Online Statistical Modeling (Regression Analysis) for Independent Responses

NASA Astrophysics Data System (ADS)

Made Tirta, I.; Anggraeni, Dian; Pandutama, Martinus

2017-06-01

Regression analysis (statistical analmodelling) are among statistical methods which are frequently needed in analyzing quantitative data, especially to model relationship between response and explanatory variables. Nowadays, statistical models have been developed into various directions to model various type and complex relationship of data. Rich varieties of advanced and recent statistical modelling are mostly available on open source software (one of them is R). However, these advanced statistical modelling, are not very friendly to novice R users, since they are based on programming script or command line interface. Our research aims to developed web interface (based on R and shiny), so that most recent and advanced statistical modelling are readily available, accessible and applicable on web. We have previously made interface in the form of e-tutorial for several modern and advanced statistical modelling on R especially for independent responses (including linear models/LM, generalized linier models/GLM, generalized additive model/GAM and generalized additive model for location scale and shape/GAMLSS). In this research we unified them in the form of data analysis, including model using Computer Intensive Statistics (Bootstrap and Markov Chain Monte Carlo/ MCMC). All are readily accessible on our online Virtual Statistics Laboratory. The web (interface) make the statistical modeling becomes easier to apply and easier to compare them in order to find the most appropriate model for the data.

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.

The Web as a Delivery Medium To Enhance Instruction.

ERIC Educational Resources Information Center

Gillani, Bijan

1998-01-01

Discusses how to design and develop an effective Web site to enhance instruction based on a graduate course at California State University at Hayward. Topics include the analysis phase, content organization, site architecture, interface design, testing, and the evaluation process. (LRW)

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

iSeq: Web-Based RNA-seq Data Analysis and Visualization.

PubMed

Zhang, Chao; Fan, Caoqi; Gan, Jingbo; Zhu, Ping; Kong, Lei; Li, Cheng

2018-01-01

Transcriptome sequencing (RNA-seq) is becoming a standard experimental methodology for genome-wide characterization and quantification of transcripts at single base-pair resolution. However, downstream analysis of massive amount of sequencing data can be prohibitively technical for wet-lab researchers. A functionally integrated and user-friendly platform is required to meet this demand. Here, we present iSeq, an R-based Web server, for RNA-seq data analysis and visualization. iSeq is a streamlined Web-based R application under the Shiny framework, featuring a simple user interface and multiple data analysis modules. Users without programming and statistical skills can analyze their RNA-seq data and construct publication-level graphs through a standardized yet customizable analytical pipeline. iSeq is accessible via Web browsers on any operating system at http://iseq.cbi.pku.edu.cn .

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.

Assessing the Quality of Academic Libraries on the Web: The Development and Testing of Criteria.

ERIC Educational Resources Information Center

Chao, Hungyune

2002-01-01

This study develops and tests an instrument useful for evaluating the quality of academic library Web sites. Discusses criteria for print materials and human-computer interfaces; user-based perspectives; the use of factor analysis; a survey of library experts; testing reliability through analysis of variance; and regression models. (Contains 53…

Optimizing real-time Web-based user interfaces for observatories

NASA Astrophysics Data System (ADS)

Gibson, J. Duane; Pickering, Timothy E.; Porter, Dallan; Schaller, Skip

2008-08-01

In using common HTML/Ajax approaches for web-based data presentation and telescope control user interfaces at the MMT Observatory (MMTO), we rapidly were confronted with web browser performance issues. Much of the operational data at the MMTO is highly dynamic and is constantly changing during normal operations. Status of telescope subsystems must be displayed with minimal latency to telescope operators and other users. A major motivation of migrating toward web-based applications at the MMTO is to provide easy access to current and past observatory subsystem data for a wide variety of users on their favorite operating system through a familiar interface, their web browser. Performance issues, especially for user interfaces that control telescope subsystems, led to investigations of more efficient use of HTML/Ajax and web server technologies as well as other web-based technologies, such as Java and Flash/Flex. The results presented here focus on techniques for optimizing HTML/Ajax web applications with near real-time data display. This study indicates that direct modification of the contents or "nodeValue" attribute of text nodes is the most efficient method of updating data values displayed on a web page. Other optimization techniques are discussed for web-based applications that display highly dynamic data.

Finding, Browsing and Getting Data Easily Using SPDF Web Services

NASA Technical Reports Server (NTRS)

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

A brief introduction to web-based genome browsers.

PubMed

Wang, Jun; Kong, Lei; Gao, Ge; Luo, Jingchu

2013-03-01

Genome browser provides a graphical interface for users to browse, search, retrieve and analyze genomic sequence and annotation data. Web-based genome browsers can be classified into general genome browsers with multiple species and species-specific genome browsers. In this review, we attempt to give an overview for the main functions and features of web-based genome browsers, covering data visualization, retrieval, analysis and customization. To give a brief introduction to the multiple-species genome browser, we describe the user interface and main functions of the Ensembl and UCSC genome browsers using the human alpha-globin gene cluster as an example. We further use the MSU and the Rice-Map genome browsers to show some special features of species-specific genome browser, taking a rice transcription factor gene OsSPL14 as an example.

Scalable web services for the PSIPRED Protein Analysis Workbench.

PubMed

Buchan, Daniel W A; Minneci, Federico; Nugent, Tim C O; Bryson, Kevin; Jones, David T

2013-07-01

Here, we present the new UCL Bioinformatics Group's PSIPRED Protein Analysis Workbench. The Workbench unites all of our previously available analysis methods into a single web-based framework. The new web portal provides a greatly streamlined user interface with a number of new features to allow users to better explore their results. We offer a number of additional services to enable computationally scalable execution of our prediction methods; these include SOAP and XML-RPC web server access and new HADOOP packages. All software and services are available via the UCL Bioinformatics Group website at http://bioinf.cs.ucl.ac.uk/.

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.

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

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.

XMM-Newton Remote Interface to Science Analysis Software: First Public Version

NASA Astrophysics Data System (ADS)

Ibarra, A.; Gabriel, C.

2011-07-01

We present the first public beta release of the XMM-Newton Remote Interface to Science Analysis (RISA) software, available through the official XMM-Newton web pages. In a nutshell, RISA is a web based application that encapsulates the XMM-Newton data analysis software. The client identifies observations and creates XMM-Newton workflows. The server processes the client request, creates job templates and sends the jobs to a computer. RISA has been designed to help, at the same time, non-expert and professional XMM-Newton users. Thanks to the predefined threads, non-expert users can easily produce light curves and spectra. And on the other hand, expert user can use the full parameter interface to tune their own analysis. In both cases, the VO compliant client/server design frees the users from having to install any specific software to analyze XMM-Newton data.

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...

Using a web-based application to define the accuracy of diagnostic tests when the gold standard is imperfect.

PubMed

Lim, Cherry; Wannapinij, Prapass; White, Lisa; Day, Nicholas P J; Cooper, Ben S; Peacock, Sharon J; Limmathurotsakul, Direk

2013-01-01

Estimates of the sensitivity and specificity for new diagnostic tests based on evaluation against a known gold standard are imprecise when the accuracy of the gold standard is imperfect. Bayesian latent class models (LCMs) can be helpful under these circumstances, but the necessary analysis requires expertise in computational programming. Here, we describe open-access web-based applications that allow non-experts to apply Bayesian LCMs to their own data sets via a user-friendly interface. Applications for Bayesian LCMs were constructed on a web server using R and WinBUGS programs. The models provided (http://mice.tropmedres.ac) include two Bayesian LCMs: the two-tests in two-population model (Hui and Walter model) and the three-tests in one-population model (Walter and Irwig model). Both models are available with simplified and advanced interfaces. In the former, all settings for Bayesian statistics are fixed as defaults. Users input their data set into a table provided on the webpage. Disease prevalence and accuracy of diagnostic tests are then estimated using the Bayesian LCM, and provided on the web page within a few minutes. With the advanced interfaces, experienced researchers can modify all settings in the models as needed. These settings include correlation among diagnostic test results and prior distributions for all unknown parameters. The web pages provide worked examples with both models using the original data sets presented by Hui and Walter in 1980, and by Walter and Irwig in 1988. We also illustrate the utility of the advanced interface using the Walter and Irwig model on a data set from a recent melioidosis study. The results obtained from the web-based applications were comparable to those published previously. The newly developed web-based applications are open-access and provide an important new resource for researchers worldwide to evaluate new diagnostic tests.

Bringing Control System User Interfaces to the Web

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

Chen, Xihui; Kasemir, Kay

With the evolution of web based technologies, especially HTML5 [1], it becomes possible to create web-based control system user interfaces (UI) that are cross-browser and cross-device compatible. This article describes two technologies that facilitate this goal. The first one is the WebOPI [2], which can seamlessly display CSS BOY [3] Operator Interfaces (OPI) in web browsers without modification to the original OPI file. The WebOPI leverages the powerful graphical editing capabilities of BOY and provides the convenience of re-using existing OPI files. On the other hand, it uses generic JavaScript and a generic communication mechanism between the web browser andmore » web server. It is not optimized for a control system, which results in unnecessary network traffic and resource usage. Our second technology is the WebSocket-based Process Data Access (WebPDA) [4]. It is a protocol that provides efficient control system data communication using WebSocket [5], so that users can create web-based control system UIs using standard web page technologies such as HTML, CSS and JavaScript. WebPDA is control system independent, potentially supporting any type of control system.« less

Draper Station Analysis Tool

NASA Technical Reports Server (NTRS)

Bedrossian, Nazareth; Jang, Jiann-Woei; McCants, Edward; Omohundro, Zachary; Ring, Tom; Templeton, Jeremy; Zoss, Jeremy; Wallace, Jonathan; Ziegler, Philip

2011-01-01

Draper Station Analysis Tool (DSAT) is a computer program, built on commercially available software, for simulating and analyzing complex dynamic systems. Heretofore used in designing and verifying guidance, navigation, and control systems of the International Space Station, DSAT has a modular architecture that lends itself to modification for application to spacecraft or terrestrial systems. DSAT consists of user-interface, data-structures, simulation-generation, analysis, plotting, documentation, and help components. DSAT automates the construction of simulations and the process of analysis. DSAT provides a graphical user interface (GUI), plus a Web-enabled interface, similar to the GUI, that enables a remotely located user to gain access to the full capabilities of DSAT via the Internet and Webbrowser software. Data structures are used to define the GUI, the Web-enabled interface, simulations, and analyses. Three data structures define the type of analysis to be performed: closed-loop simulation, frequency response, and/or stability margins. DSAT can be executed on almost any workstation, desktop, or laptop computer. DSAT provides better than an order of magnitude improvement in cost, schedule, and risk assessment for simulation based design and verification of complex dynamic systems.

Customizable scientific web-portal for DIII-D nuclear fusion experiment

NASA Astrophysics Data System (ADS)

Abla, G.; Kim, E. N.; Schissel, D. P.

2010-04-01

Increasing utilization of the Internet and convenient web technologies has made the web-portal a major application interface for remote participation and control of scientific instruments. While web-portals have provided a centralized gateway for multiple computational services, the amount of visual output often is overwhelming due to the high volume of data generated by complex scientific instruments and experiments. Since each scientist may have different priorities and areas of interest in the experiment, filtering and organizing information based on the individual user's need can increase the usability and efficiency of a web-portal. DIII-D is the largest magnetic nuclear fusion device in the US. A web-portal has been designed to support the experimental activities of DIII-D researchers worldwide. It offers a customizable interface with personalized page layouts and list of services for users to select. Each individual user can create a unique working environment to fit his own needs and interests. Customizable services are: real-time experiment status monitoring, diagnostic data access, interactive data analysis and visualization. The web-portal also supports interactive collaborations by providing collaborative logbook, and online instant announcement services. The DIII-D web-portal development utilizes multi-tier software architecture, and Web 2.0 technologies and tools, such as AJAX and Django, to develop a highly-interactive and customizable user interface.

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

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

PubMed Central

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

2015-01-01

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

Metadata tables to enable dynamic data modeling and web interface design: the SEER example.

PubMed

Weiner, Mark; Sherr, Micah; Cohen, Abigail

2002-04-01

A wealth of information addressing health status, outcomes and resource utilization is compiled and made available by various government agencies. While exploration of the data is possible using existing tools, in general, would-be users of the resources must acquire CD-ROMs or download data from the web, and upload the data into their own database. Where web interfaces exist, they are highly structured, limiting the kinds of queries that can be executed. This work develops a web-based database interface engine whose content and structure is generated through interaction with a metadata table. The result is a dynamically generated web interface that can easily accommodate changes in the underlying data model by altering the metadata table, rather than requiring changes to the interface code. This paper discusses the background and implementation of the metadata table and web-based front end and provides examples of its use with the NCI's Surveillance, Epidemiology and End-Results (SEER) database.

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.

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

ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data

PubMed Central

2016-01-01

ProXL is a Web application and accompanying database designed for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data with an emphasis on structural analysis and quality control. ProXL is designed to be independent of any particular software pipeline. The import process is simplified by the use of the ProXL XML data format, which shields developers of data importers from the relative complexity of the relational database schema. The database and Web interfaces function equally well for any software pipeline and allow data from disparate pipelines to be merged and contrasted. ProXL includes robust public and private data sharing capabilities, including a project-based interface designed to ensure security and facilitate collaboration among multiple researchers. ProXL provides multiple interactive and highly dynamic data visualizations that facilitate structural-based analysis of the observed cross-links as well as quality control. ProXL is open-source, well-documented, and freely available at https://github.com/yeastrc/proxl-web-app. PMID:27302480

ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data.

PubMed

Riffle, Michael; Jaschob, Daniel; Zelter, Alex; Davis, Trisha N

2016-08-05

ProXL is a Web application and accompanying database designed for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data with an emphasis on structural analysis and quality control. ProXL is designed to be independent of any particular software pipeline. The import process is simplified by the use of the ProXL XML data format, which shields developers of data importers from the relative complexity of the relational database schema. The database and Web interfaces function equally well for any software pipeline and allow data from disparate pipelines to be merged and contrasted. ProXL includes robust public and private data sharing capabilities, including a project-based interface designed to ensure security and facilitate collaboration among multiple researchers. ProXL provides multiple interactive and highly dynamic data visualizations that facilitate structural-based analysis of the observed cross-links as well as quality control. ProXL is open-source, well-documented, and freely available at https://github.com/yeastrc/proxl-web-app .

Trends in Culturally Relevant Interface Design Features for Latino Web Site Users

ERIC Educational Resources Information Center

Sachau, Lori L.; Hutchinson, Susan R.

2012-01-01

There is a lack of published research on designing Web-based instruction for the adult U.S. Latino population. Instructional designers need guidance on how to design culturally relevant learning environments for this audience, particularly for Latino people from Mexican heritage. The authors used content analysis to investigate the extent to which…

Focused sunlight factor of forest fire danger assessment using Web-GIS and RS technologies

NASA Astrophysics Data System (ADS)

Baranovskiy, Nikolay V.; Sherstnyov, Vladislav S.; Yankovich, Elena P.; Engel, Marina V.; Belov, Vladimir V.

2016-08-01

Timiryazevskiy forestry of Tomsk region (Siberia, Russia) is a study area elaborated in current research. Forest fire danger assessment is based on unique technology using probabilistic criterion, statistical data on forest fires, meteorological conditions, forest sites classification and remote sensing data. MODIS products are used for estimating some meteorological conditions and current forest fire situation. Geonformation technologies are used for geospatial analysis of forest fire danger situation on controlled forested territories. GIS-engine provides opportunities to construct electronic maps with different levels of forest fire probability and support raster layer for satellite remote sensing data on current forest fires. Web-interface is used for data loading on specific web-site and for forest fire danger data representation via World Wide Web. Special web-forms provide interface for choosing of relevant input data in order to process the forest fire danger data and assess the forest fire probability.

Space Physics Data Facility Web Services

NASA Technical Reports Server (NTRS)

Candey, Robert M.; Harris, Bernard T.; Chimiak, Reine A.

2005-01-01

The Space Physics Data Facility (SPDF) Web services provides a distributed programming interface to a portion of the SPDF software. (A general description of Web services is available at http://www.w3.org/ and in many current software-engineering texts and articles focused on distributed programming.) The SPDF Web services distributed programming interface enables additional collaboration and integration of the SPDF software system with other software systems, in furtherance of the SPDF mission to lead collaborative efforts in the collection and utilization of space physics data and mathematical models. This programming interface conforms to all applicable Web services specifications of the World Wide Web Consortium. The interface is specified by a Web Services Description Language (WSDL) file. The SPDF Web services software consists of the following components: 1) A server program for implementation of the Web services; and 2) A software developer s kit that consists of a WSDL file, a less formal description of the interface, a Java class library (which further eases development of Java-based client software), and Java source code for an example client program that illustrates the use of the interface.

STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence

PubMed Central

Neshich, Goran; Togawa, Roberto C.; Mancini, Adauto L.; Kuser, Paula R.; Yamagishi, Michel E. B.; Pappas, Georgios; Torres, Wellington V.; Campos, Tharsis Fonseca e; Ferreira, Leonardo L.; Luna, Fabio M.; Oliveira, Adilton G.; Miura, Ronald T.; Inoue, Marcus K.; Horita, Luiz G.; de Souza, Dimas F.; Dominiquini, Fabiana; Álvaro, Alexandre; Lima, Cleber S.; Ogawa, Fabio O.; Gomes, Gabriel B.; Palandrani, Juliana F.; dos Santos, Gabriela F.; de Freitas, Esther M.; Mattiuz, Amanda R.; Costa, Ivan C.; de Almeida, Celso L.; Souza, Savio; Baudet, Christian; Higa, Roberto H.

2003-01-01

STING Millennium Suite (SMS) is a new web-based suite of programs and databases providing visualization and a complex analysis of molecular sequence and structure for the data deposited at the Protein Data Bank (PDB). SMS operates with a collection of both publicly available data (PDB, HSSP, Prosite) and its own data (contacts, interface contacts, surface accessibility). Biologists find SMS useful because it provides a variety of algorithms and validated data, wrapped-up in a user friendly web interface. Using SMS it is now possible to analyze sequence to structure relationships, the quality of the structure, nature and volume of atomic contacts of intra and inter chain type, relative conservation of amino acids at the specific sequence position based on multiple sequence alignment, indications of folding essential residue (FER) based on the relationship of the residue conservation to the intra-chain contacts and Cα–Cα and Cβ–Cβ distance geometry. Specific emphasis in SMS is given to interface forming residues (IFR)—amino acids that define the interactive portion of the protein surfaces. SMS may simultaneously display and analyze previously superimposed structures. PDB updates trigger SMS updates in a synchronized fashion. SMS is freely accessible for public data at http://www.cbi.cnptia.embrapa.br, http://mirrors.rcsb.org/SMS and http://trantor.bioc.columbia.edu/SMS. PMID:12824333

A web-based platform for virtual screening.

PubMed

Watson, Paul; Verdonk, Marcel; Hartshorn, Michael J

2003-09-01

A fully integrated, web-based, virtual screening platform has been developed to allow rapid virtual screening of large numbers of compounds. ORACLE is used to store information at all stages of the process. The system includes a large database of historical compounds from high throughput screenings (HTS) chemical suppliers, ATLAS, containing over 3.1 million unique compounds with their associated physiochemical properties (ClogP, MW, etc.). The database can be screened using a web-based interface to produce compound subsets for virtual screening or virtual library (VL) enumeration. In order to carry out the latter task within ORACLE a reaction data cartridge has been developed. Virtual libraries can be enumerated rapidly using the web-based interface to the cartridge. The compound subsets can be seamlessly submitted for virtual screening experiments, and the results can be viewed via another web-based interface allowing ad hoc querying of the virtual screening data stored in ORACLE.

Monitoring and controlling ATLAS data management: The Rucio web user interface

NASA Astrophysics Data System (ADS)

Lassnig, M.; Beermann, T.; Vigne, R.; Barisits, M.; Garonne, V.; Serfon, C.

2015-12-01

The monitoring and controlling interfaces of the previous data management system DQ2 followed the evolutionary requirements and needs of the ATLAS collaboration. The new data management system, Rucio, has put in place a redesigned web-based interface based upon the lessons learnt from DQ2, and the increased volume of managed information. This interface encompasses both a monitoring and controlling component, and allows easy integration for usergenerated views. The interface follows three design principles. First, the collection and storage of data from internal and external systems is asynchronous to reduce latency. This includes the use of technologies like ActiveMQ or Nagios. Second, analysis of the data into information is done massively parallel due to its volume, using a combined approach with an Oracle database and Hadoop MapReduce. Third, sharing of the information does not distinguish between human or programmatic access, making it easy to access selective parts of the information both in constrained frontends like web-browsers as well as remote services. This contribution will detail the reasons for these principles and the design choices taken. Additionally, the implementation, the interactions with external systems, and an evaluation of the system in production, both from a technological and user perspective, conclude this contribution.

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.

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

NASA Astrophysics Data System (ADS)

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

2011-03-01

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

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

PubMed

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

2014-12-12

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

SeWeR: a customizable and integrated dynamic HTML interface to bioinformatics services.

PubMed

Basu, M K

2001-06-01

Sequence analysis using Web Resources (SeWeR) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser.

Intuitive web-based experimental design for high-throughput biomedical data.

PubMed

Friedrich, Andreas; Kenar, Erhan; Kohlbacher, Oliver; Nahnsen, Sven

2015-01-01

Big data bioinformatics aims at drawing biological conclusions from huge and complex biological datasets. Added value from the analysis of big data, however, is only possible if the data is accompanied by accurate metadata annotation. Particularly in high-throughput experiments intelligent approaches are needed to keep track of the experimental design, including the conditions that are studied as well as information that might be interesting for failure analysis or further experiments in the future. In addition to the management of this information, means for an integrated design and interfaces for structured data annotation are urgently needed by researchers. Here, we propose a factor-based experimental design approach that enables scientists to easily create large-scale experiments with the help of a web-based system. We present a novel implementation of a web-based interface allowing the collection of arbitrary metadata. To exchange and edit information we provide a spreadsheet-based, humanly readable format. Subsequently, sample sheets with identifiers and metainformation for data generation facilities can be created. Data files created after measurement of the samples can be uploaded to a datastore, where they are automatically linked to the previously created experimental design model.

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.

Relax with CouchDB - Into the non-relational DBMS era of Bioinformatics

PubMed Central

Manyam, Ganiraju; Payton, Michelle A.; Roth, Jack A.; Abruzzo, Lynne V.; Coombes, Kevin R.

2012-01-01

With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. PMID:22609849

Development of web-GIS system for analysis of georeferenced geophysical data

NASA Astrophysics Data System (ADS)

Okladnikov, I.; Gordov, E. P.; Titov, A. G.; Bogomolov, V. Y.; Genina, E.; Martynova, Y.; Shulgina, T. M.

2012-12-01

Georeferenced datasets (meteorological databases, modeling and reanalysis results, remote sensing products, etc.) are currently actively used in numerous applications including modeling, interpretation and forecast of climatic and ecosystem changes for various spatial and temporal scales. Due to inherent heterogeneity of environmental datasets as well as their huge size which might constitute up to tens terabytes for a single dataset at present studies in the area of climate and environmental change require a special software support. A dedicated web-GIS information-computational system for analysis of georeferenced climatological and meteorological data has been created. The information-computational system consists of 4 basic parts: computational kernel developed using GNU Data Language (GDL), a set of PHP-controllers run within specialized web-portal, JavaScript class libraries for development of typical components of web mapping application graphical user interface (GUI) based on AJAX technology, and an archive of geophysical datasets. Computational kernel comprises of a number of dedicated modules for querying and extraction of data, mathematical and statistical data analysis, visualization, and preparing output files in geoTIFF and netCDF format containing processing results. Specialized web-portal consists of a web-server Apache, complying OGC standards Geoserver software which is used as a base for presenting cartographical information over the Web, and a set of PHP-controllers implementing web-mapping application logic and governing computational kernel. JavaScript libraries aiming at graphical user interface development are based on GeoExt library combining ExtJS Framework and OpenLayers software. The archive of geophysical data consists of a number of structured environmental datasets represented by data files in netCDF, HDF, GRIB, ESRI Shapefile formats. For processing by the system are available: two editions of NCEP/NCAR Reanalysis, JMA/CRIEPI JRA-25 Reanalysis, ECMWF ERA-40 Reanalysis, ECMWF ERA Interim Reanalysis, MRI/JMA APHRODITE's Water Resources Project Reanalysis, DWD Global Precipitation Climatology Centre's data, GMAO Modern Era-Retrospective analysis for Research and Applications, meteorological observational data for the territory of the former USSR for the 20th century, results of modeling by global and regional climatological models, and others. The system is already involved into a scientific research process. Particularly, recently the system was successfully used for analysis of Siberia climate changes and its impact in the region. The Web-GIS information-computational system for geophysical data analysis provides specialists involved into multidisciplinary research projects with reliable and practical instruments for complex analysis of climate and ecosystems changes on global and regional scales. Using it even unskilled user without specific knowledge can perform computational processing and visualization of large meteorological, climatological and satellite monitoring datasets through unified web-interface in a common graphical web-browser. This work is partially supported by the Ministry of education and science of the Russian Federation (contract #07.514.114044), projects IV.31.1.5, IV.31.2.7, RFBR grants #10-07-00547a, #11-05-01190a, and integrated project SB RAS #131.

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

PubMed Central

Kuzniar, Arnold; Kanaar, Roland

2014-01-01

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

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

PubMed

Kuzniar, Arnold; Kanaar, Roland

2014-07-01

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

Architecture, Design, and Development of an HTML/JavaScript Web-Based Group Support System.

ERIC Educational Resources Information Center

Romano, Nicholas C., Jr.; Nunamaker, Jay F., Jr.; Briggs, Robert O.; Vogel, Douglas R.

1998-01-01

Examines the need for virtual workspaces and describes the architecture, design, and development of GroupSystems for the World Wide Web (GSWeb), an HTML/JavaScript Web-based Group Support System (GSS). GSWeb, an application interface similar to a Graphical User Interface (GUI), is currently used by teams around the world and relies on user…

phpMs: A PHP-Based Mass Spectrometry Utilities Library.

PubMed

Collins, Andrew; Jones, Andrew R

2018-03-02

The recent establishment of cloud computing, high-throughput networking, and more versatile web standards and browsers has led to a renewed interest in web-based applications. While traditionally big data has been the domain of optimized desktop and server applications, it is now possible to store vast amounts of data and perform the necessary calculations offsite in cloud storage and computing providers, with the results visualized in a high-quality cross-platform interface via a web browser. There are number of emerging platforms for cloud-based mass spectrometry data analysis; however, there is limited pre-existing code accessible to web developers, especially for those that are constrained to a shared hosting environment where Java and C applications are often forbidden from use by the hosting provider. To remedy this, we provide an open-source mass spectrometry library for one of the most commonly used web development languages, PHP. Our new library, phpMs, provides objects for storing and manipulating spectra and identification data as well as utilities for file reading, file writing, calculations, peptide fragmentation, and protein digestion as well as a software interface for controlling search engines. We provide a working demonstration of some of the capabilities at http://pgb.liv.ac.uk/phpMs .

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.

InterProSurf: a web server for predicting interacting sites on protein surfaces

PubMed Central

Negi, Surendra S.; Schein, Catherine H.; Oezguen, Numan; Power, Trevor D.; Braun, Werner

2009-01-01

Summary A new web server, InterProSurf, predicts interacting amino acid residues in proteins that are most likely to interact with other proteins, given the 3D structures of subunits of a protein complex. The prediction method is based on solvent accessible surface area of residues in the isolated subunits, a propensity scale for interface residues and a clustering algorithm to identify surface regions with residues of high interface propensities. Here we illustrate the application of InterProSurf to determine which areas of Bacillus anthracis toxins and measles virus hemagglutinin protein interact with their respective cell surface receptors. The computationally predicted regions overlap with those regions previously identified as interface regions by sequence analysis and mutagenesis experiments. PMID:17933856

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.

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

PubMed Central

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

2012-01-01

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

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

PubMed

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

2012-07-01

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

WEbcoli: an interactive and asynchronous web application for in silico design and analysis of genome-scale E.coli model.

PubMed

Jung, Tae-Sung; Yeo, Hock Chuan; Reddy, Satty G; Cho, Wan-Sup; Lee, Dong-Yup

2009-11-01

WEbcoli is a WEb application for in silico designing, analyzing and engineering Escherichia coli metabolism. It is devised and implemented using advanced web technologies, thereby leading to enhanced usability and dynamic web accessibility. As a main feature, the WEbcoli system provides a user-friendly rich web interface, allowing users to virtually design and synthesize mutant strains derived from the genome-scale wild-type E.coli model and to customize pathways of interest through a graph editor. In addition, constraints-based flux analysis can be conducted for quantifying metabolic fluxes and charactering the physiological and metabolic states under various genetic and/or environmental conditions. WEbcoli is freely accessible at http://webcoli.org. cheld@nus.edu.sg.

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.

WImpiBLAST: web interface for mpiBLAST to help biologists perform large-scale annotation using high performance computing.

PubMed

Sharma, Parichit; Mantri, Shrikant S

2014-01-01

The function of a newly sequenced gene can be discovered by determining its sequence homology with known proteins. BLAST is the most extensively used sequence analysis program for sequence similarity search in large databases of sequences. With the advent of next generation sequencing technologies it has now become possible to study genes and their expression at a genome-wide scale through RNA-seq and metagenome sequencing experiments. Functional annotation of all the genes is done by sequence similarity search against multiple protein databases. This annotation task is computationally very intensive and can take days to obtain complete results. The program mpiBLAST, an open-source parallelization of BLAST that achieves superlinear speedup, can be used to accelerate large-scale annotation by using supercomputers and high performance computing (HPC) clusters. Although many parallel bioinformatics applications using the Message Passing Interface (MPI) are available in the public domain, researchers are reluctant to use them due to lack of expertise in the Linux command line and relevant programming experience. With these limitations, it becomes difficult for biologists to use mpiBLAST for accelerating annotation. No web interface is available in the open-source domain for mpiBLAST. We have developed WImpiBLAST, a user-friendly open-source web interface for parallel BLAST searches. It is implemented in Struts 1.3 using a Java backbone and runs atop the open-source Apache Tomcat Server. WImpiBLAST supports script creation and job submission features and also provides a robust job management interface for system administrators. It combines script creation and modification features with job monitoring and management through the Torque resource manager on a Linux-based HPC cluster. Use case information highlights the acceleration of annotation analysis achieved by using WImpiBLAST. Here, we describe the WImpiBLAST web interface features and architecture, explain design decisions, describe workflows and provide a detailed analysis.

WImpiBLAST: Web Interface for mpiBLAST to Help Biologists Perform Large-Scale Annotation Using High Performance Computing

PubMed Central

Sharma, Parichit; Mantri, Shrikant S.

2014-01-01

The function of a newly sequenced gene can be discovered by determining its sequence homology with known proteins. BLAST is the most extensively used sequence analysis program for sequence similarity search in large databases of sequences. With the advent of next generation sequencing technologies it has now become possible to study genes and their expression at a genome-wide scale through RNA-seq and metagenome sequencing experiments. Functional annotation of all the genes is done by sequence similarity search against multiple protein databases. This annotation task is computationally very intensive and can take days to obtain complete results. The program mpiBLAST, an open-source parallelization of BLAST that achieves superlinear speedup, can be used to accelerate large-scale annotation by using supercomputers and high performance computing (HPC) clusters. Although many parallel bioinformatics applications using the Message Passing Interface (MPI) are available in the public domain, researchers are reluctant to use them due to lack of expertise in the Linux command line and relevant programming experience. With these limitations, it becomes difficult for biologists to use mpiBLAST for accelerating annotation. No web interface is available in the open-source domain for mpiBLAST. We have developed WImpiBLAST, a user-friendly open-source web interface for parallel BLAST searches. It is implemented in Struts 1.3 using a Java backbone and runs atop the open-source Apache Tomcat Server. WImpiBLAST supports script creation and job submission features and also provides a robust job management interface for system administrators. It combines script creation and modification features with job monitoring and management through the Torque resource manager on a Linux-based HPC cluster. Use case information highlights the acceleration of annotation analysis achieved by using WImpiBLAST. Here, we describe the WImpiBLAST web interface features and architecture, explain design decisions, describe workflows and provide a detailed analysis. PMID:24979410

Broadband network on-line data acquisition system with web based interface for control and basic analysis

NASA Astrophysics Data System (ADS)

Polkowski, Marcin; Grad, Marek

2016-04-01

Passive seismic experiment "13BB Star" is operated since mid 2013 in northern Poland and consists of 13 broadband seismic stations. One of the elements of this experiment is dedicated on-line data acquisition system comprised of both client (station) side and server side modules with web based interface that allows monitoring of network status and provides tools for preliminary data analysis. Station side is controlled by ARM Linux board that is programmed to maintain 3G/EDGE internet connection, receive data from digitizer, send data do central server among with additional auxiliary parameters like temperatures, voltages and electric current measurements. Station side is controlled by set of easy to install PHP scripts. Data is transmitted securely over SSH protocol to central server. Central server is a dedicated Linux based machine. Its duty is receiving and processing all data from all stations including auxiliary parameters. Server side software is written in PHP and Python. Additionally, it allows remote station configuration and provides web based interface for user friendly interaction. All collected data can be displayed for each day and station. It also allows manual creation of event oriented plots with different filtering abilities and provides numerous status and statistic information. Our solution is very flexible and easy to modify. In this presentation we would like to share our solution and experience. National Science Centre Poland provided financial support for this work via NCN grant DEC-2011/02/A/ST10/00284.

Web OPAC Interfaces: An Overview.

ERIC Educational Resources Information Center

Babu, B. Ramesh; O'Brien, Ann

2000-01-01

Discussion of Web-based online public access catalogs (OPACs) focuses on a review of six Web OPAC interfaces in use in academic libraries in the United Kingdom. Presents a checklist and guidelines of important features and functions that are currently available, including search strategies, access points, display, links, and layout. (Author/LRW)

Implementation of an Embedded Web Server Application for Wireless Control of Brain Computer Interface Based Home Environments.

PubMed

Aydın, Eda Akman; Bay, Ömer Faruk; Güler, İnan

2016-01-01

Brain Computer Interface (BCI) based environment control systems could facilitate life of people with neuromuscular diseases, reduces dependence on their caregivers, and improves their quality of life. As well as easy usage, low-cost, and robust system performance, mobility is an important functionality expected from a practical BCI system in real life. In this study, in order to enhance users' mobility, we propose internet based wireless communication between BCI system and home environment. We designed and implemented a prototype of an embedded low-cost, low power, easy to use web server which is employed in internet based wireless control of a BCI based home environment. The embedded web server provides remote access to the environmental control module through BCI and web interfaces. While the proposed system offers to BCI users enhanced mobility, it also provides remote control of the home environment by caregivers as well as the individuals in initial stages of neuromuscular disease. The input of BCI system is P300 potentials. We used Region Based Paradigm (RBP) as stimulus interface. Performance of the BCI system is evaluated on data recorded from 8 non-disabled subjects. The experimental results indicate that the proposed web server enables internet based wireless control of electrical home appliances successfully through BCIs.

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.

CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis.

PubMed

Li, Pei; Ji, Guoli; Dong, Min; Schmidt, Emily; Lenox, Douglas; Chen, Liangliang; Liu, Qi; Liu, Lin; Zhang, Jie; Liang, Chun

2012-09-15

To address the impending need for exploring rapidly increased transcriptomics data generated for non-model organisms, we developed CBrowse, an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs. Designed in a standard three-tier architecture with a data pre-processing pipeline, CBrowse is essentially a Rich Internet Application that offers many seamlessly integrated web interfaces and allows users to navigate, sort, filter, search and visualize data smoothly. The pre-processing pipeline takes the contig sequence file in FASTA format and its relevant SAM/BAM file as the input; detects putative polymorphisms, simple sequence repeats and sequencing errors in contigs and generates image, JSON and database-compatible CSV text files that are directly utilized by different web interfaces. CBowse is a generic visualization and analysis tool that facilitates close examination of assembly quality, genetic polymorphisms, sequence repeats and/or sequencing errors in transcriptome sequencing projects. CBrowse is distributed under the GNU General Public License, available at http://bioinfolab.muohio.edu/CBrowse/ liangc@muohio.edu or liangc.mu@gmail.com; glji@xmu.edu.cn Supplementary data are available at Bioinformatics online.

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

PubMed

Gordon, Paul M K; Sensen, Christoph W

2007-06-18

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

Seahawk: moving beyond HTML in Web-based bioinformatics analysis

PubMed Central

Gordon, Paul MK; Sensen, Christoph W

2007-01-01

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

Software Framework for Development of Web-GIS Systems for Analysis of Georeferenced Geophysical Data

NASA Astrophysics Data System (ADS)

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

2011-12-01

Georeferenced datasets (meteorological databases, modeling and reanalysis results, remote sensing products, etc.) are currently actively used in numerous applications including modeling, interpretation and forecast of climatic and ecosystem changes for various spatial and temporal scales. Due to inherent heterogeneity of environmental datasets as well as their size which might constitute up to tens terabytes for a single dataset at present studies in the area of climate and environmental change require a special software support. A dedicated software framework for rapid development of providing such support information-computational systems based on Web-GIS technologies has been created. The software framework consists of 3 basic parts: computational kernel developed using ITTVIS Interactive Data Language (IDL), a set of PHP-controllers run within specialized web portal, and JavaScript class library for development of typical components of web mapping application graphical user interface (GUI) based on AJAX technology. Computational kernel comprise of number of modules for datasets access, mathematical and statistical data analysis and visualization of results. Specialized web-portal consists of web-server Apache, complying OGC standards Geoserver software which is used as a base for presenting cartographical information over the Web, and a set of PHP-controllers implementing web-mapping application logic and governing computational kernel. JavaScript library aiming at graphical user interface development is based on GeoExt library combining ExtJS Framework and OpenLayers software. Based on the software framework an information-computational system for complex analysis of large georeferenced data archives was developed. Structured environmental datasets available for processing now include two editions of NCEP/NCAR Reanalysis, JMA/CRIEPI JRA-25 Reanalysis, ECMWF ERA-40 Reanalysis, ECMWF ERA Interim Reanalysis, MRI/JMA APHRODITE's Water Resources Project Reanalysis, meteorological observational data for the territory of the former USSR for the 20th century, and others. Current version of the system is already involved into a scientific research process. Particularly, recently the system was successfully used for analysis of Siberia climate changes and its impact in the region. The software framework presented allows rapid development of Web-GIS systems for geophysical data analysis thus providing specialists involved into multidisciplinary research projects with reliable and practical instruments for complex analysis of climate and ecosystems changes on global and regional scales. This work is partially supported by RFBR grants #10-07-00547, #11-05-01190, and SB RAS projects 4.31.1.5, 4.31.2.7, 4, 8, 9, 50 and 66.

Web-Based Interface for Command and Control of Network Sensors

NASA Technical Reports Server (NTRS)

Wallick, Michael N.; Doubleday, Joshua R.; Shams, Khawaja S.

2010-01-01

This software allows for the visualization and control of a network of sensors through a Web browser interface. It is currently being deployed for a network of sensors monitoring Mt. Saint Helen s volcano; however, this innovation is generic enough that it can be deployed for any type of sensor Web. From this interface, the user is able to fully control and monitor the sensor Web. This includes, but is not limited to, sending "test" commands to individual sensors in the network, monitoring for real-world events, and reacting to those events

web cellHTS2: a web-application for the analysis of high-throughput screening data.

PubMed

Pelz, Oliver; Gilsdorf, Moritz; Boutros, Michael

2010-04-12

The analysis of high-throughput screening data sets is an expanding field in bioinformatics. High-throughput screens by RNAi generate large primary data sets which need to be analyzed and annotated to identify relevant phenotypic hits. Large-scale RNAi screens are frequently used to identify novel factors that influence a broad range of cellular processes, including signaling pathway activity, cell proliferation, and host cell infection. Here, we present a web-based application utility for the end-to-end analysis of large cell-based screening experiments by cellHTS2. The software guides the user through the configuration steps that are required for the analysis of single or multi-channel experiments. The web-application provides options for various standardization and normalization methods, annotation of data sets and a comprehensive HTML report of the screening data analysis, including a ranked hit list. Sessions can be saved and restored for later re-analysis. The web frontend for the cellHTS2 R/Bioconductor package interacts with it through an R-server implementation that enables highly parallel analysis of screening data sets. web cellHTS2 further provides a file import and configuration module for common file formats. The implemented web-application facilitates the analysis of high-throughput data sets and provides a user-friendly interface. web cellHTS2 is accessible online at http://web-cellHTS2.dkfz.de. A standalone version as a virtual appliance and source code for platforms supporting Java 1.5.0 can be downloaded from the web cellHTS2 page. web cellHTS2 is freely distributed under GPL.

Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial

PubMed Central

Miller, Benjamin T.; Singh, Rishi P.; Schalk, Vinushka; Pevzner, Yuri; Sun, Jingjun; Miller, Carrie S.; Boresch, Stefan; Ichiye, Toshiko; Brooks, Bernard R.; Woodcock, H. Lee

2014-01-01

This article describes the development, implementation, and use of web-based “lessons” to introduce students and other newcomers to computer simulations of biological macromolecules. These lessons, i.e., interactive step-by-step instructions for performing common molecular simulation tasks, are integrated into the collaboratively developed CHARMM INterface and Graphics (CHARMMing) web user interface (http://www.charmming.org). Several lessons have already been developed with new ones easily added via a provided Python script. In addition to CHARMMing's new lessons functionality, web-based graphical capabilities have been overhauled and are fully compatible with modern mobile web browsers (e.g., phones and tablets), allowing easy integration of these advanced simulation techniques into coursework. Finally, one of the primary objections to web-based systems like CHARMMing has been that “point and click” simulation set-up does little to teach the user about the underlying physics, biology, and computational methods being applied. In response to this criticism, we have developed a freely available tutorial to bridge the gap between graphical simulation setup and the technical knowledge necessary to perform simulations without user interface assistance. PMID:25057988

Web-based computational chemistry education with CHARMMing I: Lessons and tutorial.

PubMed

Miller, Benjamin T; Singh, Rishi P; Schalk, Vinushka; Pevzner, Yuri; Sun, Jingjun; Miller, Carrie S; Boresch, Stefan; Ichiye, Toshiko; Brooks, Bernard R; Woodcock, H Lee

2014-07-01

This article describes the development, implementation, and use of web-based "lessons" to introduce students and other newcomers to computer simulations of biological macromolecules. These lessons, i.e., interactive step-by-step instructions for performing common molecular simulation tasks, are integrated into the collaboratively developed CHARMM INterface and Graphics (CHARMMing) web user interface (http://www.charmming.org). Several lessons have already been developed with new ones easily added via a provided Python script. In addition to CHARMMing's new lessons functionality, web-based graphical capabilities have been overhauled and are fully compatible with modern mobile web browsers (e.g., phones and tablets), allowing easy integration of these advanced simulation techniques into coursework. Finally, one of the primary objections to web-based systems like CHARMMing has been that "point and click" simulation set-up does little to teach the user about the underlying physics, biology, and computational methods being applied. In response to this criticism, we have developed a freely available tutorial to bridge the gap between graphical simulation setup and the technical knowledge necessary to perform simulations without user interface assistance.

deFUME: Dynamic exploration of functional metagenomic sequencing data.

PubMed

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

2015-07-31

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

The Effects of Metaphorical Interface on Germane Cognitive Load in Web-Based Instruction

ERIC Educational Resources Information Center

Cheon, Jongpil; Grant, Michael M.

2012-01-01

The purpose of this study was to examine the effects of a metaphorical interface on germane cognitive load in Web-based instruction. Based on cognitive load theory, germane cognitive load is a cognitive investment for schema construction and automation. A new instrument developed in a previous study was used to measure students' mental activities…

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 CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes.

PubMed

Olechnovič, Kliment; Venclovas, Ceslovas

2014-07-01

The Contact Area Difference score (CAD-score) web server provides a universal framework to compute and analyze discrepancies between different 3D structures of the same biological macromolecule or complex. The server accepts both single-subunit and multi-subunit structures and can handle all the major types of macromolecules (proteins, RNA, DNA and their complexes). It can perform numerical comparison of both structures and interfaces. In addition to entire structures and interfaces, the server can assess user-defined subsets. The CAD-score server performs both global and local numerical evaluations of structural differences between structures or interfaces. The results can be explored interactively using sortable tables of global scores, profiles of local errors, superimposed contact maps and 3D structure visualization. The web server could be used for tasks such as comparison of models with the native (reference) structure, comparison of X-ray structures of the same macromolecule obtained in different states (e.g. with and without a bound ligand), analysis of nuclear magnetic resonance (NMR) structural ensemble or structures obtained in the course of molecular dynamics simulation. The web server is freely accessible at: http://www.ibt.lt/bioinformatics/cad-score. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Migration of the ATLAS Metadata Interface (AMI) to Web 2.0 and cloud

NASA Astrophysics Data System (ADS)

Odier, J.; Albrand, S.; Fulachier, J.; Lambert, F.

2015-12-01

The ATLAS Metadata Interface (AMI), a mature application of more than 10 years of existence, is currently under adaptation to some recently available technologies. The web interfaces, which previously manipulated XML documents using XSL transformations, are being migrated to Asynchronous JavaScript (AJAX). Web development is considerably simplified by the introduction of a framework based on JQuery and Twitter Bootstrap. Finally, the AMI services are being migrated to an OpenStack cloud infrastructure.

A database for the monitoring of thermal anomalies over the Amazon forest and adjacent intertropical oceans

PubMed Central

Jiménez-Muñoz, Juan C.; Mattar, Cristian; Sobrino, José A.; Malhi, Yadvinder

2015-01-01

Advances in information technologies and accessibility to climate and satellite data in recent years have favored the development of web-based tools with user-friendly interfaces in order to facilitate the dissemination of geo/biophysical products. These products are useful for the analysis of the impact of global warming over different biomes. In particular, the study of the Amazon forest responses to drought have recently received attention by the scientific community due to the occurrence of two extreme droughts and sustained warming over the last decade. Thermal Amazoni@ is a web-based platform for the visualization and download of surface thermal anomalies products over the Amazon forest and adjacent intertropical oceans using Google Earth as a baseline graphical interface (http://ipl.uv.es/thamazon/web). This platform is currently operational at the servers of the University of Valencia (Spain), and it includes both satellite (MODIS) and climatic (ERA-Interim) datasets. Thermal Amazoni@ is composed of the viewer system and the web and ftp sites with ancillary information and access to product download. PMID:26029379

Relax with CouchDB--into the non-relational DBMS era of bioinformatics.

PubMed

Manyam, Ganiraju; Payton, Michelle A; Roth, Jack A; Abruzzo, Lynne V; Coombes, Kevin R

2012-07-01

With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. Copyright © 2012 Elsevier Inc. All rights reserved.

A database for the monitoring of thermal anomalies over the Amazon forest and adjacent intertropical oceans.

