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.

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

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 .

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.

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.

MareyMap Online: A User-Friendly Web Application and Database Service for Estimating Recombination Rates Using Physical and Genetic Maps.

PubMed

Siberchicot, Aurélie; Bessy, Adrien; Guéguen, Laurent; Marais, Gabriel A B

2017-10-01

Given the importance of meiotic recombination in biology, there is a need to develop robust methods to estimate meiotic recombination rates. A popular approach, called the Marey map approach, relies on comparing genetic and physical maps of a chromosome to estimate local recombination rates. In the past, we have implemented this approach in an R package called MareyMap, which includes many functionalities useful to get reliable recombination rate estimates in a semi-automated way. MareyMap has been used repeatedly in studies looking at the effect of recombination on genome evolution. Here, we propose a simpler user-friendly web service version of MareyMap, called MareyMap Online, which allows a user to get recombination rates from her/his own data or from a publicly available database that we offer in a few clicks. When the analysis is done, the user is asked whether her/his curated data can be placed in the database and shared with other users, which we hope will make meta-analysis on recombination rates including many species easy in the future. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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…

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.

PubMed

van Zundert, G C P; Rodrigues, J P G L M; Trellet, M; Schmitz, C; Kastritis, P L; Karaca, E; Melquiond, A S J; van Dijk, M; de Vries, S J; Bonvin, A M J J

2016-02-22

The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

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 DAQ systems: connecting the user and electronics front-ends

NASA Astrophysics Data System (ADS)

Lenzi, Thomas

2016-12-01

Web technologies are quickly evolving and are gaining in computational power and flexibility, allowing for a paradigm shift in the field of Data Acquisition (DAQ) systems design. Modern web browsers offer the possibility to create intricate user interfaces and are able to process and render complex data. Furthermore, new web standards such as WebSockets allow for fast real-time communication between the server and the user with minimal overhead. Those improvements make it possible to move the control and monitoring operations from the back-end servers directly to the user and to the front-end electronics, thus reducing the complexity of the data acquisition chain. Moreover, web-based DAQ systems offer greater flexibility, accessibility, and maintainability on the user side than traditional applications which often lack portability and ease of use. As proof of concept, we implemented a simplified DAQ system on a mid-range Spartan6 Field Programmable Gate Array (FPGA) development board coupled to a digital front-end readout chip. The system is connected to the Internet and can be accessed from any web browser. It is composed of custom code to control the front-end readout and of a dual soft-core Microblaze processor to communicate with the client.

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.

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

Empirical analysis of web-based user-object bipartite networks

NASA Astrophysics Data System (ADS)

Shang, Ming-Sheng; Lü, Linyuan; Zhang, Yi-Cheng; Zhou, Tao

2010-05-01

Understanding the structure and evolution of web-based user-object networks is a significant task since they play a crucial role in e-commerce nowadays. This letter reports the empirical analysis on two large-scale web sites, audioscrobbler.com and del.icio.us, where users are connected with music groups and bookmarks, respectively. The degree distributions and degree-degree correlations for both users and objects are reported. We propose a new index, named collaborative similarity, to quantify the diversity of tastes based on the collaborative selection. Accordingly, the correlation between degree and selection diversity is investigated. We report some novel phenomena well characterizing the selection mechanism of web users and outline the relevance of these phenomena to the information recommendation problem.

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.

User Needs of Digital Service Web Portals: A Case Study

ERIC Educational Resources Information Center

Heo, Misook; Song, Jung-Sook; Seol, Moon-Won

2013-01-01

The authors examined the needs of digital information service web portal users. More specifically, the needs of Korean cultural portal users were examined as a case study. The conceptual framework of a web-based portal is that it is a complex, web-based service application with characteristics of information systems and service agents. In…

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 Design in Medical Distributed Web Applications.

