Its scope falls within the domain of air quality management and aims to develop a federated air quality information sharing network that includes data from NASA, EPA, US States and others. Project goals were achieved through a access of satellite and ground observation data, web services information technology, interoperability standards, and air quality community collaboration. In contributing to a network of NASA ESE data in support of particulate air quality management, the project will develop access to distributed data, build Web infrastructure, and create tools for data processing and analysis. The key technologies used in the project include emerging web services for developing self describing and modular data access and processing tools, and service oriented architecture for chaining web services together to assemble customized air quality management applications. The technology and tools required for this project were developed within DataFed.net, a shared infrastructure that supports collaborative atmospheric data sharing and processing web services. Much of the collaboration was facilitated through community interactions through the Federation of Earth Science Information Partners (ESIP) Air Quality Workgroup. The main activities during the project that successfully advanced DataFed, enabled air quality applications and established community-oriented infrastructures were: develop access to distributed data (surface and satellite), build Web infrastructure to support data access, processing and analysis create tools for data processing and analysis foster air quality community collaboration and interoperability.

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.

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

PubMed

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

2009-03-01

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

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.

Providing Observation Context via Kernel Visualization and Informatics for Planning and Data Analysis

NASA Astrophysics Data System (ADS)

Kidd, J. N.; Selznick, S.; Hergenrother, C. W.

2018-04-01

From our lessons learned and SPICE expertise, we lay out the features and capabilities of a new web-based tool to provide an accessible platform to obtain context and informatics from a planetary mission's SPICE kernels.

Collaborative GIS for flood susceptibility mapping: An example from Mekong river basin of Viet Nam

NASA Astrophysics Data System (ADS)

Thanh, B.

2016-12-01

Flooding is one of the most dangerous natural disasters in Vietnam. Floods have caused serious damages to people and made adverse impact on social economic development across the country, especially in lower river basin where there is high risk of flooding as consequences of the climate change and social activities. This paper presents a collaborative platform of a combination of an interactive web-GIS framework and a multi-criteria evaluation (MCE) tool. MCE is carried out in server side through web interface, in which parameters used for evaluation are groups into three major categories, including (1) climatic factor: precipitation, typhoon frequency, temperature, humidity (2) physiographic data: DEM, topographic wetness index, NDVI, stream power index, soil texture, distance to river (3) social factor: NDBI, land use pattern. Web-based GIS is based on open-source technology that includes an information page, a page for MCE tool that users can interactively alter parameters in flood susceptible mapping, and a discussion page. The system is designed for local participation in prediction of the flood risk magnitude under impacts of natural processes and human intervention. The proposed flood susceptibility assessment prototype was implemented in the Mekong river basin, Viet Nam. Index images were calculated using Landsat data, and other were collected from authorized agencies. This study shows the potential to combine web-GIS and spatial analysis tool to flood hazard risk assessment. The combination can be a supportive solution that potentially assists the interaction between stakeholders in information exchange and in disaster management, thus provides for better analysis, control and decision-making.

VAAPA: a web platform for visualization and analysis of alternative polyadenylation.

PubMed

Guan, Jinting; Fu, Jingyi; Wu, Mingcheng; Chen, Longteng; Ji, Guoli; Quinn Li, Qingshun; Wu, Xiaohui

2015-02-01

Polyadenylation [poly(A)] is an essential process during the maturation of most mRNAs in eukaryotes. Alternative polyadenylation (APA) as an important layer of gene expression regulation has been increasingly recognized in various species. Here, a web platform for visualization and analysis of alternative polyadenylation (VAAPA) was developed. This platform can visualize the distribution of poly(A) sites and poly(A) clusters of a gene or a section of a chromosome. It can also highlight genes with switched APA sites among different conditions. VAAPA is an easy-to-use web-based tool that provides functions of poly(A) site query, data uploading, downloading, and APA sites visualization. It was designed in a multi-tier architecture and developed based on Smart GWT (Google Web Toolkit) using Java as the development language. VAAPA will be a valuable addition to the community for the comprehensive study of APA, not only by making the high quality poly(A) site data more accessible, but also by providing users with numerous valuable functions for poly(A) site analysis and visualization. Copyright © 2014 Elsevier Ltd. All rights reserved.

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.

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

PubMed

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

2014-01-01

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

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).

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

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

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

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

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

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

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

Leung, Elo; Huang, Amy; Cadag, Eithon

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

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

DOE PAGES

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

2016-01-20

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

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

AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis

PubMed Central

Badidi, Elarbi; De Sousa, Cristina; Lang, B Franz; Burger, Gertraud

2003-01-01

Background Sequence data analyses such as gene identification, structure modeling or phylogenetic tree inference involve a variety of bioinformatics software tools. Due to the heterogeneity of bioinformatics tools in usage and data requirements, scientists spend much effort on technical issues including data format, storage and management of input and output, and memorization of numerous parameters and multi-step analysis procedures. Results In this paper, we present the design and implementation of AnaBench, an interactive, Web-based bioinformatics Analysis workBench allowing streamlined data analysis. Our philosophy was to minimize the technical effort not only for the scientist who uses this environment to analyze data, but also for the administrator who manages and maintains the workbench. With new bioinformatics tools published daily, AnaBench permits easy incorporation of additional tools. This flexibility is achieved by employing a three-tier distributed architecture and recent technologies including CORBA middleware, Java, JDBC, and JSP. A CORBA server permits transparent access to a workbench management database, which stores information about the users, their data, as well as the description of all bioinformatics applications that can be launched from the workbench. Conclusion AnaBench is an efficient and intuitive interactive bioinformatics environment, which offers scientists application-driven, data-driven and protocol-driven analysis approaches. The prototype of AnaBench, managed by a team at the Université de Montréal, is accessible on-line at: . Please contact the authors for details about setting up a local-network AnaBench site elsewhere. PMID:14678565

Remote Sensing Image Analysis Without Expert Knowledge - A Web-Based Classification Tool On Top of Taverna Workflow Management System

NASA Astrophysics Data System (ADS)

Selsam, Peter; Schwartze, Christian

2016-10-01

Providing software solutions via internet has been known for quite some time and is now an increasing trend marketed as "software as a service". A lot of business units accept the new methods and streamlined IT strategies by offering web-based infrastructures for external software usage - but geospatial applications featuring very specialized services or functionalities on demand are still rare. Originally applied in desktop environments, the ILMSimage tool for remote sensing image analysis and classification was modified in its communicating structures and enabled for running on a high-power server and benefiting from Tavema software. On top, a GIS-like and web-based user interface guides the user through the different steps in ILMSimage. ILMSimage combines object oriented image segmentation with pattern recognition features. Basic image elements form a construction set to model for large image objects with diverse and complex appearance. There is no need for the user to set up detailed object definitions. Training is done by delineating one or more typical examples (templates) of the desired object using a simple vector polygon. The template can be large and does not need to be homogeneous. The template is completely independent from the segmentation. The object definition is done completely by the software.

SYNCSA--R tool for analysis of metacommunities based on functional traits and phylogeny of the community components.

PubMed

Debastiani, Vanderlei J; Pillar, Valério D

2012-08-01

SYNCSA is an R package for the analysis of metacommunities based on functional traits and phylogeny of the community components. It offers tools to calculate several matrix correlations that express trait-convergence assembly patterns, trait-divergence assembly patterns and phylogenetic signal in functional traits at the species pool level and at the metacommunity level. SYNCSA is a package for the R environment, under a GPL-2 open-source license and freely available on CRAN official web server for R (http://cran.r-project.org). vanderleidebastiani@yahoo.com.br.

Recent advancements on the development of web-based applications for the implementation of seismic analysis and surveillance systems

NASA Astrophysics Data System (ADS)

Friberg, P. A.; Luis, R. S.; Quintiliani, M.; Lisowski, S.; Hunter, S.

2014-12-01

Recently, a novel set of modules has been included in the Open Source Earthworm seismic data processing system, supporting the use of web applications. These include the Mole sub-system, for storing relevant event data in a MySQL database (see M. Quintiliani and S. Pintore, SRL, 2013), and an embedded webserver, Moleserv, for serving such data to web clients in QuakeML format. These modules have enabled, for the first time using Earthworm, the use of web applications for seismic data processing. These can greatly simplify the operation and maintenance of seismic data processing centers by having one or more servers providing the relevant data as well as the data processing applications themselves to client machines running arbitrary operating systems.Web applications with secure online web access allow operators to work anywhere, without the often cumbersome and bandwidth hungry use of secure shell or virtual private networks. Furthermore, web applications can seamlessly access third party data repositories to acquire additional information, such as maps. Finally, the usage of HTML email brought the possibility of specialized web applications, to be used in email clients. This is the case of EWHTMLEmail, which produces event notification emails that are in fact simple web applications for plotting relevant seismic data.Providing web services as part of Earthworm has enabled a number of other tools as well. One is ISTI's EZ Earthworm, a web based command and control system for an otherwise command line driven system; another is a waveform web service. The waveform web service serves Earthworm data to additional web clients for plotting, picking, and other web-based processing tools. The current Earthworm waveform web service hosts an advanced plotting capability for providing views of event-based waveforms from a Mole database served by Moleserve.The current trend towards the usage of cloud services supported by web applications is driving improvements in JavaScript, css and HTML, as well as faster and more efficient web browsers, including mobile. It is foreseeable that in the near future, web applications are as powerful and efficient as native applications. Hence the work described here has been the first step towards bringing the Open Source Earthworm seismic data processing system to this new paradigm.

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

PubMed

Zhou, Anbo; Zhang, Yeting; Sun, Yazhou; Xing, Jinchuan

2018-05-01

Analysis pipelines are an essential part of bioinformatics research, and ad hoc pipelines are frequently created by researchers for prototyping and proof-of-concept purposes. However, most existing pipeline management system or workflow engines are too complex for rapid prototyping or learning the pipeline concept. A lightweight, user-friendly and flexible solution is thus desirable. In this study, we developed a new pipeline construction and maintenance tool, PipelineDog. This is a web-based integrated development environment with a modern web graphical user interface. It offers cross-platform compatibility, project management capabilities, code formatting and error checking functions and an online repository. It uses an easy-to-read/write script system that encourages code reuse. With the online repository, it also encourages sharing of pipelines, which enhances analysis reproducibility and accountability. For most users, PipelineDog requires no software installation. Overall, this web application provides a way to rapidly create and easily manage pipelines. PipelineDog web app is freely available at http://web.pipeline.dog. The command line version is available at http://www.npmjs.com/package/pipelinedog and online repository at http://repo.pipeline.dog. ysun@kean.edu or xing@biology.rutgers.edu or ysun@diagnoa.com. Supplementary data are available at Bioinformatics online.

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

EPA Science Inventory

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

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

PubMed Central

2010-01-01

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

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

PubMed

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

2010-05-18

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

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

Interactive text mining with Pipeline Pilot: a bibliographic web-based tool for PubMed.

PubMed

Vellay, S G P; Latimer, N E Miller; Paillard, G

2009-06-01

Text mining has become an integral part of all research in the medical field. Many text analysis software platforms support particular use cases and only those. We show an example of a bibliographic tool that can be used to support virtually any use case in an agile manner. Here we focus on a Pipeline Pilot web-based application that interactively analyzes and reports on PubMed search results. This will be of interest to any scientist to help identify the most relevant papers in a topical area more quickly and to evaluate the results of query refinement. Links with Entrez databases help both the biologist and the chemist alike. We illustrate this application with Leishmaniasis, a neglected tropical disease, as a case study.