PubMed

Jiménez-Muñoz, Juan C; Mattar, Cristian; Sobrino, José A; Malhi, Yadvinder

2015-01-01

Advances in information technologies and accessibility to climate and satellite data in recent years have favored the development of web-based tools with user-friendly interfaces in order to facilitate the dissemination of geo/biophysical products. These products are useful for the analysis of the impact of global warming over different biomes. In particular, the study of the Amazon forest responses to drought have recently received attention by the scientific community due to the occurrence of two extreme droughts and sustained warming over the last decade. Thermal Amazoni@ is a web-based platform for the visualization and download of surface thermal anomalies products over the Amazon forest and adjacent intertropical oceans using Google Earth as a baseline graphical interface (http://ipl.uv.es/thamazon/web). This platform is currently operational at the servers of the University of Valencia (Spain), and it includes both satellite (MODIS) and climatic (ERA-Interim) datasets. Thermal Amazoni@ is composed of the viewer system and the web and ftp sites with ancillary information and access to product download.

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

76 FR 10628 - Self-Regulatory Organizations; the Depository Trust Company; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-25

... Change Regarding Providing Participants With a New Optional Settlement Web Interface February 22, 2011... Rule Change The proposed rule change will establish a new browser-based interface, the ``Settlement Web... Browser System (``PBS'').\\4\\ Based on request from its Participants, DTC has created a more user-friendly...

Web-Based Interactive Electronic Technical Manual (IETM) Common User Interface Style Guide, Version 2.0

DTIC Science & Technology

2003-07-01

Technical Report WEB-BASED INTERACTIVE ELECTRONIC TECHNICAL MANUAL (IETM) COMMON USER INTERFACE STYLE GUIDE Version 2.0 – July 2003 by L. John Junod ...ACKNOWLEDGEMENTS The principal authors of this document were: John Junod – NSWC, Carderock Division, Phil Deuell – AMSEC LLC, Kathleen Moore

Construction of a Linux based chemical and biological information system.

PubMed

Molnár, László; Vágó, István; Fehér, András

2003-01-01

A chemical and biological information system with a Web-based easy-to-use interface and corresponding databases has been developed. The constructed system incorporates all chemical, numerical and textual data related to the chemical compounds, including numerical biological screen results. Users can search the database by traditional textual/numerical and/or substructure or similarity queries through the web interface. To build our chemical database management system, we utilized existing IT components such as ORACLE or Tripos SYBYL for database management and Zope application server for the web interface. We chose Linux as the main platform, however, almost every component can be used under various operating systems.

[A web-based biomedical image mosaicing system].

PubMed

Zhang, Meng; Yan, Zhuang-zhi; Pan, Zhi-jun; Shao, Shi-jie

2006-11-01

This paper describes a web service for biomedical image mosaicing. A web site based on CGI (Common Gateway Interface) is implemented. The system is based on Browser/Server model and is tested in www. Finally implementation examples and experiment results are provided.

Analysis and Development of a Web-Enabled Planning and Scheduling Database Application

DTIC Science & Technology

2013-09-01

establishes an entity—relationship diagram for the desired process, constructs an operable database using MySQL , and provides a web- enabled interface for...development, develop, design, process, re- engineering, reengineering, MySQL , structured query language, SQL, myPHPadmin. 15. NUMBER OF PAGES 107 16...relationship diagram for the desired process, constructs an operable database using MySQL , and provides a web-enabled interface for the population of

Web-based access to near real-time and archived high-density time-series data: cyber infrastructure challenges & developments in the open-source Waveform Server

NASA Astrophysics Data System (ADS)

Reyes, J. C.; Vernon, F. L.; Newman, R. L.; Steidl, J. H.

2010-12-01

The Waveform Server is an interactive web-based interface to multi-station, multi-sensor and multi-channel high-density time-series data stored in Center for Seismic Studies (CSS) 3.0 schema relational databases (Newman et al., 2009). In the last twelve months, based on expanded specifications and current user feedback, both the server-side infrastructure and client-side interface have been extensively rewritten. The Python Twisted server-side code-base has been fundamentally modified to now present waveform data stored in cluster-based databases using a multi-threaded architecture, in addition to supporting the pre-existing single database model. This allows interactive web-based access to high-density (broadband @ 40Hz to strong motion @ 200Hz) waveform data that can span multiple years; the common lifetime of broadband seismic networks. The client-side interface expands on it's use of simple JSON-based AJAX queries to now incorporate a variety of User Interface (UI) improvements including standardized calendars for defining time ranges, applying on-the-fly data calibration to display SI-unit data, and increased rendering speed. This presentation will outline the various cyber infrastructure challenges we have faced while developing this application, the use-cases currently in existence, and the limitations of web-based application development.

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

NASA Astrophysics Data System (ADS)

Stoltz, Peter; Veitzer, Seth

2008-04-01

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

Service-oriented model-encapsulation strategy for sharing and integrating heterogeneous geo-analysis models in an open web environment

NASA Astrophysics Data System (ADS)

Yue, Songshan; Chen, Min; Wen, Yongning; Lu, Guonian

2016-04-01

Earth environment is extremely complicated and constantly changing; thus, it is widely accepted that the use of a single geo-analysis model cannot accurately represent all details when solving complex geo-problems. Over several years of research, numerous geo-analysis models have been developed. However, a collaborative barrier between model providers and model users still exists. The development of cloud computing has provided a new and promising approach for sharing and integrating geo-analysis models across an open web environment. To share and integrate these heterogeneous models, encapsulation studies should be conducted that are aimed at shielding original execution differences to create services which can be reused in the web environment. Although some model service standards (such as Web Processing Service (WPS) and Geo Processing Workflow (GPW)) have been designed and developed to help researchers construct model services, various problems regarding model encapsulation remain. (1) The descriptions of geo-analysis models are complicated and typically require rich-text descriptions and case-study illustrations, which are difficult to fully represent within a single web request (such as the GetCapabilities and DescribeProcess operations in the WPS standard). (2) Although Web Service technologies can be used to publish model services, model users who want to use a geo-analysis model and copy the model service into another computer still encounter problems (e.g., they cannot access the model deployment dependencies information). This study presents a strategy for encapsulating geo-analysis models to reduce problems encountered when sharing models between model providers and model users and supports the tasks with different web service standards (e.g., the WPS standard). A description method for heterogeneous geo-analysis models is studied. Based on the model description information, the methods for encapsulating the model-execution program to model services and for describing model-service deployment information are also included in the proposed strategy. Hence, the model-description interface, model-execution interface and model-deployment interface are studied to help model providers and model users more easily share, reuse and integrate geo-analysis models in an open web environment. Finally, a prototype system is established, and the WPS standard is employed as an example to verify the capability and practicability of the model-encapsulation strategy. The results show that it is more convenient for modellers to share and integrate heterogeneous geo-analysis models in cloud computing platforms.

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.

User Interface Composition with COTS-UI and Trading Approaches: Application for Web-Based Environmental Information Systems

NASA Astrophysics Data System (ADS)

Criado, Javier; Padilla, Nicolás; Iribarne, Luis; Asensio, Jose-Andrés

Due to the globalization of the information and knowledge society on the Internet, modern Web-based Information Systems (WIS) must be flexible and prepared to be easily accessible and manageable in real-time. In recent times it has received a special interest the globalization of information through a common vocabulary (i.e., ontologies), and the standardized way in which information is retrieved on the Web (i.e., powerful search engines, and intelligent software agents). These same principles of globalization and standardization should also be valid for the user interfaces of the WIS, but they are built on traditional development paradigms. In this paper we present an approach to reduce the gap of globalization/standardization in the generation of WIS user interfaces by using a real-time "bottom-up" composition perspective with COTS-interface components (type interface widgets) and trading services.

UIVerify: A Web-Based Tool for Verification and Automatic Generation of User Interfaces

NASA Technical Reports Server (NTRS)

Shiffman, Smadar; Degani, Asaf; Heymann, Michael

2004-01-01

In this poster, we describe a web-based tool for verification and automatic generation of user interfaces. The verification component of the tool accepts as input a model of a machine and a model of its interface, and checks that the interface is adequate (correct). The generation component of the tool accepts a model of a given machine and the user's task, and then generates a correct and succinct interface. This write-up will demonstrate the usefulness of the tool by verifying the correctness of a user interface to a flight-control system. The poster will include two more examples of using the tool: verification of the interface to an espresso machine, and automatic generation of a succinct interface to a large hypothetical machine.

Development of Web Interfaces for Analysis Codes

NASA Astrophysics Data System (ADS)

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

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

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

PubMed Central

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

2014-01-01

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

First Prototype of a Web Map Interface for ESA's Planetary Science Archive (PSA)

NASA Astrophysics Data System (ADS)

Manaud, N.; Gonzalez, J.

2014-04-01

We present a first prototype of a Web Map Interface that will serve as a proof of concept and design for ESA's future fully web-based Planetary Science Archive (PSA) User Interface. The PSA is ESA's planetary science archiving authority and central repository for all scientific and engineering data returned by ESA's Solar System missions [1]. All data are compliant with NASA's Planetary Data System (PDS) Standards and are accessible through several interfaces [2]: in addition to serving all public data via FTP and the Planetary Data Access Protocol (PDAP), a Java-based User Interface provides advanced search, preview, download, notification and delivery-basket functionality. It allows the user to query and visualise instrument observations footprints using a map-based interface (currently only available for Mars Express HRSC and OMEGA instruments). During the last decade, the planetary mapping science community has increasingly been adopting Geographic Information System (GIS) tools and standards, originally developed for and used in Earth science. There is an ongoing effort to produce and share cartographic products through Open Geospatial Consortium (OGC) Web Services, or as standalone data sets, so that they can be readily used in existing GIS applications [3,4,5]. Previous studies conducted at ESAC [6,7] have helped identify the needs of Planetary GIS users, and define key areas of improvement for the future Web PSA User Interface. Its web map interface shall will provide access to the full geospatial content of the PSA, including (1) observation geometry footprints of all remote sensing instruments, and (2) all georeferenced cartographic products, such as HRSC map-projected data or OMEGA global maps from Mars Express. It shall aim to provide a rich user experience for search and visualisation of this content using modern and interactive web mapping technology. A comprehensive set of built-in context maps from external sources, such as MOLA topography, TES infrared maps or planetary surface nomenclature, provided in both simple cylindrical and polar stereographic projections, shall enhance this user experience. In addition, users should be able to import and export data in commonly used open- GIS formats. It is also intended to serve all PSA geospatial data through OGC-compliant Web Services so that they can be captured, visualised and analysed directly from GIS software, along with data from other sources. The following figure illustrates how the PSA web map interface and services shall fit in a typical Planetary GIS user working environment.

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.

Web-4D-QSAR: A web-based application to generate 4D-QSAR descriptors.

PubMed

Ataide Martins, João Paulo; Rougeth de Oliveira, Marco Antônio; Oliveira de Queiroz, Mário Sérgio

2018-06-05

A web-based application is developed to generate 4D-QSAR descriptors using the LQTA-QSAR methodology, based on molecular dynamics (MD) trajectories and topology information retrieved from the GROMACS package. The LQTAGrid module calculates the intermolecular interaction energies at each grid point, considering probes and all aligned conformations resulting from MD simulations. These interaction energies are the independent variables or descriptors employed in a QSAR analysis. A friendly front end web interface, built using the Django framework and Python programming language, integrates all steps of the LQTA-QSAR methodology in a way that is transparent to the user, and in the backend, GROMACS and LQTAGrid are executed to generate 4D-QSAR descriptors to be used later in the process of QSAR model building. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

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…

The Research on Automatic Construction of Domain Model Based on Deep Web Query Interfaces

NASA Astrophysics Data System (ADS)

JianPing, Gu

The integration of services is transparent, meaning that users no longer face the millions of Web services, do not care about the required data stored, but do not need to learn how to obtain these data. In this paper, we analyze the uncertainty of schema matching, and then propose a series of similarity measures. To reduce the cost of execution, we propose the type-based optimization method and schema matching pruning method of numeric data. Based on above analysis, we propose the uncertain schema matching method. The experiments prove the effectiveness and efficiency of our method.

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.

KFC Server: interactive forecasting of protein interaction hot spots.

PubMed

Darnell, Steven J; LeGault, Laura; Mitchell, Julie C

2008-07-01

The KFC Server is a web-based implementation of the KFC (Knowledge-based FADE and Contacts) model-a machine learning approach for the prediction of binding hot spots, or the subset of residues that account for most of a protein interface's; binding free energy. The server facilitates the automated analysis of a user submitted protein-protein or protein-DNA interface and the visualization of its hot spot predictions. For each residue in the interface, the KFC Server characterizes its local structural environment, compares that environment to the environments of experimentally determined hot spots and predicts if the interface residue is a hot spot. After the computational analysis, the user can visualize the results using an interactive job viewer able to quickly highlight predicted hot spots and surrounding structural features within the protein structure. The KFC Server is accessible at http://kfc.mitchell-lab.org.

KFC Server: interactive forecasting of protein interaction hot spots

PubMed Central

Darnell, Steven J.; LeGault, Laura; Mitchell, Julie C.

2008-01-01

The KFC Server is a web-based implementation of the KFC (Knowledge-based FADE and Contacts) model—a machine learning approach for the prediction of binding hot spots, or the subset of residues that account for most of a protein interface's; binding free energy. The server facilitates the automated analysis of a user submitted protein–protein or protein–DNA interface and the visualization of its hot spot predictions. For each residue in the interface, the KFC Server characterizes its local structural environment, compares that environment to the environments of experimentally determined hot spots and predicts if the interface residue is a hot spot. After the computational analysis, the user can visualize the results using an interactive job viewer able to quickly highlight predicted hot spots and surrounding structural features within the protein structure. The KFC Server is accessible at http://kfc.mitchell-lab.org. PMID:18539611

A Web-based Data Intensive Visualization of Real-time River Drainage Network Response to Rainfall

NASA Astrophysics Data System (ADS)

Demir, I.; Krajewski, W. F.

2012-04-01

The Iowa Flood Information System (IFIS) is a web-based platform developed by the Iowa Flood Center (IFC) to provide access to and visualization of flood inundation maps, real-time flood conditions, flood forecasts both short-term and seasonal, and other flood-related data for communities in Iowa. The key element of the system's architecture is the notion of community. Locations of the communities, those near streams and rivers, define basin boundaries. The IFIS streams rainfall data from NEXRAD radar, and provides three interfaces including animation for rainfall intensity, daily rainfall totals and rainfall accumulations for past 14 days for Iowa. A real-time interactive visualization interface is developed using past rainfall intensity data. The interface creates community-based rainfall products on-demand using watershed boundaries of each community as a mask. Each individual rainfall pixel is tracked in the interface along the drainage network, and the ones drains to same pixel location are accumulated. The interface loads recent rainfall data in five minute intervals that are combined with current values. Latest web technologies are utilized for the development of the interface including HTML 5 Canvas, and JavaScript. The performance of the interface is optimized to run smoothly on modern web browsers. The interface controls allow users to change internal parameters of the system, and operation conditions of the animation. The interface will help communities understand the effects of rainfall on water transport in stream and river networks and make better-informed decisions regarding the threat of floods. This presentation provides an overview of a unique visualization interface and discusses future plans for real-time dynamic presentations of streamflow forecasting.

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.

Automatic geospatial information Web service composition based on ontology interface matching

NASA Astrophysics Data System (ADS)

Xu, Xianbin; Wu, Qunyong; Wang, Qinmin

2008-10-01

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

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.

Secure web book to store structural genomics research data.

PubMed

Manjasetty, Babu A; Höppner, Klaus; Mueller, Uwe; Heinemann, Udo

2003-01-01

Recently established collaborative structural genomics programs aim at significantly accelerating the crystal structure analysis of proteins. These large-scale projects require efficient data management systems to ensure seamless collaboration between different groups of scientists working towards the same goal. Within the Berlin-based Protein Structure Factory, the synchrotron X-ray data collection and the subsequent crystal structure analysis tasks are located at BESSY, a third-generation synchrotron source. To organize file-based communication and data transfer at the BESSY site of the Protein Structure Factory, we have developed the web-based BCLIMS, the BESSY Crystallography Laboratory Information Management System. BCLIMS is a relational data management system which is powered by MySQL as the database engine and Apache HTTP as the web server. The database interface routines are written in Python programing language. The software is freely available to academic users. Here we describe the storage, retrieval and manipulation of laboratory information, mainly pertaining to the synchrotron X-ray diffraction experiments and the subsequent protein structure analysis, using BCLIMS.

A RESTful interface to pseudonymization services in modern web applications.

PubMed

Lablans, Martin; Borg, Andreas; Ückert, Frank

2015-02-07

Medical research networks rely on record linkage and pseudonymization to determine which records from different sources relate to the same patient. To establish informational separation of powers, the required identifying data are redirected to a trusted third party that has, in turn, no access to medical data. This pseudonymization service receives identifying data, compares them with a list of already reported patient records and replies with a (new or existing) pseudonym. We found existing solutions to be technically outdated, complex to implement or not suitable for internet-based research infrastructures. In this article, we propose a new RESTful pseudonymization interface tailored for use in web applications accessed by modern web browsers. The interface is modelled as a resource-oriented architecture, which is based on the representational state transfer (REST) architectural style. We translated typical use-cases into resources to be manipulated with well-known HTTP verbs. Patients can be re-identified in real-time by authorized users' web browsers using temporary identifiers. We encourage the use of PID strings for pseudonyms and the EpiLink algorithm for record linkage. As a proof of concept, we developed a Java Servlet as reference implementation. The following resources have been identified: Sessions allow data associated with a client to be stored beyond a single request while still maintaining statelessness. Tokens authorize for a specified action and thus allow the delegation of authentication. Patients are identified by one or more pseudonyms and carry identifying fields. Relying on HTTP calls alone, the interface is firewall-friendly. The reference implementation has proven to be production stable. The RESTful pseudonymization interface fits the requirements of web-based scenarios and allows building applications that make pseudonymization transparent to the user using ordinary web technology. The open-source reference implementation implements the web interface as well as a scientifically grounded algorithm to generate non-speaking pseudonyms.

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.

A demanding web-based PACS supported by web services technology

NASA Astrophysics Data System (ADS)

Costa, Carlos M. A.; Silva, Augusto; Oliveira, José L.; Ribeiro, Vasco G.; Ribeiro, José

2006-03-01

During the last years, the ubiquity of web interfaces have pushed practically all PACS suppliers to develop client applications in which clinical practitioners can receive and analyze medical images, using conventional personal computers and Web browsers. However, due to security and performance issues, the utilization of these software packages has been restricted to Intranets. Paradigmatically, one of the most important advantages of digital image systems is to simplify the widespread sharing and remote access of medical data between healthcare institutions. This paper analyses the traditional PACS drawbacks that contribute to their reduced usage in the Internet and describes a PACS based on Web Services technology that supports a customized DICOM encoding syntax and a specific compression scheme providing all historical patient data in a unique Web interface.

Designing Web-Based Educative Curriculum Materials for the Social Studies

ERIC Educational Resources Information Center

Callahan, Cory; Saye, John; Brush, Thomas

2013-01-01

This paper reports on a design experiment of web-based curriculum materials explicitly created to help social studies teachers develop their professional teaching knowledge. Web-based social studies curriculum reform efforts, human-centered interface design, and investigations into educative curriculum materials are reviewed, as well as…

A web based Radiation Oncology Dose Manager with a rich User Interface developed using AJAX, ruby, dynamic XHTML and the new Yahoo/EXT User Interface Library.

PubMed

Vali, Faisal; Hong, Robert

2007-10-11

With the evolution of AJAX, ruby on rails, advanced dynamic XHTML technologies and the advent of powerful user interface libraries for javascript (EXT, Yahoo User Interface Library), developers now have the ability to provide truly rich interfaces within web browsers, with reasonable effort and without third-party plugins. We designed and developed an example of such a solution. The User Interface allows radiation oncology practices to intuitively manage different dose fractionation schemes by helping estimate total dose to irradiated organs.

XML-Based Visual Specification of Multidisciplinary Applications

NASA Technical Reports Server (NTRS)

Al-Theneyan, Ahmed; Jakatdar, Amol; Mehrotra, Piyush; Zubair, Mohammad

2001-01-01

The advancements in the Internet and Web technologies have fueled a growing interest in developing a web-based distributed computing environment. We have designed and developed Arcade, a web-based environment for designing, executing, monitoring, and controlling distributed heterogeneous applications, which is easy to use and access, portable, and provides support through all phases of the application development and execution. A major focus of the environment is the specification of heterogeneous, multidisciplinary applications. In this paper we focus on the visual and script-based specification interface of Arcade. The web/browser-based visual interface is designed to be intuitive to use and can also be used for visual monitoring during execution. The script specification is based on XML to: (1) make it portable across different frameworks, and (2) make the development of our tools easier by using the existing freely available XML parsers and editors. There is a one-to-one correspondence between the visual and script-based interfaces allowing users to go back and forth between the two. To support this we have developed translators that translate a script-based specification to a visual-based specification, and vice-versa. These translators are integrated with our tools and are transparent to users.

A highly scalable information system as extendable framework solution for medical R&D projects.

PubMed

Holzmüller-Laue, Silke; Göde, Bernd; Stoll, Regina; Thurow, Kerstin

2009-01-01

For research projects in preventive medicine a flexible information management is needed that offers a free planning and documentation of project specific examinations. The system should allow a simple, preferably automated data acquisition from several distributed sources (e.g., mobile sensors, stationary diagnostic systems, questionnaires, manual inputs) as well as an effective data management, data use and analysis. An information system fulfilling these requirements has been developed at the Center for Life Science Automation (celisca). This system combines data of multiple investigations and multiple devices and displays them on a single screen. The integration of mobile sensor systems for comfortable, location-independent capture of time-based physiological parameter and the possibility of observation of these measurements directly by this system allow new scenarios. The web-based information system presented in this paper is configurable by user interfaces. It covers medical process descriptions, operative process data visualizations, a user-friendly process data processing, modern online interfaces (data bases, web services, XML) as well as a comfortable support of extended data analysis with third-party applications.

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

PubMed

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

2016-07-08

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

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.

Understanding the Requirements for Open Source Software

DTIC Science & Technology

2009-06-17

GNOME and K Development Environment ( KDE ) for end-user interfaces, the Eclipse and NetBeans interactive development environments for Java-based Web...17 4.1. Informal Post-hoc Assertion of OSS Requirements vs . Requirements Elicitation...18 4.2. Requirements Reading, Sense-making, and Accountability vs . Requirements Analysis

The APA Style Converter: a Web-based interface for converting articles to APA style for publication.

PubMed

Li, Ping; Cunningham, Krystal

2005-05-01

The APA Style Converter is a Web-based tool with which authors may prepare their articles in APA style according to the APA Publication Manual (5th ed.). The Converter provides a user-friendly interface that allows authors to copy and paste text and upload figures through the Web, and it automatically converts all texts, references, and figures to a structured article in APA style. The output is saved in PDF or RTF format, ready for either electronic submission or hardcopy printing.

Towards the Interoperability of Web, Database, and Mass Storage Technologies for Petabyte Archives

NASA Technical Reports Server (NTRS)

Moore, Reagan; Marciano, Richard; Wan, Michael; Sherwin, Tom; Frost, Richard

1996-01-01

At the San Diego Supercomputer Center, a massive data analysis system (MDAS) is being developed to support data-intensive applications that manipulate terabyte sized data sets. The objective is to support scientific application access to data whether it is located at a Web site, stored as an object in a database, and/or storage in an archival storage system. We are developing a suite of demonstration programs which illustrate how Web, database (DBMS), and archival storage (mass storage) technologies can be integrated. An application presentation interface is being designed that integrates data access to all of these sources. We have developed a data movement interface between the Illustra object-relational database and the NSL UniTree archival storage system running in a production mode at the San Diego Supercomputer Center. With this interface, an Illustra client can transparently access data on UniTree under the control of the Illustr DBMS server. The current implementation is based on the creation of a new DBMS storage manager class, and a set of library functions that allow the manipulation and migration of data stored as Illustra 'large objects'. We have extended this interface to allow a Web client application to control data movement between its local disk, the Web server, the DBMS Illustra server, and the UniTree mass storage environment. This paper describes some of the current approaches successfully integrating these technologies. This framework is measured against a representative sample of environmental data extracted from the San Diego Ba Environmental Data Repository. Practical lessons are drawn and critical research areas are highlighted.

Pathview Web: user friendly pathway visualization and data integration

PubMed Central

Pant, Gaurav; Bhavnasi, Yeshvant K.; Blanchard, Steven G.; Brouwer, Cory

2017-01-01

Abstract Pathway analysis is widely used in omics studies. Pathway-based data integration and visualization is a critical component of the analysis. To address this need, we recently developed a novel R package called Pathview. Pathview maps, integrates and renders a large variety of biological data onto molecular pathway graphs. Here we developed the Pathview Web server, as to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources. Pathview Web features an intuitive graphical web interface and a user centered design. The server not only expands the core functions of Pathview, but also provides many useful features not available in the offline R package. Importantly, the server presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data. In addition, the server also provides a RESTful API for programmatic access and conveniently integration in third-party software or workflows. Pathview Web is openly and freely accessible at https://pathview.uncc.edu/. PMID:28482075

mySyntenyPortal: an application package to construct websites for synteny block analysis.

PubMed

Lee, Jongin; Lee, Daehwan; Sim, Mikang; Kwon, Daehong; Kim, Juyeon; Ko, Younhee; Kim, Jaebum

2018-06-05

Advances in sequencing technologies have facilitated large-scale comparative genomics based on whole genome sequencing. Constructing and investigating conserved genomic regions among multiple species (called synteny blocks) are essential in the comparative genomics. However, they require significant amounts of computational resources and time in addition to bioinformatics skills. Many web interfaces have been developed to make such tasks easier. However, these web interfaces cannot be customized for users who want to use their own set of genome sequences or definition of synteny blocks. To resolve this limitation, we present mySyntenyPortal, a stand-alone application package to construct websites for synteny block analyses by using users' own genome data. mySyntenyPortal provides both command line and web-based interfaces to build and manage websites for large-scale comparative genomic analyses. The websites can be also easily published and accessed by other users. To demonstrate the usability of mySyntenyPortal, we present an example study for building websites to compare genomes of three mammalian species (human, mouse, and cow) and show how they can be easily utilized to identify potential genes affected by genome rearrangements. mySyntenyPortal will contribute for extended comparative genomic analyses based on large-scale whole genome sequences by providing unique functionality to support the easy creation of interactive websites for synteny block analyses from user's own genome data.

Modelling Safe Interface Interactions in Web Applications

NASA Astrophysics Data System (ADS)

Brambilla, Marco; Cabot, Jordi; Grossniklaus, Michael

Current Web applications embed sophisticated user interfaces and business logic. The original interaction paradigm of the Web based on static content pages that are browsed by hyperlinks is, therefore, not valid anymore. In this paper, we advocate a paradigm shift for browsers and Web applications, that improves the management of user interaction and browsing history. Pages are replaced by States as basic navigation nodes, and Back/Forward navigation along the browsing history is replaced by a full-fledged interactive application paradigm, supporting transactions at the interface level and featuring Undo/Redo capabilities. This new paradigm offers a safer and more precise interaction model, protecting the user from unexpected behaviours of the applications and the browser.

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

NASA Astrophysics Data System (ADS)

Huang, L. Xinglai; Sheng, Grant

2006-10-01

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

Online Hydrologic Impact Assessment Decision Support System using Internet and Web-GIS Capability

NASA Astrophysics Data System (ADS)

Choi, J.; Engel, B. A.; Harbor, J.

2002-05-01

Urban sprawl and the corresponding land use change from lower intensity uses, such as agriculture and forests, to higher intensity uses including high density residential and commercial has various long- and short-term environment impacts on ground water recharge, water pollution, and storm water drainage. A web-based Spatial Decision Support System, SDSS, for Web-based operation of long-term hydrologic impact modeling and analysis was developed. The system combines a hydrologic model, databases, web-GIS capability and HTML user interfaces to create a comprehensive hydrologic analysis system. The hydrologic model estimates daily direct runoff using the NRCS Curve Number technique and annual nonpoint source pollution loading by an event mean concentration approach. This is supported by a rainfall database with over 30 years of daily rainfall for the continental US. A web-GIS interface and a robust Web-based watershed delineation capability were developed to simplify the spatial data preparation task that is often a barrier to hydrologic model operation. The web-GIS supports browsing of map layers including hydrologic soil groups, roads, counties, streams, lakes and railroads, as well as on-line watershed delineation for any geographic point the user selects with a simple mouse click. The watershed delineation results can also be used to generate data for the hydrologic and water quality models available in the DSS. This system is already being used by city and local government planners for hydrologic impact evaluation of land use change from urbanization, and can be found at http://pasture.ecn.purdue.edu/~watergen/hymaps. This system can assist local community, city and watershed planners, and even professionals when they are examining impacts of land use change on water resources. They can estimate the hydrologic impact of possible land use changes using this system with readily available data supported through the Internet. This system provides a cost effective approach to serve potential users who require easy-to-use tools.

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/.

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/.

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.

Adding a Visualization Feature to Web Search Engines: It’s Time

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

Wong, Pak C.

Since the first world wide web (WWW) search engine quietly entered our lives in 1994, the “information need” behind web searching has rapidly grown into a multi-billion dollar business that dominates the internet landscape, drives e-commerce traffic, propels global economy, and affects the lives of the whole human race. Today’s search engines are faster, smarter, and more powerful than those released just a few years ago. With the vast investment pouring into research and development by leading web technology providers and the intense emotion behind corporate slogans such as “win the web” or “take back the web,” I can’t helpmore » but ask why are we still using the very same “text-only” interface that was used 13 years ago to browse our search engine results pages (SERPs)? Why has the SERP interface technology lagged so far behind in the web evolution when the corresponding search technology has advanced so rapidly? In this article I explore some current SERP interface issues, suggest a simple but practical visual-based interface design approach, and argue why a visual approach can be a strong candidate for tomorrow’s SERP interface.« less

An open source web interface for linking models to infrastructure system databases

NASA Astrophysics Data System (ADS)

Knox, S.; Mohamed, K.; Harou, J. J.; Rheinheimer, D. E.; Medellin-Azuara, J.; Meier, P.; Tilmant, A.; Rosenberg, D. E.

2016-12-01

Models of networked engineered resource systems such as water or energy systems are often built collaboratively with developers from different domains working at different locations. These models can be linked to large scale real world databases, and they are constantly being improved and extended. As the development and application of these models becomes more sophisticated, and the computing power required for simulations and/or optimisations increases, so has the need for online services and tools which enable the efficient development and deployment of these models. Hydra Platform is an open source, web-based data management system, which allows modellers of network-based models to remotely store network topology and associated data in a generalised manner, allowing it to serve multiple disciplines. Hydra Platform uses a web API using JSON to allow external programs (referred to as `Apps') to interact with its stored networks and perform actions such as importing data, running models, or exporting the networks to different formats. Hydra Platform supports multiple users accessing the same network and has a suite of functions for managing users and data. We present ongoing development in Hydra Platform, the Hydra Web User Interface, through which users can collaboratively manage network data and models in a web browser. The web interface allows multiple users to graphically access, edit and share their networks, run apps and view results. Through apps, which are located on the server, the web interface can give users access to external data sources and models without the need to install or configure any software. This also ensures model results can be reproduced by removing platform or version dependence. Managing data and deploying models via the web interface provides a way for multiple modellers to collaboratively manage data, deploy and monitor model runs and analyse results.

A comprehensive physiologically based pharmacokinetic ...

EPA Pesticide Factsheets

Published physiologically based pharmacokinetic (PBPK) models from peer-reviewed articles are often well-parameterized, thoroughly-vetted, and can be utilized as excellent resources for the construction of models pertaining to related chemicals. Specifically, chemical-specific parameters and in vivo pharmacokinetic data used to calibrate these published models can act as valuable starting points for model development of new chemicals with similar molecular structures. A knowledgebase for published PBPK-related articles was compiled to support PBPK model construction for new chemicals based on their close analogues within the knowledgebase, and a web-based interface was developed to allow users to query those close analogues. A list of 689 unique chemicals and their corresponding 1751 articles was created after analysis of 2,245 PBPK-related articles. For each model, the PMID, chemical name, major metabolites, species, gender, life stages and tissue compartments were extracted from the published articles. PaDEL-Descriptor, a Chemistry Development Kit based software, was used to calculate molecular fingerprints. Tanimoto index was implemented in the user interface as measurement of structural similarity. The utility of the PBPK knowledgebase and web-based user interface was demonstrated using two case studies with ethylbenzene and gefitinib. Our PBPK knowledgebase is a novel tool for ranking chemicals based on similarities to other chemicals associated with existi

An integrated and accessible sample data library for Mars sample return science

NASA Astrophysics Data System (ADS)

Tuite, M. L., Jr.; Williford, K. H.

2015-12-01

Over the course of the next decade or more, many thousands of geological samples will be collected and analyzed in a variety of ways by researchers at the Jet Propulsion Laboratory (California Institute of Technology) in order to facilitate discovery and contextualize observations made of Mars rocks both in situ and here on Earth if samples are eventually returned. Integration of data from multiple analyses of samples including petrography, thin section and SEM imaging, isotope and organic geochemistry, XRF, XRD, and Raman spectrometry is a challenge and a potential obstacle to discoveries that require supporting lines of evidence. We report the development of a web-accessible repository, the Sample Data Library (SDL) for the sample-based data that are generated by the laboratories and instruments that comprise JPL's Center for Analysis of Returned Samples (CARS) in order to facilitate collaborative interpretation of potential biosignatures in Mars-analog geological samples. The SDL is constructed using low-cost, open-standards-based Amazon Web Services (AWS), including web-accessible storage, relational data base services, and a virtual web server. The data structure is sample-centered with a shared registry for assigning unique identifiers to all samples including International Geo-Sample Numbers. Both raw and derived data produced by instruments and post-processing workflows are automatically uploaded to online storage and linked via the unique identifiers. Through the web interface, users are able to find all the analyses associated with a single sample or search across features shared by multiple samples, sample localities, and analysis types. Planned features include more sophisticated search and analytical interfaces as well as data discoverability through NSF's EarthCube program.

An advanced web query interface for biological databases

PubMed Central

Latendresse, Mario; Karp, Peter D.

2010-01-01

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

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features.

PubMed

Simovski, Boris; Kanduri, Chakravarthi; Gundersen, Sveinung; Titov, Dmytro; Domanska, Diana; Bock, Christoph; Bossini-Castillo, Lara; Chikina, Maria; Favorov, Alexander; Layer, Ryan M; Mironov, Andrey A; Quinlan, Aaron R; Sheffield, Nathan C; Trynka, Gosia; Sandve, Geir K

2018-06-05

Functional genomics assays produce sets of genomic regions as one of their main outputs. To biologically interpret such region-sets, researchers often use colocalization analysis, where the statistical significance of colocalization (overlap, spatial proximity) between two or more region-sets is tested. Existing colocalization analysis tools vary in the statistical methodology and analysis approaches, thus potentially providing different conclusions for the same research question. As the findings of colocalization analysis are often the basis for follow-up experiments, it is helpful to use several tools in parallel and to compare the results. We developed the Coloc-stats web service to facilitate such analyses. Coloc-stats provides a unified interface to perform colocalization analysis across various analytical methods and method-specific options (e.g. colocalization measures, resolution, null models). Coloc-stats helps the user to find a method that supports their experimental requirements and allows for a straightforward comparison across methods. Coloc-stats is implemented as a web server with a graphical user interface that assists users with configuring their colocalization analyses. Coloc-stats is freely available at https://hyperbrowser.uio.no/coloc-stats/.

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.

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.

Secure Web-based Ground System User Interfaces over the Open Internet

NASA Technical Reports Server (NTRS)

Langston, James H.; Murray, Henry L.; Hunt, Gary R.

1998-01-01

A prototype has been developed which makes use of commercially available products in conjunction with the Java programming language to provide a secure user interface for command and control over the open Internet. This paper reports successful demonstration of: (1) Security over the Internet, including encryption and certification; (2) Integration of Java applets with a COTS command and control product; (3) Remote spacecraft commanding using the Internet. The Java-based Spacecraft Web Interface to Telemetry and Command Handling (Jswitch) ground system prototype provides these capabilities. This activity demonstrates the use and integration of current technologies to enable a spacecraft engineer or flight operator to monitor and control a spacecraft from a user interface communicating over the open Internet using standard World Wide Web (WWW) protocols and commercial off-the-shelf (COTS) products. The core command and control functions are provided by the COTS Epoch 2000 product. The standard WWW tools and browsers are used in conjunction with the Java programming technology. Security is provided with the current encryption and certification technology. This system prototype is a step in the direction of giving scientist and flight operators Web-based access to instrument, payload, and spacecraft data.

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.

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

Kargupta, H.; Stafford, B.; Hamzaoglu, I.

This paper describes an experimental parallel/distributed data mining system PADMA (PArallel Data Mining Agents) that uses software agents for local data accessing and analysis and a web based interface for interactive data visualization. It also presents the results of applying PADMA for detecting patterns in unstructured texts of postmortem reports and laboratory test data for Hepatitis C patients.

A web-based biosignal data management system for U-health data integration.

PubMed

Ro, Dongwoo; Yoo, Sooyoung; Choi, Jinwook

2008-11-06

In the ubiquitous healthcare environment, the biosignal data should be easily accessed and properly maintained. This paper describes a web-based data management system. It consists of a device interface, a data upload control, a central repository, and a web server. For the user-specific web services, a MFER Upload ActiveX Control was developed.

Concepts and Technologies for a Comprehensive Information System for Historical Research and Heritage Documentation

NASA Astrophysics Data System (ADS)

Henze, F.; Magdalinski, N.; Schwarzbach, F.; Schulze, A.; Gerth, Ph.; Schäfer, F.

2013-07-01

Information systems play an important role in historical research as well as in heritage documentation. As part of a joint research project of the German Archaeological Institute, the Brandenburg University of Technology Cottbus and the Dresden University of Applied Sciences a web-based documentation system is currently being developed, which can easily be adapted to the needs of different projects with individual scientific concepts, methods and questions. Based on open source and standardized technologies it will focus on open and well-documented interfaces to ease the dissemination and re-use of its content via web-services and to communicate with desktop applications for further evaluation and analysis. Core of the system is a generic data model that represents a wide range of topics and methods of archaeological work. By the provision of a concerted amount of initial themes and attributes a cross project analysis of research data will be possible. The development of enhanced search and retrieval functionalities will simplify the processing and handling of large heterogeneous data sets. To achieve a high degree of interoperability with existing external data, systems and applications, standardized interfaces will be integrated. The analysis of spatial data shall be possible through the integration of web-based GIS functions. As an extension to this, customized functions for storage, processing and provision of 3D geo data are being developed. As part of the contribution system requirements and concepts will be presented and discussed. A particular focus will be on introducing the generic data model and the derived database schema. The research work on enhanced search and retrieval capabilities will be illustrated by prototypical developments, as well as concepts and first implementations for an integrated 2D/3D Web-GIS.

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

PubMed

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

2011-07-01

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

Mars Data analysis and visualization with Marsoweb

NASA Astrophysics Data System (ADS)

Gulick, V. G.; Deardorff, D. G.

2003-04-01

Marsoweb is a collaborative web environment that has been developed for the Mars research community to better visualize and analyze Mars orbiter data. Its goal is to enable online data discovery by providing an intuitive, interactive interface to data from the Mars Global Surveyor and other orbiters. Recently Marsoweb has served a prominent role as a resource center for the site selection process for the Mars Explorer Rover 2003 missions. In addition to hosting a repository of landing site memoranda and workshop talks, it includes a Java-based interface to a variety of data maps and images. This interface enables the display and numerical querying of data, and allows data profiles to be rendered from user-drawn cross-sections. High-resolution Mars Orbiter Camera (MOC) images (currently, over 100,000) can be graphically perused; browser-based image processing tools can be used on MOC images of potential landing sites. An automated VRML atlas allows users to construct "flyovers" of their own regions-of-interest in 3D. These capabilities enable Marsoweb to be used for general global data studies, in addition to those specific to landing site selection. As of December 2002, Marsoweb has been viewed by 88,000 distinct users with a total of 3.3 million hits (801,000 page requests in all) from NASA, USGS, academia, and the general public have accessed Marsoweb. The High Resolution Imaging Experiment team for the Mars 2005 Orbiter (HiRISE, PI Alfred McEwen) plans to cast a wide net to collect targeting suggestions. Members of the general public as well as the broad Mars science community will be able to submit suggestions of high resolution imaging targets. The web-based interface for target suggestion input (HiWeb) will be based upon Marsoweb (http://marsoweb.nas.nasa.gov).

A Mediator-Based Approach to Resolving Interface Heterogeneity of Web Services

NASA Astrophysics Data System (ADS)

Leitner, Philipp; Rosenberg, Florian; Michlmayr, Anton; Huber, Andreas; Dustdar, Schahram

In theory, service-oriented architectures are based on the idea of increasing flexibility in the selection of internal and external business partners using loosely-coupled services. However, in practice this flexibility is limited by the fact that partners need not only to provide the same service, but to do so via virtually the same interface in order to actually be interchangeable easily. Invocation-level mediation may be used to overcome this issue — by using mediation interface differences can be resolved transparently at runtime. In this chapter we discuss the basic ideas of mediation, with a focus on interface-level mediation. We show how interface mediation is integrated into our dynamic Web service invocation framework DAIOS, and present three different mediation strategies, one based on structural message similarity, one based on semantically annotated WSDL, and one which is embedded into the VRESCo SOA runtime, a larger research project with explicit support for service mediation.

Web-based Hyper Suprime-Cam Data Providing System

NASA Astrophysics Data System (ADS)

Koike, M.; Furusawa, H.; Takata, T.; Price, P.; Okura, Y.; Yamada, Y.; Yamanoi, H.; Yasuda, N.; Bickerton, S.; Katayama, N.; Mineo, S.; Lupton, R.; Bosch, J.; Loomis, C.

2014-05-01

We describe a web-based user interface to retrieve Hyper Suprime-Cam data products, including images and. Users can access data directly from a graphical user interface or by writing a database SQL query. The system provides raw images, reduced images and stacked images (from multiple individual exposures), with previews available. Catalog queries can be executed in preview or queue mode, allowing for both exploratory and comprehensive investigations.

PmiRExAt: plant miRNA expression atlas database and web applications

PubMed Central

Gurjar, Anoop Kishor Singh; Panwar, Abhijeet Singh; Gupta, Rajinder; Mantri, Shrikant S.

2016-01-01

High-throughput small RNA (sRNA) sequencing technology enables an entirely new perspective for plant microRNA (miRNA) research and has immense potential to unravel regulatory networks. Novel insights gained through data mining in publically available rich resource of sRNA data will help in designing biotechnology-based approaches for crop improvement to enhance plant yield and nutritional value. Bioinformatics resources enabling meta-analysis of miRNA expression across multiple plant species are still evolving. Here, we report PmiRExAt, a new online database resource that caters plant miRNA expression atlas. The web-based repository comprises of miRNA expression profile and query tool for 1859 wheat, 2330 rice and 283 maize miRNA. The database interface offers open and easy access to miRNA expression profile and helps in identifying tissue preferential, differential and constitutively expressing miRNAs. A feature enabling expression study of conserved miRNA across multiple species is also implemented. Custom expression analysis feature enables expression analysis of novel miRNA in total 117 datasets. New sRNA dataset can also be uploaded for analysing miRNA expression profiles for 73 plant species. PmiRExAt application program interface, a simple object access protocol web service allows other programmers to remotely invoke the methods written for doing programmatic search operations on PmiRExAt database. Database URL: http://pmirexat.nabi.res.in. PMID:27081157

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

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

UCbase 2.0: ultraconserved sequences database (2014 update)

PubMed Central

Lomonaco, Vincenzo; Martoglia, Riccardo; Mandreoli, Federica; Anderlucci, Laura; Emmett, Warren; Bicciato, Silvio; Taccioli, Cristian

2014-01-01

UCbase 2.0 (http://ucbase.unimore.it) is an update, extension and evolution of UCbase, a Web tool dedicated to the analysis of ultraconserved sequences (UCRs). UCRs are 481 sequences >200 bases sharing 100% identity among human, mouse and rat genomes. They are frequently located in genomic regions known to be involved in cancer or differentially expressed in human leukemias and carcinomas. UCbase 2.0 is a platform-independent Web resource that includes the updated version of the human genome annotation (hg19), information linking disorders to chromosomal coordinates based on the Systematized Nomenclature of Medicine classification, a query tool to search for Single Nucleotide Polymorphisms (SNPs) and a new text box to directly interrogate the database using a MySQL interface. To facilitate the interactive visual interpretation of UCR chromosomal positioning, UCbase 2.0 now includes a graph visualization interface directly linked to UCSC genome browser. Database URL: http://ucbase.unimore.it PMID:24951797

Validating the usability of an interactive Earth Observation based web service for landslide investigation

NASA Astrophysics Data System (ADS)

Albrecht, Florian; Weinke, Elisabeth; Eisank, Clemens; Vecchiotti, Filippo; Hölbling, Daniel; Friedl, Barbara; Kociu, Arben

2017-04-01

Regional authorities and infrastructure maintainers in almost all mountainous regions of the Earth need detailed and up-to-date landslide inventories for hazard and risk management. Landslide inventories usually are compiled through ground surveys and manual image interpretation following landslide triggering events. We developed a web service that uses Earth Observation (EO) data to support the mapping and monitoring tasks for improving the collection of landslide information. The planned validation of the EO-based web service does not only cover the analysis of the achievable landslide information quality but also the usability and user friendliness of the user interface. The underlying validation criteria are based on the user requirements and the defined tasks and aims in the work description of the FFG project Land@Slide (EO-based landslide mapping: from methodological developments to automated web-based information delivery). The service will be validated in collaboration with stakeholders, decision makers and experts. Users are requested to test the web service functionality and give feedback with a web-based questionnaire by following the subsequently described workflow. The users will operate the web-service via the responsive user interface and can extract landslide information from EO data. They compare it to reference data for quality assessment, for monitoring changes and for assessing landslide-affected infrastructure. An overview page lets the user explore a list of example projects with resulting landslide maps and mapping workflow descriptions. The example projects include mapped landslides in several test areas in Austria and Northern Italy. Landslides were extracted from high resolution (HR) and very high resolution (VHR) satellite imagery, such as Landsat, Sentinel-2, SPOT-5, WorldView-2/3 or Pléiades. The user can create his/her own project by selecting available satellite imagery or by uploading new data. Subsequently, a new landslide extraction workflow can be initiated through the functionality that the web service provides: (1) a segmentation of the image into spectrally homogeneous objects, (2) a classification of the objects into landslide and non-landslide areas and (3) an editing tool for the manual refinement of extracted landslide boundaries. In addition, the user interface of the web service provides tools that enable the user (4) to perform a monitoring that identifies changes between landslide maps of different points in time, (5) to perform a validation of the landslide maps by comparing them to reference data, and (6) to perform an assessment of affected infrastructure by comparing the landslide maps to respective infrastructure data. After exploring the web service functionality, the users are asked to fill in the online validation protocol in form of a questionnaire in order to provide their feedback. Concerning usability, we evaluate how intuitive the web service functionality can be operated, how well the integrated help information guides the users, and what kind of background information, e.g. remote sensing concepts and theory, is necessary for a practitioner to fully exploit the value of EO data. The feedback will be used for improving the user interface and for the implementation of additional functionality.