PubMed

Serban, Alexandru; Crisan-Vida, Mihaela; Mada, Leonard; Stoicu-Tivadar, Lacramioara

2016-01-01

User interfaces are important to facilitate easy learning and operating with an IT application especially in the medical world. An easy to use interface has to be simple and to customize the user needs and mode of operation. The technology in the background is an important tool to accomplish this. The present work aims to creating a web interface using specific technology (HTML table design combined with CSS3) to provide an optimized responsive interface for a complex web application. In the first phase, the current icMED web medical application layout is analyzed, and its structure is designed using specific tools, on source files. In the second phase, a new graphic adaptable interface to different mobile terminals is proposed, (using HTML table design (TD) and CSS3 method) that uses no source files, just lines of code for layout design, improving the interaction in terms of speed and simplicity. For a complex medical software application a new prototype layout was designed and developed using HTML tables. The method uses a CSS code with only CSS classes applied to one or multiple HTML table elements, instead of CSS styles that can be applied to just one DIV tag at once. The technique has the advantage of a simplified CSS code, and a better adaptability to different media resolutions compared to DIV-CSS style method. The presented work is a proof that adaptive web interfaces can be developed just using and combining different types of design methods and technologies, using HTML table design, resulting in a simpler to learn and use interface, suitable for healthcare services.

Toward Exposing Timing-Based Probing Attacks in Web Applications.

PubMed

Mao, Jian; Chen, Yue; Shi, Futian; Jia, Yaoqi; Liang, Zhenkai

2017-02-25

Web applications have become the foundation of many types of systems, ranging from cloud services to Internet of Things (IoT) systems. Due to the large amount of sensitive data processed by web applications, user privacy emerges as a major concern in web security. Existing protection mechanisms in modern browsers, e.g., the same origin policy, prevent the users' browsing information on one website from being directly accessed by another website. However, web applications executed in the same browser share the same runtime environment. Such shared states provide side channels for malicious websites to indirectly figure out the information of other origins. Timing is a classic side channel and the root cause of many recent attacks, which rely on the variations in the time taken by the systems to process different inputs. In this paper, we propose an approach to expose the timing-based probing attacks in web applications. It monitors the browser behaviors and identifies anomalous timing behaviors to detect browser probing attacks. We have prototyped our system in the Google Chrome browser and evaluated the effectiveness of our approach by using known probing techniques. We have applied our approach on a large number of top Alexa sites and reported the suspicious behavior patterns with corresponding analysis results. Our theoretical analysis illustrates that the effectiveness of the timing-based probing attacks is dramatically limited by our approach.

Alkahest NuclearBLAST : a user-friendly BLAST management and analysis system

PubMed Central

Diener, Stephen E; Houfek, Thomas D; Kalat, Sam E; Windham, DE; Burke, Mark; Opperman, Charles; Dean, Ralph A

2005-01-01

Background - Sequencing of EST and BAC end datasets is no longer limited to large research groups. Drops in per-base pricing have made high throughput sequencing accessible to individual investigators. However, there are few options available which provide a free and user-friendly solution to the BLAST result storage and data mining needs of biologists. Results - Here we describe NuclearBLAST, a batch BLAST analysis, storage and management system designed for the biologist. It is a wrapper for NCBI BLAST which provides a user-friendly web interface which includes a request wizard and the ability to view and mine the results. All BLAST results are stored in a MySQL database which allows for more advanced data-mining through supplied command-line utilities or direct database access. NuclearBLAST can be installed on a single machine or clustered amongst a number of machines to improve analysis throughput. NuclearBLAST provides a platform which eases data-mining of multiple BLAST results. With the supplied scripts, the program can export data into a spreadsheet-friendly format, automatically assign Gene Ontology terms to sequences and provide bi-directional best hits between two datasets. Users with SQL experience can use the database to ask even more complex questions and extract any subset of data they require. Conclusion - This tool provides a user-friendly interface for requesting, viewing and mining of BLAST results which makes the management and data-mining of large sets of BLAST analyses tractable to biologists. PMID:15958161

FASH: A web application for nucleotides sequence search.

PubMed

Veksler-Lublinksy, Isana; Barash, Danny; Avisar, Chai; Troim, Einav; Chew, Paul; Kedem, Klara

2008-05-27

: FASH (Fourier Alignment Sequence Heuristics) is a web application, based on the Fast Fourier Transform, for finding remote homologs within a long nucleic acid sequence. Given a query sequence and a long text-sequence (e.g, the human genome), FASH detects subsequences within the text that are remotely-similar to the query. FASH offers an alternative approach to Blast/Fasta for querying long RNA/DNA sequences. FASH differs from these other approaches in that it does not depend on the existence of contiguous seed-sequences in its initial detection phase. The FASH web server is user friendly and very easy to operate. FASH can be accessed athttps://fash.bgu.ac.il:8443/fash/default.jsp (secured website).

RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application.

PubMed

D'Antonio, Mattia; D'Onorio De Meo, Paolo; Pallocca, Matteo; Picardi, Ernesto; D'Erchia, Anna Maria; Calogero, Raffaele A; Castrignanò, Tiziana; Pesole, Graziano

2015-01-01

The study of RNA has been dramatically improved by the introduction of Next Generation Sequencing platforms allowing massive and cheap sequencing of selected RNA fractions, also providing information on strand orientation (RNA-Seq). The complexity of transcriptomes and of their regulative pathways make RNA-Seq one of most complex field of NGS applications, addressing several aspects of the expression process (e.g. identification and quantification of expressed genes and transcripts, alternative splicing and polyadenylation, fusion genes and trans-splicing, post-transcriptional events, etc.). In order to provide researchers with an effective and friendly resource for analyzing RNA-Seq data, we present here RAP (RNA-Seq Analysis Pipeline), a cloud computing web application implementing a complete but modular analysis workflow. This pipeline integrates both state-of-the-art bioinformatics tools for RNA-Seq analysis and in-house developed scripts to offer to the user a comprehensive strategy for data analysis. RAP is able to perform quality checks (adopting FastQC and NGS QC Toolkit), identify and quantify expressed genes and transcripts (with Tophat, Cufflinks and HTSeq), detect alternative splicing events (using SpliceTrap) and chimeric transcripts (with ChimeraScan). This pipeline is also able to identify splicing junctions and constitutive or alternative polyadenylation sites (implementing custom analysis modules) and call for statistically significant differences in genes and transcripts expression, splicing pattern and polyadenylation site usage (using Cuffdiff2 and DESeq). Through a user friendly web interface, the RAP workflow can be suitably customized by the user and it is automatically executed on our cloud computing environment. This strategy allows to access to bioinformatics tools and computational resources without specific bioinformatics and IT skills. RAP provides a set of tabular and graphical results that can be helpful to browse, filter and export

Development and usability testing of a web-based decision support for users and health professionals in psychiatric services.

PubMed

Grim, Katarina; Rosenberg, David; Svedberg, Petra; Schön, Ulla-Karin

2017-09-01

Shared decision making (SMD) related to treatment and rehabilitation is considered a central component in recovery-oriented practice. Although decision aids are regarded as an essential component for successfully implementing SDM, these aids are often lacking within psychiatric services. The aim of this study was to use a participatory design to facilitate the development of a user-generated, web-based decision aid for individuals receiving psychiatric services. The results of this effort as well as the lessons learned during the development and usability processes are reported. The participatory design included 4 iterative cycles of development. Various qualitative methods for data collection were used with potential end users participating as informants in focus group and individual interviews and as usability and pilot testers. Interviewing and testing identified usability problems that then led to refinements and making the subsequent prototypes increasingly user-friendly and relevant. In each phase of the process, feedback from potential end-users provided guidance in developing the formation of the web-based decision aid that strengthens the position of users by integrating access to information regarding alternative supports, interactivity between staff and users, and user preferences as a continual focus in the tool. This web-based decision aid has the potential to strengthen service users' experience of self-efficacy and control as well as provide staff access to user knowledge and preferences. Studies employing participatory models focusing on usability have potential to significantly contribute to the development and implementation of tools that reflect user perspectives. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Conceptual Web Users' Actions Prediction for Ontology-Based Browsing Recommendations

NASA Astrophysics Data System (ADS)

Robal, Tarmo; Kalja, Ahto

The Internet consists of thousands of web sites with different kinds of structures. However, users are browsing the web according to their informational expectations towards the web site searched, having an implicit conceptual model of the domain in their minds. Nevertheless, people tend to repeat themselves and have partially shared conceptual views while surfing the web, finding some areas of web sites more interesting than others. Herein, we take advantage of the latter and provide a model and a study on predicting users' actions based on the web ontology concepts and their relations.