Exploratory Study of Web-Based Planning and Mobile Text Reminders in an Overweight Population

PubMed Central

Murray, Peter; Cobain, Mark; Chinapaw, Mai; van Mechelen, Willem; Hurling, Robert

2011-01-01

Background Forming specific health plans can help translate good intentions into action. Mobile text reminders can further enhance the effects of planning on behavior. Objective Our aim was to explore the combined impact of a Web-based, fully automated planning tool and mobile text reminders on intention to change saturated fat intake, self-reported saturated fat intake, and portion size changes over 4 weeks. Methods Of 1013 men and women recruited online, 858 were randomly allocated to 1 of 3 conditions: a planning tool (PT), combined planning tool and text reminders (PTT), and a control group. All outcome measures were assessed by online self-reports. Analysis of covariance was used to analyze the data. Results Participants allocated to the PT (meansat urated fat 3.6, meancopingplanning 3) and PTT (meansaturatedfat 3.5, meancopingplanning 3.1) reported a lower consumption of high-fat foods (F 2,571 = 4.74, P = .009) and higher levels of coping planning (F 2,571 = 7.22, P < .001) than the control group (meansat urated f at 3.9, meancopingplanning 2.8). Participants in the PTT condition also reported smaller portion sizes of high-fat foods (mean 2.8; F 2, 569 = 4.12, P = .0) than the control group (meanportions 3.1). The reduction in portion size was driven primarily by the male participants in the PTT (P = .003). We found no significant group differences in terms of percentage saturated fat intake, intentions, action planning, self-efficacy, or feedback on the intervention. Conclusions These findings support the use of Web-based tools and mobile technologies to change dietary behavior. The combination of a fully automated Web-based planning tool with mobile text reminders led to lower self-reported consumption of high-fat foods and greater reductions in portion sizes than in a control condition. Trial Registration International Standard Randomized Controlled Trial Number (ISRCTN): 61819220; http://www.controlled-trials.com/ISRCTN61819220 (Archived by WebCite at http://www.webcitation.org/63YiSy6R8) PMID:22182483

The PBL-Evaluator: A Web-Based Tool for Assessment in Tutorials.

ERIC Educational Resources Information Center

Chaves, John F.; Chaves, John A.; Lantz, Marilyn S.

1998-01-01

Describes design and use of the PBL Evaluator, a computer-based method of evaluating dental students' clinical problem-solving skills. Analysis of Indiana University students' self-, peer, and tutor ratings for one iteration of a course in critical thinking and professional behavior shows differences in these ratings. The method is found useful…

The potential of the internet.

PubMed

Coleman, Jamie J; McDowell, Sarah E

2012-06-01

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

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

PubMed

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

2015-01-01

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

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

PubMed Central

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

2008-01-01

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

Renewable Energy Data Explorer User Guide

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

Cox, Sarah L; Grue, Nicholas W; Tran, July

This publication provides a user guide for the Renewable Energy Data Explorer and technical potential tool within the Explorer. The Renewable Energy Data Explorer is a dynamic, web-based geospatial analysis tool that facilitates renewable energy decision-making, investment, and deployment. It brings together renewable energy resource data and other modeled or measured geographic information system (GIS) layers, including land use, weather, environmental, population density, administrative, and grid data.

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.

Your Personal Analysis Toolkit - An Open Source Solution

NASA Astrophysics Data System (ADS)

Mitchell, T.

2009-12-01

Open source software is commonly known for its web browsers, word processors and programming languages. However, there is a vast array of open source software focused on geographic information management and geospatial application building in general. As geo-professionals, having easy access to tools for our jobs is crucial. Open source software provides the opportunity to add a tool to your tool belt and carry it with you for your entire career - with no license fees, a supportive community and the opportunity to test, adopt and upgrade at your own pace. OSGeo is a US registered non-profit representing more than a dozen mature geospatial data management applications and programming resources. Tools cover areas such as desktop GIS, web-based mapping frameworks, metadata cataloging, spatial database analysis, image processing and more. Learn about some of these tools as they apply to AGU members, as well as how you can join OSGeo and its members in getting the job done with powerful open source tools. If you haven't heard of OSSIM, MapServer, OpenLayers, PostGIS, GRASS GIS or the many other projects under our umbrella - then you need to hear this talk. Invest in yourself - use open source!

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

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

Cox, Sarah L

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

RxPATROL: a Web-based tool for combating pharmacy theft.

PubMed

Smith, Meredith Y; Graham, J Aaron; Haddox, J David; Steffey, Amy

2009-01-01

To report the incidence of pharmacy-related burglaries and robberies and characteristics of pharmacies where such crimes have occurred using recent data from Rx Pattern Analysis Tracking Robberies & Other Losses (RxPATROL), a national Web-based information clearinghouse on pharmacy-related theft of prescription medications and over-the-counter products. Descriptive, nonexperimental study. United States between 2005 and 2006. Not applicable. Not applicable. Number of pharmacy theft reports received; incident type, date, and location; point of entry; and pharmacy security features. Between 2005 and 2006, 202 pharmacy burglary and 299 pharmacy robbery reports from 45 different states were filed with RxPATROL. More than 70% of pharmacies reporting such crimes lacked a security camera. Among those reporting a burglary, 60% lacked dead bolt locks, a solid exterior door, a motion detector device, or a safe or vault for storage of controlled substances. Burglars most often obtained access to the pharmacy via the front door. RxPATROL is a Web-based tool that can assist pharmacies and law enforcement in collaborating more effectively to combat and prevent pharmacy-related crimes.

Software Tools to Support Research on Airport Departure Planning

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

Web-GIS-based SARS epidemic situation visualization

NASA Astrophysics Data System (ADS)

Lu, Xiaolin

2004-03-01

In order to research, perform statistical analysis and broadcast the information of SARS epidemic situation according to the relevant spatial position, this paper proposed a unified global visualization information platform for SARS epidemic situation based on Web-GIS and scientific virtualization technology. To setup the unified global visual information platform, the architecture of Web-GIS based interoperable information system is adopted to enable public report SARS virus information to health cure center visually by using the web visualization technology. A GIS java applet is used to visualize the relationship between spatial graphical data and virus distribution, and other web based graphics figures such as curves, bars, maps and multi-dimensional figures are used to visualize the relationship between SARS virus tendency with time, patient number or locations. The platform is designed to display the SARS information in real time, simulate visually for real epidemic situation and offer an analyzing tools for health department and the policy-making government department to support the decision-making for preventing against the SARS epidemic virus. It could be used to analyze the virus condition through visualized graphics interface, isolate the areas of virus source, and control the virus condition within shortest time. It could be applied to the visualization field of SARS preventing systems for SARS information broadcasting, data management, statistical analysis, and decision supporting.

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…

Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples.

PubMed

Lin, Jake; Kramna, Lenka; Autio, Reija; Hyöty, Heikki; Nykter, Matti; Cinek, Ondrej

2017-05-15

Next generation sequencing (NGS) technology allows laboratories to investigate virome composition in clinical and environmental samples in a culture-independent way. There is a need for bioinformatic tools capable of parallel processing of virome sequencing data by exactly identical methods: this is especially important in studies of multifactorial diseases, or in parallel comparison of laboratory protocols. We have developed a web-based application allowing direct upload of sequences from multiple virome samples using custom parameters. The samples are then processed in parallel using an identical protocol, and can be easily reanalyzed. The pipeline performs de-novo assembly, taxonomic classification of viruses as well as sample analyses based on user-defined grouping categories. Tables of virus abundance are produced from cross-validation by remapping the sequencing reads to a union of all observed reference viruses. In addition, read sets and reports are created after processing unmapped reads against known human and bacterial ribosome references. Secured interactive results are dynamically plotted with population and diversity charts, clustered heatmaps and a sortable and searchable abundance table. The Vipie web application is a unique tool for multi-sample metagenomic analysis of viral data, producing searchable hits tables, interactive population maps, alpha diversity measures and clustered heatmaps that are grouped in applicable custom sample categories. Known references such as human genome and bacterial ribosomal genes are optionally removed from unmapped ('dark matter') reads. Secured results are accessible and shareable on modern browsers. Vipie is a freely available web-based tool whose code is open source.

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…

The EnviroAtlas: Connecting ecosystems, people, and well-being

EPA Science Inventory

The EnviroAtlas is a web-based application containing a collection of geospatial data, analysis tools, and interpretive information focused on ecosystem goods and services. Ecosystem goods and services are essentially defined as the benefits that humans receive from nature and en...

SMARTE 2007 TUTORIAL - JANUARY 2007 REVISION

EPA Science Inventory

SMARTe 2007 is a web-based decision support tool intended to help revitalization practitioners find information, perform data analysis, communicate, and evaluate future reuse options for a site or area. This tutorial CD was developed to help users navigate SMARTe 2007. It is appr...

Forensic massively parallel sequencing data analysis tool: Implementation of MyFLq as a standalone web- and Illumina BaseSpace(®)-application.

PubMed

Van Neste, Christophe; Gansemans, Yannick; De Coninck, Dieter; Van Hoofstat, David; Van Criekinge, Wim; Deforce, Dieter; Van Nieuwerburgh, Filip

2015-03-01

Routine use of massively parallel sequencing (MPS) for forensic genomics is on the horizon. The last few years, several algorithms and workflows have been developed to analyze forensic MPS data. However, none have yet been tailored to the needs of the forensic analyst who does not possess an extensive bioinformatics background. We developed our previously published forensic MPS data analysis framework MyFLq (My-Forensic-Loci-queries) into an open-source, user-friendly, web-based application. It can be installed as a standalone web application, or run directly from the Illumina BaseSpace environment. In the former, laboratories can keep their data on-site, while in the latter, data from forensic samples that are sequenced on an Illumina sequencer can be uploaded to Basespace during acquisition, and can subsequently be analyzed using the published MyFLq BaseSpace application. Additional features were implemented such as an interactive graphical report of the results, an interactive threshold selection bar, and an allele length-based analysis in addition to the sequenced-based analysis. Practical use of the application is demonstrated through the analysis of four 16-plex short tandem repeat (STR) samples, showing the complementarity between the sequence- and length-based analysis of the same MPS data. Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

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…

Web-based network analysis and visualization using CellMaps

PubMed Central

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

2016-01-01

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

Web-based network analysis and visualization using CellMaps.

PubMed

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

2016-10-01

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

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

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…

CoP Sensing Framework on Web-Based Environment

NASA Astrophysics Data System (ADS)

Mustapha, S. M. F. D. Syed

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

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…

Online characterization of planetary surfaces: PlanetServer, an open-source analysis and visualization tool

NASA Astrophysics Data System (ADS)

Marco Figuera, R.; Pham Huu, B.; Rossi, A. P.; Minin, M.; Flahaut, J.; Halder, A.

2018-01-01

The lack of open-source tools for hyperspectral data visualization and analysis creates a demand for new tools. In this paper we present the new PlanetServer, a set of tools comprising a web Geographic Information System (GIS) and a recently developed Python Application Programming Interface (API) capable of visualizing and analyzing a wide variety of hyperspectral data from different planetary bodies. Current WebGIS open-source tools are evaluated in order to give an overview and contextualize how PlanetServer can help in this matters. The web client is thoroughly described as well as the datasets available in PlanetServer. Also, the Python API is described and exposed the reason of its development. Two different examples of mineral characterization of different hydrosilicates such as chlorites, prehnites and kaolinites in the Nili Fossae area on Mars are presented. As the obtained results show positive outcome in hyperspectral analysis and visualization compared to previous literature, we suggest using the PlanetServer approach for such investigations.

How to Boost Engineering Support Via Web 2.0 - Seeds for the Ares Project...and/or Yours?

NASA Technical Reports Server (NTRS)

Scott, David W.