Development of Web GIS for complex processing and visualization of climate geospatial datasets as an integral part of dedicated Virtual Research Environment

NASA Astrophysics Data System (ADS)

Gordov, Evgeny; Okladnikov, Igor; Titov, Alexander

2017-04-01

For comprehensive usage of large geospatial meteorological and climate datasets it is necessary to create a distributed software infrastructure based on the spatial data infrastructure (SDI) approach. Currently, it is generally accepted that the development of client applications as integrated elements of such infrastructure should be based on the usage of modern web and GIS technologies. The paper describes the Web GIS for complex processing and visualization of geospatial (mainly in NetCDF and PostGIS formats) datasets as an integral part of the dedicated Virtual Research Environment for comprehensive study of ongoing and possible future climate change, and analysis of their implications, providing full information and computing support for the study of economic, political and social consequences of global climate change at the global and regional levels. The Web GIS consists of two basic software parts: 1. Server-side part representing PHP applications of the SDI geoportal and realizing the functionality of interaction with computational core backend, WMS/WFS/WPS cartographical services, as well as implementing an open API for browser-based client software. Being the secondary one, this part provides a limited set of procedures accessible via standard HTTP interface. 2. Front-end part representing Web GIS client developed according to a "single page application" technology based on JavaScript libraries OpenLayers (http://openlayers.org/), ExtJS (https://www.sencha.com/products/extjs), GeoExt (http://geoext.org/). It implements application business logic and provides intuitive user interface similar to the interface of such popular desktop GIS applications, as uDIG, QuantumGIS etc. Boundless/OpenGeo architecture was used as a basis for Web-GIS client development. According to general INSPIRE requirements to data visualization Web GIS provides such standard functionality as data overview, image navigation, scrolling, scaling and graphical overlay, displaying map legends and corresponding metadata information. The specialized Web GIS client contains three basic tires: • Tier of NetCDF metadata in JSON format • Middleware tier of JavaScript objects implementing methods to work with: o NetCDF metadata o XML file of selected calculations configuration (XML task) o WMS/WFS/WPS cartographical services • Graphical user interface tier representing JavaScript objects realizing general application business logic Web-GIS developed provides computational processing services launching to support solving tasks in the area of environmental monitoring, as well as presenting calculation results in the form of WMS/WFS cartographical layers in raster (PNG, JPG, GeoTIFF), vector (KML, GML, Shape), and binary (NetCDF) formats. It has shown its effectiveness in the process of solving real climate change research problems and disseminating investigation results in cartographical formats. The work is supported by the Russian Science Foundation grant No 16-19-10257.

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

NASA Technical Reports Server (NTRS)

Heinrichs, W.; Smith, J.

1999-01-01

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

Evaluating a Web-Based Interface for Internet Telemedicine

NASA Technical Reports Server (NTRS)

Lathan, Corinna E.; Newman, Dava J.; Sebrechts, Marc M.; Doarn, Charles R.

1997-01-01

The objective is to introduce the usability engineering methodology, heuristic evaluation, to the design and development of a web-based telemedicine system. Using a set of usability criteria, or heuristics, one evaluator examined the Spacebridge to Russia web-site for usability problems. Thirty-four usability problems were found in this preliminary study and all were assigned a severity rating. The value of heuristic analysis in the iterative design of a system is shown because the problems can be fixed before deployment of a system and the problems are of a different nature than those found by actual users of the system. It was therefore determined that there is potential value of heuristic evaluation paired with user testing as a strategy for optimal system performance design.

Remote Thermal Analysis Through the Internet

NASA Astrophysics Data System (ADS)

Malroy, Eric T.

2002-07-01

The Heater of the Hypersonic Tunnel Facility (HTF) was modeled using SINDA/FLUINT thermal software. A description of the model is given. The project presented the opportunity of interfacing the thermal model with the Internet and was a demonstration that complex analysis is possible through the Internet. Some of the issues that need to be addressed related to interfacing software with the Internet are the following: justification for using the Internet, selection of the web server, choice of the CGI language, security of the system, communication among the parties, maintenance of state between web pages, and simultaneous users on the Internet system. The opportunities available for using the Internet for analysis are many and can present a significant jump in technology. This paper presents a vision how interfacing with the Internet could develop in the future. Using a separate Optical Internet (OI) for analysis, coupled with virtual reality analysis rooms (VRAR), could provide a synergistic environment to couple together engineering analysis within industry, academia, and government. The process of analysis could be broken down into sub-components so that specialization could occur resulting in superior quality, minimized cost and reduced time for engineering analysis and manufacturing. Some possible subcomponents of the system are solver routines, databases, Graphical User Interfaces, engineering design software, VRARs, computer processing, CAD systems, manufacturing, and a plethora of other options only limited by ones imagination. On a larger scope, the specialization of companies on the optical network would allow companies to rapidly construct and reconstruct their infrastructure based on changing economic conditions. This could transform business.

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

PubMed

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

2014-01-01

Mechanistic 'whole-cell' models are needed to develop a complete understanding of cell physiology. However, extracting biological insights from whole-cell models requires running and analyzing large numbers of simulations. We developed WholeCellSimDB, a database for organizing whole-cell simulations. WholeCellSimDB was designed to enable researchers to search simulation metadata to identify simulations for further analysis, and quickly slice and aggregate simulation results data. In addition, WholeCellSimDB enables users to share simulations with the broader research community. The database uses a hybrid relational/hierarchical data format architecture to efficiently store and retrieve both simulation setup metadata and results data. WholeCellSimDB provides a graphical Web-based interface to search, browse, plot and export simulations; a JavaScript Object Notation (JSON) Web service to retrieve data for Web-based visualizations; a command-line interface to deposit simulations; and a Python API to retrieve data for advanced analysis. Overall, we believe WholeCellSimDB will help researchers use whole-cell models to advance basic biological science and bioengineering. http://www.wholecellsimdb.org SOURCE CODE REPOSITORY: URL: http://github.com/CovertLab/WholeCellSimDB. © The Author(s) 2014. Published by Oxford University Press.

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

PubMed

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

2015-11-01

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

User interface and patient involvement.

PubMed

Andreassen, Hege Kristin; Lundvoll Nilsen, Line

2013-01-01

Increased patient involvement is a goal in contemporary health care, and of importance to the development of patient oriented ICT. In this paper we discuss how the design of patient-user interfaces can affect patient involvement. Our discussion is based on 12 semi-structured interviews with patient users of a web-based solution for patient--doctor communication piloted in Norway. We argue ICT solutions offering a choice of user interfaces on the patient side are preferable to ensure individual accommodation and a high degree of patient involvement. When introducing web-based tools for patient--health professional communication a free-text option should be provided to the patient users.

A Web-based interface to calculate phonotactic probability for words and nonwords in English

PubMed Central

VITEVITCH, MICHAEL S.; LUCE, PAUL A.

2008-01-01

Phonotactic probability refers to the frequency with which phonological segments and sequences of phonological segments occur in words in a given language. We describe one method of estimating phonotactic probabilities based on words in American English. These estimates of phonotactic probability have been used in a number of previous studies and are now being made available to other researchers via a Web-based interface. Instructions for using the interface, as well as details regarding how the measures were derived, are provided in the present article. The Phonotactic Probability Calculator can be accessed at http://www.people.ku.edu/~mvitevit/PhonoProbHome.html. PMID:15641436

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Natural Language Search Interfaces: Health Data Needs Single-Field Variable Search.

PubMed

Jay, Caroline; Harper, Simon; Dunlop, Ian; Smith, Sam; Sufi, Shoaib; Goble, Carole; Buchan, Iain

2016-01-14

Data discovery, particularly the discovery of key variables and their inter-relationships, is key to secondary data analysis, and in-turn, the evolving field of data science. Interface designers have presumed that their users are domain experts, and so they have provided complex interfaces to support these "experts." Such interfaces hark back to a time when searches needed to be accurate first time as there was a high computational cost associated with each search. Our work is part of a governmental research initiative between the medical and social research funding bodies to improve the use of social data in medical research. The cross-disciplinary nature of data science can make no assumptions regarding the domain expertise of a particular scientist, whose interests may intersect multiple domains. Here we consider the common requirement for scientists to seek archived data for secondary analysis. This has more in common with search needs of the "Google generation" than with their single-domain, single-tool forebears. Our study compares a Google-like interface with traditional ways of searching for noncomplex health data in a data archive. Two user interfaces are evaluated for the same set of tasks in extracting data from surveys stored in the UK Data Archive (UKDA). One interface, Web search, is "Google-like," enabling users to browse, search for, and view metadata about study variables, whereas the other, traditional search, has standard multioption user interface. Using a comprehensive set of tasks with 20 volunteers, we found that the Web search interface met data discovery needs and expectations better than the traditional search. A task × interface repeated measures analysis showed a main effect indicating that answers found through the Web search interface were more likely to be correct (F1,19=37.3, P<.001), with a main effect of task (F3,57=6.3, P<.001). Further, participants completed the task significantly faster using the Web search interface (F1,19=18.0, P<.001). There was also a main effect of task (F2,38=4.1, P=.025, Greenhouse-Geisser correction applied). Overall, participants were asked to rate learnability, ease of use, and satisfaction. Paired mean comparisons showed that the Web search interface received significantly higher ratings than the traditional search interface for learnability (P=.002, 95% CI [0.6-2.4]), ease of use (P<.001, 95% CI [1.2-3.2]), and satisfaction (P<.001, 95% CI [1.8-3.5]). The results show superior cross-domain usability of Web search, which is consistent with its general familiarity and with enabling queries to be refined as the search proceeds, which treats serendipity as part of the refinement. The results provide clear evidence that data science should adopt single-field natural language search interfaces for variable search supporting in particular: query reformulation; data browsing; faceted search; surrogates; relevance feedback; summarization, analytics, and visual presentation.

Natural Language Search Interfaces: Health Data Needs Single-Field Variable Search

PubMed Central

Smith, Sam; Sufi, Shoaib; Goble, Carole; Buchan, Iain

2016-01-01

Background Data discovery, particularly the discovery of key variables and their inter-relationships, is key to secondary data analysis, and in-turn, the evolving field of data science. Interface designers have presumed that their users are domain experts, and so they have provided complex interfaces to support these “experts.” Such interfaces hark back to a time when searches needed to be accurate first time as there was a high computational cost associated with each search. Our work is part of a governmental research initiative between the medical and social research funding bodies to improve the use of social data in medical research. Objective The cross-disciplinary nature of data science can make no assumptions regarding the domain expertise of a particular scientist, whose interests may intersect multiple domains. Here we consider the common requirement for scientists to seek archived data for secondary analysis. This has more in common with search needs of the “Google generation” than with their single-domain, single-tool forebears. Our study compares a Google-like interface with traditional ways of searching for noncomplex health data in a data archive. Methods Two user interfaces are evaluated for the same set of tasks in extracting data from surveys stored in the UK Data Archive (UKDA). One interface, Web search, is “Google-like,” enabling users to browse, search for, and view metadata about study variables, whereas the other, traditional search, has standard multioption user interface. Results Using a comprehensive set of tasks with 20 volunteers, we found that the Web search interface met data discovery needs and expectations better than the traditional search. A task × interface repeated measures analysis showed a main effect indicating that answers found through the Web search interface were more likely to be correct (F 1,19=37.3, P<.001), with a main effect of task (F 3,57=6.3, P<.001). Further, participants completed the task significantly faster using the Web search interface (F 1,19=18.0, P<.001). There was also a main effect of task (F 2,38=4.1, P=.025, Greenhouse-Geisser correction applied). Overall, participants were asked to rate learnability, ease of use, and satisfaction. Paired mean comparisons showed that the Web search interface received significantly higher ratings than the traditional search interface for learnability (P=.002, 95% CI [0.6-2.4]), ease of use (P<.001, 95% CI [1.2-3.2]), and satisfaction (P<.001, 95% CI [1.8-3.5]). The results show superior cross-domain usability of Web search, which is consistent with its general familiarity and with enabling queries to be refined as the search proceeds, which treats serendipity as part of the refinement. Conclusions The results provide clear evidence that data science should adopt single-field natural language search interfaces for variable search supporting in particular: query reformulation; data browsing; faceted search; surrogates; relevance feedback; summarization, analytics, and visual presentation. PMID:26769334

Data Access System for Hydrology

NASA Astrophysics Data System (ADS)

Whitenack, T.; Zaslavsky, I.; Valentine, D.; Djokic, D.

2007-12-01

As part of the CUAHSI HIS (Consortium of Universities for the Advancement of Hydrologic Science, Inc., Hydrologic Information System), the CUAHSI HIS team has developed Data Access System for Hydrology or DASH. DASH is based on commercial off the shelf technology, which has been developed in conjunction with a commercial partner, ESRI. DASH is a web-based user interface, developed in ASP.NET developed using ESRI ArcGIS Server 9.2 that represents a mapping, querying and data retrieval interface over observation and GIS databases, and web services. This is the front end application for the CUAHSI Hydrologic Information System Server. The HIS Server is a software stack that organizes observation databases, geographic data layers, data importing and management tools, and online user interfaces such as the DASH application, into a flexible multi- tier application for serving both national-level and locally-maintained observation data. The user interface of the DASH web application allows online users to query observation networks by location and attributes, selecting stations in a user-specified area where a particular variable was measured during a given time interval. Once one or more stations and variables are selected, the user can retrieve and download the observation data for further off-line analysis. The DASH application is highly configurable. The mapping interface can be configured to display map services from multiple sources in multiple formats, including ArcGIS Server, ArcIMS, and WMS. The observation network data is configured in an XML file where you specify the network's web service location and its corresponding map layer. Upon initial deployment, two national level observation networks (USGS NWIS daily values and USGS NWIS Instantaneous values) are already pre-configured. There is also an optional login page which can be used to restrict access as well as providing a alternative to immediate downloads. For large request, users would be notified via email with a link to their data when it is ready.

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.

C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search.

PubMed

Sowpati, Divya Tej; Srivastava, Surabhi; Dhawan, Jyotsna; Mishra, Rakesh K

2017-09-13

Comparative epigenomic analysis across multiple genes presents a bottleneck for bench biologists working with NGS data. Despite the development of standardized peak analysis algorithms, the identification of novel epigenetic patterns and their visualization across gene subsets remains a challenge. We developed a fast and interactive web app, C-State (Chromatin-State), to query and plot chromatin landscapes across multiple loci and cell types. C-State has an interactive, JavaScript-based graphical user interface and runs locally in modern web browsers that are pre-installed on all computers, thus eliminating the need for cumbersome data transfer, pre-processing and prior programming knowledge. C-State is unique in its ability to extract and analyze multi-gene epigenetic information. It allows for powerful GUI-based pattern searching and visualization. We include a case study to demonstrate its potential for identifying user-defined epigenetic trends in context of gene expression profiles.

mirEX: a platform for comparative exploration of plant pri-miRNA expression data.

PubMed

Bielewicz, Dawid; Dolata, Jakub; Zielezinski, Andrzej; Alaba, Sylwia; Szarzynska, Bogna; Szczesniak, Michal W; Jarmolowski, Artur; Szweykowska-Kulinska, Zofia; Karlowski, Wojciech M

2012-01-01

mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data. RT-qPCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. A new way of accessing gene expression data in mirEX includes a simple mouse operated querying system and dynamic graphs for data mining analyses. In contrast to other publicly available databases, the mirEX interface allows a simultaneous comparison of expression levels between various microRNA genes in diverse organs and developmental stages. Currently, mirEX integrates information about the expression profile of 190 Arabidopsis thaliana pri-miRNAs in seven different developmental stages: seeds, seedlings and various organs of mature plants. Additionally, by providing RNA structural models, publicly available deep sequencing results, experimental procedure details and careful selection of auxiliary data in the form of web links, mirEX can function as a one-stop solution for Arabidopsis microRNA information. A web-based mirEX interface can be accessed at http://bioinfo.amu.edu.pl/mirex.

XMM-Newton Science Analysis Software: How to Bring New Technologies to Long-life Satellite Missions

NASA Astrophysics Data System (ADS)

Ibarra, A.; Calle, I.; Gabriel, C.; Salgado, J.; Osuna, P.

2009-09-01

We present here the beta version of the Remote Interface to SAS Analysis (RISA), a web service-based system that allows users the analysis of XMM-Newton data making use of all of the existing SAS functionalities. RISA takes advantage of GRID architecture to run SAS, achieving high performance in resource management. We are also making the SAS remote analysis compatible with present and future VO standards.

Integrating UIMA annotators in a web-based text processing framework.

PubMed

Chen, Xiang; Arnold, Corey W

2013-01-01

The Unstructured Information Management Architecture (UIMA) [1] framework is a growing platform for natural language processing (NLP) applications. However, such applications may be difficult for non-technical users deploy. This project presents a web-based framework that wraps UIMA-based annotator systems into a graphical user interface for researchers and clinicians, and a web service for developers. An annotator that extracts data elements from lung cancer radiology reports is presented to illustrate the use of the system. Annotation results from the web system can be exported to multiple formats for users to utilize in other aspects of their research and workflow. This project demonstrates the benefits of a lay-user interface for complex NLP applications. Efforts such as this can lead to increased interest and support for NLP work in the clinical domain.

Students Using a Novel Web-Based Laboratory Class Support System: A Case Study in Food Chemistry Education

ERIC Educational Resources Information Center

van der Kolk, Koos; Beldman, Gerrit; Hartog, Rob; Gruppen, Harry

2012-01-01

The design, usage, and evaluation of a Web-based laboratory manual (WebLM) are described. The main aim of the WebLM is to support students while working in the laboratory by providing them with just-in-time information. Design guidelines for this electronic manual were derived from literature on cognitive load and user interface design. The WebLM…

Description and testing of the Geo Data Portal: Data integration framework and Web processing services for environmental science collaboration

USGS Publications Warehouse

Blodgett, David L.; Booth, Nathaniel L.; Kunicki, Thomas C.; Walker, Jordan I.; Viger, Roland J.

2011-01-01

Interest in sharing interdisciplinary environmental modeling results and related data is increasing among scientists. The U.S. Geological Survey Geo Data Portal project enables data sharing by assembling open-standard Web services into an integrated data retrieval and analysis Web application design methodology that streamlines time-consuming and resource-intensive data management tasks. Data-serving Web services allow Web-based processing services to access Internet-available data sources. The Web processing services developed for the project create commonly needed derivatives of data in numerous formats. Coordinate reference system manipulation and spatial statistics calculation components implemented for the Web processing services were confirmed using ArcGIS 9.3.1, a geographic information science software package. Outcomes of the Geo Data Portal project support the rapid development of user interfaces for accessing and manipulating environmental data.

SEM (Symmetry Equivalent Molecules): a web-based GUI to generate and visualize the macromolecules

PubMed Central

Hussain, A. S. Z.; Kumar, Ch. Kiran; Rajesh, C. K.; Sheik, S. S.; Sekar, K.

2003-01-01

SEM, Symmetry Equivalent Molecules, is a web-based graphical user interface to generate and visualize the symmetry equivalent molecules (proteins and nucleic acids). In addition, the program allows the users to save the three-dimensional atomic coordinates of the symmetry equivalent molecules in the local machine. The widely recognized graphics program RasMol has been deployed to visualize the reference (input atomic coordinates) and the symmetry equivalent molecules. This program is written using CGI/Perl scripts and has been interfaced with all the three-dimensional structures (solved using X-ray crystallography) available in the Protein Data Bank. The program, SEM, can be accessed over the World Wide Web interface at http://dicsoft2.physics.iisc.ernet.in/sem/ or http://144.16.71.11/sem/. PMID:12824326

CFGP: a web-based, comparative fungal genomics platform

PubMed Central

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. PMID:17947331

THttpServer class in ROOT

NASA Astrophysics Data System (ADS)

Adamczewski-Musch, Joern; Linev, Sergey

2015-12-01

The new THttpServer class in ROOT implements HTTP server for arbitrary ROOT applications. It is based on Civetweb embeddable HTTP server and provides direct access to all objects registered for the server. Objects data could be provided in different formats: binary, XML, GIF/PNG, and JSON. A generic user interface for THttpServer has been implemented with HTML/JavaScript based on JavaScript ROOT development. With any modern web browser one could list, display, and monitor objects available on the server. THttpServer is used in Go4 framework to provide HTTP interface to the online analysis.

The Interface Design and the Usability Testing of a Fossilization Web-Based Learning Environment

ERIC Educational Resources Information Center

Wang, Shiang-Kwei; Yang, Chiachi

2005-01-01

This article describes practical issues related to the design and the development of a Web-Based Learning Environment (Web-LE) for high school students. The purpose of the Fossilization Web-LE was to help students understand the process of fossilization, which is a complex phenomenon and is affected by many factors. The instructional design team…

BrainIACS: a system for web-based medical image processing

NASA Astrophysics Data System (ADS)

Kishore, Bhaskar; Bazin, Pierre-Louis; Pham, Dzung L.

2009-02-01

We describe BrainIACS, a web-based medical image processing system that permits and facilitates algorithm developers to quickly create extensible user interfaces for their algorithms. Designed to address the challenges faced by algorithm developers in providing user-friendly graphical interfaces, BrainIACS is completely implemented using freely available, open-source software. The system, which is based on a client-server architecture, utilizes an AJAX front-end written using the Google Web Toolkit (GWT) and Java Servlets running on Apache Tomcat as its back-end. To enable developers to quickly and simply create user interfaces for configuring their algorithms, the interfaces are described using XML and are parsed by our system to create the corresponding user interface elements. Most of the commonly found elements such as check boxes, drop down lists, input boxes, radio buttons, tab panels and group boxes are supported. Some elements such as the input box support input validation. Changes to the user interface such as addition and deletion of elements are performed by editing the XML file or by using the system's user interface creator. In addition to user interface generation, the system also provides its own interfaces for data transfer, previewing of input and output files, and algorithm queuing. As the system is programmed using Java (and finally Java-script after compilation of the front-end code), it is platform independent with the only requirements being that a Servlet implementation be available and that the processing algorithms can execute on the server platform.

Migrating Department of Defense (DoD) Web Service Based Applications to Mobile Computing Platforms

DTIC Science & Technology

2012-03-01

World Wide Web Consortium (W3C) Geolocation API to identify the device’s location and then center the map on the device. Finally, we modify the entry...THIS PAGE INTENTIONALLY LEFT BLANK xii List of Acronyms and Abbreviations API Application Programming Interface CSS Cascading Style Sheets CLIMO...Java API for XML Web Services Reference Implementation JS JavaScript JSNI JavaScript Native Interface METOC Meteorological and Oceanographic MAA Mobile

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

Clinic expert information extraction based on domain model and block importance model.

PubMed

Zhang, Yuanpeng; Wang, Li; Qian, Danmin; Geng, Xingyun; Yao, Dengfu; Dong, Jiancheng

2015-11-01

To extract expert clinic information from the Deep Web, there are two challenges to face. The first one is to make a judgment on forms. A novel method based on a domain model, which is a tree structure constructed by the attributes of query interfaces is proposed. With this model, query interfaces can be classified to a domain and filled in with domain keywords. Another challenge is to extract information from response Web pages indexed by query interfaces. To filter the noisy information on a Web page, a block importance model is proposed, both content and spatial features are taken into account in this model. The experimental results indicate that the domain model yields a precision 4.89% higher than that of the rule-based method, whereas the block importance model yields an F1 measure 10.5% higher than that of the XPath method. Copyright © 2015 Elsevier Ltd. All rights reserved.

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.

Aided generation of search interfaces to astronomical archives

NASA Astrophysics Data System (ADS)

Zorba, Sonia; Bignamini, Andrea; Cepparo, Francesco; Knapic, Cristina; Molinaro, Marco; Smareglia, Riccardo

2016-07-01

Astrophysical data provider organizations that host web based interfaces to provide access to data resources have to cope with possible changes in data management that imply partial rewrites of web applications. To avoid doing this manually it was decided to develop a dynamically configurable Java EE web application that can set itself up reading needed information from configuration files. Specification of what information the astronomical archive database has to expose is managed using the TAP SCHEMA schema from the IVOA TAP recommendation, that can be edited using a graphical interface. When configuration steps are done the tool will build a war file to allow easy deployment of the application.

ClusterControl: a web interface for distributing and monitoring bioinformatics applications on a Linux cluster.

PubMed

Stocker, Gernot; Rieder, Dietmar; Trajanoski, Zlatko

2004-03-22

ClusterControl is a web interface to simplify distributing and monitoring bioinformatics applications on Linux cluster systems. We have developed a modular concept that enables integration of command line oriented program into the application framework of ClusterControl. The systems facilitate integration of different applications accessed through one interface and executed on a distributed cluster system. The package is based on freely available technologies like Apache as web server, PHP as server-side scripting language and OpenPBS as queuing system and is available free of charge for academic and non-profit institutions. http://genome.tugraz.at/Software/ClusterControl

Molray--a web interface between O and the POV-Ray ray tracer.

PubMed

Harris, M; Jones, T A

2001-08-01

A publicly available web-based interface is presented for producing high-quality ray-traced images and movies from the molecular-modelling program O [Jones et al. (1991), Acta Cryst. A47, 110-119]. The interface allows the user to select O-plot files and set parameters to create standard input files for the popular ray-tracing renderer POV-Ray, which can then produce publication-quality still images or simple movies. To ensure ease of use, we have made this service available to the O user community via the World Wide Web. The public Molray server is available at http://xray.bmc.uu.se/molray.

KONAGAbase: a genomic and transcriptomic database for the diamondback moth, Plutella xylostella.

PubMed

Jouraku, Akiya; Yamamoto, Kimiko; Kuwazaki, Seigo; Urio, Masahiro; Suetsugu, Yoshitaka; Narukawa, Junko; Miyamoto, Kazuhisa; Kurita, Kanako; Kanamori, Hiroyuki; Katayose, Yuichi; Matsumoto, Takashi; Noda, Hiroaki

2013-07-09

The diamondback moth (DBM), Plutella xylostella, is one of the most harmful insect pests for crucifer crops worldwide. DBM has rapidly evolved high resistance to most conventional insecticides such as pyrethroids, organophosphates, fipronil, spinosad, Bacillus thuringiensis, and diamides. Therefore, it is important to develop genomic and transcriptomic DBM resources for analysis of genes related to insecticide resistance, both to clarify the mechanism of resistance of DBM and to facilitate the development of insecticides with a novel mode of action for more effective and environmentally less harmful insecticide rotation. To contribute to this goal, we developed KONAGAbase, a genomic and transcriptomic database for DBM (KONAGA is the Japanese word for DBM). KONAGAbase provides (1) transcriptomic sequences of 37,340 ESTs/mRNAs and 147,370 RNA-seq contigs which were clustered and assembled into 84,570 unigenes (30,695 contigs, 50,548 pseudo singletons, and 3,327 singletons); and (2) genomic sequences of 88,530 WGS contigs with 246,244 degenerate contigs and 106,455 singletons from which 6,310 de novo identified repeat sequences and 34,890 predicted gene-coding sequences were extracted. The unigenes and predicted gene-coding sequences were clustered and 32,800 representative sequences were extracted as a comprehensive putative gene set. These sequences were annotated with BLAST descriptions, Gene Ontology (GO) terms, and Pfam descriptions, respectively. KONAGAbase contains rich graphical user interface (GUI)-based web interfaces for easy and efficient searching, browsing, and downloading sequences and annotation data. Five useful search interfaces consisting of BLAST search, keyword search, BLAST result-based search, GO tree-based search, and genome browser are provided. KONAGAbase is publicly available from our website (http://dbm.dna.affrc.go.jp/px/) through standard web browsers. KONAGAbase provides DBM comprehensive transcriptomic and draft genomic sequences with useful annotation information with easy-to-use web interfaces, which helps researchers to efficiently search for target sequences such as insect resistance-related genes. KONAGAbase will be continuously updated and additional genomic/transcriptomic resources and analysis tools will be provided for further efficient analysis of the mechanism of insecticide resistance and the development of effective insecticides with a novel mode of action for DBM.

FERMI/GLAST Integrated Trending and Plotting System Release 5.0

NASA Technical Reports Server (NTRS)

Ritter, Sheila; Brumer, Haim; Reitan, Denise

2012-01-01

An Integrated Trending and Plotting System (ITPS) is a trending, analysis, and plotting system used by space missions to determine performance and status of spacecraft and its instruments. ITPS supports several NASA mission operational control centers providing engineers, ground controllers, and scientists with access to the entire spacecraft telemetry data archive for the life of the mission, and includes a secure Web component for remote access. FERMI/GLAST ITPS Release 5.0 features include the option to display dates (yyyy/ddd) instead of orbit numbers along orbital Long-Term Trend (LTT) plot axis, the ability to save statistics from daily production plots as image files, and removal of redundant edit/create Input Definition File (IDF) screens. Other features are a fix to address invalid packet lengths, a change in naming convention of image files in order to use in script, the ability to save all ITPS plot images (from Windows or the Web) as GIF or PNG format, the ability to specify ymin and ymax on plots where previously only the desired range could be specified, Web interface capability to plot IDFs that contain out-oforder page and plot numbers, and a fix to change all default file names to show yyyydddhhmmss time stamps instead of hhmmssdddyyyy. A Web interface capability sorts files based on modification date (with newest one at top), and the statistics block can be displayed via a Web interface. Via the Web, users can graphically view the volume of telemetry data from each day contained in the ITPS archive in the Web digest. The ITPS could be also used in nonspace fields that need to plot data or trend data, including financial and banking systems, aviation and transportation systems, healthcare and educational systems, sales and marketing, and housing and construction.

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

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.

A Web Based Approach to Integrate Space Culture and Education

NASA Astrophysics Data System (ADS)

Gerla, F.

2002-01-01

Our intention is to dedicate a large section of our web site to space education. As the national User Support and Operation Center (USOC) for the International Space Station, MARS Center is also willing to provide material, such as videos and data, for educational purposes. In order to base our initiative on authoritative precedents, our first step has been a comparative analysis between different space agency education web sites, such as ESA and NASA. As is well known, Internet is a powerful reality, capable of connecting people all over the world and rendering public a huge amount of information. The first problem, then, is to organize this information, in order to use the web as an efficient education tool. That is why studies such as User Modeling (UM), Human Computer Interaction (HCI) and Semantic Web have become more important in Information Technology and Science. Traditional search engines are unable to provide an optimal retrieval of contents really searched for by users. Semantic Web is a valid alternative: according to its theories, web information should be represented using metadata language. Users should be able and enabled to successfully search, obtain and study new information from web. Forging knowledge in an intelligent manner, preventing users from making errors, and making this formidable quantity of information easily available have also been the starting points for HCI methodologies for defining Adaptable Interfaces. Here the information is divided into different sets, on the basis of the intended user profile, in order to prevent users from getting lost. Realized as an adaptable interface, an education web site can help users to effectively retrieve the information necessary for their scopes (teaching for a teacher and learning for a student). For students it's a great advantage to use interfaces designed on the basis of their age and scholastic level. Indeed, an adaptable interface is intended not just for students, but also for teachers, who can use it to prepare their lessons, retrieve information and organize the didactic material in order to support their lessons. We think it important to use a user centered "psychology" based on UM: we have to know the needs and expectations of the students. Our intent is to use usability tests not just to prove the site effectiveness and clearness, but also to investigate aesthetical preferences of children and young people. Physics, mathematics, chemistry are just some of the difficult learning fields connected with space technologies. Space culture is a potentially never-ending field, and our scope will be to lead students by hand in this universe of knowledge. This paper will present MARS activities in the framework of the above methodologies aimed at implementing a web based approach to integrate space culture and education. The activities are already in progress and some results will be presented in the final paper.

DLSanalysis.org: a web interface for analysis of dynamic light scattering data.

PubMed

Hansen, Steen

2018-03-01

A web interface ( www.DLSanalysis.org ) for indirect Laplace transformation of dynamic light scattering data is presented. When experimental data are uploaded to the server they are processed in a few seconds, and the result is displayed on the screen in the form of a size distribution together with the experimental data and the fit to the data. No other user input than the experimental data is necessary, but various options for the analysis may be selected. No local installation of software or registration is necessary. The result of the analysis can be downloaded.

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

PubMed Central

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

2016-01-01

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

gQTL: A Web Application for QTL Analysis Using the Collaborative Cross Mouse Genetic Reference Population.

PubMed

Konganti, Kranti; Ehrlich, Andre; Rusyn, Ivan; Threadgill, David W

2018-06-07

Multi-parental recombinant inbred populations, such as the Collaborative Cross (CC) mouse genetic reference population, are increasingly being used for analysis of quantitative trait loci (QTL). However specialized analytic software for these complex populations is typically built in R that works only on command-line, which limits the utility of these powerful resources for many users. To overcome analytic limitations, we developed gQTL, a web accessible, simple graphical user interface application based on the DOQTL platform in R to perform QTL mapping using data from CC mice. Copyright © 2018, G3: Genes, Genomes, Genetics.

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.

TMFoldWeb: a web server for predicting transmembrane protein fold class.

PubMed

Kozma, Dániel; Tusnády, Gábor E

2015-09-17

Here we present TMFoldWeb, the web server implementation of TMFoldRec, a transmembrane protein fold recognition algorithm. TMFoldRec uses statistical potentials and utilizes topology filtering and a gapless threading algorithm. It ranks template structures and selects the most likely candidates and estimates the reliability of the obtained lowest energy model. The statistical potential was developed in a maximum likelihood framework on a representative set of the PDBTM database. According to the benchmark test the performance of TMFoldRec is about 77 % in correctly predicting fold class for a given transmembrane protein sequence. An intuitive web interface has been developed for the recently published TMFoldRec algorithm. The query sequence goes through a pipeline of topology prediction and a systematic sequence to structure alignment (threading). Resulting templates are ordered by energy and reliability values and are colored according to their significance level. Besides the graphical interface, a programmatic access is available as well, via a direct interface for developers or for submitting genome-wide data sets. The TMFoldWeb web server is unique and currently the only web server that is able to predict the fold class of transmembrane proteins while assigning reliability scores for the prediction. This method is prepared for genome-wide analysis with its easy-to-use interface, informative result page and programmatic access. Considering the info-communication evolution in the last few years, the developed web server, as well as the molecule viewer, is responsive and fully compatible with the prevalent tablets and mobile devices.

Future View: Web Navigation based on Learning User's Browsing Strategy

NASA Astrophysics Data System (ADS)

Nagino, Norikatsu; Yamada, Seiji

In this paper, we propose a Future View system that assists user's usual Web browsing. The Future View will prefetch Web pages based on user's browsing strategies and present them to a user in order to assist Web browsing. To learn user's browsing strategy, the Future View uses two types of learning classifier systems: a content-based classifier system for contents change patterns and an action-based classifier system for user's action patterns. The results of learning is applied to crawling by Web robots, and the gathered Web pages are presented to a user through a Web browser interface. We experimentally show effectiveness of navigation using the Future View.

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.

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.

NPIDB: Nucleic acid-Protein Interaction DataBase.

PubMed

Kirsanov, Dmitry D; Zanegina, Olga N; Aksianov, Evgeniy A; Spirin, Sergei A; Karyagina, Anna S; Alexeevski, Andrei V

2013-01-01

The Nucleic acid-Protein Interaction DataBase (http://npidb.belozersky.msu.ru/) contains information derived from structures of DNA-protein and RNA-protein complexes extracted from the Protein Data Bank (3846 complexes in October 2012). It provides a web interface and a set of tools for extracting biologically meaningful characteristics of nucleoprotein complexes. The content of the database is updated weekly. The current version of the Nucleic acid-Protein Interaction DataBase is an upgrade of the version published in 2007. The improvements include a new web interface, new tools for calculation of intermolecular interactions, a classification of SCOP families that contains DNA-binding protein domains and data on conserved water molecules on the DNA-protein interface.

Patscanui: an intuitive web interface for searching patterns in DNA and protein data.

PubMed

Blin, Kai; Wohlleben, Wolfgang; Weber, Tilmann

2018-05-02

Patterns in biological sequences frequently signify interesting features in the underlying molecule. Many tools exist to search for well-known patterns. Less support is available for exploratory analysis, where no well-defined patterns are known yet. PatScanUI (https://patscan.secondarymetabolites.org/) provides a highly interactive web interface to the powerful generic pattern search tool PatScan. The complex PatScan-patterns are created in a drag-and-drop aware interface allowing researchers to do rapid prototyping of the often complicated patterns useful to identifying features of interest.

[Study on Information Extraction of Clinic Expert Information from Hospital Portals].

PubMed

Zhang, Yuanpeng; Dong, Jiancheng; Qian, Danmin; Geng, Xingyun; Wu, Huiqun; Wang, Li

2015-12-01

Clinic expert information provides important references for residents in need of hospital care. Usually, such information is hidden in the deep web and cannot be directly indexed by search engines. To extract clinic expert information from the deep web, the first challenge is to make a judgment on forms. This paper proposes a novel method based on a domain model, which is a tree structure constructed by the attributes of search interfaces. With this model, search interfaces can be classified to a domain and filled in with domain keywords. Another challenge is to extract information from the returned web pages indexed by search interfaces. To filter the noise information on a web page, a block importance model is proposed. The experiment results indicated that the domain model yielded a precision 10.83% higher than that of the rule-based method, whereas the block importance model yielded an F₁ measure 10.5% higher than that of the XPath method.

A GIS-Interface Web Site: Exploratory Learning for Geography Curriculum

ERIC Educational Resources Information Center

Huang, Kuo Hung

2011-01-01

Although Web-based instruction provides learners with sufficient resources for self-paced learning, previous studies have confirmed that browsing navigation-oriented Web sites possibly hampers users' comprehension of information. Web sites designed as "categories of materials" for navigation demand more cognitive effort from users to orient their…

Haptic interface of web-based training system for interventional radiology procedures

NASA Astrophysics Data System (ADS)

Ma, Xin; Lu, Yiping; Loe, KiaFock; Nowinski, Wieslaw L.

2004-05-01

The existing web-based medical training systems and surgical simulators can provide affordable and accessible medical training curriculum, but they seldom offer the trainee realistic and affordable haptic feedback. Therefore, they cannot offer the trainee a suitable practicing environment. In this paper, a haptic solution for interventional radiology (IR) procedures is proposed. System architecture of a web-based training system for IR procedures is briefly presented first. Then, the mechanical structure, the working principle and the application of a haptic device are discussed in detail. The haptic device works as an interface between the training environment and the trainees and is placed at the end user side. With the system, the user can be trained on the interventional radiology procedures - navigating catheters, inflating balloons, deploying coils and placing stents on the web and get surgical haptic feedback in real time.

Pathview Web: user friendly pathway visualization and data integration.

PubMed

Luo, Weijun; Pant, Gaurav; Bhavnasi, Yeshvant K; Blanchard, Steven G; Brouwer, Cory

2017-07-03

Pathway analysis is widely used in omics studies. Pathway-based data integration and visualization is a critical component of the analysis. To address this need, we recently developed a novel R package called Pathview. Pathview maps, integrates and renders a large variety of biological data onto molecular pathway graphs. Here we developed the Pathview Web server, as to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources. Pathview Web features an intuitive graphical web interface and a user centered design. The server not only expands the core functions of Pathview, but also provides many useful features not available in the offline R package. Importantly, the server presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data. In addition, the server also provides a RESTful API for programmatic access and conveniently integration in third-party software or workflows. Pathview Web is openly and freely accessible at https://pathview.uncc.edu/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

The Live Access Server - A Web-Services Framework for Earth Science Data

NASA Astrophysics Data System (ADS)

Schweitzer, R.; Hankin, S. C.; Callahan, J. S.; O'Brien, K.; Manke, A.; Wang, X. Y.

2005-12-01

The Live Access Server (LAS) is a general purpose Web-server for delivering services related to geo-science data sets. Data providers can use the LAS architecture to build custom Web interfaces to their scientific data. Users and client programs can then access the LAS site to search the provider's on-line data holdings, make plots of data, create sub-sets in a variety of formats, compare data sets and perform analysis on the data. The Live Access server software has continued to evolve by expanding the types of data (in-situ observations and curvilinear grids) it can serve and by taking advantages of advances in software infrastructure both in the earth sciences community (THREDDS, the GrADS Data Server, the Anagram framework and Java netCDF 2.2) and in the Web community (Java Servlet and the Apache Jakarta frameworks). This presentation will explore the continued evolution of the LAS architecture towards a complete Web-services-based framework. Additionally, we will discuss the redesign and modernization of some of the support tools available to LAS installers. Soon after the initial implementation, the LAS architecture was redesigned to separate the components that are responsible for the user interaction (the User Interface Server) from the components that are responsible for interacting with the data and producing the output requested by the user (the Product Server). During this redesign, we changed the implementation of the User Interface Server from CGI and JavaScript to the Java Servlet specification using Apache Jakarta Velocity backed by a database store for holding the user interface widget components. The User Interface server is now quite flexible and highly configurable because we modernized the components used for the implementation. Meanwhile, the implementation of the Product Server has remained a Perl CGI-based system. Clearly, the time has come to modernize this part of the LAS architecture. Before undertaking such a modernization it is important to understand what we hope to gain. Specifically we would like to make it even easier to add new output products into our core system based on the Ferret analysis and visualization package. By carefully factoring the tasks needed to create a product we will be able to create new products simply by adding a description of the product into the configuration and by writing the Ferret script needed to create the product. No code will need to be added to the Product Server to bring the new product on-line. The new architecture should be faster at extracting and processing configuration information needed to address each request. Finally, the new Product Server architecture should make it even easier to pass specialized configuration information to the Product Server to deal with unanticipated special data structures or processing requirements.

Providing Web Interfaces to the NSF EarthScope USArray Transportable Array

NASA Astrophysics Data System (ADS)

Vernon, Frank; Newman, Robert; Lindquist, Kent

2010-05-01

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

VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements.

PubMed

Christley, Scott; Scarborough, Walter; Salinas, Eddie; Rounds, William H; Toby, Inimary T; Fonner, John M; Levin, Mikhail K; Kim, Min; Mock, Stephen A; Jordan, Christopher; Ostmeyer, Jared; Buntzman, Adam; Rubelt, Florian; Davila, Marco L; Monson, Nancy L; Scheuermann, Richard H; Cowell, Lindsay G

2018-01-01

Recent technological advances in immune repertoire sequencing have created tremendous potential for advancing our understanding of adaptive immune response dynamics in various states of health and disease. Immune repertoire sequencing produces large, highly complex data sets, however, which require specialized methods and software tools for their effective analysis and interpretation. VDJServer is a cloud-based analysis portal for immune repertoire sequence data that provide access to a suite of tools for a complete analysis workflow, including modules for preprocessing and quality control of sequence reads, V(D)J gene segment assignment, repertoire characterization, and repertoire comparison. VDJServer also provides sophisticated visualizations for exploratory analysis. It is accessible through a standard web browser via a graphical user interface designed for use by immunologists, clinicians, and bioinformatics researchers. VDJServer provides a data commons for public sharing of repertoire sequencing data, as well as private sharing of data between users. We describe the main functionality and architecture of VDJServer and demonstrate its capabilities with use cases from cancer immunology and autoimmunity. VDJServer provides a complete analysis suite for human and mouse T-cell and B-cell receptor repertoire sequencing data. The combination of its user-friendly interface and high-performance computing allows large immune repertoire sequencing projects to be analyzed with no programming or software installation required. VDJServer is a web-accessible cloud platform that provides access through a graphical user interface to a data management infrastructure, a collection of analysis tools covering all steps in an analysis, and an infrastructure for sharing data along with workflows, results, and computational provenance. VDJServer is a free, publicly available, and open-source licensed resource.

COV2HTML: a visualization and analysis tool of bacterial next generation sequencing (NGS) data for postgenomics life scientists.

PubMed

Monot, Marc; Orgeur, Mickael; Camiade, Emilie; Brehier, Clément; Dupuy, Bruno

2014-03-01

COV2HTML is an interactive web interface, which is addressed to biologists, and allows performing both coverage visualization and analysis of NGS alignments performed on prokaryotic organisms (bacteria and phages). It combines two processes: a tool that converts the huge NGS mapping or coverage files into light specific coverage files containing information on genetic elements; and a visualization interface allowing a real-time analysis of data with optional integration of statistical results. To demonstrate the scope of COV2HTML, the program was tested with data from two published studies. The first data were from RNA-seq analysis of Campylobacter jejuni, based on comparison of two conditions with two replicates. We were able to recover 26 out of 27 genes highlighted in the publication using COV2HTML. The second data comprised of stranded TSS and RNA-seq data sets on the Archaea Sulfolobus solfataricus. COV2HTML was able to highlight most of the TSSs from the article and allows biologists to visualize both TSS and RNA-seq on the same screen. The strength of the COV2HTML interface is making possible NGS data analysis without software installation, login, or a long training period. A web version is accessible at https://mmonot.eu/COV2HTML/ . This website is free and open to users without any login requirement.

Pinyon, Version 0

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

Ward, Logan; Hackenberg, Robert

2017-02-13

Pinyon is a tool that stores steps involved in creating a model derived from a collection of data. The main function of Pinyon is to store descriptions of calculations used to analyze or visualize the data in a database, and allow users to view the results of these calculations via a web interface. Additionally, users may also use the web interface to make adjustments to the calculations and rerun the entire collection of analysis steps automatically.

Advancing Collaboration through Hydrologic Data and Model Sharing

NASA Astrophysics Data System (ADS)

Tarboton, D. G.; Idaszak, R.; Horsburgh, J. S.; Ames, D. P.; Goodall, J. L.; Band, L. E.; Merwade, V.; Couch, A.; Hooper, R. P.; Maidment, D. R.; Dash, P. K.; Stealey, M.; Yi, H.; Gan, T.; Castronova, A. M.; Miles, B.; Li, Z.; Morsy, M. M.

2015-12-01

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

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

PubMed Central

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

2011-01-01

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

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.

VISA--Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing.

PubMed

Hocum, Jonah D; Battrell, Logan R; Maynard, Ryan; Adair, Jennifer E; Beard, Brian C; Rawlings, David J; Kiem, Hans-Peter; Miller, Daniel G; Trobridge, Grant D

2015-07-07

Analyzing the integration profile of retroviral vectors is a vital step in determining their potential genotoxic effects and developing safer vectors for therapeutic use. Identifying retroviral vector integration sites is also important for retroviral mutagenesis screens. We developed VISA, a vector integration site analysis server, to analyze next-generation sequencing data for retroviral vector integration sites. Sequence reads that contain a provirus are mapped to the human genome, sequence reads that cannot be localized to a unique location in the genome are filtered out, and then unique retroviral vector integration sites are determined based on the alignment scores of the remaining sequence reads. VISA offers a simple web interface to upload sequence files and results are returned in a concise tabular format to allow rapid analysis of retroviral vector integration sites.

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/ .

Dynamic online surveys and experiments with the free open-source software dynQuest.

PubMed

Rademacher, Jens D M; Lippke, Sonia

2007-08-01

With computers and the World Wide Web widely available, collecting data through Web browsers is an attractive method utilized by the social sciences. In this article, conducting PC- and Web-based trials with the software package dynQuest is described. The software manages dynamic questionnaire-based trials over the Internet or on single computers, possibly as randomized control trials (RCT), if two or more groups are involved. The choice of follow-up questions can depend on previous responses, as needed for matched interventions. Data are collected in a simple text-based database that can be imported easily into other programs for postprocessing and statistical analysis. The software consists of platform-independent scripts written in the programming language PERL that use the common gateway interface between Web browser and server for submission of data through HTML forms. Advantages of dynQuest are parsimony, simplicity in use and installation, transparency, and reliability. The program is available as open-source freeware from the authors.

Map-IT! A Web-Based GIS Tool for Watershed Science Education.

ERIC Educational Resources Information Center

Curtis, David H.; Hewes, Christopher M.; Lossau, Matthew J.