Using Qualitative Methods to Create a Home Health Web Application User Interface for Patients with Low Computer Proficiency.

PubMed

Baier, Rosa R; Cooper, Emily; Wysocki, Andrea; Gravenstein, Stefan; Clark, Melissa

2015-01-01

Despite the investment in public reporting for a number of healthcare settings, evidence indicates that consumers do not routinely use available data to select providers. This suggests that existing reports do not adequately incorporate recommendations for consumer-facing reports or web applications. Healthcentric Advisors and Brown University undertook a multi-phased approach to create a consumer-facing home health web application in Rhode Island. This included reviewing the evidence base review to identify design recommendations and then creating a paper prototype and wireframe. We performed qualitative research to iteratively test our proposed user interface with two user groups, home health consumers and hospital case managers, refining our design to create the final web application. To test our prototype, we conducted two focus groups, with a total of 13 consumers, and 28 case manager interviews. Both user groups responded favorably to the prototype, with the majority commenting that they felt this type of tool would be useful. Case managers suggested revisions to ensure the application conformed to laws requiring Medicare patients to have the freedom to choose among providers and could be incorporated into hospital workflow. After incorporating changes and creating the wireframe, we conducted usability testing interviews with 14 home health consumers and six hospital case managers. We found that consumers needed prompting to navigate through the wireframe; they demonstrated confusion through both their words and body language. As a result, we modified the web application's sequence, navigation, and function to provide additional instructions and prompts. Although we designed our web application for low literacy and low health literacy, using recommendations from the evidence base, we overestimated the extent to which older adults were familiar with using computers. Some of our key learnings and recommendations run counter to general web design principles

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

feedr and animalnexus.ca: A paired R package and user-friendly Web application for transforming and visualizing animal movement data from static stations.

PubMed

LaZerte, Stefanie E; Reudink, Matthew W; Otter, Ken A; Kusack, Jackson; Bailey, Jacob M; Woolverton, Austin; Paetkau, Mark; de Jong, Adriaan; Hill, David J

2017-10-01

Radio frequency identification (RFID) provides a simple and inexpensive approach for examining the movements of tagged animals, which can provide information on species behavior and ecology, such as habitat/resource use and social interactions. In addition, tracking animal movements is appealing to naturalists, citizen scientists, and the general public and thus represents a tool for public engagement in science and science education. Although a useful tool, the large amount of data collected using RFID may quickly become overwhelming. Here, we present an R package (feedr) we have developed for loading, transforming, and visualizing time-stamped, georeferenced data, such as RFID data collected from static logger stations. Using our package, data can be transformed from raw RFID data to visits, presence (regular detections by a logger over time), movements between loggers, displacements, and activity patterns. In addition, we provide several conversion functions to allow users to format data for use in functions from other complementary R packages. Data can also be visualized through static or interactive maps or as animations over time. To increase accessibility, data can be transformed and visualized either through R directly, or through the companion site: http://animalnexus.ca, an online, user-friendly, R-based Shiny Web application. This system can be used by professional and citizen scientists alike to view and study animal movements. We have designed this package to be flexible and to be able to handle data collected from other stationary sources (e.g., hair traps, static very high frequency (VHF) telemetry loggers, observations of marked individuals in colonies or staging sites), and we hope this framework will become a meeting point for science, education, and community awareness of the movements of animals. We aim to inspire citizen engagement while simultaneously enabling robust scientific analysis.

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

Web-based interactive drone control using hand gesture

NASA Astrophysics Data System (ADS)

Zhao, Zhenfei; Luo, Hao; Song, Guang-Hua; Chen, Zhou; Lu, Zhe-Ming; Wu, Xiaofeng

2018-01-01

This paper develops a drone control prototype based on web technology with the aid of hand gesture. The uplink control command and downlink data (e.g., video) are transmitted by WiFi communication, and all the information exchange is realized on web. The control command is translated from various predetermined hand gestures. Specifically, the hardware of this friendly interactive control system is composed by a quadrotor drone, a computer vision-based hand gesture sensor, and a cost-effective computer. The software is simplified as a web-based user interface program. Aided by natural hand gestures, this system significantly reduces the complexity of traditional human-computer interaction, making remote drone operation more intuitive. Meanwhile, a web-based automatic control mode is provided in addition to the hand gesture control mode. For both operation modes, no extra application program is needed to be installed on the computer. Experimental results demonstrate the effectiveness and efficiency of the proposed system, including control accuracy, operation latency, etc. This system can be used in many applications such as controlling a drone in global positioning system denied environment or by handlers without professional drone control knowledge since it is easy to get started.