2010-01-01

The Mission Operations Laboratory (MOL) at Marshall Space Flight Center (MSFC) is responsible for Engineering Support capability for NASA s Ares launch system development. In pursuit of this, MOL is building the Ares Engineering and Operations Network (AEON), a web-based portal intended to provide a seamless interface to support and simplify two critical activities: a) Access and analyze Ares manufacturing, test, and flight performance data, with access to Shuttle data for comparison. b) Provide archive storage for engineering instrumentation data to support engineering design, development, and test. A mix of NASA-written and COTS software provides engineering analysis tools. A by-product of using a data portal to access and display data is access to collaborative tools inherent in a Web 2.0 environment. This paper discusses how Web 2.0 techniques, particularly social media, might be applied to the traditionally conservative and formal engineering support arena. A related paper by the author [1] considers use

Internet-based Modeling, Mapping, and Analysis for the Greater Everglades (IMMAGE; Version 1.0): web-based tools to assess the impact of sea level rise in south Florida

USGS Publications Warehouse

Hearn, Paul; Strong, David; Swain, Eric; Decker, Jeremy

2013-01-01

South Florida's Greater Everglades area is particularly vulnerable to sea level rise, due to its rich endowment of animal and plant species and its heavily populated urban areas along the coast. Rising sea levels are expected to have substantial impacts on inland flooding, the depth and extent of surge from coastal storms, the degradation of water supplies by saltwater intrusion, and the integrity of plant and animal habitats. Planners and managers responsible for mitigating these impacts require advanced tools to help them more effectively identify areas at risk. The U.S. Geological Survey's (USGS) Internet-based Modeling, Mapping, and Analysis for the Greater Everglades (IMMAGE) Web site has been developed to address these needs by providing more convenient access to projections from models that forecast the effects of sea level rise on surface water and groundwater, the extent of surge and resulting economic losses from coastal storms, and the distribution of habitats. IMMAGE not only provides an advanced geographic information system (GIS) interface to support decision making, but also includes topic-based modules that explain and illustrate key concepts for nontechnical users. The purpose of this report is to familiarize both technical and nontechnical users with the IMMAGE Web site and its various applications.

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

NASA Technical Reports Server (NTRS)

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

2000-01-01

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

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…

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.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

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

PubMed Central

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

2018-01-01

Background Women with chronic medical conditions, such as diabetes and hypertension, have a higher risk of pregnancy-related complications compared with women without medical conditions and should be offered contraception if desired. Although evidence based guidelines for contraceptive selection in the presence of medical conditions are available via the United States Medical Eligibility Criteria (US MEC), these guidelines are underutilized. Research also supports the use of decision tools to promote shared decision making between patients and providers during contraceptive counseling. Objective The overall goal of the MiHealth, MiChoice project is to design and implement a theory-driven, Web-based tool that incorporates the US MEC (provider-level intervention) within the vehicle of a contraceptive decision tool for women with chronic medical conditions (patient-level intervention) in community-based primary care settings (practice-level intervention). This will be a 3-phase study that includes a predesign phase, a design phase, and a testing phase in a randomized controlled trial. This study protocol describes phase 1 and aim 1, which is to determine patient-, provider-, and practice-level factors that are relevant to the design and implementation of the contraceptive decision tool. Methods This is a mixed methods implementation study. To customize the delivery of the US MEC in the decision tool, we selected high-priority constructs from the Consolidated Framework for Implementation Research and the Theoretical Domains Framework to drive data collection and analysis at the practice and provider level, respectively. A conceptual model that incorporates constructs from the transtheoretical model and the health beliefs model undergirds patient-level data collection and analysis and will inform customization of the decision tool for this population. We will recruit 6 community-based primary care practices and conduct quantitative surveys and semistructured qualitative interviews with women who have chronic medical conditions, their primary care providers (PCPs), and clinic staff, as well as field observations of practice activities. Quantitative survey data will be summarized with simple descriptive statistics and relationships between participant characteristics and contraceptive recommendations (for PCPs), and current contraceptive use (for patients) will be examined using Fisher exact test. We will conduct thematic analysis of qualitative data from interviews and field observations. The integration of data will occur by comparing, contrasting, and synthesizing qualitative and quantitative findings to inform the future development and implementation of the intervention. Results We are currently enrolling practices and anticipate study completion in 15 months. Conclusions This protocol describes the first phase of a multiphase mixed methods study to develop and implement a Web-based decision tool that is customized to meet the needs of women with chronic medical conditions in primary care settings. Study findings will promote contraceptive counseling via shared decision making and reflect evidence-based guidelines for contraceptive selection. Trial Registration ClinicalTrials.gov NCT03153644; https://clinicaltrials.gov/ct2/show/NCT03153644 (Archived by WebCite at http://www.webcitation.org/6yUkA5lK8) PMID:29669707

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.

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

PubMed

Zaldivar, Andrew; Krichmar, Jeffrey L

2014-01-01

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

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.

Use of Web-based training for quality improvement between a field immunohistochemistry laboratory in Nigeria and its United States-based partner institution.

PubMed

Oluwasola, Abideen O; Malaka, David; Khramtsov, Andrey Ilyich; Ikpatt, Offiong Francis; Odetunde, Abayomi; Adeyanju, Oyinlolu Olorunsogo; Sveen, Walmy Elisabeth; Falusi, Adeyinka Gloria; Huo, Dezheng; Olopade, Olufunmilayo Ibironke

2013-12-01

The importance of hormone receptor status in assigning treatment and the potential use of human epidermal growth factor receptor 2 (HER2)-targeted therapy have made it beneficial for laboratories to improve detection techniques. Because interlaboratory variability in immunohistochemistry (IHC) tests may also affect studies of breast cancer subtypes in different countries, we undertook a Web-based quality improvement training and a comparative study of accuracy of immunohistochemical tests of breast cancer biomarkers between a well-established laboratory in the United States (University of Chicago) and a field laboratory in Ibadan, Nigeria. Two hundred and thirty-two breast tumor blocks were evaluated for estrogen receptors (ERs), progesterone receptors (PRs), and HER2 status at both laboratories using tissue microarray technique. Initially, concordance analysis revealed κ scores of 0.42 (moderate agreement) for ER, 0.41 (moderate agreement) for PR, and 0.39 (fair agreement) for HER2 between the 2 laboratories. Antigen retrieval techniques and scoring methods were identified as important reasons for discrepancy. Web-based conferences using Web conferencing tools such as Skype and WebEx were then held periodically to discuss IHC staining protocols and standard scoring systems and to resolve discrepant cases. After quality assurance and training, the agreement improved to 0.64 (substantial agreement) for ER, 0.60 (moderate agreement) for PR, and 0.75 (substantial agreement) for HER2. We found Web-based conferences and digital microscopy useful and cost-effective tools for quality assurance of IHC, consultation, and collaboration between distant laboratories. Quality improvement exercises in testing of tumor biomarkers will reduce misclassification in epidemiologic studies of breast cancer subtypes and provide much needed capacity building in resource-poor countries. © 2013.

NASA's Lunar and Planetary Mapping and Modeling Program

NASA Astrophysics Data System (ADS)

Law, E.; Day, B. H.; Kim, R. M.; Bui, B.; Malhotra, S.; Chang, G.; Sadaqathullah, S.; Arevalo, E.; Vu, Q. A.

2016-12-01

NASA's Lunar and Planetary Mapping and Modeling Program produces a suite of online visualization and analysis tools. Originally designed for mission planning and science, these portals offer great benefits for education and public outreach (EPO), providing access to data from a wide range of instruments aboard a variety of past and current missions. As a component of NASA's Science EPO Infrastructure, they are available as resources for NASA STEM EPO programs, and to the greater EPO community. As new missions are planned to a variety of planetary bodies, these tools are facilitating the public's understanding of the missions and engaging the public in the process of identifying and selecting where these missions will land. There are currently three web portals in the program: the Lunar Mapping and Modeling Portal or LMMP (http://lmmp.nasa.gov), Vesta Trek (http://vestatrek.jpl.nasa.gov), and Mars Trek (http://marstrek.jpl.nasa.gov). Portals for additional planetary bodies are planned. As web-based toolsets, the portals do not require users to purchase or install any software beyond current web browsers. The portals provide analysis tools for measurement and study of planetary terrain. They allow data to be layered and adjusted to optimize visualization. Visualizations are easily stored and shared. The portals provide 3D visualization and give users the ability to mark terrain for generation of STL files that can be directed to 3D printers. Such 3D prints are valuable tools in museums, public exhibits, and classrooms - especially for the visually impaired. Along with the web portals, the program supports additional clients, web services, and APIs that facilitate dissemination of planetary data to a range of external applications and venues. NASA challenges and hackathons are also providing members of the software development community opportunities to participate in tool development and leverage data from the portals.

Improving Conceptual Design for Launch Vehicles

NASA Technical Reports Server (NTRS)

Olds, John R.

1998-01-01

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

The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications

PubMed Central

Bare, J Christopher; Shannon, Paul T; Schmid, Amy K; Baliga, Nitin S

2007-01-01

Background Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoing maintenance of local copies of public databases. Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data. Results The Firegoose, an extension to the Mozilla Firefox web browser, enables data transfer between web sites and desktop tools. As a component of the Gaggle integration framework, Firegoose can also exchange data with Cytoscape, the R statistical package, Multiexperiment Viewer (MeV), and several other popular desktop software tools. Firegoose adds the capability to easily use local data to query KEGG, EMBL STRING, DAVID, and other widely-used bioinformatics web sites. Query results from these web sites can be transferred to desktop tools for further analysis with a few clicks. Firegoose acquires data from the web by screen scraping, microformats, embedded XML, or web services. We define a microformat, which allows structured information compatible with the Gaggle to be embedded in HTML documents. We demonstrate the capabilities of this software by performing an analysis of the genes activated in the microbe Halobacterium salinarum NRC-1 in response to anaerobic environments. Starting with microarray data, we explore functions of differentially expressed genes by combining data from several public web resources and construct an integrated view of the cellular processes involved. Conclusion The Firegoose incorporates Mozilla Firefox into the Gaggle environment and enables interactive sharing of data between diverse web resources and desktop software tools without maintaining local copies. Additional web sites can be incorporated easily into the framework using the scripting platform of the Firefox browser. Performing data integration in the browser allows the excellent search and navigation capabilities of the browser to be used in combination with powerful desktop tools. PMID:18021453

The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications.

PubMed

Bare, J Christopher; Shannon, Paul T; Schmid, Amy K; Baliga, Nitin S

2007-11-19

Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoing maintenance of local copies of public databases. Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data. The Firegoose, an extension to the Mozilla Firefox web browser, enables data transfer between web sites and desktop tools. As a component of the Gaggle integration framework, Firegoose can also exchange data with Cytoscape, the R statistical package, Multiexperiment Viewer (MeV), and several other popular desktop software tools. Firegoose adds the capability to easily use local data to query KEGG, EMBL STRING, DAVID, and other widely-used bioinformatics web sites. Query results from these web sites can be transferred to desktop tools for further analysis with a few clicks. Firegoose acquires data from the web by screen scraping, microformats, embedded XML, or web services. We define a microformat, which allows structured information compatible with the Gaggle to be embedded in HTML documents. We demonstrate the capabilities of this software by performing an analysis of the genes activated in the microbe Halobacterium salinarum NRC-1 in response to anaerobic environments. Starting with microarray data, we explore functions of differentially expressed genes by combining data from several public web resources and construct an integrated view of the cellular processes involved. The Firegoose incorporates Mozilla Firefox into the Gaggle environment and enables interactive sharing of data between diverse web resources and desktop software tools without maintaining local copies. Additional web sites can be incorporated easily into the framework using the scripting platform of the Firefox browser. Performing data integration in the browser allows the excellent search and navigation capabilities of the browser to be used in combination with powerful desktop tools.

PanWeb: A web interface for pan-genomic analysis.

PubMed

Pantoja, Yan; Pinheiro, Kenny; Veras, Allan; Araújo, Fabrício; Lopes de Sousa, Ailton; Guimarães, Luis Carlos; Silva, Artur; Ramos, Rommel T J

2017-01-01

With increased production of genomic data since the advent of next-generation sequencing (NGS), there has been a need to develop new bioinformatics tools and areas, such as comparative genomics. In comparative genomics, the genetic material of an organism is directly compared to that of another organism to better understand biological species. Moreover, the exponentially growing number of deposited prokaryote genomes has enabled the investigation of several genomic characteristics that are intrinsic to certain species. Thus, a new approach to comparative genomics, termed pan-genomics, was developed. In pan-genomics, various organisms of the same species or genus are compared. Currently, there are many tools that can perform pan-genomic analyses, such as PGAP (Pan-Genome Analysis Pipeline), Panseq (Pan-Genome Sequence Analysis Program) and PGAT (Prokaryotic Genome Analysis Tool). Among these software tools, PGAP was developed in the Perl scripting language and its reliance on UNIX platform terminals and its requirement for an extensive parameterized command line can become a problem for users without previous computational knowledge. Thus, the aim of this study was to develop a web application, known as PanWeb, that serves as a graphical interface for PGAP. In addition, using the output files of the PGAP pipeline, the application generates graphics using custom-developed scripts in the R programming language. PanWeb is freely available at http://www.computationalbiology.ufpa.br/panweb.