This paper describes the development of a prototypic, Web-accessible GIS solution for K-12 science education and citizen-based watershed monitoring. The server side consists of ArcView IMS running on an NT workstation. The client is built around MapCafe. The client interface, which runs through a standard Web browser, supports standard MapCafe…

Chemozart: a web-based 3D molecular structure editor and visualizer platform.

PubMed

Mohebifar, Mohamad; Sajadi, Fatemehsadat

2015-01-01

Chemozart is a 3D Molecule editor and visualizer built on top of native web components. It offers an easy to access service, user-friendly graphical interface and modular design. It is a client centric web application which communicates with the server via a representational state transfer style web service. Both client-side and server-side application are written in JavaScript. A combination of JavaScript and HTML is used to draw three-dimensional structures of molecules. With the help of WebGL, three-dimensional visualization tool is provided. Using CSS3 and HTML5, a user-friendly interface is composed. More than 30 packages are used to compose this application which adds enough flexibility to it to be extended. Molecule structures can be drawn on all types of platforms and is compatible with mobile devices. No installation is required in order to use this application and it can be accessed through the internet. This application can be extended on both server-side and client-side by implementing modules in JavaScript. Molecular compounds are drawn on the HTML5 Canvas element using WebGL context. Chemozart is a chemical platform which is powerful, flexible, and easy to access. It provides an online web-based tool used for chemical visualization along with result oriented optimization for cloud based API (application programming interface). JavaScript libraries which allow creation of web pages containing interactive three-dimensional molecular structures has also been made available. The application has been released under Apache 2 License and is available from the project website https://chemozart.com.

GALT protein database, a bioinformatics resource for the management and analysis of structural features of a galactosemia-related protein and its mutants.

PubMed

d'Acierno, Antonio; Facchiano, Angelo; Marabotti, Anna

2009-06-01

We describe the GALT-Prot database and its related web-based application that have been developed to collect information about the structural and functional effects of mutations on the human enzyme galactose-1-phosphate uridyltransferase (GALT) involved in the genetic disease named galactosemia type I. Besides a list of missense mutations at gene and protein sequence levels, GALT-Prot reports the analysis results of mutant GALT structures. In addition to the structural information about the wild-type enzyme, the database also includes structures of over 100 single point mutants simulated by means of a computational procedure, and the analysis to each mutant was made with several bioinformatics programs in order to investigate the effect of the mutations. The web-based interface allows querying of the database, and several links are also provided in order to guarantee a high integration with other resources already present on the web. Moreover, the architecture of the database and the web application is flexible and can be easily adapted to store data related to other proteins with point mutations. GALT-Prot is freely available at http://bioinformatica.isa.cnr.it/GALT/.

A Web-Based Interactive Mapping System of State Wide School Performance: Integrating Google Maps API Technology into Educational Achievement Data

ERIC Educational Resources Information Center

Wang, Kening; Mulvenon, Sean W.; Stegman, Charles; Anderson, Travis

2008-01-01

Google Maps API (Application Programming Interface), released in late June 2005 by Google, is an amazing technology that allows users to embed Google Maps in their own Web pages with JavaScript. Google Maps API has accelerated the development of new Google Maps based applications. This article reports a Web-based interactive mapping system…

The ACE multi-user web-based Robotic Observatory Control System

NASA Astrophysics Data System (ADS)

Mack, P.

2003-05-01

We have developed an observatory control system that can be operated in interactive, remote or robotic modes. In interactive and remote mode the observer typically acquires the first object then creates a script through a window interface to complete observations for the rest of the night. The system closes early in the event of bad weather. In robotic mode observations are submitted ahead of time through a web-based interface. We present observations made with a 1.0-m telescope using these methods.

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform, Version 1.5 and 1.x.

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

Chain, Patrick; Lo, Chien-Chi; Li, Po-E

EDGE bioinformatics was developed to help biologists process Next Generation Sequencing data (in the form of raw FASTQ files), even if they have little to no bioinformatics expertise. EDGE is a highly integrated and interactive web-based platform that is capable of running many of the standard analyses that biologists require for viral, bacterial/archaeal, and metagenomic samples. EDGE provides the following analytical workflows: quality trimming and host removal, assembly and annotation, comparisons against known references, taxonomy classification of reads and contigs, whole genome SNP-based phylogenetic analysis, and PCR analysis. EDGE provides an intuitive web-based interface for user input, allows users tomore » visualize and interact with selected results (e.g. JBrowse genome browser), and generates a final detailed PDF report. Results in the form of tables, text files, graphic files, and PDFs can be downloaded. A user management system allows tracking of an individual’s EDGE runs, along with the ability to share, post publicly, delete, or archive their results.« less

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

On Building a Search Interface Discovery System

NASA Astrophysics Data System (ADS)

Shestakov, Denis

A huge portion of the Web known as the deep Web is accessible via search interfaces to myriads of databases on the Web. While relatively good approaches for querying the contents of web databases have been recently proposed, one cannot fully utilize them having most search interfaces unlocated. Thus, the automatic recognition of search interfaces to online databases is crucial for any application accessing the deep Web. This paper describes the architecture of the I-Crawler, a system for finding and classifying search interfaces. The I-Crawler is intentionally designed to be used in the deep web characterization surveys and for constructing directories of deep web resources.

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

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…

The Management of the Scientific Information Environment: The Role of the Research Library Web Site.

ERIC Educational Resources Information Center

Arte, Assunta

2001-01-01

Describes the experiences of the Italian National Research Council Library staff in the successful development and implementation of its Web site. Discusses electronic information sources that interface with the Web site; library services; technical infrastructure; and the choice of a Web-based library management system. (Author/LRW)

A simple versatile solution for collecting multidimensional clinical data based on the CakePHP web application framework.

PubMed

Biermann, Martin

2014-04-01

Clinical trials aiming for regulatory approval of a therapeutic agent must be conducted according to Good Clinical Practice (GCP). Clinical Data Management Systems (CDMS) are specialized software solutions geared toward GCP-trials. They are however less suited for data management in small non-GCP research projects. For use in researcher-initiated non-GCP studies, we developed a client-server database application based on the public domain CakePHP framework. The underlying MySQL database uses a simple data model based on only five data tables. The graphical user interface can be run in any web browser inside the hospital network. Data are validated upon entry. Data contained in external database systems can be imported interactively. Data are automatically anonymized on import, and the key lists identifying the subjects being logged to a restricted part of the database. Data analysis is performed by separate statistics and analysis software connecting to the database via a generic Open Database Connectivity (ODBC) interface. Since its first pilot implementation in 2011, the solution has been applied to seven different clinical research projects covering different clinical problems in different organ systems such as cancer of the thyroid and the prostate glands. This paper shows how the adoption of a generic web application framework is a feasible, flexible, low-cost, and user-friendly way of managing multidimensional research data in researcher-initiated non-GCP clinical projects. Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Effects of Mobile Phone-Based App Learning Compared to Computer-Based Web Learning on Nursing Students: Pilot Randomized Controlled Trial

PubMed Central

2015-01-01

Objectives This study aimed to determine the effect of mobile-based discussion versus computer-based discussion on self-directed learning readiness, academic motivation, learner-interface interaction, and flow state. Methods This randomized controlled trial was conducted at one university. Eighty-six nursing students who were able to use a computer, had home Internet access, and used a mobile phone were recruited. Participants were randomly assigned to either the mobile phone app-based discussion group (n = 45) or a computer web-based discussion group (n = 41). The effect was measured at before and after an online discussion via self-reported surveys that addressed academic motivation, self-directed learning readiness, time distortion, learner-learner interaction, learner-interface interaction, and flow state. Results The change in extrinsic motivation on identified regulation in the academic motivation (p = 0.011) as well as independence and ability to use basic study (p = 0.047) and positive orientation to the future in self-directed learning readiness (p = 0.021) from pre-intervention to post-intervention was significantly more positive in the mobile phone app-based group compared to the computer web-based discussion group. Interaction between learner and interface (p = 0.002), having clear goals (p = 0.012), and giving and receiving unambiguous feedback (p = 0.049) in flow state was significantly higher in the mobile phone app-based discussion group than it was in the computer web-based discussion group at post-test. Conclusions The mobile phone might offer more valuable learning opportunities for discussion teaching and learning methods in terms of self-directed learning readiness, academic motivation, learner-interface interaction, and the flow state of the learning process compared to the computer. PMID:25995965

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

DOE PAGES

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

2016-08-31

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

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

PubMed

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

2016-08-31

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

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

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

Peng, Jiajie; Li, Hongxiang; Liu, Yongzhuang

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

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

PubMed

Beveridge, Allan

2006-01-01

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

Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools.

PubMed

Ham, Timothy S; Dmytriv, Zinovii; Plahar, Hector; Chen, Joanna; Hillson, Nathan J; Keasling, Jay D

2012-10-01

The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about 'legacy' parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects.

Sign language Web pages.

PubMed

Fels, Deborah I; Richards, Jan; Hardman, Jim; Lee, Daniel G

2006-01-01

The WORLD WIDE WEB has changed the way people interact. It has also become an important equalizer of information access for many social sectors. However, for many people, including some sign language users, Web accessing can be difficult. For some, it not only presents another barrier to overcome but has left them without cultural equality. The present article describes a system that allows sign language-only Web pages to be created and linked through a video-based technique called sign-linking. In two studies, 14 Deaf participants examined two iterations of signlinked Web pages to gauge the usability and learnability of a signing Web page interface. The first study indicated that signing Web pages were usable by sign language users but that some interface features required improvement. The second study showed increased usability for those features; users consequently couldnavigate sign language information with ease and pleasure.

mORCA: sailing bioinformatics world with mobile devices.

PubMed

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

2018-03-01

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

Open ISEmeter: An open hardware high-impedance interface for potentiometric detection.

PubMed

Salvador, C; Mesa, M S; Durán, E; Alvarez, J L; Carbajo, J; Mozo, J D

2016-05-01

In this work, a new open hardware interface based on Arduino to read electromotive force (emf) from potentiometric detectors is presented. The interface has been fully designed with the open code philosophy and all documentation will be accessible on web. The paper describes a comprehensive project including the electronic design, the firmware loaded on Arduino, and the Java-coded graphical user interface to load data in a computer (PC or Mac) for processing. The prototype was tested by measuring the calibration curve of a detector. As detection element, an active poly(vinyl chloride)-based membrane was used, doped with cetyltrimethylammonium dodecylsulphate (CTA(+)-DS(-)). The experimental measures of emf indicate Nernstian behaviour with the CTA(+) content of test solutions, as it was described in the literature, proving the validity of the developed prototype. A comparative analysis of performance was made by using the same chemical detector but changing the measurement instrumentation.

The OGC Sensor Web Enablement framework

NASA Astrophysics Data System (ADS)

Cox, S. J.; Botts, M.

2006-12-01

Sensor observations are at the core of natural sciences. Improvements in data-sharing technologies offer the promise of much greater utilisation of observational data. A key to this is interoperable data standards. The Open Geospatial Consortium's (OGC) Sensor Web Enablement initiative (SWE) is developing open standards for web interfaces for the discovery, exchange and processing of sensor observations, and tasking of sensor systems. The goal is to support the construction of complex sensor applications through real-time composition of service chains from standard components. The framework is based around a suite of standard interfaces, and standard encodings for the message transferred between services. The SWE interfaces include: Sensor Observation Service (SOS)-parameterized observation requests (by observation time, feature of interest, property, sensor); Sensor Planning Service (SPS)-tasking a sensor- system to undertake future observations; Sensor Alert Service (SAS)-subscription to an alert, usually triggered by a sensor result exceeding some value. The interface design generally follows the pattern established in the OGC Web Map Service (WMS) and Web Feature Service (WFS) interfaces, where the interaction between a client and service follows a standard sequence of requests and responses. The first obtains a general description of the service capabilities, followed by obtaining detail required to formulate a data request, and finally a request for a data instance or stream. These may be implemented in a stateless "REST" idiom, or using conventional "web-services" (SOAP) messaging. In a deployed system, the SWE interfaces are supplemented by Catalogue, data (WFS) and portrayal (WMS) services, as well as authentication and rights management. The standard SWE data formats are Observations and Measurements (O&M) which encodes observation metadata and results, Sensor Model Language (SensorML) which describes sensor-systems, Transducer Model Language (TML) which covers low-level data streams, and domain-specific GML Application Schemas for definitions of the target feature types. The SWE framework has been demonstrated in several interoperability testbeds. These were based around emergency management, security, contamination and environmental monitoring scenarios.

DEApp: an interactive web interface for differential expression analysis of next generation sequence data.

PubMed

Li, Yan; Andrade, Jorge

2017-01-01

A growing trend in the biomedical community is the use of Next Generation Sequencing (NGS) technologies in genomics research. The complexity of downstream differential expression (DE) analysis is however still challenging, as it requires sufficient computer programing and command-line knowledge. Furthermore, researchers often need to evaluate and visualize interactively the effect of using differential statistical and error models, assess the impact of selecting different parameters and cutoffs, and finally explore the overlapping consensus of cross-validated results obtained with different methods. This represents a bottleneck that slows down or impedes the adoption of NGS technologies in many labs. We developed DEApp, an interactive and dynamic web application for differential expression analysis of count based NGS data. This application enables models selection, parameter tuning, cross validation and visualization of results in a user-friendly interface. DEApp enables labs with no access to full time bioinformaticians to exploit the advantages of NGS applications in biomedical research. This application is freely available at https://yanli.shinyapps.io/DEAppand https://gallery.shinyapps.io/DEApp.

A Semiotic Analysis of Icons on the World Wide Web.

ERIC Educational Resources Information Center

Ma, Yan

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

A Web interface generator for molecular biology programs in Unix.

PubMed

Letondal, C

2001-01-01

Almost all users encounter problems using sequence analysis programs. Not only are they difficult to learn because of the parameters, syntax and semantic, but many are different. That is why we have developed a Web interface generator for more than 150 molecular biology command-line driven programs, including: phylogeny, gene prediction, alignment, RNA, DNA and protein analysis, motif discovery, structure analysis and database searching programs. The generator uses XML as a high-level description language of the legacy software parameters. Its aim is to provide users with the equivalent of a basic Unix environment, with program combination, customization and basic scripting through macro registration. The program has been used for three years by about 15000 users throughout the world; it has recently been installed on other sites and evaluated as a standard user interface for EMBOSS programs.

UCbase 2.0: ultraconserved sequences database (2014 update).

PubMed

Lomonaco, Vincenzo; Martoglia, Riccardo; Mandreoli, Federica; Anderlucci, Laura; Emmett, Warren; Bicciato, Silvio; Taccioli, Cristian

2014-01-01

UCbase 2.0 (http://ucbase.unimore.it) is an update, extension and evolution of UCbase, a Web tool dedicated to the analysis of ultraconserved sequences (UCRs). UCRs are 481 sequences >200 bases sharing 100% identity among human, mouse and rat genomes. They are frequently located in genomic regions known to be involved in cancer or differentially expressed in human leukemias and carcinomas. UCbase 2.0 is a platform-independent Web resource that includes the updated version of the human genome annotation (hg19), information linking disorders to chromosomal coordinates based on the Systematized Nomenclature of Medicine classification, a query tool to search for Single Nucleotide Polymorphisms (SNPs) and a new text box to directly interrogate the database using a MySQL interface. To facilitate the interactive visual interpretation of UCR chromosomal positioning, UCbase 2.0 now includes a graph visualization interface directly linked to UCSC genome browser. Database URL: http://ucbase.unimore.it. © The Author(s) 2014. Published by Oxford University Press.

The IVTANTHERMO-Online database for thermodynamic properties of individual substances with web interface

NASA Astrophysics Data System (ADS)

Belov, G. V.; Dyachkov, S. A.; Levashov, P. R.; Lomonosov, I. V.; Minakov, D. V.; Morozov, I. V.; Sineva, M. A.; Smirnov, V. N.

2018-01-01

The database structure, main features and user interface of an IVTANTHERMO-Online system are reviewed. This system continues the series of the IVTANTHERMO packages developed in JIHT RAS. It includes the database for thermodynamic properties of individual substances and related software for analysis of experimental results, data fitting, calculation and estimation of thermodynamical functions and thermochemistry quantities. In contrast to the previous IVTANTHERMO versions it has a new extensible database design, the client-server architecture, a user-friendly web interface with a number of new features for online and offline data processing.

The Design and Application of a Web-Based Self- And Peer-Assessment System

ERIC Educational Resources Information Center

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

2005-01-01

This study describes the web-based self- and peer-assessments system, or the Web-SPA, which has been shown to provide teachers with a flexible interface with which to arrange various self- and peer-assessment procedures. Secondly, this study examines the effects of the application of the progressively focused self- and peer-assessment (PFSPA)…

Embedded Web Technology: Applying World Wide Web Standards to Embedded Systems

NASA Technical Reports Server (NTRS)

Ponyik, Joseph G.; York, David W.

2002-01-01

Embedded Systems have traditionally been developed in a highly customized manner. The user interface hardware and software along with the interface to the embedded system are typically unique to the system for which they are built, resulting in extra cost to the system in terms of development time and maintenance effort. World Wide Web standards have been developed in the passed ten years with the goal of allowing servers and clients to intemperate seamlessly. The client and server systems can consist of differing hardware and software platforms but the World Wide Web standards allow them to interface without knowing about the details of system at the other end of the interface. Embedded Web Technology is the merging of Embedded Systems with the World Wide Web. Embedded Web Technology decreases the cost of developing and maintaining the user interface by allowing the user to interface to the embedded system through a web browser running on a standard personal computer. Embedded Web Technology can also be used to simplify an Embedded System's internal network.

A Web Browser Interface to Manage the Searching and Organizing of Information on the Web by Learners

ERIC Educational Resources Information Center

Li, Liang-Yi; Chen, Gwo-Dong

2010-01-01

Information Gathering is a knowledge construction process. Web learners make a plan for their Information Gathering task based on their prior knowledge. The plan is evolved with new information encountered and their mental model is constructed through continuously assimilating and accommodating new information gathered from different Web pages. In…

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

PubMed

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

2010-05-01

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

Caching strategies for improving performance of web-based Geographic applications

NASA Astrophysics Data System (ADS)

Liu, M.; Brodzik, M.; Collins, J. A.; Lewis, S.; Oldenburg, J.

2012-12-01

The NASA Operation IceBridge mission collects airborne remote sensing measurements to bridge the gap between NASA's Ice, Cloud and Land Elevation Satellite (ICESat) mission and the upcoming ICESat-2 mission. The IceBridge Data Portal from the National Snow and Ice Data Center provides an intuitive web interface for accessing IceBridge mission observations and measurements. Scientists and users usually do not have knowledge about the individual campaigns but are interested in data collected in a specific place. We have developed a high-performance map interface to allow users to quickly zoom to an area of interest and see any Operation IceBridge overflights. The map interface consists of two layers: the user can pan and zoom on the base map layer; the flight line layer that overlays the base layer provides all the campaign missions that intersect with the current map view. The user can click on the flight campaigns and download the data as needed. The OpenGIS® Web Map Service Interface Standard (WMS) provides a simple HTTP interface for requesting geo-registered map images from one or more distributed geospatial databases. Web Feature Service (WFS) provides an interface allowing requests for geographical features across the web using platform-independent calls. OpenLayers provides vector support (points, polylines and polygons) to build a WMS/WFS client for displaying both layers on the screen. Map Server, an open source development environment for building spatially enabled internet applications, is serving the WMS and WFS spatial data to OpenLayers. Early releases of the portal displayed unacceptably poor load time performance for flight lines and the base map tiles. This issue was caused by long response times from the map server in generating all map tiles and flight line vectors. We resolved the issue by implementing various caching strategies on top of the WMS and WFS services, including the use of Squid (www.squid-cache.org) to cache frequently-used content. Our presentation includes the architectural design of the application, and how we use OpenLayers, WMS and WFS with Squid to build a responsive web application capable of efficiently displaying geospatial data to allow the user to quickly interact with the displayed information. We describe the design, implementation and performance improvement of our caching strategies, and the tools and techniques developed to assist our data caching strategies.

A new open-source Python-based Space Weather data access, visualization, and analysis toolkit

NASA Astrophysics Data System (ADS)

de Larquier, S.; Ribeiro, A.; Frissell, N. A.; Spaleta, J.; Kunduri, B.; Thomas, E. G.; Ruohoniemi, J.; Baker, J. B.

2013-12-01

Space weather research relies heavily on combining and comparing data from multiple observational platforms. Current frameworks exist to aggregate some of the data sources, most based on file downloads via web or ftp interfaces. Empirical models are mostly fortran based and lack interfaces with more useful scripting languages. In an effort to improve data and model access, the SuperDARN community has been developing a Python-based Space Science Data Visualization Toolkit (DaViTpy). At the center of this development was a redesign of how our data (from 30 years of SuperDARN radars) was made available. Several access solutions are now wrapped into one convenient Python interface which probes local directories, a new remote NoSQL database, and an FTP server to retrieve the requested data based on availability. Motivated by the efficiency of this interface and the inherent need for data from multiple instruments, we implemented similar modules for other space science datasets (POES, OMNI, Kp, AE...), and also included fundamental empirical models with Python interfaces to enhance data analysis (IRI, HWM, MSIS...). All these modules and more are gathered in a single convenient toolkit, which is collaboratively developed and distributed using Github and continues to grow. While still in its early stages, we expect this toolkit will facilitate multi-instrument space weather research and improve scientific productivity.

A web-based 3D geological information visualization system

NASA Astrophysics Data System (ADS)

Song, Renbo; Jiang, Nan

2013-03-01

Construction of 3D geological visualization system has attracted much more concern in GIS, computer modeling, simulation and visualization fields. It not only can effectively help geological interpretation and analysis work, but also can it can help leveling up geosciences professional education. In this paper, an applet-based method was introduced for developing a web-based 3D geological information visualization system. The main aims of this paper are to explore a rapid and low-cost development method for constructing a web-based 3D geological system. First, the borehole data stored in Excel spreadsheets was extracted and then stored in SQLSERVER database of a web server. Second, the JDBC data access component was utilized for providing the capability of access the database. Third, the user interface was implemented with applet component embedded in JSP page and the 3D viewing and querying functions were implemented with PickCanvas of Java3D. Last, the borehole data acquired from geological survey were used for test the system, and the test results has shown that related methods of this paper have a certain application values.

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.

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

PubMed Central

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

2010-01-01

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

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

PubMed

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

2010-07-01

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

Entrez Neuron RDFa: a pragmatic semantic web application for data integration in neuroscience research.

PubMed

Samwald, Matthias; Lim, Ernest; Masiar, Peter; Marenco, Luis; Chen, Huajun; Morse, Thomas; Mutalik, Pradeep; Shepherd, Gordon; Miller, Perry; Cheung, Kei-Hoi

2009-01-01

The amount of biomedical data available in Semantic Web formats has been rapidly growing in recent years. While these formats are machine-friendly, user-friendly web interfaces allowing easy querying of these data are typically lacking. We present "Entrez Neuron", a pilot neuron-centric interface that allows for keyword-based queries against a coherent repository of OWL ontologies. These ontologies describe neuronal structures, physiology, mathematical models and microscopy images. The returned query results are organized hierarchically according to brain architecture. Where possible, the application makes use of entities from the Open Biomedical Ontologies (OBO) and the 'HCLS knowledgebase' developed by the W3C Interest Group for Health Care and Life Science. It makes use of the emerging RDFa standard to embed ontology fragments and semantic annotations within its HTML-based user interface. The application and underlying ontologies demonstrate how Semantic Web technologies can be used for information integration within a curated information repository and between curated information repositories. It also demonstrates how information integration can be accomplished on the client side, through simple copying and pasting of portions of documents that contain RDFa markup.

Building a Web-based drug ordering system for hospitals: from requirements engineering to prototyping.

PubMed

Hübner, U; Klein, F; Hofstetter, J; Kammeyer, G; Seete, H

2000-01-01

Web-based drug ordering allows a growing number of hospitals without pharmacy to communicate seamlessly with their external pharmacy. Business process analysis and object oriented modelling performed together with the users at a pilot hospital resulted in a comprehensive picture of the user and business requirements for electronic drug ordering. The user requirements were further validated with the help of a software prototype. In order to capture the needs of a large number of users CAP10, a new method making use of pre-built models, is proposed. Solutions for coping with the technical requirements (interfacing the business software at the pharmacy) and with the legal requirements (signing the orders) are presented.

A Web-based system for the intelligent management of diabetic patients.

PubMed

Riva, A; Bellazzi, R; Stefanelli, M

1997-01-01

We describe the design and implementation of a distributed computer-based system for the management of insulin-dependent diabetes mellitus. The goal of the system is to support the normal activities of the physicians and patients involved in the care of diabetes by providing them with a set of automated services ranging from data collection and transmission to data analysis and decision support. The system is highly integrated with current practices in the management of diabetes, and it uses Internet technology to achieve high availability and ease of use. In particular, the user interaction takes place through dynamically generated World Wide Web pages, so that all the system's functions share an intuitive graphic user interface.

YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface

PubMed Central

Abdulrehman, Dário; Monteiro, Pedro Tiago; Teixeira, Miguel Cacho; Mira, Nuno Pereira; Lourenço, Artur Bastos; dos Santos, Sandra Costa; Cabrito, Tânia Rodrigues; Francisco, Alexandre Paulo; Madeira, Sara Cordeiro; Aires, Ricardo Santos; Oliveira, Arlindo Limede; Sá-Correia, Isabel; Freitas, Ana Teresa

2011-01-01

The YEAst Search for Transcriptional Regulators And Consensus Tracking (YEASTRACT) information system (http://www.yeastract.com) was developed to support the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Last updated in June 2010, this database contains over 48 200 regulatory associations between transcription factors (TFs) and target genes, including 298 specific DNA-binding sites for 110 characterized TFs. All regulatory associations stored in the database were revisited and detailed information on the experimental evidences that sustain those associations was added and classified as direct or indirect evidences. The inclusion of this new data, gathered in response to the requests of YEASTRACT users, allows the user to restrict its queries to subsets of the data based on the existence or not of experimental evidences for the direct action of the TFs in the promoter region of their target genes. Another new feature of this release is the availability of all data through a machine readable web-service interface. Users are no longer restricted to the set of available queries made available through the existing web interface, and can use the web service interface to query, retrieve and exploit the YEASTRACT data using their own implementation of additional functionalities. The YEASTRACT information system is further complemented with several computational tools that facilitate the use of the curated data when answering a number of important biological questions. Since its first release in 2006, YEASTRACT has been extensively used by hundreds of researchers from all over the world. We expect that by making the new data and services available, the system will continue to be instrumental for yeast biologists and systems biology researchers. PMID:20972212

BioFET-SIM web interface: implementation and two applications.

PubMed

Hediger, Martin R; Jensen, Jan H; De Vico, Luca

2012-01-01

We present a web interface which allows us to conveniently set up calculations based on the BioFET-SIM model. With the interface, the signal of a BioFET sensor can be calculated depending on its parameters, as well as the signal dependence on pH. As an illustration, two case studies are presented. In the first case, a generic peptide with opposite charges on both ends is inverted in orientation on a semiconducting nanowire surface leading to a corresponding change in sign of the computed sensitivity of the device. In the second case, the binding of an antibody/antigen complex on the nanowire surface is studied in terms of orientation and analyte/nanowire surface distance. We demonstrate how the BioFET-SIM web interface can aid in the understanding of experimental data and postulate alternative ways of antibody/antigen orientation on the nanowire surface.

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

PubMed

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

2018-06-01

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

CREDO: a structural interactomics database for drug discovery

PubMed Central

Schreyer, Adrian M.; Blundell, Tom L.

2013-01-01

CREDO is a unique relational database storing all pairwise atomic interactions of inter- as well as intra-molecular contacts between small molecules and macromolecules found in experimentally determined structures from the Protein Data Bank. These interactions are integrated with further chemical and biological data. The database implements useful data structures and algorithms such as cheminformatics routines to create a comprehensive analysis platform for drug discovery. The database can be accessed through a web-based interface, downloads of data sets and web services at http://www-cryst.bioc.cam.ac.uk/credo. Database URL: http://www-cryst.bioc.cam.ac.uk/credo PMID:23868908

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.

BeefTracker: Spatial Tracking and Geodatabase for Beef Herd Sustainability and Lifecycle Analysis

NASA Astrophysics Data System (ADS)

Oltjen, J. W.; Stackhouse, J.; Forero, L.; Stackhouse-Lawson, K.

2015-12-01

We have developed a web-based mapping platform named "BeefTracker" to provide beef cattle ranchers a tool to determine how cattle production fits within sustainable ecosystems and to provide regional data to update beef sustainability lifecycle analysis. After initial identification and mapping of pastures, herd data (class and number of animals) are input on a mobile device in the field with a graphical pasture interface, stored in the cloud, and linked via the web to a personal computer for inventory tracking and analysis. Pasture use calculated on an animal basis provides quantifiable data regarding carrying capacity and subsequent beef production to provide more accurate data inputs for beef sustainability lifecycle analysis. After initial testing by university range scientists and ranchers we have enhanced the BeefTracker application to work when cell service is unavailable and to improve automation for increased ease of use. Thus far experiences with BeefTracker have been largely positive, due to livestock producers' perception of the need for this type of software application and its intuitive interface. We are now in the process of education to increase its use throughout the U.S.

Development of a user-friendly system for image processing of electron microscopy by integrating a web browser and PIONE with Eos.

PubMed

Tsukamoto, Takafumi; Yasunaga, Takuo

2014-11-01

Eos (Extensible object-oriented system) is one of the powerful applications for image processing of electron micrographs. In usual cases, Eos works with only character user interfaces (CUI) under the operating systems (OS) such as OS-X or Linux, not user-friendly. Thus, users of Eos need to be expert at image processing of electron micrographs, and have a little knowledge of computer science, as well. However, all the persons who require Eos does not an expert for CUI. Thus we extended Eos to a web system independent of OS with graphical user interfaces (GUI) by integrating web browser.Advantage to use web browser is not only to extend Eos with GUI, but also extend Eos to work under distributed computational environment. Using Ajax (Asynchronous JavaScript and XML) technology, we implemented more comfortable user-interface on web browser. Eos has more than 400 commands related to image processing for electron microscopy, and the usage of each command is different from each other. Since the beginning of development, Eos has managed their user-interface by using the interface definition file of "OptionControlFile" written in CSV (Comma-Separated Value) format, i.e., Each command has "OptionControlFile", which notes information for interface and its usage generation. Developed GUI system called "Zephyr" (Zone for Easy Processing of HYpermedia Resources) also accessed "OptionControlFIle" and produced a web user-interface automatically, because its mechanism is mature and convenient,The basic actions of client side system was implemented properly and can supply auto-generation of web-form, which has functions of execution, image preview, file-uploading to a web server. Thus the system can execute Eos commands with unique options for each commands, and process image analysis. There remain problems of image file format for visualization and workspace for analysis: The image file format information is useful to check whether the input/output file is correct and we also need to provide common workspace for analysis because the client is physically separated from a server. We solved the file format problem by extension of rules of OptionControlFile of Eos. Furthermore, to solve workspace problems, we have developed two type of system. The first system is to use only local environments. The user runs a web server provided by Eos, access to a web client through a web browser, and manipulate the local files with GUI on the web browser. The second system is employing PIONE (Process-rule for Input/Output Negotiation Environment), which is our developing platform that works under heterogenic distributed environment. The users can put their resources, such as microscopic images, text files and so on, into the server-side environment supported by PIONE, and so experts can write PIONE rule definition, which defines a workflow of image processing. PIONE run each image processing on suitable computers, following the defined rule. PIONE has the ability of interactive manipulation, and user is able to try a command with various setting values. In this situation, we contribute to auto-generation of GUI for a PIONE workflow.As advanced functions, we have developed a module to log user actions. The logs include information such as setting values in image processing, procedure of commands and so on. If we use the logs effectively, we can get a lot of advantages. For example, when an expert may discover some know-how of image processing, other users can also share logs including his know-hows and so we may obtain recommendation workflow of image analysis, if we analyze logs. To implement social platform of image processing for electron microscopists, we have developed system infrastructure, as well. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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.

HAWQS Beta Flyer

EPA Pesticide Factsheets

HAWQS is a web-based interactive water quantity and quality modeling system that provides users with interactive web interfaces and maps; pre-loaded input data; outputs that include tables, charts, graphs and raw output data; and a user guide.

HAWQS beta flyer

EPA Pesticide Factsheets

HAWQS is a web-based interactive water quantity and quality modeling system that provides users with interactive web interfaces and maps; pre-loaded input data; outputs that include tables, charts, graphs and raw output data; and a user guide.

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.

ODI - Portal, Pipeline, and Archive (ODI-PPA): a web-based astronomical compute archive, visualization, and analysis service

NASA Astrophysics Data System (ADS)

Gopu, Arvind; Hayashi, Soichi; Young, Michael D.; Harbeck, Daniel R.; Boroson, Todd; Liu, Wilson; Kotulla, Ralf; Shaw, Richard; Henschel, Robert; Rajagopal, Jayadev; Stobie, Elizabeth; Knezek, Patricia; Martin, R. Pierre; Archbold, Kevin

2014-07-01

The One Degree Imager-Portal, Pipeline, and Archive (ODI-PPA) is a web science gateway that provides astronomers a modern web interface that acts as a single point of access to their data, and rich computational and visualization capabilities. Its goal is to support scientists in handling complex data sets, and to enhance WIYN Observatory's scientific productivity beyond data acquisition on its 3.5m telescope. ODI-PPA is designed, with periodic user feedback, to be a compute archive that has built-in frameworks including: (1) Collections that allow an astronomer to create logical collations of data products intended for publication, further research, instructional purposes, or to execute data processing tasks (2) Image Explorer and Source Explorer, which together enable real-time interactive visual analysis of massive astronomical data products within an HTML5 capable web browser, and overlaid standard catalog and Source Extractor-generated source markers (3) Workflow framework which enables rapid integration of data processing pipelines on an associated compute cluster and users to request such pipelines to be executed on their data via custom user interfaces. ODI-PPA is made up of several light-weight services connected by a message bus; the web portal built using Twitter/Bootstrap, AngularJS and jQuery JavaScript libraries, and backend services written in PHP (using the Zend framework) and Python; it leverages supercomputing and storage resources at Indiana University. ODI-PPA is designed to be reconfigurable for use in other science domains with large and complex datasets, including an ongoing offshoot project for electron microscopy data.

A performance study of WebDav access to storages within the Belle II collaboration

NASA Astrophysics Data System (ADS)

Pardi, S.; Russo, G.

2017-10-01

WebDav and HTTP are becoming popular protocols for data access in the High Energy Physics community. The most used Grid and Cloud storage solutions provide such kind of interfaces, in this scenario tuning and performance evaluation became crucial aspects to promote the adoption of these protocols within the Belle II community. In this work, we present the results of a large-scale test activity, made with the goal to evaluate performances and reliability of the WebDav protocol, and study a possible adoption for the user analysis. More specifically, we considered a pilot infrastructure composed by a set of storage elements configured with the WebDav interface, hosted at the Belle II sites. The performance tests include a comparison with xrootd and gridftp. As reference tests we used a set of analysis jobs running under the Belle II software framework, accessing the input data with the ROOT I/O library, in order to simulate as much as possible a realistic user activity. The final analysis shows the possibility to achieve promising performances with WebDav on different storage systems, and gives an interesting feedback, for Belle II community and for other high energy physics experiments.

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

Ground System Architectures Workshop GMSEC SERVICES SUITE (GSS): an Agile Development Story

NASA Technical Reports Server (NTRS)

Ly, Vuong

2017-01-01

The GMSEC (Goddard Mission Services Evolution Center) Services Suite (GSS) is a collection of tools and software services along with a robust customizable web-based portal that enables the user to capture, monitor, report, and analyze system-wide GMSEC data. Given our plug-and-play architecture and the needs for rapid system development, we opted to follow the Scrum Agile Methodology for software development. Being one of the first few projects to implement the Agile methodology at NASA GSFC, in this presentation we will present our approaches, tools, successes, and challenges in implementing this methodology. The GMSEC architecture provides a scalable, extensible ground and flight system for existing and future missions. GMSEC comes with a robust Application Programming Interface (GMSEC API) and a core set of Java-based GMSEC components that facilitate the development of a GMSEC-based ground system. Over the past few years, we have seen an upbeat in the number of customers who are moving from a native desktop application environment to a web based environment particularly for data monitoring and analysis. We also see a need to provide separation of the business logic from the GUI display for our Java-based components and also to consolidate all the GUI displays into one interface. This combination of separation and consolidation brings immediate value to a GMSEC-based ground system through increased ease of data access via a uniform interface, built-in security measures, centralized configuration management, and ease of feature extensibility.

ChemDoodle Web Components: HTML5 toolkit for chemical graphics, interfaces, and informatics.

PubMed

Burger, Melanie C

2015-01-01

ChemDoodle Web Components (abbreviated CWC, iChemLabs, LLC) is a light-weight (~340 KB) JavaScript/HTML5 toolkit for chemical graphics, structure editing, interfaces, and informatics based on the proprietary ChemDoodle desktop software. The library uses and WebGL technologies and other HTML5 features to provide solutions for creating chemistry-related applications for the web on desktop and mobile platforms. CWC can serve a broad range of scientific disciplines including crystallography, materials science, organic and inorganic chemistry, biochemistry and chemical biology. CWC is freely available for in-house use and is open source (GPL v3) for all other uses.Graphical abstractAdd interactive 2D and 3D chemical sketchers, graphics, and spectra to websites and apps with ChemDoodle Web Components.

VKCDB: voltage-gated K+ channel database updated and upgraded.

PubMed

Gallin, Warren J; Boutet, Patrick A

2011-01-01

The Voltage-gated K(+) Channel DataBase (VKCDB) (http://vkcdb.biology.ualberta.ca) makes a comprehensive set of sequence data readily available for phylogenetic and comparative analysis. The current update contains 2063 entries for full-length or nearly full-length unique channel sequences from Bacteria (477), Archaea (18) and Eukaryotes (1568), an increase from 346 solely eukaryotic entries in the original release. In addition to protein sequences for channels, corresponding nucleotide sequences of the open reading frames corresponding to the amino acid sequences are now available and can be extracted in parallel with sets of protein sequences. Channels are categorized into subfamilies by phylogenetic analysis and by using hidden Markov model analyses. Although the raw database contains a number of fragmentary, duplicated, obsolete and non-channel sequences that were collected in early steps of data collection, the web interface will only return entries that have been validated as likely K(+) channels. The retrieval function of the web interface allows retrieval of entries that contain a substantial fraction of the core structural elements of VKCs, fragmentary entries, or both. The full database can be downloaded as either a MySQL dump or as an XML dump from the web site. We have now implemented automated updates at quarterly intervals.

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.

Novel Web-based Education Platforms for Information Communication utilizing Gamification, Virtual and Immersive Reality

NASA Astrophysics Data System (ADS)

Demir, I.

2015-12-01

Recent developments in internet technologies make it possible to manage and visualize large data on the web. Novel visualization techniques and interactive user interfaces allow users to create realistic environments, and interact with data to gain insight from simulations and environmental observations. This presentation showcase information communication interfaces, games, and virtual and immersive reality applications for supporting teaching and learning of concepts in atmospheric and hydrological sciences. The information communication platforms utilizes latest web technologies and allow accessing and visualizing large scale data on the web. The simulation system is a web-based 3D interactive learning environment for teaching hydrological and atmospheric processes and concepts. The simulation systems provides a visually striking platform with realistic terrain and weather information, and water simulation. The web-based simulation system provides an environment for students to learn about the earth science processes, and effects of development and human activity on the terrain. Users can access the system in three visualization modes including virtual reality, augmented reality, and immersive reality using heads-up display. The system provides various scenarios customized to fit the age and education level of various users.

Advanced Query and Data Mining Capabilities for MaROS

NASA Technical Reports Server (NTRS)

Wang, Paul; Wallick, Michael N.; Allard, Daniel A.; Gladden, Roy E.; Hy, Franklin H.

2013-01-01

The Mars Relay Operational Service (MaROS) comprises a number of tools to coordinate, plan, and visualize various aspects of the Mars Relay network. These levels include a Web-based user interface, a back-end "ReSTlet" built in Java, and databases that store the data as it is received from the network. As part of MaROS, the innovators have developed and implemented a feature set that operates on several levels of the software architecture. This new feature is an advanced querying capability through either the Web-based user interface, or through a back-end REST interface to access all of the data gathered from the network. This software is not meant to replace the REST interface, but to augment and expand the range of available data. The current REST interface provides specific data that is used by the MaROS Web application to display and visualize the information; however, the returned information from the REST interface has typically been pre-processed to return only a subset of the entire information within the repository, particularly only the information that is of interest to the GUI (graphical user interface). The new, advanced query and data mining capabilities allow users to retrieve the raw data and/or to perform their own data processing. The query language used to access the repository is a restricted subset of the structured query language (SQL) that can be built safely from the Web user interface, or entered as freeform SQL by a user. The results are returned in a CSV (Comma Separated Values) format for easy exporting to third party tools and applications that can be used for data mining or user-defined visualization and interpretation. This is the first time that a service is capable of providing access to all cross-project relay data from a single Web resource. Because MaROS contains the data for a variety of missions from the Mars network, which span both NASA and ESA, the software also establishes an access control list (ACL) on each data record in the database repository to enforce user access permissions through a multilayered approach.

A Model for Web-based Information Systems in E-Retailing.

ERIC Educational Resources Information Center

Wang, Fang; Head, Milena M.

2001-01-01

Discusses the use of Web-based information systems (WIS) by electronic retailers to attract and retain consumers and deliver business functions and strategy. Presents an abstract model for WIS design in electronic retailing; discusses customers, business determinants, and business interface; and suggests future research. (Author/LRW)

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.

DHLAS: A web-based information system for statistical genetic analysis of HLA population data.

PubMed

Thriskos, P; Zintzaras, E; Germenis, A

2007-03-01

DHLAS (database HLA system) is a user-friendly, web-based information system for the analysis of human leukocyte antigens (HLA) data from population studies. DHLAS has been developed using JAVA and the R system, it runs on a Java Virtual Machine and its user-interface is web-based powered by the servlet engine TOMCAT. It utilizes STRUTS, a Model-View-Controller framework and uses several GNU packages to perform several of its tasks. The database engine it relies upon for fast access is MySQL, but others can be used a well. The system estimates metrics, performs statistical testing and produces graphs required for HLA population studies: (i) Hardy-Weinberg equilibrium (calculated using both asymptotic and exact tests), (ii) genetics distances (Euclidian or Nei), (iii) phylogenetic trees using the unweighted pair group method with averages and neigbor-joining method, (iv) linkage disequilibrium (pairwise and overall, including variance estimations), (v) haplotype frequencies (estimate using the expectation-maximization algorithm) and (vi) discriminant analysis. The main merit of DHLAS is the incorporation of a database, thus, the data can be stored and manipulated along with integrated genetic data analysis procedures. In addition, it has an open architecture allowing the inclusion of other functions and procedures.

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.

Unified web-based network management based on distributed object orientated software agents

NASA Astrophysics Data System (ADS)

Djalalian, Amir; Mukhtar, Rami; Zukerman, Moshe

2002-09-01

This paper presents an architecture that provides a unified web interface to managed network devices that support CORBA, OSI or Internet-based network management protocols. A client gains access to managed devices through a web browser, which is used to issue management operations and receive event notifications. The proposed architecture is compatible with both the OSI Management reference Model and CORBA. The steps required for designing the building blocks of such architecture are identified.

IntegratedMap: a Web interface for integrating genetic map data.

PubMed

Yang, Hongyu; Wang, Hongyu; Gingle, Alan R

2005-05-01

IntegratedMap is a Web application and database schema for storing and interactively displaying genetic map data. Its Web interface includes a menu for direct chromosome/linkage group selection, a search form for selection based on mapped object location and linkage group displays. An overview display provides convenient access to the full range of mapped and anchored object types with genetic locus details, such as numbers, types and names of mapped/anchored objects displayed in a compact scrollable list box that automatically updates based on selected map location and object type. Also, multilinkage group and localized map views are available along with links that can be configured for integration with other Web resources. IntegratedMap is implemented in C#/ASP.NET and the package, including a MySQL schema creation script, is available from http://cggc.agtec.uga.edu/Data/download.asp

WebIntera-Classroom: An Interaction-Aware Virtual Learning Environment for Augmenting Learning Interactions

ERIC Educational Resources Information Center

Chen, Jingjing; Xu, Jianliang; Tang, Tao; Chen, Rongchao

2017-01-01

Interaction is critical for successful teaching and learning in a virtual learning environment (VLE). This paper presents a web-based interaction-aware VLE--WebIntera-classroom--which aims to augment learning interactions by increasing the learner-to-content and learner-to-instructor interactions. We design a ubiquitous interactive interface that…

Vaxjo: a web-based vaccine adjuvant database and its application for analysis of vaccine adjuvants and their uses in vaccine development.

PubMed

Sayers, Samantha; Ulysse, Guerlain; Xiang, Zuoshuang; He, Yongqun

2012-01-01

Vaccine adjuvants are compounds that enhance host immune responses to co-administered antigens in vaccines. Vaxjo is a web-based central database and analysis system that curates, stores, and analyzes vaccine adjuvants and their usages in vaccine development. Basic information of a vaccine adjuvant stored in Vaxjo includes adjuvant name, components, structure, appearance, storage, preparation, function, safety, and vaccines that use this adjuvant. Reliable references are curated and cited. Bioinformatics scripts are developed and used to link vaccine adjuvants to different adjuvanted vaccines stored in the general VIOLIN vaccine database. Presently, 103 vaccine adjuvants have been curated in Vaxjo. Among these adjuvants, 98 have been used in 384 vaccines stored in VIOLIN against over 81 pathogens, cancers, or allergies. All these vaccine adjuvants are categorized and analyzed based on adjuvant types, pathogens used, and vaccine types. As a use case study of vaccine adjuvants in infectious disease vaccines, the adjuvants used in Brucella vaccines are specifically analyzed. A user-friendly web query and visualization interface is developed for interactive vaccine adjuvant search. To support data exchange, the information of vaccine adjuvants is stored in the Vaccine Ontology (VO) in the Web Ontology Language (OWL) format.

Vaxjo: A Web-Based Vaccine Adjuvant Database and Its Application for Analysis of Vaccine Adjuvants and Their Uses in Vaccine Development

PubMed Central

Sayers, Samantha; Ulysse, Guerlain; Xiang, Zuoshuang; He, Yongqun

2012-01-01

Vaccine adjuvants are compounds that enhance host immune responses to co-administered antigens in vaccines. Vaxjo is a web-based central database and analysis system that curates, stores, and analyzes vaccine adjuvants and their usages in vaccine development. Basic information of a vaccine adjuvant stored in Vaxjo includes adjuvant name, components, structure, appearance, storage, preparation, function, safety, and vaccines that use this adjuvant. Reliable references are curated and cited. Bioinformatics scripts are developed and used to link vaccine adjuvants to different adjuvanted vaccines stored in the general VIOLIN vaccine database. Presently, 103 vaccine adjuvants have been curated in Vaxjo. Among these adjuvants, 98 have been used in 384 vaccines stored in VIOLIN against over 81 pathogens, cancers, or allergies. All these vaccine adjuvants are categorized and analyzed based on adjuvant types, pathogens used, and vaccine types. As a use case study of vaccine adjuvants in infectious disease vaccines, the adjuvants used in Brucella vaccines are specifically analyzed. A user-friendly web query and visualization interface is developed for interactive vaccine adjuvant search. To support data exchange, the information of vaccine adjuvants is stored in the Vaccine Ontology (VO) in the Web Ontology Language (OWL) format. PMID:22505817

Realising the Uncertainty Enabled Model Web

NASA Astrophysics Data System (ADS)

Cornford, D.; Bastin, L.; Pebesma, E. J.; Williams, M.; Stasch, C.; Jones, R.; Gerharz, L.