Web-based interactive drone control using hand gesture.

PubMed

Zhao, Zhenfei; Luo, Hao; Song, Guang-Hua; Chen, Zhou; Lu, Zhe-Ming; Wu, Xiaofeng

2018-01-01

This paper develops a drone control prototype based on web technology with the aid of hand gesture. The uplink control command and downlink data (e.g., video) are transmitted by WiFi communication, and all the information exchange is realized on web. The control command is translated from various predetermined hand gestures. Specifically, the hardware of this friendly interactive control system is composed by a quadrotor drone, a computer vision-based hand gesture sensor, and a cost-effective computer. The software is simplified as a web-based user interface program. Aided by natural hand gestures, this system significantly reduces the complexity of traditional human-computer interaction, making remote drone operation more intuitive. Meanwhile, a web-based automatic control mode is provided in addition to the hand gesture control mode. For both operation modes, no extra application program is needed to be installed on the computer. Experimental results demonstrate the effectiveness and efficiency of the proposed system, including control accuracy, operation latency, etc. This system can be used in many applications such as controlling a drone in global positioning system denied environment or by handlers without professional drone control knowledge since it is easy to get started.

Web services in the U.S. geological survey streamstats web application

USGS Publications Warehouse

Guthrie, J.D.; Dartiguenave, C.; Ries, Kernell G.

2009-01-01

StreamStats is a U.S. Geological Survey Web-based GIS application developed as a tool for waterresources planning and management, engineering design, and other applications. StreamStats' primary functionality allows users to obtain drainage-basin boundaries, basin characteristics, and streamflow statistics for gaged and ungaged sites. Recently, Web services have been developed that provide the capability to remote users and applications to access comprehensive GIS tools that are available in StreamStats, including delineating drainage-basin boundaries, computing basin characteristics, estimating streamflow statistics for user-selected locations, and determining point features that coincide with a National Hydrography Dataset (NHD) reach address. For the state of Kentucky, a web service also has been developed that provides users the ability to estimate daily time series of drainage-basin average values of daily precipitation and temperature. The use of web services allows the user to take full advantage of the datasets and processes behind the Stream Stats application without having to develop and maintain them. ?? 2009 IEEE.

A user-friendly tool for medical-related patent retrieval.

PubMed

Pasche, Emilie; Gobeill, Julien; Teodoro, Douglas; Gaudinat, Arnaud; Vishnyakova, Dina; Lovis, Christian; Ruch, Patrick

2012-01-01

Health-related information retrieval is complicated by the variety of nomenclatures available to name entities, since different communities of users will use different ways to name a same entity. We present in this report the development and evaluation of a user-friendly interactive Web application aiming at facilitating health-related patent search. Our tool, called TWINC, relies on a search engine tuned during several patent retrieval competitions, enhanced with intelligent interaction modules, such as chemical query, normalization and expansion. While the functionality of related article search showed promising performances, the ad hoc search results in fairly contrasted results. Nonetheless, TWINC performed well during the PatOlympics competition and was appreciated by intellectual property experts. This result should be balanced by the limited evaluation sample. We can also assume that it can be customized to be applied in corporate search environments to process domain and company-specific vocabularies, including non-English literature and patents reports.

Framework for Supporting Web-Based Collaborative Applications

NASA Astrophysics Data System (ADS)

Dai, Wei

The article proposes an intelligent framework for supporting Web-based applications. The framework focuses on innovative use of existing resources and technologies in the form of services and takes the leverage of theoretical foundation of services science and the research from services computing. The main focus of the framework is to deliver benefits to users with various roles such as service requesters, service providers, and business owners to maximize their productivity when engaging with each other via the Web. The article opens up with research motivations and questions, analyses the existing state of research in the field, and describes the approach in implementing the proposed framework. Finally, an e-health application is discussed to evaluate the effectiveness of the framework where participants such as general practitioners (GPs), patients, and health-care workers collaborate via the Web.