WEBnm@ v2.0: Web server and services for comparing protein flexibility.

PubMed

Tiwari, Sandhya P; Fuglebakk, Edvin; Hollup, Siv M; Skjærven, Lars; Cragnolini, Tristan; Grindhaug, Svenn H; Tekle, Kidane M; Reuter, Nathalie

2014-12-30

Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dynamics-function relationship can be gained by comparing protein motions between protein homologs and functional classifications. This can be achieved by comparing normal modes obtained from sets of evolutionary related proteins. We have developed an automated tool for comparative NMA of a set of pre-aligned protein structures. The user can submit a sequence alignment in the FASTA format and the corresponding coordinate files in the Protein Data Bank (PDB) format. The computed normalised squared atomic fluctuations and atomic deformation energies of the submitted structures can be easily compared on graphs provided by the web user interface. The web server provides pairwise comparison of the dynamics of all proteins included in the submitted set using two measures: the Root Mean Squared Inner Product and the Bhattacharyya Coefficient. The Comparative Analysis has been implemented on our web server for NMA, WEBnm@, which also provides recently upgraded functionality for NMA of single protein structures. This includes new visualisations of protein motion, visualisation of inter-residue correlations and the analysis of conformational change using the overlap analysis. In addition, programmatic access to WEBnm@ is now available through a SOAP-based web service. Webnm@ is available at http://apps.cbu.uib.no/webnma . WEBnm@ v2.0 is an online tool offering unique capability for comparative NMA on multiple protein structures. Along with a convenient web interface, powerful computing resources, and several methods for mode analyses, WEBnm@ facilitates the assessment of protein flexibility within protein families and superfamilies. These analyses can give a good view of how the structures move and how the flexibility is conserved over the different structures.

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.

The aware toolbox for the detection of law infringements on web pages

NASA Astrophysics Data System (ADS)

Shahab, Asif; Kieninger, Thomas; Dengel, Andreas

2010-01-01

In the project Aware we aim to develop an automatic assistant for the detection of law infringements on web pages. The motivation for this project is that many authors of web pages are at some points infringing copyrightor other laws, mostly without being aware of that fact, and are more and more often confronted with costly legal warnings. As the legal environment is constantly changing, an important requirement of Aware is that the domain knowledge can be maintained (and initially defined) by numerous legal experts remotely working without further assistance of the computer scientists. Consequently, the software platform was chosen to be a web-based generic toolbox that can be configured to suit individual analysis experts, definitions of analysis flow, information gathering and report generation. The report generated by the system summarizes all critical elements of a given web page and provides case specific hints to the page author and thus forms a new type of service. Regarding the analysis subsystems, Aware mainly builds on existing state-of-the-art technologies. Their usability has been evaluated for each intended task. In order to control the heterogeneous analysis components and to gather the information, a lightweight scripting shell has been developed. This paper describes the analysis technologies, ranging from text based information extraction, over optical character recognition and phonetic fuzzy string matching to a set of image analysis and retrieval tools; as well as the scripting language to define the analysis flow.

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."

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

PubMed

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

2015-01-01

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

Development of a Web-based question database for students' self-assessment.

PubMed

Hammoud, Maya M; Barclay, Mel L

2002-09-01

Computer-based testing (CBT) for the purpose of the national licensure examination has increased interest among medical students in this modality of testing. The advent of Web-based question-delivery systems for self-assessment and learning has made it possible for students to practice this technology and participate in self-directed learning. Test Pilot(TM) is a Web-based program that provides a fast and easy tool for the development and deployment of online testing. Our objectives for introducing the program were to (1) develop a large database of questions for students' practice and self-assessment; (2) include multimedia tools such as illustrations and short videos to enhance learning; (3) provide a feedback tool for clerkship and site directors regarding student performance; and (4) evaluate this tool in terms of students' frequency of use, students' satisfaction, and its potential effectiveness in enhancing learning. The Obstetrics and Gynecology clerkship at the University of Michigan is held at four different sites. In the past, students have been provided with access to floppy disks that contain about 500 self-assessment questions. These questions have been reformatted, updated, and transferred to Test Pilot. Visual illustrations have been added to the questions along with more varied formats, including extended matching, fill-in, and essay questions. The questions are divided into ten-question quizzes. The students get immediate feedback after answering each question and a summary of performance at the end of each quiz. Security, access, and analysis are facilitated because the questions and responses are stored centrally. In addition, Test Pilot captures information regarding individual and collective students' performances. At the end of the rotation, students fill out a form evaluating the Test Pilot program and comparing it with the quiz disks. In addition, we are collecting data regarding the actual use of Test Pilot, which will be compared with the students' surveys and final exam scores. Test Pilot has many benefits, including access control, immediate feedback, automated scoring, interactive learning, and data analysis. The enhancement of material permitted by a Web-based system increases the depth and variety of the learning experience by adding perceptual dimensions. Test Pilot also provides the clerkship director with the capability to obtain improved measurements of student performance and captures the student's self-learning and testing process. It can potentially identify weaknesses or inconsistencies across the different sites and recognize students who may need additional help early in the rotation. Over a one-year period, most students have switched from the quiz disks to Test Pilot. The students reported satisfaction with the Web-based format and found it user friendly. They especially liked the immediate feedback. The students have requested more questions and multimedia options be added. We plan to continue the development and assessment of this learning tool.

GobyWeb: Simplified Management and Analysis of Gene Expression and DNA Methylation Sequencing Data

PubMed Central

Dorff, Kevin C.; Chambwe, Nyasha; Zeno, Zachary; Simi, Manuele; Shaknovich, Rita; Campagne, Fabien

2013-01-01

We present GobyWeb, a web-based system that facilitates the management and analysis of high-throughput sequencing (HTS) projects. The software provides integrated support for a broad set of HTS analyses and offers a simple plugin extension mechanism. Analyses currently supported include quantification of gene expression for messenger and small RNA sequencing, estimation of DNA methylation (i.e., reduced bisulfite sequencing and whole genome methyl-seq), or the detection of pathogens in sequenced data. In contrast to previous analysis pipelines developed for analysis of HTS data, GobyWeb requires significantly less storage space, runs analyses efficiently on a parallel grid, scales gracefully to process tens or hundreds of multi-gigabyte samples, yet can be used effectively by researchers who are comfortable using a web browser. We conducted performance evaluations of the software and found it to either outperform or have similar performance to analysis programs developed for specialized analyses of HTS data. We found that most biologists who took a one-hour GobyWeb training session were readily able to analyze RNA-Seq data with state of the art analysis tools. GobyWeb can be obtained at http://gobyweb.campagnelab.org and is freely available for non-commercial use. GobyWeb plugins are distributed in source code and licensed under the open source LGPL3 license to facilitate code inspection, reuse and independent extensions http://github.com/CampagneLaboratory/gobyweb2-plugins. PMID:23936070

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

PubMed

Carpenter, Suzanne H

2016-01-01

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

Cloud-Based Orchestration of a Model-Based Power and Data Analysis Toolchain

NASA Technical Reports Server (NTRS)

Post, Ethan; Cole, Bjorn; Dinkel, Kevin; Kim, Hongman; Lee, Erich; Nairouz, Bassem

2016-01-01

The proposed Europa Mission concept contains many engineering and scientific instruments that consume varying amounts of power and produce varying amounts of data throughout the mission. System-level power and data usage must be well understood and analyzed to verify design requirements. Numerous cross-disciplinary tools and analysis models are used to simulate the system-level spacecraft power and data behavior. This paper addresses the problem of orchestrating a consistent set of models, tools, and data in a unified analysis toolchain when ownership is distributed among numerous domain experts. An analysis and simulation environment was developed as a way to manage the complexity of the power and data analysis toolchain and to reduce the simulation turnaround time. A system model data repository is used as the trusted store of high-level inputs and results while other remote servers are used for archival of larger data sets and for analysis tool execution. Simulation data passes through numerous domain-specific analysis tools and end-to-end simulation execution is enabled through a web-based tool. The use of a cloud-based service facilitates coordination among distributed developers and enables scalable computation and storage needs, and ensures a consistent execution environment. Configuration management is emphasized to maintain traceability between current and historical simulation runs and their corresponding versions of models, tools and data.

Enhancing efficiency and quality of statistical estimation of immunogenicity assay cut points through standardization and automation.

PubMed

Su, Cheng; Zhou, Lei; Hu, Zheng; Weng, Winnie; Subramani, Jayanthi; Tadkod, Vineet; Hamilton, Kortney; Bautista, Ami; Wu, Yu; Chirmule, Narendra; Zhong, Zhandong Don

2015-10-01

Biotherapeutics can elicit immune responses, which can alter the exposure, safety, and efficacy of the therapeutics. A well-designed and robust bioanalytical method is critical for the detection and characterization of relevant anti-drug antibody (ADA) and the success of an immunogenicity study. As a fundamental criterion in immunogenicity testing, assay cut points need to be statistically established with a risk-based approach to reduce subjectivity. This manuscript describes the development of a validated, web-based, multi-tier customized assay statistical tool (CAST) for assessing cut points of ADA assays. The tool provides an intuitive web interface that allows users to import experimental data generated from a standardized experimental design, select the assay factors, run the standardized analysis algorithms, and generate tables, figures, and listings (TFL). It allows bioanalytical scientists to perform complex statistical analysis at a click of the button to produce reliable assay parameters in support of immunogenicity studies. Copyright © 2015 Elsevier B.V. All rights reserved.

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

HC StratoMineR: A Web-Based Tool for the Rapid Analysis of High-Content Datasets.

PubMed

Omta, Wienand A; van Heesbeen, Roy G; Pagliero, Romina J; van der Velden, Lieke M; Lelieveld, Daphne; Nellen, Mehdi; Kramer, Maik; Yeong, Marley; Saeidi, Amir M; Medema, Rene H; Spruit, Marco; Brinkkemper, Sjaak; Klumperman, Judith; Egan, David A

2016-10-01

High-content screening (HCS) can generate large multidimensional datasets and when aligned with the appropriate data mining tools, it can yield valuable insights into the mechanism of action of bioactive molecules. However, easy-to-use data mining tools are not widely available, with the result that these datasets are frequently underutilized. Here, we present HC StratoMineR, a web-based tool for high-content data analysis. It is a decision-supportive platform that guides even non-expert users through a high-content data analysis workflow. HC StratoMineR is built by using My Structured Query Language for storage and querying, PHP: Hypertext Preprocessor as the main programming language, and jQuery for additional user interface functionality. R is used for statistical calculations, logic and data visualizations. Furthermore, C++ and graphical processor unit power is diffusely embedded in R by using the rcpp and rpud libraries for operations that are computationally highly intensive. We show that we can use HC StratoMineR for the analysis of multivariate data from a high-content siRNA knock-down screen and a small-molecule screen. It can be used to rapidly filter out undesirable data; to select relevant data; and to perform quality control, data reduction, data exploration, morphological hit picking, and data clustering. Our results demonstrate that HC StratoMineR can be used to functionally categorize HCS hits and, thus, provide valuable information for hit prioritization.