2012-12-01

The FP7 funded UncertWeb project aims to create the "uncertainty enabled model web". The central concept here is that geospatial models and data resources are exposed via standard web service interfaces, such as the Open Geospatial Consortium (OGC) suite of encodings and interface standards, allowing the creation of complex workflows combining both data and models. The focus of UncertWeb is on the issue of managing uncertainty in such workflows, and providing the standards, architecture, tools and software support necessary to realise the "uncertainty enabled model web". In this paper we summarise the developments in the first two years of UncertWeb, illustrating several key points with examples taken from the use case requirements that motivate the project. Firstly we address the issue of encoding specifications. We explain the usage of UncertML 2.0, a flexible encoding for representing uncertainty based on a probabilistic approach. This is designed to be used within existing standards such as Observations and Measurements (O&M) and data quality elements of ISO19115 / 19139 (geographic information metadata and encoding specifications) as well as more broadly outside the OGC domain. We show profiles of O&M that have been developed within UncertWeb and how UncertML 2.0 is used within these. We also show encodings based on NetCDF and discuss possible future directions for encodings in JSON. We then discuss the issues of workflow construction, considering discovery of resources (both data and models). We discuss why a brokering approach to service composition is necessary in a world where the web service interfaces remain relatively heterogeneous, including many non-OGC approaches, in particular the more mainstream SOAP and WSDL approaches. We discuss the trade-offs between delegating uncertainty management functions to the service interfaces themselves and integrating the functions in the workflow management system. We describe two utility services to address conversion between uncertainty types, and between the spatial / temporal support of service inputs / outputs. Finally we describe the tools being generated within the UncertWeb project, considering three main aspects: i) Elicitation of uncertainties on model inputs. We are developing tools to enable domain experts to provide judgements about input uncertainties from UncertWeb model components (e.g. parameters in meteorological models) which allow panels of experts to engage in the process and reach a consensus view on the current knowledge / beliefs about that parameter or variable. We are developing systems for continuous and categorical variables as well as stationary spatial fields. ii) Visualisation of the resulting uncertain outputs from the end of the workflow, but also at intermediate steps. At this point we have prototype implementations driven by the requirements from the use cases that motivate UncertWeb. iii) Sensitivity and uncertainty analysis on model outputs. Here we show the design of the overall system we are developing, including the deployment of an emulator framework to allow computationally efficient approaches. We conclude with a summary of the open issues and remaining challenges we are facing in UncertWeb, and provide a brief overview of how we plan to tackle these.

Model My Watershed and BiG CZ Data Portal: Interactive geospatial analysis and hydrological modeling web applications that leverage the Amazon cloud for scientists, resource managers and students

NASA Astrophysics Data System (ADS)

Aufdenkampe, A. K.; Mayorga, E.; Tarboton, D. G.; Sazib, N. S.; Horsburgh, J. S.; Cheetham, R.

2016-12-01

The Model My Watershed Web app (http://wikiwatershed.org/model/) was designed to enable citizens, conservation practitioners, municipal decision-makers, educators, and students to interactively select any area of interest anywhere in the continental USA to: (1) analyze real land use and soil data for that area; (2) model stormwater runoff and water-quality outcomes; and (3) compare how different conservation or development scenarios could modify runoff and water quality. The BiG CZ Data Portal is a web application for scientists for intuitive, high-performance map-based discovery, visualization, access and publication of diverse earth and environmental science data via a map-based interface that simultaneously performs geospatial analysis of selected GIS and satellite raster data for a selected area of interest. The two web applications share a common codebase (https://github.com/WikiWatershed and https://github.com/big-cz), high performance geospatial analysis engine (http://geotrellis.io/ and https://github.com/geotrellis) and deployment on the Amazon Web Services (AWS) cloud cyberinfrastructure. Users can use "on-the-fly" rapid watershed delineation over the national elevation model to select their watershed or catchment of interest. The two web applications also share the goal of enabling the scientists, resource managers and students alike to share data, analyses and model results. We will present these functioning web applications and their potential to substantially lower the bar for studying and understanding our water resources. We will also present work in progress, including a prototype system for enabling citizen-scientists to register open-source sensor stations (http://envirodiy.org/mayfly/) to stream data into these systems, so that they can be reshared using Water One Flow web services.

A Web-Based System for Monitoring and Controlling Multidisciplinary Design Projects

NASA Technical Reports Server (NTRS)

Salas, Andrea O.; Rogers, James L.

1997-01-01

In today's competitive environment, both industry and government agencies are under enormous pressure to reduce the time and cost of multidisciplinary design projects. A number of frameworks have been introduced to assist in this process by facilitating the integration of and communication among diverse disciplinary codes. An examination of current frameworks reveals weaknesses in various areas such as sequencing, displaying, monitoring, and controlling the design process. The objective of this research is to explore how Web technology, in conjunction with an existing framework, can improve these areas of weakness. This paper describes a system that executes a sequence of programs, monitors and controls the design process through a Web-based interface, and visualizes intermediate and final results through the use of Java(Tm) applets. A small sample problem, which includes nine processes with two analysis programs that are coupled to an optimizer, is used to demonstrate the feasibility of this approach.

Web based tools for visualizing imaging data and development of XNATView, a zero footprint image viewer

PubMed Central

Gutman, David A.; Dunn, William D.; Cobb, Jake; Stoner, Richard M.; Kalpathy-Cramer, Jayashree; Erickson, Bradley

2014-01-01

Advances in web technologies now allow direct visualization of imaging data sets without necessitating the download of large file sets or the installation of software. This allows centralization of file storage and facilitates image review and analysis. XNATView is a light framework recently developed in our lab to visualize DICOM images stored in The Extensible Neuroimaging Archive Toolkit (XNAT). It consists of a PyXNAT-based framework to wrap around the REST application programming interface (API) and query the data in XNAT. XNATView was developed to simplify quality assurance, help organize imaging data, and facilitate data sharing for intra- and inter-laboratory collaborations. Its zero-footprint design allows the user to connect to XNAT from a web browser, navigate through projects, experiments, and subjects, and view DICOM images with accompanying metadata all within a single viewing instance. PMID:24904399

3D-SURFER: software for high-throughput protein surface comparison and analysis

PubMed Central

La, David; Esquivel-Rodríguez, Juan; Venkatraman, Vishwesh; Li, Bin; Sael, Lee; Ueng, Stephen; Ahrendt, Steven; Kihara, Daisuke

2009-01-01

Summary: We present 3D-SURFER, a web-based tool designed to facilitate high-throughput comparison and characterization of proteins based on their surface shape. As each protein is effectively represented by a vector of 3D Zernike descriptors, comparison times for a query protein against the entire PDB take, on an average, only a couple of seconds. The web interface has been designed to be as interactive as possible with displays showing animated protein rotations, CATH codes and structural alignments using the CE program. In addition, geometrically interesting local features of the protein surface, such as pockets that often correspond to ligand binding sites as well as protrusions and flat regions can also be identified and visualized. Availability: 3D-SURFER is a web application that can be freely accessed from: http://dragon.bio.purdue.edu/3d-surfer Contact: dkihara@purdue.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19759195

3D-SURFER: software for high-throughput protein surface comparison and analysis.

PubMed

La, David; Esquivel-Rodríguez, Juan; Venkatraman, Vishwesh; Li, Bin; Sael, Lee; Ueng, Stephen; Ahrendt, Steven; Kihara, Daisuke

2009-11-01

We present 3D-SURFER, a web-based tool designed to facilitate high-throughput comparison and characterization of proteins based on their surface shape. As each protein is effectively represented by a vector of 3D Zernike descriptors, comparison times for a query protein against the entire PDB take, on an average, only a couple of seconds. The web interface has been designed to be as interactive as possible with displays showing animated protein rotations, CATH codes and structural alignments using the CE program. In addition, geometrically interesting local features of the protein surface, such as pockets that often correspond to ligand binding sites as well as protrusions and flat regions can also be identified and visualized. 3D-SURFER is a web application that can be freely accessed from: http://dragon.bio.purdue.edu/3d-surfer dkihara@purdue.edu Supplementary data are available at Bioinformatics online.

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

NASA Astrophysics Data System (ADS)

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

2008-12-01

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

Development of RESTful services and map-based user interface tools for access and delivery of data and metadata from the Marine-Geo Digital Library

NASA Astrophysics Data System (ADS)

Morton, J. J.; Ferrini, V. L.

2015-12-01

The Marine Geoscience Data System (MGDS, www.marine-geo.org) operates an interactive digital data repository and metadata catalog that provides access to a variety of marine geology and geophysical data from throughout the global oceans. Its Marine-Geo Digital Library includes common marine geophysical data types and supporting data and metadata, as well as complementary long-tail data. The Digital Library also includes community data collections and custom data portals for the GeoPRISMS, MARGINS and Ridge2000 programs, for active source reflection data (Academic Seismic Portal), and for marine data acquired by the US Antarctic Program (Antarctic and Southern Ocean Data Portal). Ensuring that these data are discoverable not only through our own interfaces but also through standards-compliant web services is critical for enabling investigators to find data of interest.Over the past two years, MGDS has developed several new RESTful web services that enable programmatic access to metadata and data holdings. These web services are compliant with the EarthCube GeoWS Building Blocks specifications and are currently used to drive our own user interfaces. New web applications have also been deployed to provide a more intuitive user experience for searching, accessing and browsing metadata and data. Our new map-based search interface combines components of the Google Maps API with our web services for dynamic searching and exploration of geospatially constrained data sets. Direct introspection of nearly all data formats for hundreds of thousands of data files curated in the Marine-Geo Digital Library has allowed for precise geographic bounds, which allow geographic searches to an extent not previously possible. All MGDS map interfaces utilize the web services of the Global Multi-Resolution Topography (GMRT) synthesis for displaying global basemap imagery and for dynamically provide depth values at the cursor location.

A Prototype Visualization of Real-time River Drainage Network Response to Rainfall

NASA Astrophysics Data System (ADS)

Demir, I.; Krajewski, W. F.

2011-12-01

The Iowa Flood Information System (IFIS) is a web-based platform developed by the Iowa Flood Center (IFC) to provide access to and visualization of flood inundation maps, real-time flood conditions, flood forecasts both short-term and seasonal, and other flood-related data for communities in Iowa. The key element of the system's architecture is the notion of community. Locations of the communities, those near streams and rivers, define basin boundaries. The IFIS streams rainfall data from NEXRAD radar, and provides three interfaces including animation for rainfall intensity, daily rainfall totals and rainfall accumulations for past 14 days for Iowa. A real-time interactive visualization interface is developed using past rainfall intensity data. The interface creates community-based rainfall products on-demand using watershed boundaries of each community as a mask. Each individual rainfall pixel is tracked in the interface along the drainage network, and the ones drains to same pixel location are accumulated. The interface loads recent rainfall data in five minute intervals that are combined with current values. Latest web technologies are utilized for the development of the interface including HTML 5 Canvas, and JavaScript. The performance of the interface is optimized to run smoothly on modern web browsers. The interface controls allow users to change internal parameters of the system, and operation conditions of the animation. The interface will help communities understand the effects of rainfall on water transport in stream and river networks and make better-informed decisions regarding the threat of floods. This presentation provides an overview of a unique visualization interface and discusses future plans for real-time dynamic presentations of streamflow forecasting.

Design of Epidemia - an Ecohealth Informatics System for Integrated Forecasting of Malaria Epidemics

NASA Astrophysics Data System (ADS)

Wimberly, M. C.; Bayabil, E.; Beyane, B.; Bishaw, M.; Henebry, G. M.; Lemma, A.; Liu, Y.; Merkord, C. L.; Mihretie, A.; Senay, G. B.; Yalew, W.

2014-12-01

Early warning of the timing and locations of malaria epidemics can facilitate the targeting of resources for prevention and emergency response. In response to this need, we are developing the Epidemic Prognosis Incorporating Disease and Environmental Monitoring for Integrated Assessment (EPIDEMIA) computer system. The system incorporates software for capturing, processing, and integrating environmental and epidemiological data from multiple sources; data assimilation techniques that continually update models and forecasts; and a web-based interface that makes the resulting information available to public health decision makers. This technology will enable forecasts based on lagged responses to environmental risk factors as well as information about recent trends in malaria cases. Environmental driving variables will include a variety of remote-sensed hydrological indicators. EPIDEMIA will be implemented and tested in the Amhara Region of Ethiopia in collaboration with local stakeholders. We conducted an initial co-design workshop in July 2014 that included environmental scientists, software engineers, and participants from the NGO, academic, and public health sectors in Ethiopia. A prototype of the EPIDEMIA web interface was presented and a requirements analysis was conducted to characterize the main use cases for the public health community, identify the critical data requirements for malaria risk modeling, and develop of a list of baseline features for the public health interface. Several critical system features were identified, including a secure web-based interface for uploading and validating surveillance data; a flexible query system to allow retrieval of environmental and epidemiological data summaries as tables, charts, and maps; and an alert system to provide automatic warnings in response to environmental and epidemiological risk factors for malaria. Future system development will involve a cycle of implementation, training, usability testing, and upgrading. This innovative translational bioinformatics approach will allow us to assess the practical effectiveness of these tools as we continually improve the technologies.

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

An Approach of Web-based Point Cloud Visualization without Plug-in

NASA Astrophysics Data System (ADS)

Ye, Mengxuan; Wei, Shuangfeng; Zhang, Dongmei

2016-11-01

With the advances in three-dimensional laser scanning technology, the demand for visualization of massive point cloud is increasingly urgent, but a few years ago point cloud visualization was limited to desktop-based solutions until the introduction of WebGL, several web renderers are available. This paper addressed the current issues in web-based point cloud visualization, and proposed a method of web-based point cloud visualization without plug-in. The method combines ASP.NET and WebGL technologies, using the spatial database PostgreSQL to store data and the open web technologies HTML5 and CSS3 to implement the user interface, a visualization system online for 3D point cloud is developed by Javascript with the web interactions. Finally, the method is applied to the real case. Experiment proves that the new model is of great practical value which avoids the shortcoming of the existing WebGIS solutions.

Open Clients for Distributed Databases

NASA Astrophysics Data System (ADS)

Chayes, D. N.; Arko, R. A.

2001-12-01

We are actively developing a collection of open source example clients that demonstrate use of our "back end" data management infrastructure. The data management system is reported elsewhere at this meeting (Arko and Chayes: A Scaleable Database Infrastructure). In addition to their primary goal of being examples for others to build upon, some of these clients may have limited utility in them selves. More information about the clients and the data infrastructure is available on line at http://data.ldeo.columbia.edu. The available examples to be demonstrated include several web-based clients including those developed for the Community Review System of the Digital Library for Earth System Education, a real-time watch standers log book, an offline interface to use log book entries, a simple client to search on multibeam metadata and others are Internet enabled and generally web-based front ends that support searches against one or more relational databases using industry standard SQL queries. In addition to the web based clients, simple SQL searches from within Excel and similar applications will be demonstrated. By defining, documenting and publishing a clear interface to the fully searchable databases, it becomes relatively easy to construct client interfaces that are optimized for specific applications in comparison to building a monolithic data and user interface system.

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.

WIFIP: a web-based user interface for automated synchrotron beamlines.

PubMed

Sallaz-Damaz, Yoann; Ferrer, Jean Luc

2017-09-01

The beamline control software, through the associated graphical user interface (GUI), is the user access point to the experiment, interacting with synchrotron beamline components and providing automated routines. FIP, the French beamline for the Investigation of Proteins, is a highly automatized macromolecular crystallography (MX) beamline at the European Synchrotron Radiation Facility. On such a beamline, a significant number of users choose to control their experiment remotely. This is often performed with a limited bandwidth and from a large choice of computers and operating systems. Furthermore, this has to be possible in a rapidly evolving experimental environment, where new developments have to be easily integrated. To face these challenges, a light, platform-independent, control software and associated GUI are required. Here, WIFIP, a web-based user interface developed at FIP, is described. Further than being the present FIP control interface, WIFIP is also a proof of concept for future MX control software.

A Development of Lightweight Grid Interface

NASA Astrophysics Data System (ADS)

Iwai, G.; Kawai, Y.; Sasaki, T.; Watase, Y.

2011-12-01

In order to help a rapid development of Grid/Cloud aware applications, we have developed API to abstract the distributed computing infrastructures based on SAGA (A Simple API for Grid Applications). SAGA, which is standardized in the OGF (Open Grid Forum), defines API specifications to access distributed computing infrastructures, such as Grid, Cloud and local computing resources. The Universal Grid API (UGAPI), which is a set of command line interfaces (CLI) and APIs, aims to offer simpler API to combine several SAGA interfaces with richer functionalities. These CLIs of the UGAPI offer typical functionalities required by end users for job management and file access to the different distributed computing infrastructures as well as local computing resources. We have also built a web interface for the particle therapy simulation and demonstrated the large scale calculation using the different infrastructures at the same time. In this paper, we would like to present how the web interface based on UGAPI and SAGA achieve more efficient utilization of computing resources over the different infrastructures with technical details and practical experiences.

WebGL Visualisation of 3D Environmental Models Based on Finnish Open Geospatial Data Sets

NASA Astrophysics Data System (ADS)

Krooks, A.; Kahkonen, J.; Lehto, L.; Latvala, P.; Karjalainen, M.; Honkavaara, E.

2014-08-01

Recent developments in spatial data infrastructures have enabled real time GIS analysis and visualization using open input data sources and service interfaces. In this study we present a new concept where metric point clouds derived from national open airborne laser scanning (ALS) and photogrammetric image data are processed, analyzed, finally visualised a through open service interfaces to produce user-driven analysis products from targeted areas. The concept is demonstrated in three environmental applications: assessment of forest storm damages, assessment of volumetric changes in open pit mine and 3D city model visualization. One of the main objectives was to study the usability and requirements of national level photogrammetric imagery in these applications. The results demonstrated that user driven 3D geospatial analyses were possible with the proposed approach and current technology, for instance, the landowner could assess the amount of fallen trees within his property borders after a storm easily using any web browser. On the other hand, our study indicated that there are still many uncertainties especially due to the insufficient standardization of photogrammetric products and processes and their quality indicators.

Entrez Neuron RDFa: a pragmatic Semantic Web application for data integration in neuroscience research

PubMed Central

Samwald, Matthias; Lim, Ernest; Masiar, Peter; Marenco, Luis; Chen, Huajun; Morse, Thomas; Mutalik, Pradeep; Shepherd, Gordon; Miller, Perry; Cheung, Kei-Hoi

2013-01-01

The amount of biomedical data available in Semantic Web formats has been rapidly growing in recent years. While these formats are machine-friendly, user-friendly web interfaces allowing easy querying of these data are typically lacking. We present “Entrez Neuron”, a pilot neuron-centric interface that allows for keyword-based queries against a coherent repository of OWL ontologies. These ontologies describe neuronal structures, physiology, mathematical models and microscopy images. The returned query results are organized hierarchically according to brain architecture. Where possible, the application makes use of entities from the Open Biomedical Ontologies (OBO) and the ‘HCLS knowledgebase’ developed by the W3C Interest Group for Health Care and Life Science. It makes use of the emerging RDFa standard to embed ontology fragments and semantic annotations within its HTML-based user interface. The application and underlying ontologies demonstrates how Semantic Web technologies can be used for information integration within a curated information repository and between curated information repositories. It also demonstrates how information integration can be accomplished on the client side, through simple copying and pasting of portions of documents that contain RDFa markup. PMID:19745321

Big data in multiple sclerosis: development of a web-based longitudinal study viewer in an imaging informatics-based eFolder system for complex data analysis and management

NASA Astrophysics Data System (ADS)

Ma, Kevin; Wang, Ximing; Lerner, Alex; Shiroishi, Mark; Amezcua, Lilyana; Liu, Brent

2015-03-01

In the past, we have developed and displayed a multiple sclerosis eFolder system for patient data storage, image viewing, and automatic lesion quantification results stored in DICOM-SR format. The web-based system aims to be integrated in DICOM-compliant clinical and research environments to aid clinicians in patient treatments and disease tracking. This year, we have further developed the eFolder system to handle big data analysis and data mining in today's medical imaging field. The database has been updated to allow data mining and data look-up from DICOM-SR lesion analysis contents. Longitudinal studies are tracked, and any changes in lesion volumes and brain parenchyma volumes are calculated and shown on the webbased user interface as graphical representations. Longitudinal lesion characteristic changes are compared with patients' disease history, including treatments, symptom progressions, and any other changes in the disease profile. The image viewer is updated such that imaging studies can be viewed side-by-side to allow visual comparisons. We aim to use the web-based medical imaging informatics eFolder system to demonstrate big data analysis in medical imaging, and use the analysis results to predict MS disease trends and patterns in Hispanic and Caucasian populations in our pilot study. The discovery of disease patterns among the two ethnicities is a big data analysis result that will help lead to personalized patient care and treatment planning.

A New User Interface for On-Demand Customizable Data Products for Sensors in a SensorWeb

NASA Technical Reports Server (NTRS)

Mandl, Daniel; Cappelaere, Pat; Frye, Stuart; Sohlberg, Rob; Ly, Vuong; Chien, Steve; Sullivan, Don

2011-01-01

A SensorWeb is a set of sensors, which can consist of ground, airborne and space-based sensors interoperating in an automated or autonomous collaborative manner. The NASA SensorWeb toolbox, developed at NASA/GSFC in collaboration with NASA/JPL, NASA/Ames and other partners, is a set of software and standards that (1) enables users to create virtual private networks of sensors over open networks; (2) provides the capability to orchestrate their actions; (3) provides the capability to customize the output data products and (4) enables automated delivery of the data products to the users desktop. A recent addition to the SensorWeb Toolbox is a new user interface, together with web services co-resident with the sensors, to enable rapid creation, loading and execution of new algorithms for processing sensor data. The web service along with the user interface follows the Open Geospatial Consortium (OGC) standard called Web Coverage Processing Service (WCPS). This presentation will detail the prototype that was built and how the WCPS was tested against a HyspIRI flight testbed and an elastic computation cloud on the ground with EO-1 data. HyspIRI is a future NASA decadal mission. The elastic computation cloud stores EO-1 data and runs software similar to Amazon online shopping.

A Smart Itsy Bitsy Spider for the Web.

ERIC Educational Resources Information Center

Chen, Hsinchun; Chung, Yi-Ming; Ramsey, Marshall; Yang, Christopher C.

1998-01-01

This study tested two Web personal spiders (i.e., agents that take users' requests and perform real-time customized searches) based on best first-search and genetic-algorithm techniques. Both results were comparable and complementary, although the genetic algorithm obtained higher recall value. The Java-based interface was found to be necessary…

User Interface Design for WWW-Based Courses: Building upon Student Evaluations.

ERIC Educational Resources Information Center

van Rennes, Linda; Collis, Betty

This paper describes how student reactions shaped the design of a WWW (World Wide Web)-based course environment at the University of Twente (Netherlands), using the example of a first year course. The first section discusses the importance of user interface (re)design for WWW-based courses. The University's focus on student evaluations of…

Ergatis: a web interface and scalable software system for bioinformatics workflows

PubMed Central

Orvis, Joshua; Crabtree, Jonathan; Galens, Kevin; Gussman, Aaron; Inman, Jason M.; Lee, Eduardo; Nampally, Sreenath; Riley, David; Sundaram, Jaideep P.; Felix, Victor; Whitty, Brett; Mahurkar, Anup; Wortman, Jennifer; White, Owen; Angiuoli, Samuel V.

2010-01-01

Motivation: The growth of sequence data has been accompanied by an increasing need to analyze data on distributed computer clusters. The use of these systems for routine analysis requires scalable and robust software for data management of large datasets. Software is also needed to simplify data management and make large-scale bioinformatics analysis accessible and reproducible to a wide class of target users. Results: We have developed a workflow management system named Ergatis that enables users to build, execute and monitor pipelines for computational analysis of genomics data. Ergatis contains preconfigured components and template pipelines for a number of common bioinformatics tasks such as prokaryotic genome annotation and genome comparisons. Outputs from many of these components can be loaded into a Chado relational database. Ergatis was designed to be accessible to a broad class of users and provides a user friendly, web-based interface. Ergatis supports high-throughput batch processing on distributed compute clusters and has been used for data management in a number of genome annotation and comparative genomics projects. Availability: Ergatis is an open-source project and is freely available at http://ergatis.sourceforge.net Contact: jorvis@users.sourceforge.net PMID:20413634

A Browser-Based Multi-User Working Environment for Physicists

NASA Astrophysics Data System (ADS)

Erdmann, M.; Fischer, R.; Glaser, C.; Klingebiel, D.; Komm, M.; Müller, G.; Rieger, M.; Steggemann, J.; Urban, M.; Winchen, T.

2014-06-01

Many programs in experimental particle physics do not yet have a graphical interface, or demand strong platform and software requirements. With the most recent development of the VISPA project, we provide graphical interfaces to existing software programs and access to multiple computing clusters through standard web browsers. The scalable clientserver system allows analyses to be performed in sizable teams, and disburdens the individual physicist from installing and maintaining a software environment. The VISPA graphical interfaces are implemented in HTML, JavaScript and extensions to the Python webserver. The webserver uses SSH and RPC to access user data, code and processes on remote sites. As example applications we present graphical interfaces for steering the reconstruction framework OFFLINE of the Pierre-Auger experiment, and the analysis development toolkit PXL. The browser based VISPA system was field-tested in biweekly homework of a third year physics course by more than 100 students. We discuss the system deployment and the evaluation by the students.

Open ISEmeter: An open hardware high-impedance interface for potentiometric detection

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

Salvador, C.; Carbajo, J.; Mozo, J. D., E-mail: jdaniel.mozo@diq.uhu.es

In this work, a new open hardware interface based on Arduino to read electromotive force (emf) from potentiometric detectors is presented. The interface has been fully designed with the open code philosophy and all documentation will be accessible on web. The paper describes a comprehensive project including the electronic design, the firmware loaded on Arduino, and the Java-coded graphical user interface to load data in a computer (PC or Mac) for processing. The prototype was tested by measuring the calibration curve of a detector. As detection element, an active poly(vinyl chloride)-based membrane was used, doped with cetyltrimethylammonium dodecylsulphate (CTA{sup +}-DS{supmore » −}). The experimental measures of emf indicate Nernstian behaviour with the CTA{sup +} content of test solutions, as it was described in the literature, proving the validity of the developed prototype. A comparative analysis of performance was made by using the same chemical detector but changing the measurement instrumentation.« less

Biotool2Web: creating simple Web interfaces for bioinformatics applications.

PubMed

Shahid, Mohammad; Alam, Intikhab; Fuellen, Georg

2006-01-01

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

Credibility judgments in web page design - a brief review.

PubMed

Selejan, O; Muresanu, D F; Popa, L; Muresanu-Oloeriu, I; Iudean, D; Buzoianu, A; Suciu, S

2016-01-01

Today, more than ever, knowledge that interfaces appearance analysis is a crucial point in human-computer interaction field has been accepted. As nowadays virtually anyone can publish information on the web, the credibility role has grown increasingly important in relation to the web-based content. Areas like trust, credibility, and behavior, doubled by overall impression and user expectation are today in the spotlight of research compared to the last period, when other pragmatic areas such as usability and utility were considered. Credibility has been discussed as a theoretical construct in the field of communication in the past decades and revealed that people tend to evaluate the credibility of communication primarily by the communicator's expertise. Other factors involved in the content communication process are trustworthiness and dynamism as well as various other criteria but to a lower extent. In this brief review, factors like web page aesthetics, browsing experiences and user experience are considered.

Developing Interoperable Air Quality Community Portals

NASA Astrophysics Data System (ADS)

Falke, S. R.; Husar, R. B.; Yang, C. P.; Robinson, E. M.; Fialkowski, W. E.

2009-04-01

Web portals are intended to provide consolidated discovery, filtering and aggregation of content from multiple, distributed web sources targeted at particular user communities. This paper presents a standards-based information architectural approach to developing portals aimed at air quality community collaboration in data access and analysis. An important characteristic of the approach is to advance beyond the present stand-alone design of most portals to achieve interoperability with other portals and information sources. We show how using metadata standards, web services, RSS feeds and other Web 2.0 technologies, such as Yahoo! Pipes and del.icio.us, helps increase interoperability among portals. The approach is illustrated within the context of the GEOSS Architecture Implementation Pilot where an air quality community portal is being developed to provide a user interface between the portals and clearinghouse of the GEOSS Common Infrastructure and the air quality community catalog of metadata and data services.

Credibility judgments in web page design – a brief review

PubMed Central

Selejan, O; Muresanu, DF; Popa, L; Muresanu-Oloeriu, I; Iudean, D; Buzoianu, A; Suciu, S

2016-01-01

Today, more than ever, knowledge that interfaces appearance analysis is a crucial point in human-computer interaction field has been accepted. As nowadays virtually anyone can publish information on the web, the credibility role has grown increasingly important in relation to the web-based content. Areas like trust, credibility, and behavior, doubled by overall impression and user expectation are today in the spotlight of research compared to the last period, when other pragmatic areas such as usability and utility were considered. Credibility has been discussed as a theoretical construct in the field of communication in the past decades and revealed that people tend to evaluate the credibility of communication primarily by the communicator’s expertise. Other factors involved in the content communication process are trustworthiness and dynamism as well as various other criteria but to a lower extent. In this brief review, factors like web page aesthetics, browsing experiences and user experience are considered. PMID:27453738

Informatic system for a global tissue–fluid biorepository with a graph theory–oriented graphical user interface

PubMed Central

Butler, William E.; Atai, Nadia; Carter, Bob; Hochberg, Fred

2014-01-01

The Richard Floor Biorepository supports collaborative studies of extracellular vesicles (EVs) found in human fluids and tissue specimens. The current emphasis is on biomarkers for central nervous system neoplasms but its structure may serve as a template for collaborative EV translational studies in other fields. The informatic system provides specimen inventory tracking with bar codes assigned to specimens and containers and projects, is hosted on globalized cloud computing resources, and embeds a suite of shared documents, calendars, and video-conferencing features. Clinical data are recorded in relation to molecular EV attributes and may be tagged with terms drawn from a network of externally maintained ontologies thus offering expansion of the system as the field matures. We fashioned the graphical user interface (GUI) around a web-based data visualization package. This system is now in an early stage of deployment, mainly focused on specimen tracking and clinical, laboratory, and imaging data capture in support of studies to optimize detection and analysis of brain tumour–specific mutations. It currently includes 4,392 specimens drawn from 611 subjects, the majority with brain tumours. As EV science evolves, we plan biorepository changes which may reflect multi-institutional collaborations, proteomic interfaces, additional biofluids, changes in operating procedures and kits for specimen handling, novel procedures for detection of tumour-specific EVs, and for RNA extraction and changes in the taxonomy of EVs. We have used an ontology-driven data model and web-based architecture with a graph theory–driven GUI to accommodate and stimulate the semantic web of EV science. PMID:25317275

Informatic system for a global tissue-fluid biorepository with a graph theory-oriented graphical user interface.

PubMed

Butler, William E; Atai, Nadia; Carter, Bob; Hochberg, Fred

2014-01-01

The Richard Floor Biorepository supports collaborative studies of extracellular vesicles (EVs) found in human fluids and tissue specimens. The current emphasis is on biomarkers for central nervous system neoplasms but its structure may serve as a template for collaborative EV translational studies in other fields. The informatic system provides specimen inventory tracking with bar codes assigned to specimens and containers and projects, is hosted on globalized cloud computing resources, and embeds a suite of shared documents, calendars, and video-conferencing features. Clinical data are recorded in relation to molecular EV attributes and may be tagged with terms drawn from a network of externally maintained ontologies thus offering expansion of the system as the field matures. We fashioned the graphical user interface (GUI) around a web-based data visualization package. This system is now in an early stage of deployment, mainly focused on specimen tracking and clinical, laboratory, and imaging data capture in support of studies to optimize detection and analysis of brain tumour-specific mutations. It currently includes 4,392 specimens drawn from 611 subjects, the majority with brain tumours. As EV science evolves, we plan biorepository changes which may reflect multi-institutional collaborations, proteomic interfaces, additional biofluids, changes in operating procedures and kits for specimen handling, novel procedures for detection of tumour-specific EVs, and for RNA extraction and changes in the taxonomy of EVs. We have used an ontology-driven data model and web-based architecture with a graph theory-driven GUI to accommodate and stimulate the semantic web of EV science.

The Water SWITCH-ON Spatial Information Platform (SIP)

NASA Astrophysics Data System (ADS)

Sala Calero, J., Sr.; Boot, G., Sr.; Dihé, P., Sr.; Arheimer, B.

2017-12-01

The amount of hydrological open data is continually growing and providing opportunities to the scientific community. Although the existing data portals (GEOSS Portal, INSPIRE community geoportal and others) enable access to open data, many users still find browsing through them difficult. Moreover, the time spent on gathering and preparing data usually is more significant than the time spent on the experiment itself. Thus, any improvement on searching, understanding, accessing or using open data is greatly beneficial. The Spatial Information Platform (SIP) has been developed to tackle these issues within the SWITCH-ON European Commission funded FP7 project. The SIP has been designed as a set of tools based on open standards that provide to the user all the necessary functionalities as described in the Publish-Find-Bind (PFB) pattern. In other words, this means that the SIP helps users to locate relevant and suitable data for their experiments analysis, to access and transform it (filtering, extraction, selection, conversion, aggregation). Moreover, the SIP can be used to provide descriptive information about the data and to publish it so others can find and use it. The SIP is based on existing open data protocols such as the OGC/CSW, OGC/WMS, OpenDAP and open-source components like PostgreSQL/PostGIS, GeoServer and pyCSW. The SIP is divided in three main user interfaces: the BYOD (Browse your open dataset) web interface, the Expert GUI tool and the Upload Data and Metadata web interface. The BYOD HTML5 client is the main entry point for users that want to browse through open data in the SIP. The BYOD has a map interface based on Leaflet JavaScript libraries so that the users can search more efficiently. The web-based Open Data Registration Tool is a user-friendly upload and metadata description interface (geographical extent, license, DOI generation). The Expert GUI is a desktop application that provides full metadata editing capabilities for the metadata moderators of the project. In conclusion, the Spatial Information Platform (SIP) provides to its community a set of tools for better understanding and ease of use of hydrological open-data. Moreover, the SIP has been based on well-known OGC standards that will allow the connection and data harvesting from popular open data portals such as the GEOSS system of systems.

Influence of Learning Styles on Graphical User Interface Preferences for e-Learners

ERIC Educational Resources Information Center

Dedic, Velimir; Markovic, Suzana

2012-01-01

Implementing Web-based educational environment requires not only developing appropriate architectures, but also incorporating human factors considerations. User interface becomes the major channel to convey information in e-learning context: a well-designed and friendly enough interface is thus the key element in helping users to get the best…

Design and development of a web-based application for diabetes patient data management.

PubMed

Deo, S S; Deobagkar, D N; Deobagkar, Deepti D

2005-01-01

A web-based database management system developed for collecting, managing and analysing information of diabetes patients is described here. It is a searchable, client-server, relational database application, developed on the Windows platform using Oracle, Active Server Pages (ASP), Visual Basic Script (VB Script) and Java Script. The software is menu-driven and allows authorized healthcare providers to access, enter, update and analyse patient information. Graphical representation of data can be generated by the system using bar charts and pie charts. An interactive web interface allows users to query the database and generate reports. Alpha- and beta-testing of the system was carried out and the system at present holds records of 500 diabetes patients and is found useful in diagnosis and treatment. In addition to providing patient data on a continuous basis in a simple format, the system is used in population and comparative analysis. It has proved to be of significant advantage to the healthcare provider as compared to the paper-based system.

Cancer Imaging Phenomics Toolkit (CaPTk) | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

CaPTk is a software toolkit to facilitate translation of quantitative image analysis methods that help us obtain rich imaging phenotypic signatures of oncologic images and relate them to precision diagnostics and prediction of clinical outcomes, as well as to underlying molecular characteristics of cancer. The stand-alone graphical user interface of CaPTk brings analysis methods from the realm of medical imaging research to the clinic, and will be extended to use web-based services for computationally-demanding pipelines.

Prototyping the graphical user interface for the operator of the Cherenkov Telescope Array

NASA Astrophysics Data System (ADS)

Sadeh, I.; Oya, I.; Schwarz, J.; Pietriga, E.

2016-07-01

The Cherenkov Telescope Array (CTA) is a planned gamma-ray observatory. CTA will incorporate about 100 imaging atmospheric Cherenkov telescopes (IACTs) at a Southern site, and about 20 in the North. Previous IACT experiments have used up to five telescopes. Subsequently, the design of a graphical user interface (GUI) for the operator of CTA involves new challenges. We present a GUI prototype, the concept for which is being developed in collaboration with experts from the field of Human-Computer Interaction (HCI). The prototype is based on Web technology; it incorporates a Python web server, Web Sockets and graphics generated with the d3.js Javascript library.

Integrated web-based viewing and secure remote access to a clinical data repository and diverse clinical systems.

PubMed

Duncan, R G; Saperia, D; Dulbandzhyan, R; Shabot, M M; Polaschek, J X; Jones, D T

2001-01-01

The advent of the World-Wide-Web protocols and client-server technology has made it easy to build low-cost, user-friendly, platform-independent graphical user interfaces to health information systems and to integrate the presentation of data from multiple systems. The authors describe a Web interface for a clinical data repository (CDR) that was moved from concept to production status in less than six months using a rapid prototyping approach, multi-disciplinary development team, and off-the-shelf hardware and software. The system has since been expanded to provide an integrated display of clinical data from nearly 20 disparate information systems.

Spider-web amphiphiles as artificial lipid clusters: design, synthesis, and accommodation of lipid components at the air-water interface.

PubMed

Ariga, Katsuhiko; Urakawa, Toshihiro; Michiue, Atsuo; Kikuchi, Jun-ichi

2004-08-03

As a novel category of two-dimensional lipid clusters, dendrimers having an amphiphilic structure in every unit were synthesized and labeled "spider-web amphiphiles". Amphiphilic units based on a Lys-Lys-Glu tripeptide with hydrophobic tails at the C-terminal and a polar head at the N-terminal are dendrically connected through stepwise peptide coupling. This structural design allowed us to separately introduce the polar head and hydrophobic tails. Accordingly, we demonstrated the synthesis of the spider-web amphiphile series in three combinations: acetyl head/C16 chain, acetyl head/C18 chain, and ammonium head/C16 chain. All the spider-web amphiphiles were synthesized in satisfactory yields, and characterized by 1H NMR, MALDI-TOFMS, GPC, and elemental analyses. Surface pressure (pi)-molecular area (A) isotherms showed the formation of expanded monolayers except for the C18-chain amphiphile at 10 degrees C, for which the molecular area in the condensed phase is consistent with the cross-sectional area assigned for all the alkyl chains. In all the spider-web amphiphiles, the molecular areas at a given pressure in the expanded phase increased in proportion to the number of units, indicating that alkyl chains freely fill the inner space of the dendritic core. The mixing of octadecanoic acid with the spider-web amphiphiles at the air-water interface induced condensation of the molecular area. From the molecular area analysis, the inclusion of the octadecanoic acid bears a stoichiometric characteristic; i.e., the number of captured octadecanoic acids in the spider-web amphiphile roughly agrees with the number of branching points in the spider-web amphiphile.

Web of Pseudostreamer and Streamer Belts and their Interplanetary Signatures

NASA Astrophysics Data System (ADS)

Crooker, N. U.; Owens, M. J.; McPherron, R. L.

2012-12-01

A new method of identifying pseudostreamer and streamer belts on potential field source surface (PFSS) maps reveals how they interconnect to form a network or web-like pattern that expands to cover the Sun at solar maximum. The method is based upon calculating the distance dS between the photospheric footpoints of field lines that are uniformly spaced in longitude at the source surface. This distance peaks sharply under the large arcades characteristic of both pseudostreamer and streamer belts, where the former (latter) mark boundaries between coronal holes with the same (different) polarities. Thus the two kinds of belts are distinguished from each other by noting whether or not a change in magnetic polarity accompanies the peak, signaling passage of the heliospheric current sheet unique to the streamer belt. To compare the plasma and composition properties of pseudostreamer and streamer belts at 1 AU, we use 12 years of ACE data to perform superposed epoch analysis centered on stream interfaces in interaction regions, where the interfaces mark the trailing boundaries of what was originally slow flow. The interfaces are sorted according to whether they bound streamers or pseudostreamers by ballistically mapping them back to traces of dS across the source surface. Preliminary results indicate sharp drops in oxygen and carbon charge state ratios as well as the elemental abundance ratio Fe/O at both streamer and pseudostreamer boundaries. Combined with the web-like pattern of streamer and pseudostreamer belts, the results are consistent with the separatrix-web model of the slow solar wind first described by Antiochos et al. [Astrophys. J., 731, 112, 2011].

Mining microarray data at NCBI's Gene Expression Omnibus (GEO)*.

PubMed

Barrett, Tanya; Edgar, Ron

2006-01-01

The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) has emerged as the leading fully public repository for gene expression data. This chapter describes how to use Web-based interfaces, applications, and graphics to effectively explore, visualize, and interpret the hundreds of microarray studies and millions of gene expression patterns stored in GEO. Data can be examined from both experiment-centric and gene-centric perspectives using user-friendly tools that do not require specialized expertise in microarray analysis or time-consuming download of massive data sets. The GEO database is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.

LAVA web-based remote simulation: enhancements for education and technology innovation

NASA Astrophysics Data System (ADS)

Lee, Sang Il; Ng, Ka Chun; Orimoto, Takashi; Pittenger, Jason; Horie, Toshi; Adam, Konstantinos; Cheng, Mosong; Croffie, Ebo H.; Deng, Yunfei; Gennari, Frank E.; Pistor, Thomas V.; Robins, Garth; Williamson, Mike V.; Wu, Bo; Yuan, Lei; Neureuther, Andrew R.

2001-09-01

The Lithography Analysis using Virtual Access (LAVA) web site at http://cuervo.eecs.berkeley.edu/Volcano/ has been enhanced with new optical and deposition applets, graphical infrastructure and linkage to parallel execution on networks of workstations. More than ten new graphical user interface applets have been designed to support education, illustrate novel concepts from research, and explore usage of parallel machines. These applets have been improved through feedback and classroom use. Over the last year LAVA provided industry and other academic communities 1,300 session and 700 rigorous simulations per month among the SPLAT, SAMPLE2D, SAMPLE3D, TEMPEST, STORM, and BEBS simulators.

Analysis of metabolomics datasets with high-performance computing and metabolite atlases

DOE PAGES

Yao, Yushu; Sun, Terence; Wang, Tony; ...

2015-07-20

Even with the widespread use of liquid chromatography mass spectrometry (LC/MS) based metabolomics, there are still a number of challenges facing this promising technique. Many, diverse experimental workflows exist; yet there is a lack of infrastructure and systems for tracking and sharing of information. Here, we describe the Metabolite Atlas framework and interface that provides highly-efficient, web-based access to raw mass spectrometry data in concert with assertions about chemicals detected to help address some of these challenges. This integration, by design, enables experimentalists to explore their raw data, specify and refine features annotations such that they can be leveraged formore » future experiments. Fast queries of the data through the web using SciDB, a parallelized database for high performance computing, make this process operate quickly. Furthermore, by using scripting containers, such as IPython or Jupyter, to analyze the data, scientists can utilize a wide variety of freely available graphing, statistics, and information management resources. In addition, the interfaces facilitate integration with systems biology tools to ultimately link metabolomics data with biological models.« less

A continuously growing web-based interface structure databank

NASA Astrophysics Data System (ADS)

Erwin, N. A.; Wang, E. I.; Osysko, A.; Warner, D. H.

2012-07-01

The macroscopic properties of materials can be significantly influenced by the presence of microscopic interfaces. The complexity of these interfaces coupled with the vast configurational space in which they reside has been a long-standing obstacle to the advancement of true bottom-up material behavior predictions. In this vein, atomistic simulations have proven to be a valuable tool for investigating interface behavior. However, before atomistic simulations can be utilized to model interface behavior, meaningful interface atomic structures must be generated. The generation of structures has historically been carried out disjointly by individual research groups, and thus, has constituted an overlap in effort across the broad research community. To address this overlap and to lower the barrier for new researchers to explore interface modeling, we introduce a web-based interface structure databank (www.isdb.cee.cornell.edu) where users can search, download and share interface structures. The databank is intended to grow via two mechanisms: (1) interface structure donations from individual research groups and (2) an automated structure generation algorithm which continuously creates equilibrium interface structures. In this paper, we describe the databank, the automated interface generation algorithm, and compare a subset of the autonomously generated structures to structures currently available in the literature. To date, the automated generation algorithm has been directed toward aluminum grain boundary structures, which can be compared with experimentally measured population densities of aluminum polycrystals.

Using NASA's Giovanni Web Portal to Access and Visualize Satellite-based Earth Science Data in the Classroom

NASA Technical Reports Server (NTRS)

Lloyd, Steven; Acker, James G.; Prados, Ana I.; Leptoukh, Gregory G.

2008-01-01

One of the biggest obstacles for the average Earth science student today is locating and obtaining satellite-based remote sensing data sets in a format that is accessible and optimal for their data analysis needs. At the Goddard Earth Sciences Data and Information Services Center (GES-DISC) alone, on the order of hundreds of Terabytes of data are available for distribution to scientists, students and the general public. The single biggest and time-consuming hurdle for most students when they begin their study of the various datasets is how to slog through this mountain of data to arrive at a properly sub-setted and manageable data set to answer their science question(s). The GES DISC provides a number of tools for data access and visualization, including the Google-like Mirador search engine and the powerful GES-DISC Interactive Online Visualization ANd aNalysis Infrastructure (Giovanni) web interface.

An interactive web-based system using cloud for large-scale visual analytics

NASA Astrophysics Data System (ADS)

Kaseb, Ahmed S.; Berry, Everett; Rozolis, Erik; McNulty, Kyle; Bontrager, Seth; Koh, Youngsol; Lu, Yung-Hsiang; Delp, Edward J.

2015-03-01

Network cameras have been growing rapidly in recent years. Thousands of public network cameras provide tremendous amount of visual information about the environment. There is a need to analyze this valuable information for a better understanding of the world around us. This paper presents an interactive web-based system that enables users to execute image analysis and computer vision techniques on a large scale to analyze the data from more than 65,000 worldwide cameras. This paper focuses on how to use both the system's website and Application Programming Interface (API). Given a computer program that analyzes a single frame, the user needs to make only slight changes to the existing program and choose the cameras to analyze. The system handles the heterogeneity of the geographically distributed cameras, e.g. different brands, resolutions. The system allocates and manages Amazon EC2 and Windows Azure cloud resources to meet the analysis requirements.

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

A knowledge base for Vitis vinifera functional analysis.