Using intervention mapping for the development of a targeted secure web-based outreach strategy named SafeFriend, for Chlamydia trachomatis testing in young people at risk

PubMed Central

2013-01-01

Background Many young people at high risk for Chlamydia trachomatis (Ct) are not reached by current sexual health care systems, such as general practitioners and public sexual health care centres (sexually transmitted infection clinics).Ct is the most frequently diagnosed bacterial sexually transmitted infection (STI) among sexually active people and in particular young heterosexuals. Innovative screening strategies are needed to interrupt the transmission of Ct among young people and connect the hidden cases to care. Methods Intervention Mapping (IM), a systematic approach to develop theory- and evidence-based interventions, was used to develop a strategy to target Ct testing towards young people who are currently hidden to care in The Netherlands. Both clinical users (i.e. sexual health care nurses) and public users (i.e., young people at risk for Ct) were closely involved in the IM process. A needs assessment study was carried out using semi-structured interviews among users (N = 21), a literature search and by taking lessons learned from existing screening programmes. Theoretical methods and practical applications to reach high risk young people and influence testing were selected and translated into specific programme components. Results The IM approach resulted in the development of a secure and web-based outreach Ct screening strategy, named SafeFriend. It is developed to target groups of high-risk young people who are currently hidden to care. Key methods include web-based Respondent Driven Sampling, starting from young Ct positive sexual health care centre clients, to reach and motivate peers (i.e., sex partners and friends) to get tested for Ct. Testing and the motivation of peers were proposed as the desired behavioural outcomes and the Precaution Adoption Process Model was chosen as theoretical framework. End users, i.e., young people and sexual health care nurses were interviewed and included in the development process to increase the success of

Using intervention mapping for the development of a targeted secure web-based outreach strategy named SafeFriend, for Chlamydia trachomatis testing in young people at risk.

PubMed

Theunissen, Kevin A T M; Hoebe, Christian J P A; Crutzen, Rik; Kara-Zaïtri, Chakib; de Vries, Nanne K; van Bergen, Jan E A M; van der Sande, Marianne A B; Dukers-Muijrers, Nicole H T M

2013-10-22

Many young people at high risk for Chlamydia trachomatis (Ct) are not reached by current sexual health care systems, such as general practitioners and public sexual health care centres (sexually transmitted infection clinics).Ct is the most frequently diagnosed bacterial sexually transmitted infection (STI) among sexually active people and in particular young heterosexuals. Innovative screening strategies are needed to interrupt the transmission of Ct among young people and connect the hidden cases to care. Intervention Mapping (IM), a systematic approach to develop theory- and evidence-based interventions, was used to develop a strategy to target Ct testing towards young people who are currently hidden to care in The Netherlands. Both clinical users (i.e. sexual health care nurses) and public users (i.e., young people at risk for Ct) were closely involved in the IM process. A needs assessment study was carried out using semi-structured interviews among users (N = 21), a literature search and by taking lessons learned from existing screening programmes. Theoretical methods and practical applications to reach high risk young people and influence testing were selected and translated into specific programme components. The IM approach resulted in the development of a secure and web-based outreach Ct screening strategy, named SafeFriend. It is developed to target groups of high-risk young people who are currently hidden to care. Key methods include web-based Respondent Driven Sampling, starting from young Ct positive sexual health care centre clients, to reach and motivate peers (i.e., sex partners and friends) to get tested for Ct. Testing and the motivation of peers were proposed as the desired behavioural outcomes and the Precaution Adoption Process Model was chosen as theoretical framework. End users, i.e., young people and sexual health care nurses were interviewed and included in the development process to increase the success of implementation. IM proved useful

A Web Service-based framework model for people-centric sensing applications applied to social networking.