The Effects of Social Presence on Adherence-Focused Guidance in Problematic Cannabis Users: Protocol for the CANreduce 2.0 Randomized Controlled Trial

PubMed Central

Amann, Manuel; Haug, Severin; Wenger, Andreas; Baumgartner, Christian; Ebert, David D; Berger, Thomas; Stark, Lars; Walter, Marc

2018-01-01

Background In European countries, including Switzerland, cannabis is the most commonly used illicit drug. Offering a Web-based self-help tool could potentially reach users who otherwise would not seek traditional help. However, such Web-based self-help tools often suffer from low adherence. Objective Through adherence-focused guidance enhancements, the aim of this study was to increase adherence in cannabis users entering a Web-based self-help tool to reduce their cannabis use and, in this way, augment its effectiveness. Methods This paper presents the protocol for a three-arm randomized controlled trial (RCT) to compare the effectiveness of (1) an adherence-focused, guidance-enhanced, Web-based self-help intervention with social presence; (2) an adherence-focused, guidance-enhanced, Web-based self-help intervention without social presence; and (3) a treatment-as-usual at reducing cannabis use in problematic users. The two active interventions, each spanning 6 weeks, consist of modules designed to reduce cannabis use and attenuate common mental disorder (CMD) symptoms, including depression, anxiety, and stress-related disorder symptoms based on the approaches of motivational interviewing and cognitive behavioral therapy. With a target sample size of 528, data will be collected at baseline, 6 weeks, and 3 months after baseline. The primary outcome measurement will be the number of days of cannabis use on the preceding 7 days. Secondary outcomes will include the quantity of cannabis used in standardized cannabis joints, the severity of cannabis dependence, changes in CMD symptoms, and adherence to the program. Data analysis will follow the intention-to-treat principle and employ (generalized) linear mixed models. Results The project commenced in August 2016; recruitment is anticipated to end by December 2018. First results are expected to be submitted for publication in summer 2019. Conclusions This study will provide detailed insights on if and how the effectiveness of a Web-based self-help intervention aiming to reduce cannabis use in frequent cannabis users can be improved by theory-driven, adherence-focused guidance enhancement. Trial Registration International Standard Randomized Controlled Trial Number Registry: ISRCTN11086185; http://www.isrctn.com/ISRCTN11086185 (Archived by WebCite at http://www.webcitation.org/6wspbuQ1M) PMID:29386176

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.

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.

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…

CoNVaQ: a web tool for copy number variation-based association studies.

PubMed

Larsen, Simon Jonas; do Canto, Luisa Matos; Rogatto, Silvia Regina; Baumbach, Jan

2018-05-18

Copy number variations (CNVs) are large segments of the genome that are duplicated or deleted. Structural variations in the genome have been linked to many complex diseases. Similar to how genome-wide association studies (GWAS) have helped discover single-nucleotide polymorphisms linked to disease phenotypes, the extension of GWAS to CNVs has aided the discovery of structural variants associated with human traits and diseases. We present CoNVaQ, an easy-to-use web-based tool for CNV-based association studies. The web service allows users to upload two sets of CNV segments and search for genomic regions where the occurrence of CNVs is significantly associated with the phenotype. CoNVaQ provides two models: a simple statistical model using Fisher's exact test and a novel query-based model matching regions to user-defined queries. For each region, the method computes a global q-value statistic by repeated permutation of samples among the populations. We demonstrate our platform by using it to analyze a data set of HPV-positive and HPV-negative penile cancer patients. CoNVaQ provides a simple workflow for performing CNV-based association studies. It is made available as a web platform in order to provide a user-friendly workflow for biologists and clinicians to carry out CNV data analysis without installing any software. Through the web interface, users are also able to analyze their results to find overrepresented GO terms and pathways. In addition, our method is also available as a package for the R programming language. CoNVaQ is available at https://convaq.compbio.sdu.dk .

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…

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.

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…

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

ERIC Educational Resources Information Center

Cakir, Mustafa; Carlsen, William S.

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

d-Omix: a mixer of generic protein domain analysis tools.

PubMed

Wichadakul, Duangdao; Numnark, Somrak; Ingsriswang, Supawadee

2009-07-01

Domain combination provides important clues to the roles of protein domains in protein function, interaction and evolution. We have developed a web server d-Omix (a Mixer of Protein Domain Analysis Tools) aiming as a unified platform to analyze, compare and visualize protein data sets in various aspects of protein domain combinations. With InterProScan files for protein sets of interest provided by users, the server incorporates four services for domain analyses. First, it constructs protein phylogenetic tree based on a distance matrix calculated from protein domain architectures (DAs), allowing the comparison with a sequence-based tree. Second, it calculates and visualizes the versatility, abundance and co-presence of protein domains via a domain graph. Third, it compares the similarity of proteins based on DA alignment. Fourth, it builds a putative protein network derived from domain-domain interactions from DOMINE. Users may select a variety of input data files and flexibly choose domain search tools (e.g. hmmpfam, superfamily) for a specific analysis. Results from the d-Omix could be interactively explored and exported into various formats such as SVG, JPG, BMP and CSV. Users with only protein sequences could prepare an InterProScan file using a service provided by the server as well. The d-Omix web server is freely available at http://www.biotec.or.th/isl/Domix.

GelScape: a web-based server for interactively annotating, manipulating, comparing and archiving 1D and 2D gel images.

PubMed

Young, Nelson; Chang, Zhan; Wishart, David S

2004-04-12

GelScape is a web-based tool that permits facile, interactive annotation, comparison, manipulation and storage of protein gel images. It uses Java applet-servlet technology to allow rapid, remote image handling and image processing in a platform-independent manner. It supports many of the features found in commercial, stand-alone gel analysis software including spot annotation, spot integration, gel warping, image resizing, HTML image mapping, image overlaying as well as the storage of gel image and gel annotation data in compliance with Federated Gel Database requirements.

GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis.

PubMed

Zheng, Qi; Wang, Xiu-Jie

2008-07-01

Gene Ontology (GO) analysis has become a commonly used approach for functional studies of large-scale genomic or transcriptomic data. Although there have been a lot of software with GO-related analysis functions, new tools are still needed to meet the requirements for data generated by newly developed technologies or for advanced analysis purpose. Here, we present a Gene Ontology Enrichment Analysis Software Toolkit (GOEAST), an easy-to-use web-based toolkit that identifies statistically overrepresented GO terms within given gene sets. Compared with available GO analysis tools, GOEAST has the following improved features: (i) GOEAST displays enriched GO terms in graphical format according to their relationships in the hierarchical tree of each GO category (biological process, molecular function and cellular component), therefore, provides better understanding of the correlations among enriched GO terms; (ii) GOEAST supports analysis for data from various sources (probe or probe set IDs of Affymetrix, Illumina, Agilent or customized microarrays, as well as different gene identifiers) and multiple species (about 60 prokaryote and eukaryote species); (iii) One unique feature of GOEAST is to allow cross comparison of the GO enrichment status of multiple experiments to identify functional correlations among them. GOEAST also provides rigorous statistical tests to enhance the reliability of analysis results. GOEAST is freely accessible at http://omicslab.genetics.ac.cn/GOEAST/

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

Lynx: a database and knowledge extraction engine for integrative medicine

PubMed Central

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

2014-01-01

We have developed Lynx (http://lynx.ci.uchicago.edu)—a web-based database and a knowledge extraction engine, supporting annotation and analysis of experimental data and generation of weighted hypotheses on molecular mechanisms contributing to human phenotypes and disorders of interest. Its underlying knowledge base (LynxKB) integrates various classes of information from >35 public databases and private collections, as well as manually curated data from our group and collaborators. Lynx provides advanced search capabilities and a variety of algorithms for enrichment analysis and network-based gene prioritization to assist the user in extracting meaningful knowledge from LynxKB and experimental data, whereas its service-oriented architecture provides public access to LynxKB and its analytical tools via user-friendly web services and interfaces. PMID:24270788

Web-based interactive access, analysis and comparison of remotely sensed and in situ measured temperature data

NASA Astrophysics Data System (ADS)

Eberle, Jonas; Urban, Marcel; Hüttich, Christian; Schmullius, Christiane

2014-05-01

Numerous datasets providing temperature information from meteorological stations or remote sensing satellites are available. However, the challenging issue is to search in the archives and process the time series information for further analysis. These steps can be automated for each individual product, if the pre-conditions are complied, e.g. data access through web services (HTTP, FTP) or legal rights to redistribute the datasets. Therefore a python-based package was developed to provide data access and data processing tools for MODIS Land Surface Temperature (LST) data, which is provided by NASA Land Processed Distributed Active Archive Center (LPDAAC), as well as the Global Surface Summary of the Day (GSOD) and the Global Historical Climatology Network (GHCN) daily datasets provided by NOAA National Climatic Data Center (NCDC). The package to access and process the information is available as web services used by an interactive web portal for simple data access and analysis. Tools for time series analysis were linked to the system, e.g. time series plotting, decomposition, aggregation (monthly, seasonal, etc.), trend analyses, and breakpoint detection. Especially for temperature data a plot was integrated for the comparison of two temperature datasets based on the work by Urban et al. (2013). As a first result, a kernel density plot compares daily MODIS LST from satellites Aqua and Terra with daily means from GSOD and GHCN datasets. Without any data download and data processing, the users can analyze different time series datasets in an easy-to-use web portal. As a first use case, we built up this complimentary system with remotely sensed MODIS data and in situ measurements from meteorological stations for Siberia within the Siberian Earth System Science Cluster (www.sibessc.uni-jena.de). References: Urban, Marcel; Eberle, Jonas; Hüttich, Christian; Schmullius, Christiane; Herold, Martin. 2013. "Comparison of Satellite-Derived Land Surface Temperature and Air Temperature from Meteorological Stations on the Pan-Arctic Scale." Remote Sens. 5, no. 5: 2348-2367. Further materials: Eberle, Jonas; Clausnitzer, Siegfried; Hüttich, Christian; Schmullius, Christiane. 2013. "Multi-Source Data Processing Middleware for Land Monitoring within a Web-Based Spatial Data Infrastructure for Siberia." ISPRS Int. J. Geo-Inf. 2, no. 3: 553-576.

Web-Based Model Visualization Tools to Aid in Model Optimization and Uncertainty Analysis

NASA Astrophysics Data System (ADS)

Alder, J.; van Griensven, A.; Meixner, T.

2003-12-01

Individuals applying hydrologic models have a need for a quick easy to use visualization tools to permit them to assess and understand model performance. We present here the Interactive Hydrologic Modeling (IHM) visualization toolbox. The IHM utilizes high-speed Internet access, the portability of the web and the increasing power of modern computers to provide an online toolbox for quick and easy model result visualization. This visualization interface allows for the interpretation and analysis of Monte-Carlo and batch model simulation results. Often times a given project will generate several thousands or even hundreds of thousands simulations. This large number of simulations creates a challenge for post-simulation analysis. IHM's goal is to try to solve this problem by loading all of the data into a database with a web interface that can dynamically generate graphs for the user according to their needs. IHM currently supports: a global samples statistics table (e.g. sum of squares error, sum of absolute differences etc.), top ten simulations table and graphs, graphs of an individual simulation using time step data, objective based dotty plots, threshold based parameter cumulative density function graphs (as used in the regional sensitivity analysis of Spear and Hornberger) and 2D error surface graphs of the parameter space. IHM is ideal for the simplest bucket model to the largest set of Monte-Carlo model simulations with a multi-dimensional parameter and model output space. By using a web interface, IHM offers the user complete flexibility in the sense that they can be anywhere in the world using any operating system. IHM can be a time saving and money saving alternative to spending time producing graphs or conducting analysis that may not be informative or being forced to purchase or use expensive and proprietary software. IHM is a simple, free, method of interpreting and analyzing batch model results, and is suitable for novice to expert hydrologic modelers.

Moon Trek: An Interactive Web Portal for Current and Future Lunar Missions

NASA Technical Reports Server (NTRS)

Day, B; Law, Emily S.

2017-01-01

NASA's Moon Trek (https://moontrek.jpl.nasa.gov) is the successor to and replacement for NASA's Lunar Mapping and Modeling Portal (LMMP). Released in 2017, Moon Trek features a new interface with improved ways to access, visualize, and analyze data. Moon Trek provides a web-based Portal and a suite of interactive visualization and analysis tools to enable mission planners, lunar scientists, and engineers to access mapped lunar data products from past and current lunar missions.