PubMed

Pulvirenti, Alfredo; Giugno, Rosalba; Distefano, Rosario; Pigola, Giuseppe; Mongiovi, Misael; Giudice, Girolamo; Vendramin, Vera; Lombardo, Alessandro; Cattonaro, Federica; Ferro, Alfredo

2015-01-01

Vitis vinifera (Grapevine) is the most important fruit species in the modern world. Wine and table grapes sales contribute significantly to the economy of major wine producing countries. The most relevant goals in wine production concern quality and safety. In order to significantly improve the achievement of these objectives and to gain biological knowledge about cultivars, a genomic approach is the most reliable strategy. The recent grapevine genome sequencing offers the opportunity to study the potential roles of genes and microRNAs in fruit maturation and other physiological and pathological processes. Although several systems allowing the analysis of plant genomes have been reported, none of them has been designed specifically for the functional analysis of grapevine genomes of cultivars under environmental stress in connection with microRNA data. Here we introduce a novel knowledge base, called BIOWINE, designed for the functional analysis of Vitis vinifera genomes of cultivars present in Sicily. The system allows the analysis of RNA-seq experiments of two different cultivars, namely Nero d'Avola and Nerello Mascalese. Samples were taken under different climatic conditions of phenological phases, diseases, and geographic locations. The BIOWINE web interface is equipped with data analysis modules for grapevine genomes. In particular users may analyze the current genome assembly together with the RNA-seq data through a customized version of GBrowse. The web interface allows users to perform gene set enrichment by exploiting third-party databases. BIOWINE is a knowledge base implementing a set of bioinformatics tools for the analysis of grapevine genomes. The system aims to increase our understanding of the grapevine varieties and species of Sicilian products focusing on adaptability to different climatic conditions, phenological phases, diseases, and geographic locations.

Web-Based Media Contents Editor for UCC Websites

NASA Astrophysics Data System (ADS)

Kim, Seoksoo

The purpose of this research is to "design web-based media contents editor for establishing UCC(User Created Contents)-based websites." The web-based editor features user-oriented interfaces and increased convenience, significantly different from previous off-line editors. It allows users to edit media contents online and can be effectively used for online promotion activities of enterprises and organizations. In addition to development of the editor, the research aims to support the entry of enterprises and public agencies to the online market by combining the technology with various UCC items.

Visual Analytics for Law Enforcement: Deploying a Service-Oriented Analytic Framework for Web-based Visualization

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

Dowson, Scott T.; Bruce, Joseph R.; Best, Daniel M.

2009-04-14

This paper presents key components of the Law Enforcement Information Framework (LEIF) that provides communications, situational awareness, and visual analytics tools in a service-oriented architecture supporting web-based desktop and handheld device users. LEIF simplifies interfaces and visualizations of well-established visual analytical techniques to improve usability. Advanced analytics capability is maintained by enhancing the underlying processing to support the new interface. LEIF development is driven by real-world user feedback gathered through deployments at three operational law enforcement organizations in the US. LEIF incorporates a robust information ingest pipeline supporting a wide variety of information formats. LEIF also insulates interface and analyticalmore » components from information sources making it easier to adapt the framework for many different data repositories.« less

WebProtégé: a collaborative Web-based platform for editing biomedical ontologies.

PubMed

Horridge, Matthew; Tudorache, Tania; Nuylas, Csongor; Vendetti, Jennifer; Noy, Natalya F; Musen, Mark A

2014-08-15

WebProtégé is an open-source Web application for editing OWL 2 ontologies. It contains several features to aid collaboration, including support for the discussion of issues, change notification and revision-based change tracking. WebProtégé also features a simple user interface, which is geared towards editing the kinds of class descriptions and annotations that are prevalent throughout biomedical ontologies. Moreover, it is possible to configure the user interface using views that are optimized for editing Open Biomedical Ontology (OBO) class descriptions and metadata. Some of these views are shown in the Supplementary Material and can be seen in WebProtégé itself by configuring the project as an OBO project. WebProtégé is freely available for use on the Web at http://webprotege.stanford.edu. It is implemented in Java and JavaScript using the OWL API and the Google Web Toolkit. All major browsers are supported. For users who do not wish to host their ontologies on the Stanford servers, WebProtégé is available as a Web app that can be run locally using a Servlet container such as Tomcat. Binaries, source code and documentation are available under an open-source license at http://protegewiki.stanford.edu/wiki/WebProtege. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Metis Hub: The Development of an Intuitive Project Planning System

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

McConnell, Rachael M.; Lawrence Livermore National Lab.

2015-08-26

The goal is to develop an intuitive, dynamic, and consistent interface for the Metis Planning System by combining user requirements and human engineering concepts. The system is largely based upon existing systems so some tools already have working models that we can follow. However, the web-based interface is completely new.

STAR: an integrated solution to management and visualization of sequencing data.

PubMed

Wang, Tao; Liu, Jie; Shen, Li; Tonti-Filippini, Julian; Zhu, Yun; Jia, Haiyang; Lister, Ryan; Whitaker, John W; Ecker, Joseph R; Millar, A Harvey; Ren, Bing; Wang, Wei

2013-12-15

Easily visualization of complex data features is a necessary step to conduct studies on next-generation sequencing (NGS) data. We developed STAR, an integrated web application that enables online management, visualization and track-based analysis of NGS data. STAR is a multilayer web service system. On the client side, STAR leverages JavaScript, HTML5 Canvas and asynchronous communications to deliver a smoothly scrolling desktop-like graphical user interface with a suite of in-browser analysis tools that range from providing simple track configuration controls to sophisticated feature detection within datasets. On the server side, STAR supports private session state retention via an account management system and provides data management modules that enable collection, visualization and analysis of third-party sequencing data from the public domain with over thousands of tracks hosted to date. Overall, STAR represents a next-generation data exploration solution to match the requirements of NGS data, enabling both intuitive visualization and dynamic analysis of data. STAR browser system is freely available on the web at http://wanglab.ucsd.edu/star/browser and https://github.com/angell1117/STAR-genome-browser.

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/.

A Framework for Integrating Oceanographic Data Repositories

NASA Astrophysics Data System (ADS)

Rozell, E.; Maffei, A. R.; Beaulieu, S. E.; Fox, P. A.

2010-12-01

Oceanographic research covers a broad range of science domains and requires a tremendous amount of cross-disciplinary collaboration. Advances in cyberinfrastructure are making it easier to share data across disciplines through the use of web services and community vocabularies. Best practices in the design of web services and vocabularies to support interoperability amongst science data repositories are only starting to emerge. Strategic design decisions in these areas are crucial to the creation of end-user data and application integration tools. We present S2S, a novel framework for deploying customizable user interfaces to support the search and analysis of data from multiple repositories. Our research methods follow the Semantic Web methodology and technology development process developed by Fox et al. This methodology stresses the importance of close scientist-technologist interactions when developing scientific use cases, keeping the project well scoped and ensuring the result meets a real scientific need. The S2S framework motivates the development of standardized web services with well-described parameters, as well as the integration of existing web services and applications in the search and analysis of data. S2S also encourages the use and development of community vocabularies and ontologies to support federated search and reduce the amount of domain expertise required in the data discovery process. S2S utilizes the Web Ontology Language (OWL) to describe the components of the framework, including web service parameters, and OpenSearch as a standard description for web services, particularly search services for oceanographic data repositories. We have created search services for an oceanographic metadata database, a large set of quality-controlled ocean profile measurements, and a biogeographic search service. S2S provides an application programming interface (API) that can be used to generate custom user interfaces, supporting data and application integration across these repositories and other web resources. Although initially targeted towards a general oceanographic audience, the S2S framework shows promise in many science domains, inspired in part by the broad disciplinary coverage of oceanography. This presentation will cover the challenges addressed by the S2S framework, the research methods used in its development, and the resulting architecture for the system. It will demonstrate how S2S is remarkably extensible, and can be generalized to many science domains. Given these characteristics, the framework can simplify the process of data discovery and analysis for the end user, and can help to shift the responsibility of search interface development away from data managers.

BMI cyberworkstation: enabling dynamic data-driven brain-machine interface research through cyberinfrastructure.

PubMed

Zhao, Ming; Rattanatamrong, Prapaporn; DiGiovanna, Jack; Mahmoudi, Babak; Figueiredo, Renato J; Sanchez, Justin C; Príncipe, José C; Fortes, José A B

2008-01-01

Dynamic data-driven brain-machine interfaces (DDDBMI) have great potential to advance the understanding of neural systems and improve the design of brain-inspired rehabilitative systems. This paper presents a novel cyberinfrastructure that couples in vivo neurophysiology experimentation with massive computational resources to provide seamless and efficient support of DDDBMI research. Closed-loop experiments can be conducted with in vivo data acquisition, reliable network transfer, parallel model computation, and real-time robot control. Behavioral experiments with live animals are supported with real-time guarantees. Offline studies can be performed with various configurations for extensive analysis and training. A Web-based portal is also provided to allow users to conveniently interact with the cyberinfrastructure, conducting both experimentation and analysis. New motor control models are developed based on this approach, which include recursive least square based (RLS) and reinforcement learning based (RLBMI) algorithms. The results from an online RLBMI experiment shows that the cyberinfrastructure can successfully support DDDBMI experiments and meet the desired real-time requirements.

A web interface for easy flexible protein-protein docking with ATTRACT.

PubMed

de Vries, Sjoerd J; Schindler, Christina E M; Chauvot de Beauchêne, Isaure; Zacharias, Martin

2015-02-03

Protein-protein docking programs can give valuable insights into the structure of protein complexes in the absence of an experimental complex structure. Web interfaces can facilitate the use of docking programs by structural biologists. Here, we present an easy web interface for protein-protein docking with the ATTRACT program. While aimed at nonexpert users, the web interface still covers a considerable range of docking applications. The web interface supports systematic rigid-body protein docking with the ATTRACT coarse-grained force field, as well as various kinds of protein flexibility. The execution of a docking protocol takes up to a few hours on a standard desktop computer. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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.

Web Based Seismological Monitoring (wbsm)

NASA Astrophysics Data System (ADS)

Giudicepietro, F.; Meglio, V.; Romano, S. P.; de Cesare, W.; Ventre, G.; Martini, M.

Over the last few decades the seismological monitoring systems have dramatically improved tanks to the technological advancements and to the scientific progresses of the seismological studies. The most modern processing systems use the network tech- nologies to realize high quality performances in data transmission and remote controls. Their architecture is designed to favor the real-time signals analysis. This is, usually, realized by adopting a modular structure that allow to easy integrate any new cal- culation algorithm, without affecting the other system functionalities. A further step in the seismic processing systems evolution is the large use of the web based appli- cations. The web technologies can be an useful support for the monitoring activities allowing to automatically publishing the results of signals processing and favoring the remote access to data, software systems and instrumentation. An application of the web technologies to the seismological monitoring has been developed at the "Os- servatorio Vesuviano" monitoring center (INGV) in collaboration with the "Diparti- mento di Informatica e Sistemistica" of the Naples University. A system named Web Based Seismological Monitoring (WBSM) has been developed. Its main objective is to automatically publish the seismic events processing results and to allow displaying, analyzing and downloading seismic data via Internet. WBSM uses the XML tech- nology for hypocentral and picking parameters representation and creates a seismic events data base containing parametric data and wave-forms. In order to give tools for the evaluation of the quality and reliability of the published locations, WBSM also supplies all the quality parameters calculated by the locating program and allow to interactively display the wave-forms and the related parameters. WBSM is a modular system in which the interface function to the data sources is performed by two spe- cific modules so that to make it working in conjunction with a generic data source it is sufficient to modify or substitute the interface modules. WBSM is running at the "Osservatorio Vesuviano" Monitoring Center since the beginning of 2001 and can be visited at http://ov.ingv.it.

SU-F-P-10: A Web-Based Radiation Safety Relational Database Module for Regulatory Compliance

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

Rosen, C; Ramsay, B; Konerth, S

Purpose: Maintaining compliance with Radioactive Materials Licenses is inherently a time-consuming task requiring focus and attention to detail. Staff tasked with these responsibilities, such as the Radiation Safety Officer and associated personnel must retain disparate records for eventual placement into one or more annual reports. Entering results and records in a relational database using a web browser as the interface, and storing that data in a cloud-based storage site, removes procedural barriers. The data becomes more adaptable for mining and sharing. Methods: Web-based code was written utilizing the web framework Django, written in Python. Additionally, the application utilizes JavaScript formore » front-end interaction, SQL, HTML and CSS. Quality assurance code testing is performed in a sequential style, and new code is only added after the successful testing of the previous goals. Separate sections of the module include data entry and analysis for audits, surveys, quality management, and continuous quality improvement. Data elements can be adapted for quarterly and annual reporting, and for immediate notification of user determined alarm settings. Results: Current advances are focusing on user interface issues, and determining the simplest manner by which to teach the user to build query forms. One solution has been to prepare library documents that a user can select or edit in place of creation a new document. Forms are being developed based upon Nuclear Regulatory Commission federal code, and will be expanded to include State Regulations. Conclusion: Establishing a secure website to act as the portal for data entry, storage and manipulation can lead to added efficiencies for a Radiation Safety Program. Access to multiple databases can lead to mining for big data programs, and for determining safety issues before they occur. Overcoming web programming challenges, a category that includes mathematical handling, is providing challenges that are being overcome.« less

Digital hand atlas for web-based bone age assessment: system design and implementation

NASA Astrophysics Data System (ADS)

Cao, Fei; Huang, H. K.; Pietka, Ewa; Gilsanz, Vicente

2000-04-01

A frequently used assessment method of skeletal age is atlas matching by a radiological examination of a hand image against a small set of Greulich-Pyle patterns of normal standards. The method however can lead to significant deviation in age assessment, due to a variety of observers with different levels of training. The Greulich-Pyle atlas based on middle upper class white populations in the 1950s, is also not fully applicable for children of today, especially regarding the standard development in other racial groups. In this paper, we present our system design and initial implementation of a digital hand atlas and computer-aided diagnostic (CAD) system for Web-based bone age assessment. The digital atlas will remove the disadvantages of the currently out-of-date one and allow the bone age assessment to be computerized and done conveniently via Web. The system consists of a hand atlas database, a CAD module and a Java-based Web user interface. The atlas database is based on a large set of clinically normal hand images of diverse ethnic groups. The Java-based Web user interface allows users to interact with the hand image database form browsers. Users can use a Web browser to push a clinical hand image to the CAD server for a bone age assessment. Quantitative features on the examined image, which reflect the skeletal maturity, is then extracted and compared with patterns from the atlas database to assess the bone age.

SOCR Analyses - an Instructional Java Web-based Statistical Analysis Toolkit.

PubMed

Chu, Annie; Cui, Jenny; Dinov, Ivo D

2009-03-01

The Statistical Online Computational Resource (SOCR) designs web-based tools for educational use in a variety of undergraduate courses (Dinov 2006). Several studies have demonstrated that these resources significantly improve students' motivation and learning experiences (Dinov et al. 2008). SOCR Analyses is a new component that concentrates on data modeling and analysis using parametric and non-parametric techniques supported with graphical model diagnostics. Currently implemented analyses include commonly used models in undergraduate statistics courses like linear models (Simple Linear Regression, Multiple Linear Regression, One-Way and Two-Way ANOVA). In addition, we implemented tests for sample comparisons, such as t-test in the parametric category; and Wilcoxon rank sum test, Kruskal-Wallis test, Friedman's test, in the non-parametric category. SOCR Analyses also include several hypothesis test models, such as Contingency tables, Friedman's test and Fisher's exact test.The code itself is open source (http://socr.googlecode.com/), hoping to contribute to the efforts of the statistical computing community. The code includes functionality for each specific analysis model and it has general utilities that can be applied in various statistical computing tasks. For example, concrete methods with API (Application Programming Interface) have been implemented in statistical summary, least square solutions of general linear models, rank calculations, etc. HTML interfaces, tutorials, source code, activities, and data are freely available via the web (www.SOCR.ucla.edu). Code examples for developers and demos for educators are provided on the SOCR Wiki website.In this article, the pedagogical utilization of the SOCR Analyses is discussed, as well as the underlying design framework. As the SOCR project is on-going and more functions and tools are being added to it, these resources are constantly improved. The reader is strongly encouraged to check the SOCR site for most updated information and newly added models.

Collaborative Interactive Visualization Exploratory Concept

DTIC Science & Technology

2015-06-01

the FIAC concepts. It consists of various DRDC-RDDC-2015-N004 intelligence analysis web services build of top of big data technologies exploited...sits on the UDS where validated common knowledge is stored. Based on the Lumify software2, this important component exploits big data technologies such...interfaces. Above this database resides the Big Data Manager responsible for transparent data transmission between the UDS and the rest of the S3

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/ .

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

New Data Products and Tools from STEREO's IMPACT Investigation

NASA Astrophysics Data System (ADS)

Schroeder, P. C.; Luhmann, J. G.; Li, Y.; Huttunen, E.; Toy, V.; Russell, C. T.; Davis, A.

2008-05-01

STEREO's IMPACT (In-situ Measurements of Particles and CME Transients) investigation provides the first opportunity for long duration, detailed observations of 1 AU magnetic field structures, plasma and suprathermal electrons, and energetic particles at points bracketing Earth's heliospheric location. The IMPACT team has developed both human-friendly web portals and API's (application program interfaces) which provide straight- foward data access to scientists and the Virtual Observatories. Several new data products and web features have been developed including the release of more and higher-level data products, a library of TPLOT-based IDL data analysis routines, and web sites devoted to event analysis and inter-mission and inter-disciplinary collaboration. A web browser integrating STEREO and L1 in situ data with imaging and models provides a powerful venue for exploring the Sun-Earth connection. These latest releases enable the larger scientific community to use STEREO's unique in-situ data in novel ways along side "third eye" data sets from Wind, ACE and other heliospheric missions contributing to a better understanding of three dimensional structures in the solar wind.

77 FR 61039 - Self-Regulatory Organizations; NASDAQ OMX PHLX LLC; Notice of Filing and Immediate Effectiveness...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-05

... adopt the new QView service. QView is a web-based, front-end application, which provides a subscribing... orders and executions provided in the QView dashboard interface. The dashboard also allows a QView... trading activity.\\5\\ \\4\\ TradeInfo PSX is a web-based tool that, among other things, allows users access...

galaxie--CGI scripts for sequence identification through automated phylogenetic analysis.

PubMed

Nilsson, R Henrik; Larsson, Karl-Henrik; Ursing, Björn M

2004-06-12

The prevalent use of similarity searches like BLAST to identify sequences and species implicitly assumes the reference database to be of extensive sequence sampling. This is often not the case, restraining the correctness of the outcome as a basis for sequence identification. Phylogenetic inference outperforms similarity searches in retrieving correct phylogenies and consequently sequence identities, and a project was initiated to design a freely available script package for sequence identification through automated Web-based phylogenetic analysis. Three CGI scripts were designed to facilitate qualified sequence identification from a Web interface. Query sequences are aligned to pre-made alignments or to alignments made by ClustalW with entries retrieved from a BLAST search. The subsequent phylogenetic analysis is based on the PHYLIP package for inferring neighbor-joining and parsimony trees. The scripts are highly configurable. A service installation and a version for local use are found at http://andromeda.botany.gu.se/galaxiewelcome.html and http://galaxie.cgb.ki.se

Availability of the OGC geoprocessing standard: March 2011 reality check

NASA Astrophysics Data System (ADS)

Lopez-Pellicer, Francisco J.; Rentería-Agualimpia, Walter; Béjar, Rubén; Muro-Medrano, Pedro R.; Zarazaga-Soria, F. Javier

2012-10-01

This paper presents an investigation about the servers available in March 2011 conforming to the Web Processing Service interface specification published by the geospatial standards organization Open Geospatial Consortium (OGC) in 2007. This interface specification gives support to standard Web-based geoprocessing. The data used in this research were collected using a focused crawler configured for finding OGC Web services. The research goals are (i) to provide a reality check of the availability of Web Processing Service servers, (ii) to provide quantitative data about the use of different features defined in the standard that are relevant for a scalable Geoprocessing Web (e.g. long-running processes, Web-accessible data outputs), and (iii) to test if the advances in the use of search engines and focused crawlers for finding Web services can be applied for finding geoscience processing systems. Research results show the feasibility of the discovery approach and provide data about the implementation of the Web Processing Service specification. These results also show extensive use of features related to scalability, except for those related to technical and semantic interoperability.

Co-Evolution of User and Organizational Interfaces: A Longitudinal Case Study of WWW Dissemination of National Statistics.

ERIC Educational Resources Information Center

Marchionini, Gary

2002-01-01

Describes how user interfaces for the Bureau of Labor Statistics (BLS) web site evolved over a 5-year period along with the larger organizational interface and how this co-evolution has influenced the institution. Interviews with BLS staff and transaction log analysis are the foci of this study, as well as user information-seeking studies and user…

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.

PubMed

Yu, Nancy Y; Wagner, James R; Laird, Matthew R; Melli, Gabor; Rey, Sébastien; Lo, Raymond; Dao, Phuong; Sahinalp, S Cenk; Ester, Martin; Foster, Leonard J; Brinkman, Fiona S L

2010-07-01

PSORTb has remained the most precise bacterial protein subcellular localization (SCL) predictor since it was first made available in 2003. However, the recall needs to be improved and no accurate SCL predictors yet make predictions for archaea, nor differentiate important localization subcategories, such as proteins targeted to a host cell or bacterial hyperstructures/organelles. Such improvements should preferably be encompassed in a freely available web-based predictor that can also be used as a standalone program. We developed PSORTb version 3.0 with improved recall, higher proteome-scale prediction coverage, and new refined localization subcategories. It is the first SCL predictor specifically geared for all prokaryotes, including archaea and bacteria with atypical membrane/cell wall topologies. It features an improved standalone program, with a new batch results delivery system complementing its web interface. We evaluated the most accurate SCL predictors using 5-fold cross validation plus we performed an independent proteomics analysis, showing that PSORTb 3.0 is the most accurate but can benefit from being complemented by Proteome Analyst predictions. http://www.psort.org/psortb (download open source software or use the web interface). psort-mail@sfu.ca Supplementary data are available at Bioinformatics online.

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

NASA Astrophysics Data System (ADS)

Fragkoulis, Marios; Spinellis, Diomidis; Louridas, Panos

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

MetaGenSense: A web-application for analysis and exploration of high throughput sequencing metagenomic data

PubMed Central

Denis, Jean-Baptiste; Vandenbogaert, Mathias; Caro, Valérie

2016-01-01

The detection and characterization of emerging infectious agents has been a continuing public health concern. High Throughput Sequencing (HTS) or Next-Generation Sequencing (NGS) technologies have proven to be promising approaches for efficient and unbiased detection of pathogens in complex biological samples, providing access to comprehensive analyses. As NGS approaches typically yield millions of putatively representative reads per sample, efficient data management and visualization resources have become mandatory. Most usually, those resources are implemented through a dedicated Laboratory Information Management System (LIMS), solely to provide perspective regarding the available information. We developed an easily deployable web-interface, facilitating management and bioinformatics analysis of metagenomics data-samples. It was engineered to run associated and dedicated Galaxy workflows for the detection and eventually classification of pathogens. The web application allows easy interaction with existing Galaxy metagenomic workflows, facilitates the organization, exploration and aggregation of the most relevant sample-specific sequences among millions of genomic sequences, allowing them to determine their relative abundance, and associate them to the most closely related organism or pathogen. The user-friendly Django-Based interface, associates the users’ input data and its metadata through a bio-IT provided set of resources (a Galaxy instance, and both sufficient storage and grid computing power). Galaxy is used to handle and analyze the user’s input data from loading, indexing, mapping, assembly and DB-searches. Interaction between our application and Galaxy is ensured by the BioBlend library, which gives API-based access to Galaxy’s main features. Metadata about samples, runs, as well as the workflow results are stored in the LIMS. For metagenomic classification and exploration purposes, we show, as a proof of concept, that integration of intuitive exploratory tools, like Krona for representation of taxonomic classification, can be achieved very easily. In the trend of Galaxy, the interface enables the sharing of scientific results to fellow team members. PMID:28451381

MetaGenSense: A web-application for analysis and exploration of high throughput sequencing metagenomic data.

PubMed

Correia, Damien; Doppelt-Azeroual, Olivia; Denis, Jean-Baptiste; Vandenbogaert, Mathias; Caro, Valérie

2015-01-01

The detection and characterization of emerging infectious agents has been a continuing public health concern. High Throughput Sequencing (HTS) or Next-Generation Sequencing (NGS) technologies have proven to be promising approaches for efficient and unbiased detection of pathogens in complex biological samples, providing access to comprehensive analyses. As NGS approaches typically yield millions of putatively representative reads per sample, efficient data management and visualization resources have become mandatory. Most usually, those resources are implemented through a dedicated Laboratory Information Management System (LIMS), solely to provide perspective regarding the available information. We developed an easily deployable web-interface, facilitating management and bioinformatics analysis of metagenomics data-samples. It was engineered to run associated and dedicated Galaxy workflows for the detection and eventually classification of pathogens. The web application allows easy interaction with existing Galaxy metagenomic workflows, facilitates the organization, exploration and aggregation of the most relevant sample-specific sequences among millions of genomic sequences, allowing them to determine their relative abundance, and associate them to the most closely related organism or pathogen. The user-friendly Django-Based interface, associates the users' input data and its metadata through a bio-IT provided set of resources (a Galaxy instance, and both sufficient storage and grid computing power). Galaxy is used to handle and analyze the user's input data from loading, indexing, mapping, assembly and DB-searches. Interaction between our application and Galaxy is ensured by the BioBlend library, which gives API-based access to Galaxy's main features. Metadata about samples, runs, as well as the workflow results are stored in the LIMS. For metagenomic classification and exploration purposes, we show, as a proof of concept, that integration of intuitive exploratory tools, like Krona for representation of taxonomic classification, can be achieved very easily. In the trend of Galaxy, the interface enables the sharing of scientific results to fellow team members.

Providing Multi-Page Data Extraction Services with XWRAPComposer

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

Liu, Ling; Zhang, Jianjun; Han, Wei

2008-04-30

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

Sharing knowledge of Planetary Datasets through the Web-Based PRoGIS

NASA Astrophysics Data System (ADS)

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

2015-10-01

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

Dynamic XML-based exchange of relational data: application to the Human Brain Project.

PubMed

Tang, Zhengming; Kadiyska, Yana; Li, Hao; Suciu, Dan; Brinkley, James F

2003-01-01

This paper discusses an approach to exporting relational data in XML format for data exchange over the web. We describe the first real-world application of SilkRoute, a middleware program that dynamically converts existing relational data to a user-defined XML DTD. The application, called XBrain, wraps SilkRoute in a Java Server Pages framework, thus permitting a web-based XQuery interface to a legacy relational database. The application is demonstrated as a query interface to the University of Washington Brain Project's Language Map Experiment Management System, which is used to manage data about language organization in the brain.

Amira: Multi-Dimensional Scientific Visualization for the GeoSciences in the 21st Century

NASA Astrophysics Data System (ADS)

Bartsch, H.; Erlebacher, G.

2003-12-01

amira (www.amiravis.com) is a general purpose framework for 3D scientific visualization that meets the needs of the non-programmer, the script writer, and the advanced programmer alike. Provided modules may be visually assembled in an interactive manner to create complex visual displays. These modules and their associated user interfaces are controlled either through a mouse, or via an interactive scripting mechanism based on Tcl. We provide interactive demonstrations of the various features of Amira and explain how these may be used to enhance the comprehension of datasets in use in the Earth Sciences community. Its features will be illustrated on scalar and vector fields on grid types ranging from Cartesian to fully unstructured. Specialized extension modules developed by some of our collaborators will be illustrated [1]. These include a module to automatically choose values for salient isosurface identification and extraction, and color maps suitable for volume rendering. During the session, we will present several demonstrations of remote networking, processing of very large spatio-temporal datasets, and various other projects that are underway. In particular, we will demonstrate WEB-IS, a java-applet interface to Amira that allows script editing via the web, and selected data analysis [2]. [1] G. Erlebacher, D. A. Yuen, F. Dubuffet, "Case Study: Visualization and Analysis of High Rayleigh Number -- 3D Convection in the Earth's Mantle", Proceedings of Visualization 2002, pp. 529--532. [2] Y. Wang, G. Erlebacher, Z. A. Garbow, D. A. Yuen, "Web-Based Service of a Visualization Package 'amira' for the Geosciences", Visual Geosciences, 2003.

A Connection Model between the Positioning Mechanism and Ultrasonic Measurement System via a Web Browser to Assess Acoustic Target Strength

NASA Astrophysics Data System (ADS)

Ishii, Ken; Imaizumi, Tomohito; Abe, Koki; Takao, Yoshimi; Tamura, Shuko

This paper details a network-controlled measurement system for use in fisheries engineering. The target strength (TS) of fish is important in order to convert acoustic integration values obtained during acoustic surveys into estimates of fish abundance. The target strength pattern is measured with the combination of the rotation system for the aspect of the sample and the echo data acquisition system using the underwater supersonic wave. The user interface of the network architecture is designed for collaborative use with researchers in other organizations. The flexible network architecture is based on the web direct-access model for the rotation mechanism. The user interface is available for monitoring and controlling via a web browser that is installed in any terminal PC (personal computer). Previously the combination of two applications was performed not by a web browser but by the exclusive interface program. So a connection model is proposed between two applications by indirect communication via the DCOM (Distributed Component Object Model) server and added in the web direct-access model. A prompt report system in the TS measurement system and a positioning and measurement system using an electric flatcar via a web browser are developed. By a secure network architecture, DCOM communications via both Intranet and LAN are successfully certificated.

PearlTrees web-based interface for teaching informatics in the radiology residency

NASA Astrophysics Data System (ADS)

Licurse, Mindy Y.; Cook, Tessa S.

2014-03-01

Radiology and imaging informatics education have rapidly evolved over the past few decades. With the increasing recognition that future growth and maintenance of radiology practices will rely heavily on radiologists with fundamentally sound informatics skills, the onus falls on radiology residency programs to properly implement and execute an informatics curriculum. In addition, the American Board of Radiology may choose to include even more informatics on the new board examinations. However, the resources available for didactic teaching and guidance most especially at the introductory level are widespread and varied. Given the breadth of informatics, a centralized web-based interface designed to serve as an adjunct to standardized informatics curriculums as well as a stand-alone for other interested audiences is desirable. We present the development of a curriculum using PearlTrees, an existing web-interface based on the concept of a visual interest graph that allows users to collect, organize, and share any URL they find online as well as to upload photos and other documents. For our purpose, the group of "pearls" includes informatics concepts linked by appropriate hierarchal relationships. The curriculum was developed using a combination of our institution's current informatics fellowship curriculum, the Practical Imaging Informatics textbook1 and other useful online resources. After development of the initial interface and curriculum has been publicized, we anticipate that involvement by the informatics community will help promote collaborations and foster mentorships at all career levels.

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

PubMed

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

2016-08-01

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

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

DOE PAGES

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

2015-01-08

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

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

PubMed Central

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

2015-01-01

Metagenomic sequencing has produced significant amounts of data in recent years. For example, as of summer 2013, MG-RAST has been used to annotate over 110,000 data sets totaling over 43 Terabases. With metagenomic sequencing finding even wider adoption in the scientific community, the existing web-based analysis tools and infrastructure in MG-RAST provide limited capability for data retrieval and analysis, such as comparative analysis between multiple data sets. Moreover, although the system provides many analysis tools, it is not comprehensive. By opening MG-RAST up via a web services API (application programmers interface) we have greatly expanded access to MG-RAST data, as well as provided a mechanism for the use of third-party analysis tools with MG-RAST data. This RESTful API makes all data and data objects created by the MG-RAST pipeline accessible as JSON objects. As part of the DOE Systems Biology Knowledgebase project (KBase, http://kbase.us) we have implemented a web services API for MG-RAST. This API complements the existing MG-RAST web interface and constitutes the basis of KBase's microbial community capabilities. In addition, the API exposes a comprehensive collection of data to programmers. This API, which uses a RESTful (Representational State Transfer) implementation, is compatible with most programming environments and should be easy to use for end users and third parties. It provides comprehensive access to sequence data, quality control results, annotations, and many other data types. Where feasible, we have used standards to expose data and metadata. Code examples are provided in a number of languages both to show the versatility of the API and to provide a starting point for users. We present an API that exposes the data in MG-RAST for consumption by our users, greatly enhancing the utility of the MG-RAST service. PMID:25569221

PROTICdb: a web-based application to store, track, query, and compare plant proteome data.

PubMed

Ferry-Dumazet, Hélène; Houel, Gwenn; Montalent, Pierre; Moreau, Luc; Langella, Olivier; Negroni, Luc; Vincent, Delphine; Lalanne, Céline; de Daruvar, Antoine; Plomion, Christophe; Zivy, Michel; Joets, Johann

2005-05-01

PROTICdb is a web-based application, mainly designed to store and analyze plant proteome data obtained by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and mass spectrometry (MS). The purposes of PROTICdb are (i) to store, track, and query information related to proteomic experiments, i.e., from tissue sampling to protein identification and quantitative measurements, and (ii) to integrate information from the user's own expertise and other sources into a knowledge base, used to support data interpretation (e.g., for the determination of allelic variants or products of post-translational modifications). Data insertion into the relational database of PROTICdb is achieved either by uploading outputs of image analysis and MS identification software, or by filling web forms. 2-D PAGE annotated maps can be displayed, queried, and compared through a graphical interface. Links to external databases are also available. Quantitative data can be easily exported in a tabulated format for statistical analyses. PROTICdb is based on the Oracle or the PostgreSQL Database Management System and is freely available upon request at the following URL: http://moulon.inra.fr/ bioinfo/PROTICdb.

A Grid job monitoring system

NASA Astrophysics Data System (ADS)

Dumitrescu, Catalin; Nowack, Andreas; Padhi, Sanjay; Sarkar, Subir

2010-04-01

This paper presents a web-based Job Monitoring framework for individual Grid sites that allows users to follow in detail their jobs in quasi-real time. The framework consists of several independent components : (a) a set of sensors that run on the site CE and worker nodes and update a database, (b) a simple yet extensible web services framework and (c) an Ajax powered web interface having a look-and-feel and control similar to a desktop application. The monitoring framework supports LSF, Condor and PBS-like batch systems. This is one of the first monitoring systems where an X.509 authenticated web interface can be seamlessly accessed by both end-users and site administrators. While a site administrator has access to all the possible information, a user can only view the jobs for the Virtual Organizations (VO) he/she is a part of. The monitoring framework design supports several possible deployment scenarios. For a site running a supported batch system, the system may be deployed as a whole, or existing site sensors can be adapted and reused with the web services components. A site may even prefer to build the web server independently and choose to use only the Ajax powered web interface. Finally, the system is being used to monitor a glideinWMS instance. This broadens the scope significantly, allowing it to monitor jobs over multiple sites.

Semantic Annotations and Querying of Web Data Sources

NASA Astrophysics Data System (ADS)

Hornung, Thomas; May, Wolfgang

A large part of the Web, actually holding a significant portion of the useful information throughout the Web, consists of views on hidden databases, provided by numerous heterogeneous interfaces that are partly human-oriented via Web forms ("Deep Web"), and partly based on Web Services (only machine accessible). In this paper we present an approach for annotating these sources in a way that makes them citizens of the Semantic Web. We illustrate how queries can be stated in terms of the ontology, and how the annotations are used to selected and access appropriate sources and to answer the queries.

Soybean Knowledge Base (SoyKB): a Web Resource for Soybean Translational Genomics

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

Joshi, Trupti; Patil, Kapil; Fitzpatrick, Michael R.

2012-01-17

Background: Soybean Knowledge Base (SoyKB) is a comprehensive all-inclusive web resource for soybean translational genomics. SoyKB is designed to handle the management and integration of soybean genomics, transcriptomics, proteomics and metabolomics data along with annotation of gene function and biological pathway. It contains information on four entities, namely genes, microRNAs, metabolites and single nucleotide polymorphisms (SNPs). Methods: SoyKB has many useful tools such as Affymetrix probe ID search, gene family search, multiple gene/ metabolite search supporting co-expression analysis, and protein 3D structure viewer as well as download and upload capacity for experimental data and annotations. It has four tiers ofmore » registration, which control different levels of access to public and private data. It allows users of certain levels to share their expertise by adding comments to the data. It has a user-friendly web interface together with genome browser and pathway viewer, which display data in an intuitive manner to the soybean researchers, producers and consumers. Conclusions: SoyKB addresses the increasing need of the soybean research community to have a one-stop-shop functional and translational omics web resource for information retrieval and analysis in a user-friendly way. SoyKB can be publicly accessed at http://soykb.org/.« less

An XML-based Generic Tool for Information Retrieval in Solar Databases

NASA Astrophysics Data System (ADS)

Scholl, Isabelle F.; Legay, Eric; Linsolas, Romain

This paper presents the current architecture of the `Solar Web Project' now in its development phase. This tool will provide scientists interested in solar data with a single web-based interface for browsing distributed and heterogeneous catalogs of solar observations. The main goal is to have a generic application that can be easily extended to new sets of data or to new missions with a low level of maintenance. It is developed with Java and XML is used as a powerful configuration language. The server, independent of any database scheme, can communicate with a client (the user interface) and several local or remote archive access systems (such as existing web pages, ftp sites or SQL databases). Archive access systems are externally described in XML files. The user interface is also dynamically generated from an XML file containing the window building rules and a simplified database description. This project is developed at MEDOC (Multi-Experiment Data and Operations Centre), located at the Institut d'Astrophysique Spatiale (Orsay, France). Successful tests have been conducted with other solar archive access systems.

Network-based real-time radiation monitoring system in Synchrotron Radiation Research Center.

PubMed

Sheu, R J; Wang, J P; Chen, C R; Liu, J; Chang, F D; Jiang, S H

2003-10-01

The real-time radiation monitoring system (RMS) in the Synchrotron Radiation Research Center (SRRC) has been upgraded significantly during the past years. The new framework of the RMS is built on the popular network technology, including Ethernet hardware connections and Web-based software interfaces. It features virtually no distance limitations, flexible and scalable equipment connections, faster response time, remote diagnosis, easy maintenance, as well as many graphic user interface software tools. This paper briefly describes the radiation environment in SRRC and presents the system configuration, basic functions, and some operational results of this real-time RMS. Besides the control of radiation exposures, it has been demonstrated that a variety of valuable information or correlations could be extracted from the measured radiation levels delivered by the RMS, including the changes of operating conditions, beam loss pattern, radiation skyshine, and so on. The real-time RMS can be conveniently accessed either using the dedicated client program or World Wide Web interface. The address of the Web site is http:// www-rms.srrc.gov.tw.

WebCIS: large scale deployment of a Web-based clinical information system.

PubMed

Hripcsak, G; Cimino, J J; Sengupta, S

1999-01-01

WebCIS is a Web-based clinical information system. It sits atop the existing Columbia University clinical information system architecture, which includes a clinical repository, the Medical Entities Dictionary, an HL7 interface engine, and an Arden Syntax based clinical event monitor. WebCIS security features include authentication with secure tokens, authorization maintained in an LDAP server, SSL encryption, permanent audit logs, and application time outs. WebCIS is currently used by 810 physicians at the Columbia-Presbyterian center of New York Presbyterian Healthcare to review and enter data into the electronic medical record. Current deployment challenges include maintaining adequate database performance despite complex queries, replacing large numbers of computers that cannot run modern Web browsers, and training users that have never logged onto the Web. Although the raised expectations and higher goals have increased deployment costs, the end result is a far more functional, far more available system.

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

PubMed Central

Reddy, T.B.K.; Thomas, Alex D.; Stamatis, Dimitri; Bertsch, Jon; Isbandi, Michelle; Jansson, Jakob; Mallajosyula, Jyothi; Pagani, Ioanna; Lobos, Elizabeth A.; Kyrpides, Nikos C.

2015-01-01

The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Here we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19 200 studies, 56 000 Biosamples, 56 000 sequencing projects and 39 400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards. PMID:25348402

Brain Tumor Database, a free relational database for collection and analysis of brain tumor patient information.

PubMed

Bergamino, Maurizio; Hamilton, David J; Castelletti, Lara; Barletta, Laura; Castellan, Lucio

2015-03-01

In this study, we describe the development and utilization of a relational database designed to manage the clinical and radiological data of patients with brain tumors. The Brain Tumor Database was implemented using MySQL v.5.0, while the graphical user interface was created using PHP and HTML, thus making it easily accessible through a web browser. This web-based approach allows for multiple institutions to potentially access the database. The BT Database can record brain tumor patient information (e.g. clinical features, anatomical attributes, and radiological characteristics) and be used for clinical and research purposes. Analytic tools to automatically generate statistics and different plots are provided. The BT Database is a free and powerful user-friendly tool with a wide range of possible clinical and research applications in neurology and neurosurgery. The BT Database graphical user interface source code and manual are freely available at http://tumorsdatabase.altervista.org. © The Author(s) 2013.

Technical development of PubMed interact: an improved interface for MEDLINE/PubMed searches.

PubMed

Muin, Michael; Fontelo, Paul

2006-11-03

The project aims to create an alternative search interface for MEDLINE/PubMed that may provide assistance to the novice user and added convenience to the advanced user. An earlier version of the project was the 'Slider Interface for MEDLINE/PubMed searches' (SLIM) which provided JavaScript slider bars to control search parameters. In this new version, recent developments in Web-based technologies were implemented. These changes may prove to be even more valuable in enhancing user interactivity through client-side manipulation and management of results. PubMed Interact is a Web-based MEDLINE/PubMed search application built with HTML, JavaScript and PHP. It is implemented on a Windows Server 2003 with Apache 2.0.52, PHP 4.4.1 and MySQL 4.1.18. PHP scripts provide the backend engine that connects with E-Utilities and parses XML files. JavaScript manages client-side functionalities and converts Web pages into interactive platforms using dynamic HTML (DHTML), Document Object Model (DOM) tree manipulation and Ajax methods. With PubMed Interact, users can limit searches with JavaScript slider bars, preview result counts, delete citations from the list, display and add related articles and create relevance lists. Many interactive features occur at client-side, which allow instant feedback without reloading or refreshing the page resulting in a more efficient user experience. PubMed Interact is a highly interactive Web-based search application for MEDLINE/PubMed that explores recent trends in Web technologies like DOM tree manipulation and Ajax. It may become a valuable technical development for online medical search applications.

The Development of Web-based Graphical User Interface for Unified Modeling Data with Multi (Correlated) Responses

NASA Astrophysics Data System (ADS)

Made Tirta, I.; Anggraeni, Dian

2018-04-01

Statistical models have been developed rapidly into various directions to accommodate various types of data. Data collected from longitudinal, repeated measured, clustered data (either continuous, binary, count, or ordinal), are more likely to be correlated. Therefore statistical model for independent responses, such as Generalized Linear Model (GLM), Generalized Additive Model (GAM) are not appropriate. There are several models available to apply for correlated responses including GEEs (Generalized Estimating Equations), for marginal model and various mixed effect model such as GLMM (Generalized Linear Mixed Models) and HGLM (Hierarchical Generalized Linear Models) for subject spesific models. These models are available on free open source software R, but they can only be accessed through command line interface (using scrit). On the othe hand, most practical researchers very much rely on menu based or Graphical User Interface (GUI). We develop, using Shiny framework, standard pull down menu Web-GUI that unifies most models for correlated responses. The Web-GUI has accomodated almost all needed features. It enables users to do and compare various modeling for repeated measure data (GEE, GLMM, HGLM, GEE for nominal responses) much more easily trough online menus. This paper discusses the features of the Web-GUI and illustrates the use of them. In General we find that GEE, GLMM, HGLM gave very closed results.

Making Your Tools Useful to a Broader Audience

NASA Astrophysics Data System (ADS)

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

2006-12-01

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

Amino Acid Interaction (INTAA) web server.

PubMed

Galgonek, Jakub; Vymetal, Jirí; Jakubec, David; Vondrášek, Jirí

2017-07-03

Large biomolecules-proteins and nucleic acids-are composed of building blocks which define their identity, properties and binding capabilities. In order to shed light on the energetic side of interactions of amino acids between themselves and with deoxyribonucleotides, we present the Amino Acid Interaction web server (http://bioinfo.uochb.cas.cz/INTAA/). INTAA offers the calculation of the residue Interaction Energy Matrix for any protein structure (deposited in Protein Data Bank or submitted by the user) and a comprehensive analysis of the interfaces in protein-DNA complexes. The Interaction Energy Matrix web application aims to identify key residues within protein structures which contribute significantly to the stability of the protein. The application provides an interactive user interface enhanced by 3D structure viewer for efficient visualization of pairwise and net interaction energies of individual amino acids, side chains and backbones. The protein-DNA interaction analysis part of the web server allows the user to view the relative abundance of various configurations of amino acid-deoxyribonucleotide pairs found at the protein-DNA interface and the interaction energies corresponding to these configurations calculated using a molecular mechanical force field. The effects of the sugar-phosphate moiety and of the dielectric properties of the solvent on the interaction energies can be studied for the various configurations. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Development of a real-time clinical decision support system upon the web mvc-based architecture for prostate cancer treatment

PubMed Central

2011-01-01

Background A real-time clinical decision support system (RTCDSS) with interactive diagrams enables clinicians to instantly and efficiently track patients' clinical records (PCRs) and improve their quality of clinical care. We propose a RTCDSS to process online clinical informatics from multiple databases for clinical decision making in the treatment of prostate cancer based on Web Model-View-Controller (MVC) architecture, by which the system can easily be adapted to different diseases and applications. Methods We designed a framework upon the Web MVC-based architecture in which the reusable and extractable models can be conveniently adapted to other hospital information systems and which allows for efficient database integration. Then, we determined the clinical variables of the prostate cancer treatment based on participating clinicians' opinions and developed a computational model to determine the pretreatment parameters. Furthermore, the components of the RTCDSS integrated PCRs and decision factors for real-time analysis to provide evidence-based diagrams upon the clinician-oriented interface for visualization of treatment guidance and health risk assessment. Results The resulting system can improve quality of clinical treatment by allowing clinicians to concurrently analyze and evaluate the clinical markers of prostate cancer patients with instantaneous clinical data and evidence-based diagrams which can automatically identify pretreatment parameters. Moreover, the proposed RTCDSS can aid interactions between patients and clinicians. Conclusions Our proposed framework supports online clinical informatics, evaluates treatment risks, offers interactive guidance, and provides real-time reference for decision making in the treatment of prostate cancer. The developed clinician-oriented interface can assist clinicians in conveniently presenting evidence-based information to patients and can be readily adapted to an existing hospital information system and be easily applied in other chronic diseases. PMID:21385459

Development of a real-time clinical decision support system upon the Web MVC-based architecture for prostate cancer treatment.

PubMed

Lin, Hsueh-Chun; Wu, Hsi-Chin; Chang, Chih-Hung; Li, Tsai-Chung; Liang, Wen-Miin; Wang, Jong-Yi Wang

2011-03-08

A real-time clinical decision support system (RTCDSS) with interactive diagrams enables clinicians to instantly and efficiently track patients' clinical records (PCRs) and improve their quality of clinical care. We propose a RTCDSS to process online clinical informatics from multiple databases for clinical decision making in the treatment of prostate cancer based on Web Model-View-Controller (MVC) architecture, by which the system can easily be adapted to different diseases and applications. We designed a framework upon the Web MVC-based architecture in which the reusable and extractable models can be conveniently adapted to other hospital information systems and which allows for efficient database integration. Then, we determined the clinical variables of the prostate cancer treatment based on participating clinicians' opinions and developed a computational model to determine the pretreatment parameters. Furthermore, the components of the RTCDSS integrated PCRs and decision factors for real-time analysis to provide evidence-based diagrams upon the clinician-oriented interface for visualization of treatment guidance and health risk assessment. The resulting system can improve quality of clinical treatment by allowing clinicians to concurrently analyze and evaluate the clinical markers of prostate cancer patients with instantaneous clinical data and evidence-based diagrams which can automatically identify pretreatment parameters. Moreover, the proposed RTCDSS can aid interactions between patients and clinicians. Our proposed framework supports online clinical informatics, evaluates treatment risks, offers interactive guidance, and provides real-time reference for decision making in the treatment of prostate cancer. The developed clinician-oriented interface can assist clinicians in conveniently presenting evidence-based information to patients and can be readily adapted to an existing hospital information system and be easily applied in other chronic diseases.

Analysis of the interface variability in NMR structure ensembles of protein-protein complexes.

PubMed

Calvanese, Luisa; D'Auria, Gabriella; Vangone, Anna; Falcigno, Lucia; Oliva, Romina

2016-06-01

NMR structures consist in ensembles of conformers, all satisfying the experimental restraints, which exhibit a certain degree of structural variability. We analyzed here the interface in NMR ensembles of protein-protein heterodimeric complexes and found it to span a wide range of different conservations. The different exhibited conservations do not simply correlate with the size of the systems/interfaces, and are most probably the result of an interplay between different factors, including the quality of experimental data and the intrinsic complex flexibility. In any case, this information is not to be missed when NMR structures of protein-protein complexes are analyzed; especially considering that, as we also show here, the first NMR conformer is usually not the one which best reflects the overall interface. To quantify the interface conservation and to analyze it, we used an approach originally conceived for the analysis and ranking of ensembles of docking models, which has now been extended to directly deal with NMR ensembles. We propose this approach, based on the conservation of the inter-residue contacts at the interface, both for the analysis of the interface in whole ensembles of NMR complexes and for the possible selection of a single conformer as the best representative of the overall interface. In order to make the analyses automatic and fast, we made the protocol available as a web tool at: https://www.molnac.unisa.it/BioTools/consrank/consrank-nmr.html. Copyright © 2016 Elsevier Inc. All rights reserved.

77 FR 47867 - Agency Information Collection Activities: Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-10

... phenology information to Nature's Notebook through a browser-based web application or via mobile applications for iPhone and Android operating systems, meeting GPEA requirements. The web application interface... techniques or other forms of information technology. Please note that the comments submitted in response to...

Web-Based Job Submission Interface for the GAMESS Computational Chemistry Program

ERIC Educational Resources Information Center

Perri, M. J.; Weber, S. H.

2014-01-01

A Web site is described that facilitates use of the free computational chemistry software: General Atomic and Molecular Electronic Structure System (GAMESS). Its goal is to provide an opportunity for undergraduate students to perform computational chemistry experiments without the need to purchase expensive software.

77 FR 18280 - Self-Regulatory Organizations; The NASDAQ Stock Market LLC; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-27

... adopted QView on December 1, 2011 at no cost to subscribers.\\3\\ QView is a Web-based, front-end... executions provided in the QView dashboard interface. The dashboard also allows a QView subscriber to track...\\ \\5\\ TradeInfo is a web-based tool that, among other things, allows users access to all of the NASDAQ...

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.

maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination.

PubMed

Hancock, David; Wilson, Michael; Velarde, Giles; Morrison, Norman; Hayes, Andrew; Hulme, Helen; Wood, A Joseph; Nashar, Karim; Kell, Douglas B; Brass, Andy

2005-11-03

maxdLoad2 is a relational database schema and Java application for microarray experimental annotation and storage. It is compliant with all standards for microarray meta-data capture; including the specification of what data should be recorded, extensive use of standard ontologies and support for data exchange formats. The output from maxdLoad2 is of a form acceptable for submission to the ArrayExpress microarray repository at the European Bioinformatics Institute. maxdBrowse is a PHP web-application that makes contents of maxdLoad2 databases accessible via web-browser, the command-line and web-service environments. It thus acts as both a dissemination and data-mining tool. maxdLoad2 presents an easy-to-use interface to an underlying relational database and provides a full complement of facilities for browsing, searching and editing. There is a tree-based visualization of data connectivity and the ability to explore the links between any pair of data elements, irrespective of how many intermediate links lie between them. Its principle novel features are: the flexibility of the meta-data that can be captured, the tools provided for importing data from spreadsheets and other tabular representations, the tools provided for the automatic creation of structured documents, the ability to browse and access the data via web and web-services interfaces. Within maxdLoad2 it is very straightforward to customise the meta-data that is being captured or change the definitions of the meta-data. These meta-data definitions are stored within the database itself allowing client software to connect properly to a modified database without having to be specially configured. The meta-data definitions (configuration file) can also be centralized allowing changes made in response to revisions of standards or terminologies to be propagated to clients without user intervention.maxdBrowse is hosted on a web-server and presents multiple interfaces to the contents of maxd databases. maxdBrowse emulates many of the browse and search features available in the maxdLoad2 application via a web-browser. This allows users who are not familiar with maxdLoad2 to browse and export microarray data from the database for their own analysis. The same browse and search features are also available via command-line and SOAP server interfaces. This both enables scripting of data export for use embedded in data repositories and analysis environments, and allows access to the maxd databases via web-service architectures. maxdLoad2 http://www.bioinf.man.ac.uk/microarray/maxd/ and maxdBrowse http://dbk.ch.umist.ac.uk/maxdBrowse are portable and compatible with all common operating systems and major database servers. They provide a powerful, flexible package for annotation of microarray experiments and a convenient dissemination environment. They are available for download and open sourced under the Artistic License.

SWS: accessing SRS sites contents through Web Services.

PubMed

Romano, Paolo; Marra, Domenico

2008-03-26

Web Services and Workflow Management Systems can support creation and deployment of network systems, able to automate data analysis and retrieval processes in biomedical research. Web Services have been implemented at bioinformatics centres and workflow systems have been proposed for biological data analysis. New databanks are often developed by taking into account these technologies, but many existing databases do not allow a programmatic access. Only a fraction of available databanks can thus be queried through programmatic interfaces. SRS is a well know indexing and search engine for biomedical databanks offering public access to many databanks and analysis tools. Unfortunately, these data are not easily and efficiently accessible through Web Services. We have developed 'SRS by WS' (SWS), a tool that makes information available in SRS sites accessible through Web Services. Information on known sites is maintained in a database, srsdb. SWS consists in a suite of WS that can query both srsdb, for information on sites and databases, and SRS sites. SWS returns results in a text-only format and can be accessed through a WSDL compliant client. SWS enables interoperability between workflow systems and SRS implementations, by also managing access to alternative sites, in order to cope with network and maintenance problems, and selecting the most up-to-date among available systems. Development and implementation of Web Services, allowing to make a programmatic access to an exhaustive set of biomedical databases can significantly improve automation of in-silico analysis. SWS supports this activity by making biological databanks that are managed in public SRS sites available through a programmatic interface.

MaROS Strategic Relay Planning and Coordination Interfaces

NASA Technical Reports Server (NTRS)

Allard, Daniel A.

2010-01-01

The Mars Relay Operations Service (MaROS) is designed to provide planning and analysis tools in support of ongoing Mars Network relay operations. Strategic relay planning requires coordination between lander and orbiter mission ground data system (GDS) teams to schedule and execute relay communications passes. MaROS centralizes this process, correlating all data relevant to relay coordination to provide a cohesive picture of the relay state. Service users interact with the system through thin-layer command line and web user interface client applications. Users provide and utilize data such as lander view periods of orbiters, Deep Space Network (DSN) antenna tracks, and reports of relay pass performance. Users upload and download relevant relay data via formally defined and documented file structures including some described in Extensible Markup Language (XML). Clients interface with the system via an http-based Representational State Transfer (ReST) pattern using Javascript Object Notation (JSON) formats. This paper will provide a general overview of the service architecture and detail the software interfaces and considerations for interface design.

The Input-Interface of Webcam Applied in 3D Virtual Reality Systems

ERIC Educational Resources Information Center

Sun, Huey-Min; Cheng, Wen-Lin

2009-01-01

Our research explores a virtual reality application based on Web camera (Webcam) input-interface. The interface can replace with the mouse to control direction intention of a user by the method of frame difference. We divide a frame into nine grids from Webcam and make use of the background registration to compute the moving object. In order to…

CUNY+ Web: Usability Study of the Web-Based GUI Version of the Bibliographic Database of the City University of New York (CUNY).

ERIC Educational Resources Information Center

Oulanov, Alexei; Pajarillo, Edmund J. Y.

2002-01-01

Describes the usability evaluation of the CUNY (City University of New York) information system in Web and Graphical User Interface (GUI) versions. Compares results to an earlier usability study of the basic information database available on CUNY's wide-area network and describes the applicability of the previous usability instrument to this…

Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize

PubMed Central

2010-01-01

Background Aspergillus flavus Link:Fr, an opportunistic fungus that produces aflatoxin, is pathogenic to maize and other oilseed crops. Aflatoxin is a potent carcinogen, and its presence markedly reduces the value of grain. Understanding and enhancing host resistance to A. flavus infection and/or subsequent aflatoxin accumulation is generally considered an efficient means of reducing grain losses to aflatoxin. Different proteomic, genomic and genetic studies of maize (Zea mays L.) have generated large data sets with the goal of identifying genes responsible for conferring resistance to A. flavus, or aflatoxin. Results In order to maximize the usage of different data sets in new studies, including association mapping, we have constructed a relational database with web interface integrating the results of gene expression, proteomic (both gel-based and shotgun), Quantitative Trait Loci (QTL) genetic mapping studies, and sequence data from the literature to facilitate selection of candidate genes for continued investigation. The Corn Fungal Resistance Associated Sequences Database (CFRAS-DB) (http://agbase.msstate.edu/) was created with the main goal of identifying genes important to aflatoxin resistance. CFRAS-DB is implemented using MySQL as the relational database management system running on a Linux server, using an Apache web server, and Perl CGI scripts as the web interface. The database and the associated web-based interface allow researchers to examine many lines of evidence (e.g. microarray, proteomics, QTL studies, SNP data) to assess the potential role of a gene or group of genes in the response of different maize lines to A. flavus infection and subsequent production of aflatoxin by the fungus. Conclusions CFRAS-DB provides the first opportunity to integrate data pertaining to the problem of A. flavus and aflatoxin resistance in maize in one resource and to support queries across different datasets. The web-based interface gives researchers different query options for mining the database across different types of experiments. The database is publically available at http://agbase.msstate.edu. PMID:20946609

Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize.

PubMed

Kelley, Rowena Y; Gresham, Cathy; Harper, Jonathan; Bridges, Susan M; Warburton, Marilyn L; Hawkins, Leigh K; Pechanova, Olga; Peethambaran, Bela; Pechan, Tibor; Luthe, Dawn S; Mylroie, J E; Ankala, Arunkanth; Ozkan, Seval; Henry, W B; Williams, W P

2010-10-07

Aspergillus flavus Link:Fr, an opportunistic fungus that produces aflatoxin, is pathogenic to maize and other oilseed crops. Aflatoxin is a potent carcinogen, and its presence markedly reduces the value of grain. Understanding and enhancing host resistance to A. flavus infection and/or subsequent aflatoxin accumulation is generally considered an efficient means of reducing grain losses to aflatoxin. Different proteomic, genomic and genetic studies of maize (Zea mays L.) have generated large data sets with the goal of identifying genes responsible for conferring resistance to A. flavus, or aflatoxin. In order to maximize the usage of different data sets in new studies, including association mapping, we have constructed a relational database with web interface integrating the results of gene expression, proteomic (both gel-based and shotgun), Quantitative Trait Loci (QTL) genetic mapping studies, and sequence data from the literature to facilitate selection of candidate genes for continued investigation. The Corn Fungal Resistance Associated Sequences Database (CFRAS-DB) (http://agbase.msstate.edu/) was created with the main goal of identifying genes important to aflatoxin resistance. CFRAS-DB is implemented using MySQL as the relational database management system running on a Linux server, using an Apache web server, and Perl CGI scripts as the web interface. The database and the associated web-based interface allow researchers to examine many lines of evidence (e.g. microarray, proteomics, QTL studies, SNP data) to assess the potential role of a gene or group of genes in the response of different maize lines to A. flavus infection and subsequent production of aflatoxin by the fungus. CFRAS-DB provides the first opportunity to integrate data pertaining to the problem of A. flavus and aflatoxin resistance in maize in one resource and to support queries across different datasets. The web-based interface gives researchers different query options for mining the database across different types of experiments. The database is publically available at http://agbase.msstate.edu.

Protein interface classification by evolutionary analysis

PubMed Central

2012-01-01

Background Distinguishing biologically relevant interfaces from lattice contacts in protein crystals is a fundamental problem in structural biology. Despite efforts towards the computational prediction of interface character, many issues are still unresolved. Results We present here a protein-protein interface classifier that relies on evolutionary data to detect the biological character of interfaces. The classifier uses a simple geometric measure, number of core residues, and two evolutionary indicators based on the sequence entropy of homolog sequences. Both aim at detecting differential selection pressure between interface core and rim or rest of surface. The core residues, defined as fully buried residues (>95% burial), appear to be fundamental determinants of biological interfaces: their number is in itself a powerful discriminator of interface character and together with the evolutionary measures it is able to clearly distinguish evolved biological contacts from crystal ones. We demonstrate that this definition of core residues leads to distinctively better results than earlier definitions from the literature. The stringent selection and quality filtering of structural and sequence data was key to the success of the method. Most importantly we demonstrate that a more conservative selection of homolog sequences - with relatively high sequence identities to the query - is able to produce a clearer signal than previous attempts. Conclusions An evolutionary approach like the one presented here is key to the advancement of the field, which so far was missing an effective method exploiting the evolutionary character of protein interfaces. Its coverage and performance will only improve over time thanks to the incessant growth of sequence databases. Currently our method reaches an accuracy of 89% in classifying interfaces of the Ponstingl 2003 datasets and it lends itself to a variety of useful applications in structural biology and bioinformatics. We made the corresponding software implementation available to the community as an easy-to-use graphical web interface at http://www.eppic-web.org. PMID:23259833

An Automated Weather Research and Forecasting (WRF)-Based Nowcasting System: Software Description

DTIC Science & Technology

2013-10-01

14. ABSTRACT A Web service /Web interface software package has been engineered to address the need for an automated means to run the Weather Research...An Automated Weather Research and Forecasting (WRF)- Based Nowcasting System: Software Description by Stephen F. Kirby, Brian P. Reen, and...Based Nowcasting System: Software Description Stephen F. Kirby, Brian P. Reen, and Robert E. Dumais Jr. Computational and Information Sciences

Mining Microarray Data at NCBI’s Gene Expression Omnibus (GEO)*

PubMed Central

Barrett, Tanya; Edgar, Ron

2006-01-01

Summary The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) has emerged as the leading fully public repository for gene expression data. This chapter describes how to use Web-based interfaces, applications, and graphics to effectively explore, visualize, and interpret the hundreds of microarray studies and millions of gene expression patterns stored in GEO. Data can be examined from both experiment-centric and gene-centric perspectives using user-friendly tools that do not require specialized expertise in microarray analysis or time-consuming download of massive data sets. The GEO database is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo. PMID:16888359

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.

Comparative study of predicted and experimentally detected interplanetary shocks

NASA Astrophysics Data System (ADS)

Kartalev, M. D.; Grigorov, K. G.; Smith, Z.; Dryer, M.; Fry, C. D.; Sun, Wei; Deehr, C. S.

2002-03-01

We compare the real time space weather prediction shock arrival times at 1 AU made by the USAF/NOAA Shock Time of Arrival (STOA) and Interplanetary Shock Propagation Model (ISPM) models, and the Exploration Physics International/University of Alaska Hakamada-Akasofu-Fry Solar Wind Model (HAF-v2) to a real time analysis analysis of plasma and field ACE data. The comparison is made using an algorithm that was developed on the basis of wavelet data analysis and MHD identification procedure. The shock parameters are estimated for selected "candidate events". An appropriate automatically performing Web-based interface periodically utilizes solar wind observations made by the ACE at L1. Near real time results as well an archive of the registered interesting events are available on a specially developed web site. A number of events are considered. These studies are essential for the validation of real time space weather forecasts made from solar data.

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

Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization.

PubMed

Veidenberg, Andres; Medlar, Alan; Löytynoja, Ari

2016-04-01

Wasabi is an open source, web-based environment for evolutionary sequence analysis. Wasabi visualizes sequence data together with a phylogenetic tree within a modern, user-friendly interface: The interface hides extraneous options, supports context sensitive menus, drag-and-drop editing, and displays additional information, such as ancestral sequences, associated with specific tree nodes. The Wasabi environment supports reproducibility by automatically storing intermediate analysis steps and includes built-in functions to share data between users and publish analysis results. For computational analysis, Wasabi supports PRANK and PAGAN for phylogeny-aware alignment and alignment extension, and it can be easily extended with other tools. Along with drag-and-drop import of local files, Wasabi can access remote data through URL and import sequence data, GeneTrees and EPO alignments directly from Ensembl. To demonstrate a typical workflow using Wasabi, we reproduce key findings from recent comparative genomics studies, including a reanalysis of the EGLN1 gene from the tiger genome study: These case studies can be browsed within Wasabi at http://wasabiapp.org:8000?id=usecases. Wasabi runs inside a web browser and does not require any installation. One can start using it at http://wasabiapp.org. All source code is licensed under the AGPLv3. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Geena 2, improved automated analysis of MALDI/TOF mass spectra.

PubMed

Romano, Paolo; Profumo, Aldo; Rocco, Mattia; Mangerini, Rosa; Ferri, Fabio; Facchiano, Angelo

2016-03-02

Mass spectrometry (MS) is producing high volumes of data supporting oncological sciences, especially for translational research. Most of related elaborations can be carried out by combining existing tools at different levels, but little is currently available for the automation of the fundamental steps. For the analysis of MALDI/TOF spectra, a number of pre-processing steps are required, including joining of isotopic abundances for a given molecular species, normalization of signals against an internal standard, background noise removal, averaging multiple spectra from the same sample, and aligning spectra from different samples. In this paper, we present Geena 2, a public software tool for the automated execution of these pre-processing steps for MALDI/TOF spectra. Geena 2 has been developed in a Linux-Apache-MySQL-PHP web development environment, with scripts in PHP and Perl. Input and output are managed as simple formats that can be consumed by any database system and spreadsheet software. Input data may also be stored in a MySQL database. Processing methods are based on original heuristic algorithms which are introduced in the paper. Three simple and intuitive web interfaces are available: the Standard Search Interface, which allows a complete control over all parameters, the Bright Search Interface, which leaves to the user the possibility to tune parameters for alignment of spectra, and the Quick Search Interface, which limits the number of parameters to a minimum by using default values for the majority of parameters. Geena 2 has been utilized, in conjunction with a statistical analysis tool, in three published experimental works: a proteomic study on the effects of long-term cryopreservation on the low molecular weight fraction of serum proteome, and two retrospective serum proteomic studies, one on the risk of developing breat cancer in patients affected by gross cystic disease of the breast (GCDB) and the other for the identification of a predictor of breast cancer mortality following breast cancer surgery, whose results were validated by ELISA, a completely alternative method. Geena 2 is a public tool for the automated pre-processing of MS data originated by MALDI/TOF instruments, with a simple and intuitive web interface. It is now under active development for the inclusion of further filtering options and for the adoption of standard formats for MS spectra.

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.

Digital hand atlas and computer-aided bone age assessment via the Web

NASA Astrophysics Data System (ADS)

Cao, Fei; Huang, H. K.; Pietka, Ewa; Gilsanz, Vicente

1999-07-01

A frequently used assessment method of bone age is atlas matching by a radiological examination of a hand image against a reference set of atlas patterns of normal standards. We are in a process of developing a digital hand atlas with a large standard set of normal hand and wrist images that reflect the skeletal maturity, race and sex difference, and current child development. The digital hand atlas will be used for a computer-aided bone age assessment via Web. We have designed and partially implemented a computer-aided diagnostic (CAD) system for Web-based bone age assessment. The system consists of a digital hand atlas, a relational image database and a Web-based user interface. The digital atlas is based on a large standard set of normal hand an wrist images with extracted bone objects and quantitative features. The image database uses a content- based indexing to organize the hand images and their attributes and present to users in a structured way. The Web-based user interface allows users to interact with the hand image database from browsers. Users can use a Web browser to push a clinical hand image to the CAD server for a bone age assessment. Quantitative features on the examined image, which reflect the skeletal maturity, will be extracted and compared with patterns from the atlas database to assess the bone age. The relevant reference imags and the final assessment report will be sent back to the user's browser via Web. The digital atlas will remove the disadvantages of the currently out-of-date one and allow the bone age assessment to be computerized and done conveniently via Web. In this paper, we present the system design and Web-based client-server model for computer-assisted bone age assessment and our initial implementation of the digital atlas database.

Design of Web-based Fuzzy Input Expert System for the analysis of serology laboratory tests.

PubMed

Başçiftçi, Fatih; Incekara, Hayri

2012-08-01

In this study, it is aimed, using the Web-based Expert System with Fuzzy Input (WESFI), to convert the patients' (users') Serology Laboratory Tests (SLT) results to linguistic statements (low, normal, high) and analyzing those, give a feedback to the user (patient) of the potential signs of disease. The feedbacks given to the patients are the existing interpretations in the database, which were prepared by doctors before. Furthermore, the SLT terms (Brucella Coombs, Ama, P-Protein etc.) are explained in a way that the user can understand. The WESFI is published with an interface on the web environment. In order to determine the rate of the success of the WESFI, users evaluated the system answering the "How do you find the evaluation?" question. The question has been answered by 461 users. As a result it is observed that 90% of female users, 92% of male users and 91% of all users found the system useful.

ST-analyzer: a web-based user interface for simulation trajectory analysis.

PubMed

Jeong, Jong Cheol; Jo, Sunhwan; Wu, Emilia L; Qi, Yifei; Monje-Galvan, Viviana; Yeom, Min Sun; Gorenstein, Lev; Chen, Feng; Klauda, Jeffery B; Im, Wonpil

2014-05-05

Molecular dynamics (MD) simulation has become one of the key tools to obtain deeper insights into biological systems using various levels of descriptions such as all-atom, united-atom, and coarse-grained models. Recent advances in computing resources and MD programs have significantly accelerated the simulation time and thus increased the amount of trajectory data. Although many laboratories routinely perform MD simulations, analyzing MD trajectories is still time consuming and often a difficult task. ST-analyzer, http://im.bioinformatics.ku.edu/st-analyzer, is a standalone graphical user interface (GUI) toolset to perform various trajectory analyses. ST-analyzer has several outstanding features compared to other existing analysis tools: (i) handling various formats of trajectory files from MD programs, such as CHARMM, NAMD, GROMACS, and Amber, (ii) intuitive web-based GUI environment--minimizing administrative load and reducing burdens on the user from adapting new software environments, (iii) platform independent design--working with any existing operating system, (iv) easy integration into job queuing systems--providing options of batch processing either on the cluster or in an interactive mode, and (v) providing independence between foreground GUI and background modules--making it easier to add personal modules or to recycle/integrate pre-existing scripts utilizing other analysis tools. The current ST-analyzer contains nine main analysis modules that together contain 18 options, including density profile, lipid deuterium order parameters, surface area per lipid, and membrane hydrophobic thickness. This article introduces ST-analyzer with its design, implementation, and features, and also illustrates practical analysis of lipid bilayer simulations. Copyright © 2014 Wiley Periodicals, Inc.

Identification of estrogen-responsive genes using a genome-wide analysis of promoter elements for transcription factor binding sites.

PubMed

Kamalakaran, Sitharthan; Radhakrishnan, Senthil K; Beck, William T

2005-06-03

We developed a pipeline to identify novel genes regulated by the steroid hormone-dependent transcription factor, estrogen receptor, through a systematic analysis of upstream regions of all human and mouse genes. We built a data base of putative promoter regions for 23,077 human and 19,984 mouse transcripts from National Center for Biotechnology Information annotation and 8793 human and 6785 mouse promoters from the Data Base of Transcriptional Start Sites. We used this data base of putative promoters to identify potential targets of estrogen receptor by identifying estrogen response elements (EREs) in their promoters. Our program correctly identified EREs in genes known to be regulated by estrogen in addition to several new genes whose putative promoters contained EREs. We validated six genes (KIAA1243, NRIP1, MADH9, NME3, TPD52L, and ABCG2) to be estrogen-responsive in MCF7 cells using reverse transcription PCR. To allow for extensibility of our program in identifying targets of other transcription factors, we have built a Web interface to access our data base and programs. Our Web-based program for Promoter Analysis of Genome, PAGen@UIC, allows a user to identify putative target genes for vertebrate transcription factors through the analysis of their upstream sequences. The interface allows the user to search the human and mouse promoter data bases for potential target genes containing one or more listed transcription factor binding sites (TFBSs) in their upstream elements, using either regular expression-based consensus or position weight matrices. The data base can also be searched for promoters harboring user-defined TFBSs given as a consensus or a position weight matrix. Furthermore, the user can retrieve putative promoter sequences for any given gene together with identified TFBSs located on its promoter. Orthologous promoters are also analyzed to determine conserved elements.

Job submission and management through web services: the experience with the CREAM service

NASA Astrophysics Data System (ADS)

Aiftimiei, C.; Andreetto, P.; Bertocco, S.; Fina, S. D.; Ronco, S. D.; Dorigo, A.; Gianelle, A.; Marzolla, M.; Mazzucato, M.; Sgaravatto, M.; Verlato, M.; Zangrando, L.; Corvo, M.; Miccio, V.; Sciaba, A.; Cesini, D.; Dongiovanni, D.; Grandi, C.

2008-07-01

Modern Grid middleware is built around components providing basic functionality, such as data storage, authentication, security, job management, resource monitoring and reservation. In this paper we describe the Computing Resource Execution and Management (CREAM) service. CREAM provides a Web service-based job execution and management capability for Grid systems; in particular, it is being used within the gLite middleware. CREAM exposes a Web service interface allowing conforming clients to submit and manage computational jobs to a Local Resource Management System. We developed a special component, called ICE (Interface to CREAM Environment) to integrate CREAM in gLite. ICE transfers job submissions and cancellations from the Workload Management System, allowing users to manage CREAM jobs from the gLite User Interface. This paper describes some recent studies aimed at assessing the performance and reliability of CREAM and ICE; those tests have been performed as part of the acceptance tests for integration of CREAM and ICE in gLite. We also discuss recent work towards enhancing CREAM with a BES and JSDL compliant interface.

CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function.

PubMed

Krüger, Dennis M; Rathi, Prakash Chandra; Pfleger, Christopher; Gohlke, Holger

2013-07-01

The Constraint Network Analysis (CNA) web server provides a user-friendly interface to the CNA approach developed in our laboratory for linking results from rigidity analyses to biologically relevant characteristics of a biomolecular structure. The CNA web server provides a refined modeling of thermal unfolding simulations that considers the temperature dependence of hydrophobic tethers and computes a set of global and local indices for quantifying biomacromolecular stability. From the global indices, phase transition points are identified where the structure switches from a rigid to a floppy state; these phase transition points can be related to a protein's (thermo-)stability. Structural weak spots (unfolding nuclei) are automatically identified, too; this knowledge can be exploited in data-driven protein engineering. The local indices are useful in linking flexibility and function and to understand the impact of ligand binding on protein flexibility. The CNA web server robustly handles small-molecule ligands in general. To overcome issues of sensitivity with respect to the input structure, the CNA web server allows performing two ensemble-based variants of thermal unfolding simulations. The web server output is provided as raw data, plots and/or Jmol representations. The CNA web server, accessible at http://cpclab.uni-duesseldorf.de/cna or http://www.cnanalysis.de, is free and open to all users with no login requirement.

CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function

PubMed Central

Krüger, Dennis M.; Rathi, Prakash Chandra; Pfleger, Christopher; Gohlke, Holger

2013-01-01

The Constraint Network Analysis (CNA) web server provides a user-friendly interface to the CNA approach developed in our laboratory for linking results from rigidity analyses to biologically relevant characteristics of a biomolecular structure. The CNA web server provides a refined modeling of thermal unfolding simulations that considers the temperature dependence of hydrophobic tethers and computes a set of global and local indices for quantifying biomacromolecular stability. From the global indices, phase transition points are identified where the structure switches from a rigid to a floppy state; these phase transition points can be related to a protein’s (thermo-)stability. Structural weak spots (unfolding nuclei) are automatically identified, too; this knowledge can be exploited in data-driven protein engineering. The local indices are useful in linking flexibility and function and to understand the impact of ligand binding on protein flexibility. The CNA web server robustly handles small-molecule ligands in general. To overcome issues of sensitivity with respect to the input structure, the CNA web server allows performing two ensemble-based variants of thermal unfolding simulations. The web server output is provided as raw data, plots and/or Jmol representations. The CNA web server, accessible at http://cpclab.uni-duesseldorf.de/cna or http://www.cnanalysis.de, is free and open to all users with no login requirement. PMID:23609541

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

ERIC Educational Resources Information Center

Chou, Chien

2002-01-01

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

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

PubMed Central

Gao, Jianjiong; Aksoy, Bülent Arman; Dogrusoz, Ugur; Dresdner, Gideon; Gross, Benjamin; Sumer, S. Onur; Sun, Yichao; Jacobsen, Anders; Sinha, Rileen; Larsson, Erik; Cerami, Ethan; Sander, Chris; Schultz, Nikolaus

2014-01-01

The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal reduces molecular profiling data from cancer tissues and cell lines into readily understandable genetic, epigenetic, gene expression, and proteomic events. The query interface combined with customized data storage enables researchers to interactively explore genetic alterations across samples, genes, and pathways and, when available in the underlying data, to link these to clinical outcomes. The portal provides graphical summaries of gene-level data from multiple platforms, network visualization and analysis, survival analysis, patient-centric queries, and software programmatic access. The intuitive Web interface of the portal makes complex cancer genomics profiles accessible to researchers and clinicians without requiring bioinformatics expertise, thus facilitating biological discoveries. Here, we provide a practical guide to the analysis and visualization features of the cBioPortal for Cancer Genomics. PMID:23550210

A Cross-Cultural Usability Study on the Internationalization of User Interfaces Based on an Empirical Five Factor Model

ERIC Educational Resources Information Center

Chakraborty, Joyram

2009-01-01

With the internationalization of e-commerce, it is no longer viable to design one user interface for all environments. Web-based applications and services can be accessed from all over the globe. To account for this globalization process, software developers need to understand that simply accounting for language translation of their websites for…

Stratification-Based Outlier Detection over the Deep Web.

PubMed

Xian, Xuefeng; Zhao, Pengpeng; Sheng, Victor S; Fang, Ligang; Gu, Caidong; Yang, Yuanfeng; Cui, Zhiming

2016-01-01

For many applications, finding rare instances or outliers can be more interesting than finding common patterns. Existing work in outlier detection never considers the context of deep web. In this paper, we argue that, for many scenarios, it is more meaningful to detect outliers over deep web. In the context of deep web, users must submit queries through a query interface to retrieve corresponding data. Therefore, traditional data mining methods cannot be directly applied. The primary contribution of this paper is to develop a new data mining method for outlier detection over deep web. In our approach, the query space of a deep web data source is stratified based on a pilot sample. Neighborhood sampling and uncertainty sampling are developed in this paper with the goal of improving recall and precision based on stratification. Finally, a careful performance evaluation of our algorithm confirms that our approach can effectively detect outliers in deep web.

Stratification-Based Outlier Detection over the Deep Web

PubMed Central

Xian, Xuefeng; Zhao, Pengpeng; Sheng, Victor S.; Fang, Ligang; Gu, Caidong; Yang, Yuanfeng; Cui, Zhiming

2016-01-01

For many applications, finding rare instances or outliers can be more interesting than finding common patterns. Existing work in outlier detection never considers the context of deep web. In this paper, we argue that, for many scenarios, it is more meaningful to detect outliers over deep web. In the context of deep web, users must submit queries through a query interface to retrieve corresponding data. Therefore, traditional data mining methods cannot be directly applied. The primary contribution of this paper is to develop a new data mining method for outlier detection over deep web. In our approach, the query space of a deep web data source is stratified based on a pilot sample. Neighborhood sampling and uncertainty sampling are developed in this paper with the goal of improving recall and precision based on stratification. Finally, a careful performance evaluation of our algorithm confirms that our approach can effectively detect outliers in deep web. PMID:27313603

BioSWR – Semantic Web Services Registry for Bioinformatics

PubMed Central

Repchevsky, Dmitry; Gelpi, Josep Ll.

2014-01-01

Despite of the variety of available Web services registries specially aimed at Life Sciences, their scope is usually restricted to a limited set of well-defined types of services. While dedicated registries are generally tied to a particular format, general-purpose ones are more adherent to standards and usually rely on Web Service Definition Language (WSDL). Although WSDL is quite flexible to support common Web services types, its lack of semantic expressiveness led to various initiatives to describe Web services via ontology languages. Nevertheless, WSDL 2.0 descriptions gained a standard representation based on Web Ontology Language (OWL). BioSWR is a novel Web services registry that provides standard Resource Description Framework (RDF) based Web services descriptions along with the traditional WSDL based ones. The registry provides Web-based interface for Web services registration, querying and annotation, and is also accessible programmatically via Representational State Transfer (REST) API or using a SPARQL Protocol and RDF Query Language. BioSWR server is located at http://inb.bsc.es/BioSWR/and its code is available at https://sourceforge.net/projects/bioswr/under the LGPL license. PMID:25233118

BioSWR--semantic web services registry for bioinformatics.

PubMed

Repchevsky, Dmitry; Gelpi, Josep Ll

2014-01-01

Despite of the variety of available Web services registries specially aimed at Life Sciences, their scope is usually restricted to a limited set of well-defined types of services. While dedicated registries are generally tied to a particular format, general-purpose ones are more adherent to standards and usually rely on Web Service Definition Language (WSDL). Although WSDL is quite flexible to support common Web services types, its lack of semantic expressiveness led to various initiatives to describe Web services via ontology languages. Nevertheless, WSDL 2.0 descriptions gained a standard representation based on Web Ontology Language (OWL). BioSWR is a novel Web services registry that provides standard Resource Description Framework (RDF) based Web services descriptions along with the traditional WSDL based ones. The registry provides Web-based interface for Web services registration, querying and annotation, and is also accessible programmatically via Representational State Transfer (REST) API or using a SPARQL Protocol and RDF Query Language. BioSWR server is located at http://inb.bsc.es/BioSWR/and its code is available at https://sourceforge.net/projects/bioswr/under the LGPL license.

Focused Crawling of the Deep Web Using Service Class Descriptions

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

Rocco, D; Liu, L; Critchlow, T

2004-06-21

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

National Scale Marine Geophysical Data Portal for the Israel EEZ with Public Access Web-GIS Platform

NASA Astrophysics Data System (ADS)

Ketter, T.; Kanari, M.; Tibor, G.

2017-12-01

Recent offshore discoveries and regulation in the Israel Exclusive Economic Zone (EEZ) are the driving forces behind increasing marine research and development initiatives such as infrastructure development, environmental protection and decision making among many others. All marine operations rely on existing seabed information, while some also generate new data. We aim to create a single platform knowledge-base to enable access to existing information, in a comprehensive, publicly accessible web-based interface. The Israel EEZ covers approx. 26,000 sqkm and has been surveyed continuously with various geophysical instruments over the past decades, including 10,000 km of multibeam survey lines, 8,000 km of sub-bottom seismic lines, and hundreds of sediment sampling stations. Our database consists of vector and raster datasets from multiple sources compiled into a repository of geophysical data and metadata, acquired nation-wide by several research institutes and universities. The repository will enable public access via a web portal based on a GIS platform, including datasets from multibeam, sub-bottom profiling, single- and multi-channel seismic surveys and sediment sampling analysis. Respective data products will also be available e.g. bathymetry, substrate type, granulometry, geological structure etc. Operating a web-GIS based repository allows retrieval of pre-existing data for potential users to facilitate planning of future activities e.g. conducting marine surveys, construction of marine infrastructure and other private or public projects. User interface is based on map oriented spatial selection, which will reveal any relevant data for designated areas of interest. Querying the database will allow the user to obtain information about the data owner and to address them for data retrieval as required. Wide and free public access to existing data and metadata can save time and funds for academia, government and commercial sectors, while aiding in cooperation and data sharing among the various stakeholders.

The Legacy Archive for Microwave Background Data Analysis (LAMBDA)

NASA Astrophysics Data System (ADS)

Miller, Nathan; LAMBDA

2018-01-01

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

Insight: An ontology-based integrated database and analysis platform for epilepsy self-management research.

PubMed

Sahoo, Satya S; Ramesh, Priya; Welter, Elisabeth; Bukach, Ashley; Valdez, Joshua; Tatsuoka, Curtis; Bamps, Yvan; Stoll, Shelley; Jobst, Barbara C; Sajatovic, Martha

2016-10-01

We present Insight as an integrated database and analysis platform for epilepsy self-management research as part of the national Managing Epilepsy Well Network. Insight is the only available informatics platform for accessing and analyzing integrated data from multiple epilepsy self-management research studies with several new data management features and user-friendly functionalities. The features of Insight include, (1) use of Common Data Elements defined by members of the research community and an epilepsy domain ontology for data integration and querying, (2) visualization tools to support real time exploration of data distribution across research studies, and (3) an interactive visual query interface for provenance-enabled research cohort identification. The Insight platform contains data from five completed epilepsy self-management research studies covering various categories of data, including depression, quality of life, seizure frequency, and socioeconomic information. The data represents over 400 participants with 7552 data points. The Insight data exploration and cohort identification query interface has been developed using Ruby on Rails Web technology and open source Web Ontology Language Application Programming Interface to support ontology-based reasoning. We have developed an efficient ontology management module that automatically updates the ontology mappings each time a new version of the Epilepsy and Seizure Ontology is released. The Insight platform features a Role-based Access Control module to authenticate and effectively manage user access to different research studies. User access to Insight is managed by the Managing Epilepsy Well Network database steering committee consisting of representatives of all current collaborating centers of the Managing Epilepsy Well Network. New research studies are being continuously added to the Insight database and the size as well as the unique coverage of the dataset allows investigators to conduct aggregate data analysis that will inform the next generation of epilepsy self-management studies. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

A prototype web-GIS application for risk analysis of natural hazards in Switzerland

NASA Astrophysics Data System (ADS)

Aye, Zar Chi; Nicolet, Pierrick; Jaboyedoff, Michel; Derron, Marc-Henri; Gerber, Christian; Lévy, Sebastien

2016-04-01

Following changes in the system of Swiss subsidy in January 2008, the Swiss cantons and the Federal Office for the Environment (FOEN) were forced to prioritize different natural hazard protection projects based on their cost-effectiveness, as a response to limited financial resources (Bründl et al., 2009). For this purpose, applications such as EconoMe (OFEV, 2016) and Valdorisk (DGE, 2016) were developed for risk evaluation and prioritization of mitigation projects. These tools serve as a useful decision-making instrument to the community of practitioners and responsible authorities for natural hazard risk management in Switzerland. However, there are several aspects which could be improved, in particular, the integration and visualization of spatial information interactively through a web-GIS interface for better risk planning and evaluation. Therefore, in this study, we aim to develop an interactive web-GIS application based on the risk concepts applied in Switzerland. The purpose of this tool is to provide a rapid evaluation of risk before and after protection measures, and to test the efficiency of measures by using a simplified cost-benefit analysis within the context of different protection projects. This application allows to integrate different layers which are necessary to calculate risk, in particular, hazard intensity (vector) maps for different scenarios (such as 30, 100 and 300 years of return periods based on Swiss guidelines), exposed objects (such as buildings) and vulnerability information of these objects. Based on provided information and additional parameters, risk is calculated automatically and results are visualized within the web-GIS interface of the application. The users can modify these input information and parameters to create different risk scenarios. Based on the resultant risk scenarios, the users can propose and visualize (preliminary) risk reduction measures before realizing the actual design and dimensions of such protective measures in the area. After designing measures, the users can re-calculate risk by updating hazard intensity and object layers. This is achieved by manual editing of shape (vector) layers in the web-GIS interface interactively. Within the application, a cost-benefit analysis tool is also integrated to support the decision-making process for the selection of different protection measures. Finally, the resultant risk information (vector layers and data) can be exported in the form of shapefiles and excel sheets. A prototype application is realized using open-source geospatial software and technologies. Boundless framework with its client-side SDK environment is applied for the rapid prototyping. Free and open source components such as PostGIS spatial database, GeoServer and GeoWebCache, GeoExt and OpenLayers are used for the development of the platform. This developed prototype is demonstrated with a case study area located in Les Diablerets, Switzerland. This research work is carried out within a project funded by the Canton of Vaud, Switzerland. References: Bründl, M., Romang, H. E., Bischof, N., and Rheinberger, C. M.: The risk concept and its application in natural hazard risk management in Switzerland, Nat. Hazards Earth Syst. Sci., 9, 801-813, 2009. DGE: Valdorisk - Direction Générale de l'Environnement, www.vd.ch, accessed 9 January 2016, 2016. OFEV: EconoMe - Office fédéral de l'environnement, www.econome.admin.ch, accessed 9 January 2016, 2016.

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.

Web accessibility and open source software.

PubMed

Obrenović, Zeljko

2009-07-01

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

Personal diabetes management system based on ubiquitous computing technology.

PubMed

Park, Kyung-Soon; Kim, Nam-Jin; Hong, Joo-Hyun; Park, Mi-Sook; Cha, Eun-Jung; Lee, Tae-Soo

2006-01-01

Assisting diabetes patients to self manage blood glucose test and insulin injection is of great importance for their healthcare. This study presented a PDA based system to manage the personal glucose level data interfaced with a small glucometer through a serial port. The data stored in the PDA can be transmitted by cradle or wireless communication to the remote web-server, where further medical analysis and service is provided. This system enables more efficient and systematic management of diabetes patients through self management and remote medical practice.

Next Generation Transport Phenomenology Model

NASA Technical Reports Server (NTRS)

Strickland, Douglas J.; Knight, Harold; Evans, J. Scott

2004-01-01

This report describes the progress made in Quarter 3 of Contract Year 3 on the development of Aeronomy Phenomenology Modeling Tool (APMT), an open-source, component-based, client-server architecture for distributed modeling, analysis, and simulation activities focused on electron and photon transport for general atmospheres. In the past quarter, column emission rate computations were implemented in Java, preexisting Fortran programs for computing synthetic spectra were embedded into APMT through Java wrappers, and work began on a web-based user interface for setting input parameters and running the photoelectron and auroral electron transport models.

CropEx Web-Based Agricultural Monitoring and Decision Support

NASA Technical Reports Server (NTRS)

Harvey. Craig; Lawhead, Joel

2011-01-01

CropEx is a Web-based agricultural Decision Support System (DSS) that monitors changes in crop health over time. It is designed to be used by a wide range of both public and private organizations, including individual producers and regional government offices with a vested interest in tracking vegetation health. The database and data management system automatically retrieve and ingest data for the area of interest. Another stores results of the processing and supports the DSS. The processing engine will allow server-side analysis of imagery with support for image sub-setting and a set of core raster operations for image classification, creation of vegetation indices, and change detection. The system includes the Web-based (CropEx) interface, data ingestion system, server-side processing engine, and a database processing engine. It contains a Web-based interface that has multi-tiered security profiles for multiple users. The interface provides the ability to identify areas of interest to specific users, user profiles, and methods of processing and data types for selected or created areas of interest. A compilation of programs is used to ingest available data into the system, classify that data, profile that data for quality, and make data available for the processing engine immediately upon the data s availability to the system (near real time). The processing engine consists of methods and algorithms used to process the data in a real-time fashion without copying, storing, or moving the raw data. The engine makes results available to the database processing engine for storage and further manipulation. The database processing engine ingests data from the image processing engine, distills those results into numerical indices, and stores each index for an area of interest. This process happens each time new data is ingested and processed for the area of interest, and upon subsequent database entries, the database processing engine qualifies each value for each area of interest and conducts a logical processing of results indicating when and where thresholds are exceeded. Reports are provided at regular, operator-determined intervals that include variances from thresholds and links to view raw data for verification, if necessary. The technology and method of development allow the code base to easily be modified for varied use in the real-time and near-real-time processing environments. In addition, the final product will be demonstrated as a means for rapid draft assessment of imagery.

Web-Based Instruction Systems: Correlation of First Year Online Student Acceptance and Use Variables Related to Intent to Use

ERIC Educational Resources Information Center

Butler, William T.

2014-01-01

The online education population is growing among all age groups but the connection that allows students to interface to the online classroom has been ignored as an issue for research. Web-based instructional systems are the key technology that enables students to enter the virtual classroom of the internet. The study of student perceptions of the…

Enabling User to User Interactions in Web Lectures with History-Aware User Awareness

ERIC Educational Resources Information Center

Ketterl, Markus; Mertens, Robert; Wiesen, Christoph; Vornberger, Oliver

2011-01-01

Purpose: The purpose of this paper is to present a user interface for web lectures for engaging with other users while working with video based learning content. The application allows its users to ask questions about the content and to get answers from those users that currently online are more familiar with it. The filtering is based on the…

Web-based Teaching Radio Interferometer for Africa

NASA Astrophysics Data System (ADS)

Carignan, Claude

2015-08-01

Practical training for the future use of the African VLBI Network (AVN) or any VLBI experiment starts by understanding the basic principles of radio observations and radio interferometry. The aim of this project is to build a basic interferometer that could be used remotely via a web interface from any country on the African continent. This should turn out as a much less expensive and much more efficient way to train AVN researchers from SKA partner countries to the principles of radio astronomy and to interferometric data analysis. The idea is based on the very successful EUHOU (European Hands-On Universe) already very successful in Europe. The former EUHOU manager, Dr Yannick Liebert, arrived for a 3 years postdoc with Prof Claude Carignan at the University of Cape Town to implement the same project on the African continent (AHI: African Hands-on Interferometry). Besides the use of AHI for the AVN researchers, this web-based system could be used be any undergraduate program on radio astronomical techniques across the African continent as the EUHOU is used all across Europe.

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.

Immunogenetic Management Software: a new tool for visualization and analysis of complex immunogenetic datasets

PubMed Central

Johnson, Z. P.; Eady, R. D.; Ahmad, S. F.; Agravat, S.; Morris, T; Else, J; Lank, S. M.; Wiseman, R. W.; O’Connor, D. H.; Penedo, M. C. T.; Larsen, C. P.