Moon Trek: An Interactive Web Portal for Current and Future Lunar Missions

NASA Astrophysics Data System (ADS)

Day, B.; Law, E.

2017-09-01

NASA's Moon Trek (https://moontrek.jpl.nasa.gov) is the successor to and replacement for NASA's Lunar Mapping and Modeling Portal (LMMP). Released in 2017, Moon Trek features a new interface with improved ways to access, visualize, and analyse data. Moon Trek provides a web-based Portal and a suite of interactive visualization and analysis tools to enable mission planners, lunar scientists, and engineers to access mapped lunar data products from past and current lunar missions.

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.

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

PubMed

Aranguren, Mikel Egaña; Wilkinson, Mark D

2015-01-01

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

Design and Testing of BACRA, a Web-Based Tool for Middle Managers at Health Care Facilities to Lead the Search for Solutions to Patient Safety Incidents

PubMed Central

Mira, José Joaquín; Vicente, Maria Asuncion; Fernandez, Cesar; Guilabert, Mercedes; Ferrús, Lena; Zavala, Elena; Silvestre, Carmen; Pérez-Pérez, Pastora

2016-01-01

Background Lack of time, lack of familiarity with root cause analysis, or suspicion that the reporting may result in negative consequences hinder involvement in the analysis of safety incidents and the search for preventive actions that can improve patient safety. Objective The aim was develop a tool that enables hospitals and primary care professionals to immediately analyze the causes of incidents and to propose and implement measures intended to prevent their recurrence. Methods The design of the Web-based tool (BACRA) considered research on the barriers for reporting, review of incident analysis tools, and the experience of eight managers from the field of patient safety. BACRA’s design was improved in successive versions (BACRA v1.1 and BACRA v1.2) based on feedback from 86 middle managers. BACRA v1.1 was used by 13 frontline professionals to analyze incidents of safety; 59 professionals used BACRA v1.2 and assessed the respective usefulness and ease of use of both versions. Results BACRA contains seven tabs that guide the user through the process of analyzing a safety incident and proposing preventive actions for similar future incidents. BACRA does not identify the person completing each analysis since the password introduced to hide said analysis only is linked to the information concerning the incident and not to any personal data. The tool was used by 72 professionals from hospitals and primary care centers. BACRA v1.2 was assessed more favorably than BACRA v1.1, both in terms of its usefulness (z=2.2, P=.03) and its ease of use (z=3.0, P=.003). Conclusions BACRA helps to analyze incidents of safety and to propose preventive actions. BACRA guarantees anonymity of the analysis and reduces the reluctance of professionals to carry out this task. BACRA is useful and easy to use. PMID:27678308

Design and Testing of BACRA, a Web-Based Tool for Middle Managers at Health Care Facilities to Lead the Search for Solutions to Patient Safety Incidents.

PubMed

Carrillo, Irene; Mira, José Joaquín; Vicente, Maria Asuncion; Fernandez, Cesar; Guilabert, Mercedes; Ferrús, Lena; Zavala, Elena; Silvestre, Carmen; Pérez-Pérez, Pastora

2016-09-27

Lack of time, lack of familiarity with root cause analysis, or suspicion that the reporting may result in negative consequences hinder involvement in the analysis of safety incidents and the search for preventive actions that can improve patient safety. The aim was develop a tool that enables hospitals and primary care professionals to immediately analyze the causes of incidents and to propose and implement measures intended to prevent their recurrence. The design of the Web-based tool (BACRA) considered research on the barriers for reporting, review of incident analysis tools, and the experience of eight managers from the field of patient safety. BACRA's design was improved in successive versions (BACRA v1.1 and BACRA v1.2) based on feedback from 86 middle managers. BACRA v1.1 was used by 13 frontline professionals to analyze incidents of safety; 59 professionals used BACRA v1.2 and assessed the respective usefulness and ease of use of both versions. BACRA contains seven tabs that guide the user through the process of analyzing a safety incident and proposing preventive actions for similar future incidents. BACRA does not identify the person completing each analysis since the password introduced to hide said analysis only is linked to the information concerning the incident and not to any personal data. The tool was used by 72 professionals from hospitals and primary care centers. BACRA v1.2 was assessed more favorably than BACRA v1.1, both in terms of its usefulness (z=2.2, P=.03) and its ease of use (z=3.0, P=.003). BACRA helps to analyze incidents of safety and to propose preventive actions. BACRA guarantees anonymity of the analysis and reduces the reluctance of professionals to carry out this task. BACRA is useful and easy to use.

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…

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.

Exploring Gendered Notions: Gender, Job Hunting and Web Searches

NASA Astrophysics Data System (ADS)

Martey, R. M.

Based on analysis of a series of interviews, this chapter suggests that in looking for jobs online, women confront gendered notions of the Internet as well as gendered notions of the jobs themselves. It argues that the social and cultural contexts of both the search tools and the search tasks should be considered in exploring how Web-based technologies serve women in a job search. For these women, the opportunities and limitations of online job-search tools were intimately related to their personal and social needs, especially needs for part-time work, maternity benefits, and career advancement. Although job-seeking services such as Monster.com were used frequently by most of these women, search services did not completely fulfill all their informational needs, and became an — often frustrating — initial starting point for a job search rather than an end-point.

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.

TSVdb: a web-tool for TCGA splicing variants analysis.

PubMed

Sun, Wenjie; Duan, Ting; Ye, Panmeng; Chen, Kelie; Zhang, Guanling; Lai, Maode; Zhang, Honghe

2018-05-29

Collaborative projects such as The Cancer Genome Atlas (TCGA) have generated various -omics and clinical data on cancer. Many computational tools have been developed to facilitate the study of the molecular characterization of tumors using data from the TCGA. Alternative splicing of a gene produces splicing variants, and accumulating evidence has revealed its essential role in cancer-related processes, implying the urgent need to discover tumor-specific isoforms and uncover their potential functions in tumorigenesis. We developed TSVdb, a web-based tool, to explore alternative splicing based on TCGA samples with 30 clinical variables from 33 tumors. TSVdb has an integrated and well-proportioned interface for visualization of the clinical data, gene expression, usage of exons/junctions and splicing patterns. Researchers can interpret the isoform expression variations between or across clinical subgroups and estimate the relationships between isoforms and patient prognosis. TSVdb is available at http://www.tsvdb.com , and the source code is available at https://github.com/wenjie1991/TSVdb . TSVdb will inspire oncologists and accelerate isoform-level advances in cancer research.

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

PubMed

Morrison, James; Kaufman, John

2016-12-01

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

IMAGE EXPLORER: Astronomical Image Analysis on an HTML5-based Web Application

NASA Astrophysics Data System (ADS)

Gopu, A.; Hayashi, S.; Young, M. D.

2014-05-01

Large datasets produced by recent astronomical imagers cause the traditional paradigm for basic visual analysis - typically downloading one's entire image dataset and using desktop clients like DS9, Aladin, etc. - to not scale, despite advances in desktop computing power and storage. This paper describes Image Explorer, a web framework that offers several of the basic visualization and analysis functionality commonly provided by tools like DS9, on any HTML5 capable web browser on various platforms. It uses a combination of the modern HTML5 canvas, JavaScript, and several layers of lossless PNG tiles producted from the FITS image data. Astronomers are able to rapidly and simultaneously open up several images on their web-browser, adjust the intensity min/max cutoff or its scaling function, and zoom level, apply color-maps, view position and FITS header information, execute typically used data reduction codes on the corresponding FITS data using the FRIAA framework, and overlay tiles for source catalog objects, etc.

miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments.

PubMed

Hackenberg, Michael; Sturm, Martin; Langenberger, David; Falcón-Pérez, Juan Manuel; Aransay, Ana M

2009-07-01

Next-generation sequencing allows now the sequencing of small RNA molecules and the estimation of their expression levels. Consequently, there will be a high demand of bioinformatics tools to cope with the several gigabytes of sequence data generated in each single deep-sequencing experiment. Given this scene, we developed miRanalyzer, a web server tool for the analysis of deep-sequencing experiments for small RNAs. The web server tool requires a simple input file containing a list of unique reads and its copy numbers (expression levels). Using these data, miRanalyzer (i) detects all known microRNA sequences annotated in miRBase, (ii) finds all perfect matches against other libraries of transcribed sequences and (iii) predicts new microRNAs. The prediction of new microRNAs is an especially important point as there are many species with very few known microRNAs. Therefore, we implemented a highly accurate machine learning algorithm for the prediction of new microRNAs that reaches AUC values of 97.9% and recall values of up to 75% on unseen data. The web tool summarizes all the described steps in a single output page, which provides a comprehensive overview of the analysis, adding links to more detailed output pages for each analysis module. miRanalyzer is available at http://web.bioinformatics.cicbiogune.es/microRNA/.

The Design of Modular Web-Based Collaboration

NASA Astrophysics Data System (ADS)

Intapong, Ploypailin; Settapat, Sittapong; Kaewkamnerdpong, Boonserm; Achalakul, Tiranee

Online collaborative systems are popular communication channels as the systems allow people from various disciplines to interact and collaborate with ease. The systems provide communication tools and services that can be integrated on the web; consequently, the systems are more convenient to use and easier to install. Nevertheless, most of the currently available systems are designed according to some specific requirements and cannot be straightforwardly integrated into various applications. This paper provides the design of a new collaborative platform, which is component-based and re-configurable. The platform is called the Modular Web-based Collaboration (MWC). MWC shares the same concept as computer supported collaborative work (CSCW) and computer-supported collaborative learning (CSCL), but it provides configurable tools for online collaboration. Each tool module can be integrated into users' web applications freely and easily. This makes collaborative system flexible, adaptable and suitable for online collaboration.

RSAT 2015: Regulatory Sequence Analysis Tools

PubMed Central

Medina-Rivera, Alejandra; Defrance, Matthieu; Sand, Olivier; Herrmann, Carl; Castro-Mondragon, Jaime A.; Delerce, Jeremy; Jaeger, Sébastien; Blanchet, Christophe; Vincens, Pierre; Caron, Christophe; Staines, Daniel M.; Contreras-Moreira, Bruno; Artufel, Marie; Charbonnier-Khamvongsa, Lucie; Hernandez, Céline; Thieffry, Denis; Thomas-Chollier, Morgane; van Helden, Jacques

2015-01-01

RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative genomics and (iv) analysis of regulatory variations. Nine new programs have been added to the 43 described in the 2011 NAR Web Software Issue, including a tool to extract sequences from a list of coordinates (fetch-sequences from UCSC), novel programs dedicated to the analysis of regulatory variants from GWAS or population genomics (retrieve-variation-seq and variation-scan), a program to cluster motifs and visualize the similarities as trees (matrix-clustering). To deal with the drastic increase of sequenced genomes, RSAT public sites have been reorganized into taxon-specific servers. The suite is well-documented with tutorials and published protocols. The software suite is available through Web sites, SOAP/WSDL Web services, virtual machines and stand-alone programs at http://www.rsat.eu/. PMID:25904632

Patient-oriented interactive E-health tools on U.S. hospital Web sites.

PubMed

Huang, Edgar; Chang, Chiu-Chi Angela

2012-01-01

The purpose of this study is to provide evidence for strategic planning regarding e-health development in U.S. hospitals. A content analysis of a representative sample of the U.S. hospital Web sites has revealed how U.S. hospitals have taken advantage of the 21 patient-oriented interactive tools identified in this study. Significant gaps between various types of hospitals have also been found. It is concluded that although the majority of the U.S. hospitals have adopted traditional functional tools, they need to make significant inroad in implementing the core e-business tools to serve their patients/users, making their Web sites more efficient marketing tools.