2012-01-01

Here we describe the Immunogenetic Management Software (IMS) system, a novel web-based application that permitsmultiplexed analysis of complex immunogenetic traits that are necessary for the accurate planning and execution of experiments involving large animal models, including nonhuman primates. IMS is capable of housing complex pedigree relationships, microsatellite-based MHC typing data, as well as MHC pyrosequencing expression analysis of class I alleles. It includes a novel, automated MHC haplotype naming algorithm and has accomplished an innovative visualization protocol that allows users to view multiple familial and MHC haplotype relationships through a single, interactive graphical interface. Detailed DNA and RNA-based data can also be queried and analyzed in a highly accessible fashion, and flexible search capabilities allow experimental choices to be made based on multiple, individualized and expandable immunogenetic factors. This web application is implemented in Java, MySQL, Tomcat, and Apache, with supported browsers including Internet Explorer and Firefox onWindows and Safari on Mac OS. The software is freely available for distribution to noncommercial users by contacting Leslie. kean@emory.edu. A demonstration site for the software is available at http://typing.emory.edu/typing_demo, user name: imsdemo7@gmail.com and password: imsdemo. PMID:22080300

Immunogenetic Management Software: a new tool for visualization and analysis of complex immunogenetic datasets.

PubMed

Johnson, Z P; Eady, R D; Ahmad, S F; Agravat, S; Morris, T; Else, J; Lank, S M; Wiseman, R W; O'Connor, D H; Penedo, M C T; Larsen, C P; Kean, L S

2012-04-01

Here we describe the Immunogenetic Management Software (IMS) system, a novel web-based application that permits multiplexed analysis of complex immunogenetic traits that are necessary for the accurate planning and execution of experiments involving large animal models, including nonhuman primates. IMS is capable of housing complex pedigree relationships, microsatellite-based MHC typing data, as well as MHC pyrosequencing expression analysis of class I alleles. It includes a novel, automated MHC haplotype naming algorithm and has accomplished an innovative visualization protocol that allows users to view multiple familial and MHC haplotype relationships through a single, interactive graphical interface. Detailed DNA and RNA-based data can also be queried and analyzed in a highly accessible fashion, and flexible search capabilities allow experimental choices to be made based on multiple, individualized and expandable immunogenetic factors. This web application is implemented in Java, MySQL, Tomcat, and Apache, with supported browsers including Internet Explorer and Firefox on Windows and Safari on Mac OS. The software is freely available for distribution to noncommercial users by contacting Leslie.kean@emory.edu. A demonstration site for the software is available at http://typing.emory.edu/typing_demo , user name: imsdemo7@gmail.com and password: imsdemo.

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

PubMed

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

2015-06-02

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

Change and Anomaly Detection in Real-Time GPS Data

NASA Astrophysics Data System (ADS)

Granat, R.; Pierce, M.; Gao, X.; Bock, Y.

2008-12-01

The California Real-Time Network (CRTN) is currently generating real-time GPS position data at a rate of 1-2Hz at over 80 locations. The CRTN data presents the possibility of studying dynamical solid earth processes in a way that complements existing seismic networks. To realize this possibility we have developed a prototype system for detecting changes and anomalies in the real-time data. Through this system, we can can correlate changes in multiple stations in order to detect signals with geographical extent. Our approach involves developing a statistical model for each GPS station in the network, and then using those models to segment the time series into a number of discrete states described by the model. We use a hidden Markov model (HMM) to describe the behavior of each station; fitting the model to the data requires neither labeled training examples nor a priori information about the system. As such, HMMs are well suited to this problem domain, in which the data remains largely uncharacterized. There are two main components to our approach. The first is the model fitting algorithm, regularized deterministic annealing expectation- maximization (RDAEM), which provides robust, high-quality results. The second is a web service infrastructure that connects the data to the statistical modeling analysis and allows us to easily present the results of that analysis through a web portal interface. This web service approach facilitates the automatic updating of station models to keep pace with dynamical changes in the data. Our web portal interface is critical to the process of interpreting the data. A Google Maps interface allows users to visually interpret state changes not only on individual stations but across the entire network. Users can drill down from the map interface to inspect detailed results for individual stations, download the time series data, and inspect fitted models. Alternatively, users can use the web portal look at the evolution of changes on the network by moving backwards and forwards in time.

The GLIMS Glacier Database

NASA Astrophysics Data System (ADS)

Raup, B. H.; Khalsa, S. S.; Armstrong, R.

2007-12-01

The Global Land Ice Measurements from Space (GLIMS) project has built a geospatial and temporal database of glacier data, composed of glacier outlines and various scalar attributes. These data are being derived primarily from satellite imagery, such as from ASTER and Landsat. Each "snapshot" of a glacier is from a specific time, and the database is designed to store multiple snapshots representative of different times. We have implemented two web-based interfaces to the database; one enables exploration of the data via interactive maps (web map server), while the other allows searches based on text-field constraints. The web map server is an Open Geospatial Consortium (OGC) compliant Web Map Server (WMS) and Web Feature Server (WFS). This means that other web sites can display glacier layers from our site over the Internet, or retrieve glacier features in vector format. All components of the system are implemented using Open Source software: Linux, PostgreSQL, PostGIS (geospatial extensions to the database), MapServer (WMS and WFS), and several supporting components such as Proj.4 (a geographic projection library) and PHP. These tools are robust and provide a flexible and powerful framework for web mapping applications. As a service to the GLIMS community, the database contains metadata on all ASTER imagery acquired over glacierized terrain. Reduced-resolution of the images (browse imagery) can be viewed either as a layer in the MapServer application, or overlaid on the virtual globe within Google Earth. The interactive map application allows the user to constrain by time what data appear on the map. For example, ASTER or glacier outlines from 2002 only, or from Autumn in any year, can be displayed. The system allows users to download their selected glacier data in a choice of formats. The results of a query based on spatial selection (using a mouse) or text-field constraints can be downloaded in any of these formats: ESRI shapefiles, KML (Google Earth), MapInfo, GML (Geography Markup Language) and GMT (Generic Mapping Tools). This "clip-and-ship" function allows users to download only the data they are interested in. Our flexible web interfaces to the database, which includes various support layers (e.g. a layer to help collaborators identify satellite imagery over their region of expertise) will facilitate enhanced analysis to be undertaken on glacier systems, their distribution, and their impacts on other Earth systems.

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

The New Web-Based Hera Data Processing System at the HEASARC

NASA Technical Reports Server (NTRS)

Pence, W.

2011-01-01

The HEASARC at NASA/GSFC has provide an on-line astronomical data processing system called Hera for several years. Hera provides a complete data processing environment, including installed software packages, local data storage, and the CPU resources needed to process the user's data. The original design of Hera, however, has 2 requirements that has limited it's usefulness for some users, namely, that 1) the user must download and install a small helper program on their own computer before using Hera, and 2) Hera requires that several computer ports/sockets be allowed to communicate through any local firewalls on the users machine. Both of these restrictions can be problematic for some users, therefore we are now migrating Hera into a purely Web based environment which only requires a standard Web browser. The first release of Web Hera is now publicly available at http://heasarc.gsfc.nasa.gov/webheara/. It currently provides a standard graphical interface for running hundreds of different data processing programs that are available in the HEASARC's ftools software package. Over the next year we to add more features to Web Hera, including an interactive command line interface, and more display and line capabilities.

Web-GIS platform for monitoring and forecasting of regional climate and ecological changes

NASA Astrophysics Data System (ADS)

Gordov, E. P.; Krupchatnikov, V. N.; Lykosov, V. N.; Okladnikov, I.; Titov, A. G.; Shulgina, T. M.

2012-12-01

Growing volume of environmental data from sensors and model outputs makes development of based on modern information-telecommunication technologies software infrastructure for information support of integrated scientific researches in the field of Earth sciences urgent and important task (Gordov et al, 2012, van der Wel, 2005). It should be considered that original heterogeneity of datasets obtained from different sources and institutions not only hampers interchange of data and analysis results but also complicates their intercomparison leading to a decrease in reliability of analysis results. However, modern geophysical data processing techniques allow combining of different technological solutions for organizing such information resources. Nowadays it becomes a generally accepted opinion that information-computational infrastructure should rely on a potential of combined usage of web- and GIS-technologies for creating applied information-computational web-systems (Titov et al, 2009, Gordov et al. 2010, Gordov, Okladnikov and Titov, 2011). Using these approaches for development of internet-accessible thematic information-computational systems, and arranging of data and knowledge interchange between them is a very promising way of creation of distributed information-computation environment for supporting of multidiscipline regional and global research in the field of Earth sciences including analysis of climate changes and their impact on spatial-temporal vegetation distribution and state. Experimental software and hardware platform providing operation of a web-oriented production and research center for regional climate change investigations which combines modern web 2.0 approach, GIS-functionality and capabilities of running climate and meteorological models, large geophysical datasets processing, visualization, joint software development by distributed research groups, scientific analysis and organization of students and post-graduate students education is presented. Platform software developed (Shulgina et al, 2012, Okladnikov et al, 2012) includes dedicated modules for numerical processing of regional and global modeling results for consequent analysis and visualization. Also data preprocessing, run and visualization of modeling results of models WRF and «Planet Simulator» integrated into the platform is provided. All functions of the center are accessible by a user through a web-portal using common graphical web-browser in the form of an interactive graphical user interface which provides, particularly, capabilities of visualization of processing results, selection of geographical region of interest (pan and zoom) and data layers manipulation (order, enable/disable, features extraction). Platform developed provides users with capabilities of heterogeneous geophysical data analysis, including high-resolution data, and discovering of tendencies in climatic and ecosystem changes in the framework of different multidisciplinary researches (Shulgina et al, 2011). Using it even unskilled user without specific knowledge can perform computational processing and visualization of large meteorological, climatological and satellite monitoring datasets through unified graphical web-interface.

CovalentDock Cloud: a web server for automated covalent docking.

PubMed

Ouyang, Xuchang; Zhou, Shuo; Ge, Zemei; Li, Runtao; Kwoh, Chee Keong

2013-07-01

Covalent binding is an important mechanism for many drugs to gain its function. We developed a computational algorithm to model this chemical event and extended it to a web server, the CovalentDock Cloud, to make it accessible directly online without any local installation and configuration. It provides a simple yet user-friendly web interface to perform covalent docking experiments and analysis online. The web server accepts the structures of both the ligand and the receptor uploaded by the user or retrieved from online databases with valid access id. It identifies the potential covalent binding patterns, carries out the covalent docking experiments and provides visualization of the result for user analysis. This web server is free and open to all users at http://docking.sce.ntu.edu.sg/.

CovalentDock Cloud: a web server for automated covalent docking

PubMed Central

Ouyang, Xuchang; Zhou, Shuo; Ge, Zemei; Li, Runtao; Kwoh, Chee Keong

2013-01-01

Covalent binding is an important mechanism for many drugs to gain its function. We developed a computational algorithm to model this chemical event and extended it to a web server, the CovalentDock Cloud, to make it accessible directly online without any local installation and configuration. It provides a simple yet user-friendly web interface to perform covalent docking experiments and analysis online. The web server accepts the structures of both the ligand and the receptor uploaded by the user or retrieved from online databases with valid access id. It identifies the potential covalent binding patterns, carries out the covalent docking experiments and provides visualization of the result for user analysis. This web server is free and open to all users at http://docking.sce.ntu.edu.sg/. PMID:23677616

STAR: an integrated solution to management and visualization of sequencing data

PubMed Central

Wang, Tao; Liu, Jie; Shen, Li; Tonti-Filippini, Julian; Zhu, Yun; Jia, Haiyang; Lister, Ryan; Whitaker, John W.; Ecker, Joseph R.; Millar, A. Harvey; Ren, Bing; Wang, Wei

2013-01-01

Motivation: Easily visualization of complex data features is a necessary step to conduct studies on next-generation sequencing (NGS) data. We developed STAR, an integrated web application that enables online management, visualization and track-based analysis of NGS data. Results: STAR is a multilayer web service system. On the client side, STAR leverages JavaScript, HTML5 Canvas and asynchronous communications to deliver a smoothly scrolling desktop-like graphical user interface with a suite of in-browser analysis tools that range from providing simple track configuration controls to sophisticated feature detection within datasets. On the server side, STAR supports private session state retention via an account management system and provides data management modules that enable collection, visualization and analysis of third-party sequencing data from the public domain with over thousands of tracks hosted to date. Overall, STAR represents a next-generation data exploration solution to match the requirements of NGS data, enabling both intuitive visualization and dynamic analysis of data. Availability and implementation: STAR browser system is freely available on the web at http://wanglab.ucsd.edu/star/browser and https://github.com/angell1117/STAR-genome-browser. Contact: wei-wang@ucsd.edu PMID:24078702

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.

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

PubMed Central

Metsalu, Tauno; Vilo, Jaak

2015-01-01

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

Analysis of Technique to Extract Data from the Web for Improved Performance

NASA Astrophysics Data System (ADS)

Gupta, Neena; Singh, Manish

2010-11-01

The World Wide Web rapidly guides the world into a newly amazing electronic world, where everyone can publish anything in electronic form and extract almost all the information. Extraction of information from semi structured or unstructured documents, such as web pages, is a useful yet complex task. Data extraction, which is important for many applications, extracts the records from the HTML files automatically. Ontologies can achieve a high degree of accuracy in data extraction. We analyze method for data extraction OBDE (Ontology-Based Data Extraction), which automatically extracts the query result records from the web with the help of agents. OBDE first constructs an ontology for a domain according to information matching between the query interfaces and query result pages from different web sites within the same domain. Then, the constructed domain ontology is used during data extraction to identify the query result section in a query result page and to align and label the data values in the extracted records. The ontology-assisted data extraction method is fully automatic and overcomes many of the deficiencies of current automatic data extraction methods.

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.

Technical development of PubMed Interact: an improved interface for MEDLINE/PubMed searches

PubMed Central

Muin, Michael; Fontelo, Paul

2006-01-01

Background The project aims to create an alternative search interface for MEDLINE/PubMed that may provide assistance to the novice user and added convenience to the advanced user. An earlier version of the project was the 'Slider Interface for MEDLINE/PubMed searches' (SLIM) which provided JavaScript slider bars to control search parameters. In this new version, recent developments in Web-based technologies were implemented. These changes may prove to be even more valuable in enhancing user interactivity through client-side manipulation and management of results. Results PubMed Interact is a Web-based MEDLINE/PubMed search application built with HTML, JavaScript and PHP. It is implemented on a Windows Server 2003 with Apache 2.0.52, PHP 4.4.1 and MySQL 4.1.18. PHP scripts provide the backend engine that connects with E-Utilities and parses XML files. JavaScript manages client-side functionalities and converts Web pages into interactive platforms using dynamic HTML (DHTML), Document Object Model (DOM) tree manipulation and Ajax methods. With PubMed Interact, users can limit searches with JavaScript slider bars, preview result counts, delete citations from the list, display and add related articles and create relevance lists. Many interactive features occur at client-side, which allow instant feedback without reloading or refreshing the page resulting in a more efficient user experience. Conclusion PubMed Interact is a highly interactive Web-based search application for MEDLINE/PubMed that explores recent trends in Web technologies like DOM tree manipulation and Ajax. It may become a valuable technical development for online medical search applications. PMID:17083729

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

Remote Control and Monitoring of VLBI Experiments by Smartphones

NASA Astrophysics Data System (ADS)

Ruztort, C. H.; Hase, H.; Zapata, O.; Pedreros, F.

2012-12-01

For the remote control and monitoring of VLBI operations, we developed a software optimized for smartphones. This is a new tool based on a client-server architecture with a Web interface optimized for smartphone screens and cellphone networks. The server uses variables of the Field System and its station specific parameters stored in the shared memory. The client running on the smartphone by a Web interface analyzes and visualizes the current status of the radio telescope, receiver, schedule, and recorder. In addition, it allows commands to be sent remotely to the Field System computer and displays the log entries. The user has full access to the entire operation process, which is important in emergency cases. The software also integrates a webcam interface.

QuadBase2: web server for multiplexed guanine quadruplex mining and visualization

PubMed Central

Dhapola, Parashar; Chowdhury, Shantanu

2016-01-01

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

LD Hub: a centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis.

PubMed

Zheng, Jie; Erzurumluoglu, A Mesut; Elsworth, Benjamin L; Kemp, John P; Howe, Laurence; Haycock, Philip C; Hemani, Gibran; Tansey, Katherine; Laurin, Charles; Pourcain, Beate St; Warrington, Nicole M; Finucane, Hilary K; Price, Alkes L; Bulik-Sullivan, Brendan K; Anttila, Verneri; Paternoster, Lavinia; Gaunt, Tom R; Evans, David M; Neale, Benjamin M

2017-01-15

LD score regression is a reliable and efficient method of using genome-wide association study (GWAS) summary-level results data to estimate the SNP heritability of complex traits and diseases, partition this heritability into functional categories, and estimate the genetic correlation between different phenotypes. Because the method relies on summary level results data, LD score regression is computationally tractable even for very large sample sizes. However, publicly available GWAS summary-level data are typically stored in different databases and have different formats, making it difficult to apply LD score regression to estimate genetic correlations across many different traits simultaneously. In this manuscript, we describe LD Hub - a centralized database of summary-level GWAS results for 173 diseases/traits from different publicly available resources/consortia and a web interface that automates the LD score regression analysis pipeline. To demonstrate functionality and validate our software, we replicated previously reported LD score regression analyses of 49 traits/diseases using LD Hub; and estimated SNP heritability and the genetic correlation across the different phenotypes. We also present new results obtained by uploading a recent atopic dermatitis GWAS meta-analysis to examine the genetic correlation between the condition and other potentially related traits. In response to the growing availability of publicly accessible GWAS summary-level results data, our database and the accompanying web interface will ensure maximal uptake of the LD score regression methodology, provide a useful database for the public dissemination of GWAS results, and provide a method for easily screening hundreds of traits for overlapping genetic aetiologies. The web interface and instructions for using LD Hub are available at http://ldsc.broadinstitute.org/ CONTACT: jie.zheng@bristol.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Molecular structure input on the web.

PubMed

Ertl, Peter

2010-02-02

A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. This review focuses on a special type of molecule editors, namely those that are used for molecule structure input on the web. Scientific computing is now moving more and more in the direction of web services and cloud computing, with servers scattered all around the Internet. Thus a web browser has become the universal scientific user interface, and a tool to edit molecules directly within the web browser is essential.The review covers a history of web-based structure input, starting with simple text entry boxes and early molecule editors based on clickable maps, before moving to the current situation dominated by Java applets. One typical example - the popular JME Molecule Editor - will be described in more detail. Modern Ajax server-side molecule editors are also presented. And finally, the possible future direction of web-based molecule editing, based on technologies like JavaScript and Flash, is discussed.

Role-Based And Adaptive User Interface Designs In A Teledermatology Consult System: A Way To Secure And A Way To Enhance

PubMed Central

Lin, Yi-Jung; Speedie, Stuart

2003-01-01

User interface design is one of the most important parts of developing applications. Nowadays, a quality user interface must not only accommodate interaction between machines and users, but also needs to recognize the differences and provide functionalities for users from role-to-role or even individual-to-individual. With the web-based application of our Teledermatology consult system, the development environment provides us highly useful opportunities to create dynamic user interfaces, which lets us to gain greater access control and has the potential to increase efficiency of the system. We will describe the two models of user interfaces in our system: Role-based and Adaptive. PMID:14728419

Design and development of an IoT-based web application for an intelligent remote SCADA system

NASA Astrophysics Data System (ADS)

Kao, Kuang-Chi; Chieng, Wei-Hua; Jeng, Shyr-Long

2018-03-01

This paper presents a design of an intelligent remote electrical power supervisory control and data acquisition (SCADA) system based on the Internet of Things (IoT), with Internet Information Services (IIS) for setting up web servers, an ASP.NET model-view- controller (MVC) for establishing a remote electrical power monitoring and control system by using responsive web design (RWD), and a Microsoft SQL Server as the database. With the web browser connected to the Internet, the sensing data is sent to the client by using the TCP/IP protocol, which supports mobile devices with different screen sizes. The users can provide instructions immediately without being present to check the conditions, which considerably reduces labor and time costs. The developed system incorporates a remote measuring function by using a wireless sensor network and utilizes a visual interface to make the human-machine interface (HMI) more instinctive. Moreover, it contains an analog input/output and a basic digital input/output that can be applied to a motor driver and an inverter for integration with a remote SCADA system based on IoT, and thus achieve efficient power management.

TOPSAN: a dynamic web database for structural genomics.

PubMed

Ellrott, Kyle; Zmasek, Christian M; Weekes, Dana; Sri Krishna, S; Bakolitsa, Constantina; Godzik, Adam; Wooley, John

2011-01-01

The Open Protein Structure Annotation Network (TOPSAN) is a web-based collaboration platform for exploring and annotating structures determined by structural genomics efforts. Characterization of those structures presents a challenge since the majority of the proteins themselves have not yet been characterized. Responding to this challenge, the TOPSAN platform facilitates collaborative annotation and investigation via a user-friendly web-based interface pre-populated with automatically generated information. Semantic web technologies expand and enrich TOPSAN's content through links to larger sets of related databases, and thus, enable data integration from disparate sources and data mining via conventional query languages. TOPSAN can be found at http://www.topsan.org.

Optimizing the Information Presentation on Mining Potential by using Web Services Technology with Restful Protocol

NASA Astrophysics Data System (ADS)

Abdillah, T.; Dai, R.; Setiawan, E.

2018-02-01

This study aims to develop the application of Web Services technology with RestFul Protocol to optimize the information presentation on mining potential. This study used User Interface Design approach for the information accuracy and relevance as well as the Web Service for the reliability in presenting the information. The results show that: the information accuracy and relevance regarding mining potential can be seen from the achievement of User Interface implementation in the application that is based on the following rules: The consideration of the appropriate colours and objects, the easiness of using the navigation, and users’ interaction with the applications that employs symbols and languages understood by the users; the information accuracy and relevance related to mining potential can be observed by the information presented by using charts and Tool Tip Text to help the users understand the provided chart/figure; the reliability of the information presentation is evident by the results of Web Services testing in Figure 4.5.6. This study finds out that User Interface Design and Web Services approaches (for the access of different Platform apps) are able to optimize the presentation. The results of this study can be used as a reference for software developers and Provincial Government of Gorontalo.

BCM Search Launcher--an integrated interface to molecular biology data base search and analysis services available on the World Wide Web.

PubMed

Smith, R F; Wiese, B A; Wojzynski, M K; Davison, D B; Worley, K C

1996-05-01

The BCM Search Launcher is an integrated set of World Wide Web (WWW) pages that organize molecular biology-related search and analysis services available on the WWW by function, and provide a single point of entry for related searches. The Protein Sequence Search Page, for example, provides a single sequence entry form for submitting sequences to WWW servers that offer remote access to a variety of different protein sequence search tools, including BLAST, FASTA, Smith-Waterman, BEAUTY, PROSITE, and BLOCKS searches. Other Launch pages provide access to (1) nucleic acid sequence searches, (2) multiple and pair-wise sequence alignments, (3) gene feature searches, (4) protein secondary structure prediction, and (5) miscellaneous sequence utilities (e.g., six-frame translation). The BCM Search Launcher also provides a mechanism to extend the utility of other WWW services by adding supplementary hypertext links to results returned by remote servers. For example, links to the NCBI's Entrez data base and to the Sequence Retrieval System (SRS) are added to search results returned by the NCBI's WWW BLAST server. These links provide easy access to auxiliary information, such as Medline abstracts, that can be extremely helpful when analyzing BLAST data base hits. For new or infrequent users of sequence data base search tools, we have preset the default search parameters to provide the most informative first-pass sequence analysis possible. We have also developed a batch client interface for Unix and Macintosh computers that allows multiple input sequences to be searched automatically as a background task, with the results returned as individual HTML documents directly to the user's system. The BCM Search Launcher and batch client are available on the WWW at URL http:@gc.bcm.tmc.edu:8088/search-launcher.html.

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.

RootJS: Node.js Bindings for ROOT 6

NASA Astrophysics Data System (ADS)

Beffart, Theo; Früh, Maximilian; Haas, Christoph; Rajgopal, Sachin; Schwabe, Jonas; Wolff, Christoph; Szuba, Marek

2017-10-01

We present rootJS, an interface making it possible to seamlessly integrate ROOT 6 into applications written for Node.js, the JavaScript runtime platform increasingly commonly used to create high-performance Web applications. ROOT features can be called both directly from Node.js code and by JIT-compiling C++ macros. All rootJS methods are invoked asynchronously and support callback functions, allowing non-blocking operation of Node.js applications using them. Last but not least, our bindings have been designed to platform-independent and should therefore work on all systems supporting both ROOT 6 and Node.js. Thanks to rootJS it is now possible to create ROOT-aware Web applications taking full advantage of the high performance and extensive capabilities of Node.js. Examples include platforms for the quality assurance of acquired, reconstructed or simulated data, book-keeping and e-log systems, and even Web browser-based data visualisation and analysis.

Virtual Classroom for Business Planning Formulation.

ERIC Educational Resources Information Center

Osorio, J.; Rubio-Royo, E.; Ocon, A.

One of the most promising possibilities of the World Wide Web resides in its potential to support distance education. In 1996, the University of Las Palmas de Gran Canaria developed the "INNOVA Project" in order to promote Web-based training and learning. As a result, the Virtual Classroom Interface (IVA) was created. Several software…

Teaching And Learning Tectonics With Web-GIS

NASA Astrophysics Data System (ADS)

Anastasio, D. J.; Sahagian, D. L.; Bodzin, A.; Teletzke, A. L.; Rutzmoser, S.; Cirucci, L.; Bressler, D.; Burrows, J. E.

2012-12-01

Tectonics is a new curriculum enhancement consisting of six Web GIS investigations designed to augment a traditional middle school Earth science curriculum. The investigations are aligned to Disciplinary Core Ideas: Earth and Space Science from the National Research Council's (2012) Framework for K-12 Science Education and to tectonics benchmark ideas articulated in the AAAS Project 2061 (2007) Atlas of Science Literacy. The curriculum emphasizes geospatial thinking and scientific inquiry and consists of the following modules: Geohazards, which plate boundary is closest to me? How do we recognize plate boundaries? How does thermal energy move around the Earth? What happens when plates diverge? What happens when plate move sideways past each other? What happens when plates collide? The Web GIS interface uses JavaScript for simplicity, intuition, and convenience for implementation on a variety of platforms making it easier for diverse middle school learners and their teachers to conduct authentic Earth science investigations, including multidisciplinary visualization, analysis, and synthesis of data. Instructional adaptations allow students who are English language learners, have disabilities, or are reluctant readers to perform advanced desktop GIS functions including spatial analysis, map visualization and query. The Web GIS interface integrates graphics, multimedia, and animation in addition to newly developed features, which allow users to explore and discover geospatial patterns that would not be easily visible using typical classroom instructional materials. The Tectonics curriculum uses a spatial learning design model that incorporates a related set of frameworks and design principles. The framework builds on the work of other successful technology-integrated curriculum projects and includes, alignment of materials and assessments with learning goals, casting key ideas in real-world problems, engaging students in scientific practices that foster the use of key ideas, uses geospatial technology, and supports for teachers in adopting and implementing GIS and inquiry-based activities.

modPDZpep: a web resource for structure based analysis of human PDZ-mediated interaction networks.

PubMed

Sain, Neetu; Mohanty, Debasisa

2016-09-21

PDZ domains recognize short sequence stretches usually present in C-terminal of their interaction partners. Because of the involvement of PDZ domains in many important biological processes, several attempts have been made for developing bioinformatics tools for genome-wide identification of PDZ interaction networks. Currently available tools for prediction of interaction partners of PDZ domains utilize machine learning approach. Since, they have been trained using experimental substrate specificity data for specific PDZ families, their applicability is limited to PDZ families closely related to the training set. These tools also do not allow analysis of PDZ-peptide interaction interfaces. We have used a structure based approach to develop modPDZpep, a program to predict the interaction partners of human PDZ domains and analyze structural details of PDZ interaction interfaces. modPDZpep predicts interaction partners by using structural models of PDZ-peptide complexes and evaluating binding energy scores using residue based statistical pair potentials. Since, it does not require training using experimental data on peptide binding affinity, it can predict substrates for diverse PDZ families. Because of the use of simple scoring function for binding energy, it is also fast enough for genome scale structure based analysis of PDZ interaction networks. Benchmarking using artificial as well as real negative datasets indicates good predictive power with ROC-AUC values in the range of 0.7 to 0.9 for a large number of human PDZ domains. Another novel feature of modPDZpep is its ability to map novel PDZ mediated interactions in human protein-protein interaction networks, either by utilizing available experimental phage display data or by structure based predictions. In summary, we have developed modPDZpep, a web-server for structure based analysis of human PDZ domains. It is freely available at http://www.nii.ac.in/modPDZpep.html or http://202.54.226.235/modPDZpep.html . This article was reviewed by Michael Gromiha and Zoltán Gáspári.

78 FR 79434 - Notice of Technical Conference

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-30

...: one that will allow EQR users to file through a web interface on the Commission's Web site, and a... the conference, staff will demonstrate how to make a filing using both the XML and web interface... Calendar of Events on the Commission's Web site, www.ferc.gov . A free webcast of the conference will be...

SAFOD Brittle Microstructure and Mechanics Knowledge Base (BM2KB)

NASA Astrophysics Data System (ADS)

Babaie, Hassan A.; Broda Cindi, M.; Hadizadeh, Jafar; Kumar, Anuj

2013-07-01

Scientific drilling near Parkfield, California has established the San Andreas Fault Observatory at Depth (SAFOD), which provides the solid earth community with short range geophysical and fault zone material data. The BM2KB ontology was developed in order to formalize the knowledge about brittle microstructures in the fault rocks sampled from the SAFOD cores. A knowledge base, instantiated from this domain ontology, stores and presents the observed microstructural and analytical data with respect to implications for brittle deformation and mechanics of faulting. These data can be searched on the knowledge base‧s Web interface by selecting a set of terms (classes, properties) from different drop-down lists that are dynamically populated from the ontology. In addition to this general search, a query can also be conducted to view data contributed by a specific investigator. A search by sample is done using the EarthScope SAFOD Core Viewer that allows a user to locate samples on high resolution images of core sections belonging to different runs and holes. The class hierarchy of the BM2KB ontology was initially designed using the Unified Modeling Language (UML), which was used as a visual guide to develop the ontology in OWL applying the Protégé ontology editor. Various Semantic Web technologies such as the RDF, RDFS, and OWL ontology languages, SPARQL query language, and Pellet reasoning engine, were used to develop the ontology. An interactive Web application interface was developed through Jena, a java based framework, with AJAX technology, jsp pages, and java servlets, and deployed via an Apache tomcat server. The interface allows the registered user to submit data related to their research on a sample of the SAFOD core. The submitted data, after initial review by the knowledge base administrator, are added to the extensible knowledge base and become available in subsequent queries to all types of users. The interface facilitates inference capabilities in the ontology, supports SPARQL queries, allows for modifications based on successive discoveries, and provides an accessible knowledge base on the Web.

SolarSoft Web Services

NASA Astrophysics Data System (ADS)

Freeland, S.; Hurlburt, N.

2005-12-01

The SolarSoft system (SSW) is a set of integrated software libraries, databases, and system utilities which provide a common programming and data analysis environment for solar physics. The system includes contributions from a large community base, representing the efforts of many NASA PI team MO&DA teams,spanning many years and multiple NASA and international orbital and ground based missions. The SSW general use libraries include Many hundreds of utilities which are instrument and mission independent. A large subset are also SOLAR independent, such as time conversions, digital detector cleanup, time series analysis, mathematics, image display, WWW server communications and the like. PI teams may draw on these general purpose libraries for analysis and application development while concentrating efforts on instrument specific calibration issues rather than reinvention of general use software. By the same token, PI teams are encouraged to contribute new applications or enhancements to existing utilities which may have more general interest. Recent areas of intense evolution include space weather applications, automated distributed data access and analysis, interfaces with the ongoing Virtual Solar Observatory efforts, and externalization of SolarSoft power through Web Services. We will discuss the current status of SSW web services and demonstrate how this facilitates accessing the underlying power of SolarSoft in more abstract terms. In this context, we will describe the use of SSW services within the Collaborative Sun Earth Connector environment.

A reliable user authentication and key agreement scheme for Web-based Hospital-acquired Infection Surveillance Information System.

PubMed

Wu, Zhen-Yu; Tseng, Yi-Ju; Chung, Yufang; Chen, Yee-Chun; Lai, Feipei

2012-08-01

With the rapid development of the Internet, both digitization and electronic orientation are required on various applications in the daily life. For hospital-acquired infection control, a Web-based Hospital-acquired Infection Surveillance System was implemented. Clinical data from different hospitals and systems were collected and analyzed. The hospital-acquired infection screening rules in this system utilized this information to detect different patterns of defined hospital-acquired infection. Moreover, these data were integrated into the user interface of a signal entry point to assist physicians and healthcare providers in making decisions. Based on Service-Oriented Architecture, web-service techniques which were suitable for integrating heterogeneous platforms, protocols, and applications, were used. In summary, this system simplifies the workflow of hospital infection control and improves the healthcare quality. However, it is probable for attackers to intercept the process of data transmission or access to the user interface. To tackle the illegal access and to prevent the information from being stolen during transmission over the insecure Internet, a password-based user authentication scheme is proposed for information integrity.

A Web-Based Treatment Decision Support Tool for Patients With Advanced Knee Arthritis: Evaluation of User Interface and Content Design

PubMed Central

Zheng, Hua; Rosal, Milagros C; Li, Wenjun; Borg, Amy; Yang, Wenyun; Ayers, David C

2018-01-01

Background Data-driven surgical decisions will ensure proper use and timing of surgical care. We developed a Web-based patient-centered treatment decision and assessment tool to guide treatment decisions among patients with advanced knee osteoarthritis who are considering total knee replacement surgery. Objective The aim of this study was to examine user experience and acceptance of the Web-based treatment decision support tool among older adults. Methods User-centered formative and summative evaluations were conducted for the tool. A sample of 28 patients who were considering total knee replacement participated in the study. Participants’ responses to the user interface design, the clarity of information, as well as usefulness, satisfaction, and acceptance of the tool were collected through qualitative (ie, individual patient interviews) and quantitative (ie, standardized Computer System Usability Questionnaire) methods. Results Participants were older adults with a mean age of 63 (SD 11) years. Three-quarters of them had no technical questions using the tool. User interface design recommendations included larger fonts, bigger buttons, less colors, simpler navigation without extra “next page” click, less mouse movement, and clearer illustrations with simple graphs. Color-coded bar charts and outcome-specific graphs with positive action were easiest for them to understand the outcomes data. Questionnaire data revealed high satisfaction with the tool usefulness and interface quality, and also showed ease of use of the tool, regardless of age or educational status. Conclusions We evaluated the usability of a patient-centered decision support tool designed for advanced knee arthritis patients to facilitate their knee osteoarthritis treatment decision making. The lessons learned can inform other decision support tools to improve interface and content design for older patients’ use. PMID:29712620

Systemic Vulnerabilities in Customer-Premises Equipment (CPE) Routers

DTIC Science & Technology

2017-07-01

equipment (CPE),1 specifically small office/home office (SOHO) routers, has become ubiquitous. CPE routers are notorious for their web interface...and enabling remote management, although all settings controllable over the web -management interface can be manipulated. • 85% (11 of 13) of...specifically small office/home office (SOHO) routers— has become ubiquitous. CPE routers are notorious for their web interface vulnerabilities, old ver- sions

VisGets: coordinated visualizations for web-based information exploration and discovery.

PubMed

Dörk, Marian; Carpendale, Sheelagh; Collins, Christopher; Williamson, Carey

2008-01-01

In common Web-based search interfaces, it can be difficult to formulate queries that simultaneously combine temporal, spatial, and topical data filters. We investigate how coordinated visualizations can enhance search and exploration of information on the World Wide Web by easing the formulation of these types of queries. Drawing from visual information seeking and exploratory search, we introduce VisGets--interactive query visualizations of Web-based information that operate with online information within a Web browser. VisGets provide the information seeker with visual overviews of Web resources and offer a way to visually filter the data. Our goal is to facilitate the construction of dynamic search queries that combine filters from more than one data dimension. We present a prototype information exploration system featuring three linked VisGets (temporal, spatial, and topical), and used it to visually explore news items from online RSS feeds.

Quarterly Performance/Technical Report of the National Marrow Donor Program

DTIC Science & Technology

2006-05-01

HapLogicTM was implemented for all search reports. This provides a real-time DNA - based match that utilizes genotype list data in the up- front match...CCN meeting held at the ASBMT/CIBMTR Tandem conference, the National Library of Medicine (NLM) demonstrated a draft of their web based version of the...making improvements to the web based interface. O Government Signature Date A . Contingency Preparedness (Hypothesis 1) Grant Award N00014-05-1-0859

Spreadsheets for Analyzing and Optimizing Space Missions

NASA Technical Reports Server (NTRS)

Some, Raphael R.; Agrawal, Anil K.; Czikmantory, Akos J.; Weisbin, Charles R.; Hua, Hook; Neff, Jon M.; Cowdin, Mark A.; Lewis, Brian S.; Iroz, Juana; Ross, Rick

2009-01-01

XCALIBR (XML Capability Analysis LIBRary) is a set of Extensible Markup Language (XML) database and spreadsheet- based analysis software tools designed to assist in technology-return-on-investment analysis and optimization of technology portfolios pertaining to outer-space missions. XCALIBR is also being examined for use in planning, tracking, and documentation of projects. An XCALIBR database contains information on mission requirements and technological capabilities, which are related by use of an XML taxonomy. XCALIBR incorporates a standardized interface for exporting data and analysis templates to an Excel spreadsheet. Unique features of XCALIBR include the following: It is inherently hierarchical by virtue of its XML basis. The XML taxonomy codifies a comprehensive data structure and data dictionary that includes performance metrics for spacecraft, sensors, and spacecraft systems other than sensors. The taxonomy contains >700 nodes representing all levels, from system through subsystem to individual parts. All entries are searchable and machine readable. There is an intuitive Web-based user interface. The software automatically matches technologies to mission requirements. The software automatically generates, and makes the required entries in, an Excel return-on-investment analysis software tool. The results of an analysis are presented in both tabular and graphical displays.

Development of Web-based Distributed Cooperative Development Environmentof Sign-Language Animation System and its Evaluation

NASA Astrophysics Data System (ADS)

Yuizono, Takaya; Hara, Kousuke; Nakayama, Shigeru

A web-based distributed cooperative development environment of sign-language animation system has been developed. We have extended the system from the previous animation system that was constructed as three tiered system which consists of sign-language animation interface layer, sign-language data processing layer, and sign-language animation database. Two components of a web client using VRML plug-in and web servlet are added to the previous system. The systems can support humanoid-model avatar for interoperability, and can use the stored sign language animation data shared on the database. It is noted in the evaluation of this system that the inverse kinematics function of web client improves the sign-language animation making.

Developing A Web-based User Interface for Semantic Information Retrieval

NASA Technical Reports Server (NTRS)

Berrios, Daniel C.; Keller, Richard M.

2003-01-01

While there are now a number of languages and frameworks that enable computer-based systems to search stored data semantically, the optimal design for effective user interfaces for such systems is still uncle ar. Such interfaces should mask unnecessary query detail from users, yet still allow them to build queries of arbitrary complexity without significant restrictions. We developed a user interface supporting s emantic query generation for Semanticorganizer, a tool used by scient ists and engineers at NASA to construct networks of knowledge and dat a. Through this interface users can select node types, node attribute s and node links to build ad-hoc semantic queries for searching the S emanticOrganizer network.

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2014-01-01

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

Designing an information search interface for younger and older adults.

PubMed

Pak, Richard; Price, Margaux M

2008-08-01

The present study examined Web-based information retrieval as a function of age for two information organization schemes: hierarchical organization and one organized around tags or keywords. Older adults' performance in information retrieval tasks has traditionally been lower compared with younger adults'. The current study examined the degree to which information organization moderated age-related performance differences on an information retrieval task. The theory of fluid and crystallized intelligence may provide insight into different kinds of information architectures that may reduce age-related differences in computer-based information retrieval performance. Fifty younger (18-23 years of age) and 50 older (55-76 years of age) participants browsed a Web site for answers to specific questions. Half of the participants browsed the hierarchically organized system (taxonomy), which maintained a one-to-one relationship between menu link and page, whereas the other half browsed the tag-based interface, with a many-to-one relationship between menu and page. This difference was expected to interact with age-related differences in fluid and crystallized intelligence. Age-related differences in information retrieval performance persisted; however, a tag-based retrieval interface reduced age-related differences, as compared with a taxonomical interface. Cognitive aging theory can lead to interface interventions that reduce age-related differences in performance with technology. In an information retrieval paradigm, older adults may be able to leverage their increased crystallized intelligence to offset fluid intelligence declines in a computer-based information search task. More research is necessary, but the results suggest that information retrieval interfaces organized around keywords may reduce age-related differences in performance.

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.

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

NASA Astrophysics Data System (ADS)

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

2009-04-01

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

Wilber 3: A Python-Django Web Application For Acquiring Large-scale Event-oriented Seismic Data

NASA Astrophysics Data System (ADS)

Newman, R. L.; Clark, A.; Trabant, C. M.; Karstens, R.; Hutko, A. R.; Casey, R. E.; Ahern, T. K.

2013-12-01

Since 2001, the IRIS Data Management Center (DMC) WILBER II system has provided a convenient web-based interface for locating seismic data related to a particular event, and requesting a subset of that data for download. Since its launch, both the scale of available data and the technology of web-based applications have developed significantly. Wilber 3 is a ground-up redesign that leverages a number of public and open-source projects to provide an event-oriented data request interface with a high level of interactivity and scalability for multiple data types. Wilber 3 uses the IRIS/Federation of Digital Seismic Networks (FDSN) web services for event data, metadata, and time-series data. Combining a carefully optimized Google Map with the highly scalable SlickGrid data API, the Wilber 3 client-side interface can load tens of thousands of events or networks/stations in a single request, and provide instantly responsive browsing, sorting, and filtering of event and meta data in the web browser, without further reliance on the data service. The server-side of Wilber 3 is a Python-Django application, one of over a dozen developed in the last year at IRIS, whose common framework, components, and administrative overhead represent a massive savings in developer resources. Requests for assembled datasets, which may include thousands of data channels and gigabytes of data, are queued and executed using the Celery distributed Python task scheduler, giving Wilber 3 the ability to operate in parallel across a large number of nodes.

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

NASA Astrophysics Data System (ADS)

Franceschini, Derrick; Riecken, Mark

2016-05-01

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

Experiment Software and Projects on the Web with VISPA

NASA Astrophysics Data System (ADS)

Erdmann, M.; Fischer, B.; Fischer, R.; Geiser, E.; Glaser, C.; Müller, G.; Rieger, M.; Urban, M.; von Cube, R. F.; Welling, C.

2017-10-01

The Visual Physics Analysis (VISPA) project defines a toolbox for accessing software via the web. It is based on latest web technologies and provides a powerful extension mechanism that enables to interface a wide range of applications. Beyond basic applications such as a code editor, a file browser, or a terminal, it meets the demands of sophisticated experiment-specific use cases that focus on physics data analyses and typically require a high degree of interactivity. As an example, we developed a data inspector that is capable of browsing interactively through event content of several data formats, e.g., MiniAOD which is utilized by the CMS collaboration. The VISPA extension mechanism can also be used to embed external web-based applications that benefit from dynamic allocation of user-defined computing resources via SSH. For example, by wrapping the JSROOT project, ROOT files located on any remote machine can be inspected directly through a VISPA server instance. We introduced domains that combine groups of users and role-based permissions. Thereby, tailored projects are enabled, e.g. for teaching where access to student’s homework is restricted to a team of tutors, or for experiment-specific data that may only be accessible for members of the collaboration. We present the extension mechanism including corresponding applications and give an outlook onto the new permission system.

SAFOD Brittle Microstructure and Mechanics Knowledge Base (SAFOD BM2KB)

NASA Astrophysics Data System (ADS)

Babaie, H. A.; Hadizadeh, J.; di Toro, G.; Mair, K.; Kumar, A.

2008-12-01

We have developed a knowledge base to store and present the data collected by a group of investigators studying the microstructures and mechanics of brittle faulting using core samples from the SAFOD (San Andreas Fault Observatory at Depth) project. The investigations are carried out with a variety of analytical and experimental methods primarily to better understand the physics of strain localization in fault gouge. The knowledge base instantiates an specially-designed brittle rock deformation ontology developed at Georgia State University. The inference rules embedded in the semantic web languages, such as OWL, RDF, and RDFS, which are used in our ontology, allow the Pellet reasoner used in this application to derive additional truths about the ontology and knowledge of this domain. Access to the knowledge base is via a public website, which is designed to provide the knowledge acquired by all the investigators involved in the project. The stored data will be products of studies such as: experiments (e.g., high-velocity friction experiment), analyses (e.g., microstructural, chemical, mass transfer, mineralogical, surface, image, texture), microscopy (optical, HRSEM, FESEM, HRTEM]), tomography, porosity measurement, microprobe, and cathodoluminesence. Data about laboratories, experimental conditions, methods, assumptions, equipments, and mechanical properties and lithology of the studied samples will also be presented on the website per investigation. The ontology was modeled applying the UML (Unified Modeling Language) in Rational Rose, and implemented in OWL-DL (Ontology Web Language) using the Protégé ontology editor. The UML model was converted to OWL-DL by first mapping it to Ecore (.ecore) and Generator model (.genmodel) with the help of the EMF (Eclipse Modeling Framework) plugin in Eclipse. The Ecore model was then mapped to a .uml file, which later was converted into an .owl file and subsequently imported into the Protégé ontology editing environment. The web-interface was developed in java using eclipse as the IDE. The web interfaces to query and submit data were implemented applying JSP, servlets, javascript, and AJAX. The Jena API, a Java framework for building Semantic Web applications, was used to develop the web-interface. Jena provided a programmatic environment for RDF, RDFS, OWL, and SPARQL query engine. Building web applications with AJAX helps retrieving data from the server asynchronously in the background without interfering with the display and behavior of the existing page. The application was deployed on an apache tomcat server at GSU. The SAFOD BM2KB website provides user-friendly search, submit, feedback, and other services. The General Search option allows users to search the knowledge base by selecting the classes (e.g., Experiment, Surface Analysis), their respective attributes (e.g., apparatus, date performed), and the relationships to other classes (e.g., Sample, Laboratory). The Search by Sample option allows users to search the knowledge base based on sample number. The Search by Investigator lets users to search the knowledge base by choosing an investigator who is involved in this project. The website also allows users to submit new data. The Submit Data option opens a page where users can submit the SAFOD data to our knowledge base by selecting specific classes and attributes. The submitted data then become available for query as part of the knowledge base. The SAFOD BM2KB can be accessed from the main SAFOD website.

Autonomous system for Web-based microarray image analysis.

PubMed

Bozinov, Daniel

2003-12-01

Software-based feature extraction from DNA microarray images still requires human intervention on various levels. Manual adjustment of grid and metagrid parameters, precise alignment of superimposed grid templates and gene spots, or simply identification of large-scale artifacts have to be performed beforehand to reliably analyze DNA signals and correctly quantify their expression values. Ideally, a Web-based system with input solely confined to a single microarray image and a data table as output containing measurements for all gene spots would directly transform raw image data into abstracted gene expression tables. Sophisticated algorithms with advanced procedures for iterative correction function can overcome imminent challenges in image processing. Herein is introduced an integrated software system with a Java-based interface on the client side that allows for decentralized access and furthermore enables the scientist to instantly employ the most updated software version at any given time. This software tool is extended from PixClust as used in Extractiff incorporated with Java Web Start deployment technology. Ultimately, this setup is destined for high-throughput pipelines in genome-wide medical diagnostics labs or microarray core facilities aimed at providing fully automated service to its users.

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

PubMed

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

2017-02-22

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