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…

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

PubMed

Senachak, Jittisak; Cheevadhanarak, Supapon; Hongsthong, Apiradee

2015-07-29

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

Leveraging Google Geo Tools for Interactive STEM Education: Insights from the GEODE Project

NASA Astrophysics Data System (ADS)

Dordevic, M.; Whitmeyer, S. J.; De Paor, D. G.; Karabinos, P.; Burgin, S.; Coba, F.; Bentley, C.; St John, K. K.

2016-12-01

Web-based imagery and geospatial tools have transformed our ability to immerse students in global virtual environments. Google's suite of geospatial tools, such as Google Earth (± Engine), Google Maps, and Street View, allow developers and instructors to create interactive and immersive environments, where students can investigate and resolve common misconceptions in STEM concepts and natural processes. The GEODE (.net) project is developing digital resources to enhance STEM education. These include virtual field experiences (VFEs), such as an interactive visualization of the breakup of the Pangaea supercontinent, a "Grand Tour of the Terrestrial Planets," and GigaPan-based VFEs of sites like the Canadian Rockies. Web-based challenges, such as EarthQuiz (.net) and the "Fold Analysis Challenge," incorporate scaffolded investigations of geoscience concepts. EarthQuiz features web-hosted imagery, such as Street View, Photo Spheres, GigaPans, and Satellite View, as the basis for guided inquiry. In the Fold Analysis Challenge, upper-level undergraduates use Google Earth to evaluate a doubly-plunging fold at Sheep Mountain, WY. GEODE.net also features: "Reasons for the Seasons"—a Google Earth-based visualization that addresses misconceptions that abound amongst students, teachers, and the public, many of whom believe that seasonality is caused by large variations in Earth's distance from the Sun; "Plate Euler Pole Finder," which helps students understand rotational motion of tectonic plates on the globe; and "Exploring Marine Sediments Using Google Earth," an exercise that uses empirical data to explore the surficial distribution of marine sediments in the modern ocean. The GEODE research team includes the authors and: Heather Almquist, Cinzia Cervato, Gene Cooper, Helen Crompton, Terry Pavlis, Jen Piatek, Bill Richards, Jeff Ryan, Ron Schott, Barb Tewksbury, and their students and collaborating colleagues. We are supported by NSF DUE 1323419 and a Google Geo Curriculum Award.

CFGP: a web-based, comparative fungal genomics platform.

PubMed

Park, Jongsun; Park, Bongsoo; Jung, Kyongyong; Jang, Suwang; Yu, Kwangyul; Choi, Jaeyoung; Kong, Sunghyung; Park, Jaejin; Kim, Seryun; Kim, Hyojeong; Kim, Soonok; Kim, Jihyun F; Blair, Jaime E; Lee, Kwangwon; Kang, Seogchan; Lee, Yong-Hwan

2008-01-01

Since the completion of the Saccharomyces cerevisiae genome sequencing project in 1996, the genomes of over 80 fungal species have been sequenced or are currently being sequenced. Resulting data provide opportunities for studying and comparing fungal biology and evolution at the genome level. To support such studies, the Comparative Fungal Genomics Platform (CFGP; http://cfgp.snu.ac.kr), a web-based multifunctional informatics workbench, was developed. The CFGP comprises three layers, including the basal layer, middleware and the user interface. The data warehouse in the basal layer contains standardized genome sequences of 65 fungal species. The middleware processes queries via six analysis tools, including BLAST, ClustalW, InterProScan, SignalP 3.0, PSORT II and a newly developed tool named BLASTMatrix. The BLASTMatrix permits the identification and visualization of genes homologous to a query across multiple species. The Data-driven User Interface (DUI) of the CFGP was built on a new concept of pre-collecting data and post-executing analysis instead of the 'fill-in-the-form-and-press-SUBMIT' user interfaces utilized by most bioinformatics sites. A tool termed Favorite, which supports the management of encapsulated sequence data and provides a personalized data repository to users, is another novel feature in the DUI.

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update).

PubMed

Pravda, Lukáš; Sehnal, David; Toušek, Dominik; Navrátilová, Veronika; Bazgier, Václav; Berka, Karel; Svobodová Vareková, Radka; Koca, Jaroslav; Otyepka, Michal

2018-04-30

MOLEonline is an interactive, web-based application for the detection and characterization of channels (pores and tunnels) within biomacromolecular structures. The updated version of MOLEonline overcomes limitations of the previous version by incorporating the recently developed LiteMol Viewer visualization engine and providing a simple, fully interactive user experience. The application enables two modes of calculation: one is dedicated to the analysis of channels while the other was specifically designed for transmembrane pores. As the application can use both PDB and mmCIF formats, it can be leveraged to analyze a wide spectrum of biomacromolecular structures, e.g. stemming from NMR, X-ray and cryo-EM techniques. The tool is interconnected with other bioinformatics tools (e.g., PDBe, CSA, ChannelsDB, OPM, UniProt) to help both setup and the analysis of acquired results. MOLEonline provides unprecedented analytics for the detection and structural characterization of channels, as well as information about their numerous physicochemical features. Here we present the application of MOLEonline for structural analyses of α-hemolysin and transient receptor potential mucolipin 1 (TRMP1) pores. The MOLEonline application is freely available via the Internet at https://mole.upol.cz.

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.

Haystack, a web-based tool for metabolomics research

PubMed Central

2014-01-01

Background Liquid chromatography coupled to mass spectrometry (LCMS) has become a widely used technique in metabolomics research for differential profiling, the broad screening of biomolecular constituents across multiple samples to diagnose phenotypic differences and elucidate relevant features. However, a significant limitation in LCMS-based metabolomics is the high-throughput data processing required for robust statistical analysis and data modeling for large numbers of samples with hundreds of unique chemical species. Results To address this problem, we developed Haystack, a web-based tool designed to visualize, parse, filter, and extract significant features from LCMS datasets rapidly and efficiently. Haystack runs in a browser environment with an intuitive graphical user interface that provides both display and data processing options. Total ion chromatograms (TICs) and base peak chromatograms (BPCs) are automatically displayed, along with time-resolved mass spectra and extracted ion chromatograms (EICs) over any mass range. Output files in the common .csv format can be saved for further statistical analysis or customized graphing. Haystack's core function is a flexible binning procedure that converts the mass dimension of the chromatogram into a set of interval variables that can uniquely identify a sample. Binned mass data can be analyzed by exploratory methods such as principal component analysis (PCA) to model class assignment and identify discriminatory features. The validity of this approach is demonstrated by comparison of a dataset from plants grown at two light conditions with manual and automated peak detection methods. Haystack successfully predicted class assignment based on PCA and cluster analysis, and identified discriminatory features based on analysis of EICs of significant bins. Conclusion Haystack, a new online tool for rapid processing and analysis of LCMS-based metabolomics data is described. It offers users a range of data visualization options and supports non-biased differential profiling studies through a unique and flexible binning function that provides an alternative to conventional peak deconvolution analysis methods. PMID:25350247

Haystack, a web-based tool for metabolomics research.

PubMed

Grace, Stephen C; Embry, Stephen; Luo, Heng

2014-01-01

Liquid chromatography coupled to mass spectrometry (LCMS) has become a widely used technique in metabolomics research for differential profiling, the broad screening of biomolecular constituents across multiple samples to diagnose phenotypic differences and elucidate relevant features. However, a significant limitation in LCMS-based metabolomics is the high-throughput data processing required for robust statistical analysis and data modeling for large numbers of samples with hundreds of unique chemical species. To address this problem, we developed Haystack, a web-based tool designed to visualize, parse, filter, and extract significant features from LCMS datasets rapidly and efficiently. Haystack runs in a browser environment with an intuitive graphical user interface that provides both display and data processing options. Total ion chromatograms (TICs) and base peak chromatograms (BPCs) are automatically displayed, along with time-resolved mass spectra and extracted ion chromatograms (EICs) over any mass range. Output files in the common .csv format can be saved for further statistical analysis or customized graphing. Haystack's core function is a flexible binning procedure that converts the mass dimension of the chromatogram into a set of interval variables that can uniquely identify a sample. Binned mass data can be analyzed by exploratory methods such as principal component analysis (PCA) to model class assignment and identify discriminatory features. The validity of this approach is demonstrated by comparison of a dataset from plants grown at two light conditions with manual and automated peak detection methods. Haystack successfully predicted class assignment based on PCA and cluster analysis, and identified discriminatory features based on analysis of EICs of significant bins. Haystack, a new online tool for rapid processing and analysis of LCMS-based metabolomics data is described. It offers users a range of data visualization options and supports non-biased differential profiling studies through a unique and flexible binning function that provides an alternative to conventional peak deconvolution analysis methods.

Computing tools for implementing standards for single-case designs.

PubMed

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

2015-11-01

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

PathCase-SB architecture and database design

PubMed Central

2011-01-01

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

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.

SurvMicro: assessment of miRNA-based prognostic signatures for cancer clinical outcomes by multivariate survival analysis.

PubMed

Aguirre-Gamboa, Raul; Trevino, Victor

2014-06-01

MicroRNAs (miRNAs) play a key role in post-transcriptional regulation of mRNA levels. Their function in cancer has been studied by high-throughput methods generating valuable sources of public information. Thus, miRNA signatures predicting cancer clinical outcomes are emerging. An important step to propose miRNA-based biomarkers before clinical validation is their evaluation in independent cohorts. Although it can be carried out using public data, such task is time-consuming and requires a specialized analysis. Therefore, to aid and simplify the evaluation of prognostic miRNA signatures in cancer, we developed SurvMicro, a free and easy-to-use web tool that assesses miRNA signatures from publicly available miRNA profiles using multivariate survival analysis. SurvMicro is composed of a wide and updated database of >40 cohorts in different tissues and a web tool where survival analysis can be done in minutes. We presented evaluations to portray the straightforward functionality of SurvMicro in liver and lung cancer. To our knowledge, SurvMicro is the only bioinformatic tool that aids the evaluation of multivariate prognostic miRNA signatures in cancer. SurvMicro and its tutorial are freely available at http://bioinformatica.mty.itesm.mx/SurvMicro. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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...

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…

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.

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

PubMed

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

2013-06-01

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

Using sentiment analysis to review patient satisfaction data located on the internet.

PubMed

Hopper, Anthony M; Uriyo, Maria

2015-01-01

The purpose of this paper is to test the usefulness of sentiment analysis and time-to-next-complaint methods in quantifying text-based information located on the internet. As important, the authors demonstrate how managers can use time-to-next-complaint techniques to organize sentiment analysis derived data into useful information, which can be shared with doctors and other staff. The authors used sentiment analysis to review patient feedback for a select group of gynecologists in Virginia. The authors utilized time-to-next-complaint methods along with other techniques to organize this data into meaningful information. The authors demonstrated that sentiment analysis and time-to-next-complaint techniques might be useful tools for healthcare managers who are interested in transforming web-based text into meaningful, quantifiable information. This study has several limitations. For one thing, neither the data set nor the techniques the authors used to analyze it will account for biases that resulted from selection issues related to gender, income, and culture, as well as from other socio-demographic concerns. Additionally, the authors lacked key data concerning patient volumes for the targeted physicians. Finally, it may be difficult to convince doctors to consider web-based comments as truthful, thereby preventing healthcare managers from using data located on the internet. The report illustrates some of the ways in which healthcare administrators can utilize sentiment analysis, along with time-to-next-complaint techniques, to mine web-based, patient comments for meaningful information. The paper is one of the first to illustrate ways in which administrators at clinics and physicians' offices can utilize sentiment analysis and time-to-next-complaint methods to analyze web-based patient comments.

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.

Biowep: a workflow enactment portal for bioinformatics applications.

PubMed

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

2007-03-08

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

Biowep: a workflow enactment portal for bioinformatics applications

PubMed Central

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

2007-01-01

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

Version VI of the ESTree db: an improved tool for peach transcriptome analysis

PubMed Central

Lazzari, Barbara; Caprera, Andrea; Vecchietti, Alberto; Merelli, Ivan; Barale, Francesca; Milanesi, Luciano; Stella, Alessandra; Pozzi, Carlo

2008-01-01

Background The ESTree database (db) is a collection of Prunus persica and Prunus dulcis EST sequences that in its current version encompasses 75,404 sequences from 3 almond and 19 peach libraries. Nine peach genotypes and four peach tissues are represented, from four fruit developmental stages. The aim of this work was to implement the already existing ESTree db by adding new sequences and analysis programs. Particular care was given to the implementation of the web interface, that allows querying each of the database features. Results A Perl modular pipeline is the backbone of sequence analysis in the ESTree db project. Outputs obtained during the pipeline steps are automatically arrayed into the fields of a MySQL database. Apart from standard clustering and annotation analyses, version VI of the ESTree db encompasses new tools for tandem repeat identification, annotation against genomic Rosaceae sequences, and positioning on the database of oligomer sequences that were used in a peach microarray study. Furthermore, known protein patterns and motifs were identified by comparison to PROSITE. Based on data retrieved from sequence annotation against the UniProtKB database, a script was prepared to track positions of homologous hits on the GO tree and build statistics on the ontologies distribution in GO functional categories. EST mapping data were also integrated in the database. The PHP-based web interface was upgraded and extended. The aim of the authors was to enable querying the database according to all the biological aspects that can be investigated from the analysis of data available in the ESTree db. This is achieved by allowing multiple searches on logical subsets of sequences that represent different biological situations or features. Conclusions The version VI of ESTree db offers a broad overview on peach gene expression. Sequence analyses results contained in the database, extensively linked to external related resources, represent a large amount of information that can be queried via the tools offered in the web interface. Flexibility and modularity of the ESTree analysis pipeline and of the web interface allowed the authors to set up similar structures for different datasets, with limited manual intervention. PMID:18387211

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

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

PubMed

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

2014-01-01

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

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.

Dairy Analytics and Nutrient Analysis (DANA) Prototype System User Manual

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

Sam Alessi; Dennis Keiser

2012-10-01

This document is a user manual for the Dairy Analytics and Nutrient Analysis (DANA) model. DANA provides an analysis of dairy anaerobic digestion technology and allows users to calculate biogas production, co-product valuation, capital costs, expenses, revenue and financial metrics, for user customizable scenarios, dairy and digester types. The model provides results for three anaerobic digester types; Covered Lagoons, Modified Plug Flow, and Complete Mix, and three main energy production technologies; electricity generation, renewable natural gas generation, and compressed natural gas generation. Additional options include different dairy types, bedding types, backend treatment type as well as numerous production, and economicmore » parameters. DANA’s goal is to extend the National Market Value of Anaerobic Digester Products analysis (informa economics, 2012; Innovation Center, 2011) to include a greater and more flexible set of regional digester scenarios and to provide a modular framework for creation of a tool to support farmer and investor needs. Users can set up scenarios from combinations of existing parameters or add new parameters, run the model and view a variety of reports, charts and tables that are automatically produced and delivered over the web interface. DANA is based in the INL’s analysis architecture entitled Generalized Environment for Modeling Systems (GEMS) , which offers extensive collaboration, analysis, and integration opportunities and greatly speeds the ability construct highly scalable web delivered user-oriented decision tools. DANA’s approach uses server-based data processing and web-based user interfaces, rather a client-based spreadsheet approach. This offers a number of benefits over the client-based approach. Server processing and storage can scale up to handle a very large number of scenarios, so that analysis of county, even field level, across the whole U.S., can be performed. Server based databases allow dairy and digester parameters be held and managed in a single managed data repository, while allows users to customize standard values and perform individual analysis. Server-based calculations can be easily extended, versions and upgrades managed, and any changes are immediately available to all users. This user manual describes how to use and/or modify input database tables, run DANA, view and modify reports.« less

FoodPro: A Web-Based Tool for Evaluating Covariance and Correlation NMR Spectra Associated with Food Processes

PubMed Central

Chikayama, Eisuke; Yamashina, Ryo; Komatsu, Keiko; Tsuboi, Yuuri; Sakata, Kenji; Kikuchi, Jun; Sekiyama, Yasuyo

2016-01-01

Foods from agriculture and fishery products are processed using various technologies. Molecular mixture analysis during food processing has the potential to help us understand the molecular mechanisms involved, thus enabling better cooking of the analyzed foods. To date, there has been no web-based tool focusing on accumulating Nuclear Magnetic Resonance (NMR) spectra from various types of food processing. Therefore, we have developed a novel web-based tool, FoodPro, that includes a food NMR spectrum database and computes covariance and correlation spectra to tasting and hardness. As a result, FoodPro has accumulated 236 aqueous (extracted in D2O) and 131 hydrophobic (extracted in CDCl3) experimental bench-top 60-MHz NMR spectra, 1753 tastings scored by volunteers, and 139 hardness measurements recorded by a penetrometer, all placed into a core database. The database content was roughly classified into fish and vegetable groups from the viewpoint of different spectrum patterns. FoodPro can query a user food NMR spectrum, search similar NMR spectra with a specified similarity threshold, and then compute estimated tasting and hardness, covariance, and correlation spectra to tasting and hardness. Querying fish spectra exemplified specific covariance spectra to tasting and hardness, giving positive covariance for tasting at 1.31 ppm for lactate and 3.47 ppm for glucose and a positive covariance for hardness at 3.26 ppm for trimethylamine N-oxide. PMID:27775560

FoodPro: A Web-Based Tool for Evaluating Covariance and Correlation NMR Spectra Associated with Food Processes.

PubMed

Chikayama, Eisuke; Yamashina, Ryo; Komatsu, Keiko; Tsuboi, Yuuri; Sakata, Kenji; Kikuchi, Jun; Sekiyama, Yasuyo

2016-10-19

Foods from agriculture and fishery products are processed using various technologies. Molecular mixture analysis during food processing has the potential to help us understand the molecular mechanisms involved, thus enabling better cooking of the analyzed foods. To date, there has been no web-based tool focusing on accumulating Nuclear Magnetic Resonance (NMR) spectra from various types of food processing. Therefore, we have developed a novel web-based tool, FoodPro, that includes a food NMR spectrum database and computes covariance and correlation spectra to tasting and hardness. As a result, FoodPro has accumulated 236 aqueous (extracted in D₂O) and 131 hydrophobic (extracted in CDCl₃) experimental bench-top 60-MHz NMR spectra, 1753 tastings scored by volunteers, and 139 hardness measurements recorded by a penetrometer, all placed into a core database. The database content was roughly classified into fish and vegetable groups from the viewpoint of different spectrum patterns. FoodPro can query a user food NMR spectrum, search similar NMR spectra with a specified similarity threshold, and then compute estimated tasting and hardness, covariance, and correlation spectra to tasting and hardness. Querying fish spectra exemplified specific covariance spectra to tasting and hardness, giving positive covariance for tasting at 1.31 ppm for lactate and 3.47 ppm for glucose and a positive covariance for hardness at 3.26 ppm for trimethylamine N -oxide.

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.

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/ .

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..

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.

Development and Field-Testing of a Study Protocol, including a Web-Based Occupant Survey Tool, for Use in Intervention Studies of Indoor Environmental Quality

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

Mendell, Mark; Eliseeva, Ekaterina; Spears, Michael

We developed and pilot-tested an overall protocol for intervention studies to evaluate the effects of indoor environmental changes in office buildings on the health symptoms and comfort of occupants. The protocol includes a web-based survey to assess the occupant's responses, as well as specific features of study design and analysis. The pilot study, carried out on two similar floors in a single building, compared two types of ventilation system filter media. With support from the building's Facilities staff, the implementation of the filter change intervention went well. While the web-based survey tool worked well also, low overall response rates (21-34percentmore » among the three work groups included) limited our ability to evaluate the filter intervention., The total number of questionnaires returned was low even though we extended the study from eight to ten weeks. Because another simultaneous study we conducted elsewhere using the same survey had a high response rate (>70percent), we conclude that the low response here resulted from issues specific to this pilot, including unexpected restrictions by some employing agencies on communication with occupants.« less

From Analysis to Impact: Challenges and Outcomes from Google's Cloud-based Platforms for Analyzing and Leveraging Petapixels of Geospatial Data

NASA Astrophysics Data System (ADS)

Thau, D.

2017-12-01

For the past seven years, Google has made petabytes of Earth observation data, and the tools to analyze it, freely available to researchers around the world via cloud computing. These data and tools were initially available via Google Earth Engine and are increasingly available on the Google Cloud Platform. We have introduced a number of APIs for both the analysis and presentation of geospatial data that have been successfully used to create impactful datasets and web applications, including studies of global surface water availability, global tree cover change, and crop yield estimation. Each of these projects used the cloud to analyze thousands to millions of Landsat scenes. The APIs support a range of publishing options, from outputting imagery and data for inclusion in papers, to providing tools for full scale web applications that provide analysis tools of their own. Over the course of developing these tools, we have learned a number of lessons about how to build a publicly available cloud platform for geospatial analysis, and about how the characteristics of an API can affect the kinds of impacts a platform can enable. This study will present an overview of how Google Earth Engine works and how Google's geospatial capabilities are extending to Google Cloud Platform. We will provide a number of case studies describing how these platforms, and the data they host, have been leveraged to build impactful decision support tools used by governments, researchers, and other institutions, and we will describe how the available APIs have shaped (or constrained) those tools. [Image Credit: Tyler A. Erickson

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…

Air Markets Program Data (AMPD)

EPA Pesticide Factsheets

The Air Markets Program Data tool allows users to search EPA data to answer scientific, general, policy, and regulatory questions about industry emissions. Air Markets Program Data (AMPD) is a web-based application that allows users easy access to both current and historical data collected as part of EPA's emissions trading programs. This site allows you to create and view reports and to download emissions data for further analysis. AMPD provides a query tool so users can create custom queries of industry source emissions data, allowance data, compliance data, and facility attributes. In addition, AMPD provides interactive maps, charts, reports, and pre-packaged datasets. AMPD does not require any additional software, plug-ins, or security controls and can be accessed using a standard web browser.

Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information

NASA Astrophysics Data System (ADS)

Sushko, Iurii; Novotarskyi, Sergii; Körner, Robert; Pandey, Anil Kumar; Rupp, Matthias; Teetz, Wolfram; Brandmaier, Stefan; Abdelaziz, Ahmed; Prokopenko, Volodymyr V.; Tanchuk, Vsevolod Y.; Todeschini, Roberto; Varnek, Alexandre; Marcou, Gilles; Ertl, Peter; Potemkin, Vladimir; Grishina, Maria; Gasteiger, Johann; Schwab, Christof; Baskin, Igor I.; Palyulin, Vladimir A.; Radchenko, Eugene V.; Welsh, William J.; Kholodovych, Vladyslav; Chekmarev, Dmitriy; Cherkasov, Artem; Aires-de-Sousa, Joao; Zhang, Qing-You; Bender, Andreas; Nigsch, Florian; Patiny, Luc; Williams, Antony; Tkachenko, Valery; Tetko, Igor V.

2011-06-01

The Online Chemical Modeling Environment is a web-based platform that aims to automate and simplify the typical steps required for QSAR modeling. The platform consists of two major subsystems: the database of experimental measurements and the modeling framework. A user-contributed database contains a set of tools for easy input, search and modification of thousands of records. The OCHEM database is based on the wiki principle and focuses primarily on the quality and verifiability of the data. The database is tightly integrated with the modeling framework, which supports all the steps required to create a predictive model: data search, calculation and selection of a vast variety of molecular descriptors, application of machine learning methods, validation, analysis of the model and assessment of the applicability domain. As compared to other similar systems, OCHEM is not intended to re-implement the existing tools or models but rather to invite the original authors to contribute their results, make them publicly available, share them with other users and to become members of the growing research community. Our intention is to make OCHEM a widely used platform to perform the QSPR/QSAR studies online and share it with other users on the Web. The ultimate goal of OCHEM is collecting all possible chemoinformatics tools within one simple, reliable and user-friendly resource. The OCHEM is free for web users and it is available online at http://www.ochem.eu.

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2018-04-18

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