PubMed

Nunes, David; Tran, Thanh-Dien; Raposo, Duarte; Pinto, André; Gomes, André; Silva, Jorge Sá

2012-01-01

As the Internet evolved, social networks (such as Facebook) have bloomed and brought together an astonishing number of users. Mashing up mobile phones and sensors with these social environments enables the creation of people-centric sensing systems which have great potential for expanding our current social networking usage. However, such systems also have many associated technical challenges, such as privacy concerns, activity detection mechanisms or intermittent connectivity, as well as limitations due to the heterogeneity of sensor nodes and networks. Considering the openness of the Web 2.0, good technical solutions for these cases consist of frameworks that expose sensing data and functionalities as common Web-Services. This paper presents our RESTful Web Service-based model for people-centric sensing frameworks, which uses sensors and mobile phones to detect users' activities and locations, sharing this information amongst the user's friends within a social networking site. We also present some screenshot results of our experimental prototype.

Development of a web-based video management and application processing system

NASA Astrophysics Data System (ADS)

Chan, Shermann S.; Wu, Yi; Li, Qing; Zhuang, Yueting

2001-07-01

How to facilitate efficient video manipulation and access in a web-based environment is becoming a popular trend for video applications. In this paper, we present a web-oriented video management and application processing system, based on our previous work on multimedia database and content-based retrieval. In particular, we extend the VideoMAP architecture with specific web-oriented mechanisms, which include: (1) Concurrency control facilities for the editing of video data among different types of users, such as Video Administrator, Video Producer, Video Editor, and Video Query Client; different users are assigned various priority levels for different operations on the database. (2) Versatile video retrieval mechanism which employs a hybrid approach by integrating a query-based (database) mechanism with content- based retrieval (CBR) functions; its specific language (CAROL/ST with CBR) supports spatio-temporal semantics of video objects, and also offers an improved mechanism to describe visual content of videos by content-based analysis method. (3) Query profiling database which records the `histories' of various clients' query activities; such profiles can be used to provide the default query template when a similar query is encountered by the same kind of users. An experimental prototype system is being developed based on the existing VideoMAP prototype system, using Java and VC++ on the PC platform.

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.

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

PubMed

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

2011-10-01

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

RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application

PubMed Central

2015-01-01

Background The study of RNA has been dramatically improved by the introduction of Next Generation Sequencing platforms allowing massive and cheap sequencing of selected RNA fractions, also providing information on strand orientation (RNA-Seq). The complexity of transcriptomes and of their regulative pathways make RNA-Seq one of most complex field of NGS applications, addressing several aspects of the expression process (e.g. identification and quantification of expressed genes and transcripts, alternative splicing and polyadenylation, fusion genes and trans-splicing, post-transcriptional events, etc.). Moreover, the huge volume of data generated by NGS platforms introduces unprecedented computational and technological challenges to efficiently analyze and store sequence data and results. Methods In order to provide researchers with an effective and friendly resource for analyzing RNA-Seq data, we present here RAP (RNA-Seq Analysis Pipeline), a cloud computing web application implementing a complete but modular analysis workflow. This pipeline integrates both state-of-the-art bioinformatics tools for RNA-Seq analysis and in-house developed scripts to offer to the user a comprehensive strategy for data analysis. RAP is able to perform quality checks (adopting FastQC and NGS QC Toolkit), identify and quantify expressed genes and transcripts (with Tophat, Cufflinks and HTSeq), detect alternative splicing events (using SpliceTrap) and chimeric transcripts (with ChimeraScan). This pipeline is also able to identify splicing junctions and constitutive or alternative polyadenylation sites (implementing custom analysis modules) and call for statistically significant differences in genes and transcripts expression, splicing pattern and polyadenylation site usage (using Cuffdiff2 and DESeq). Results Through a user friendly web interface, the RAP workflow can be suitably customized by the user and it is automatically executed on our cloud computing environment. This strategy

SLIMS--a user-friendly sample operations and inventory management system for genotyping labs.

PubMed

Van Rossum, Thea; Tripp, Ben; Daley, Denise

2010-07-15

We present the Sample-based Laboratory Information Management System (SLIMS), a powerful and user-friendly open source web application that provides all members of a laboratory with an interface to view, edit and create sample information. SLIMS aims to simplify common laboratory tasks with tools such as a user-friendly shopping cart for subjects, samples and containers that easily generates reports, shareable lists and plate designs for genotyping. Further key features include customizable data views, database change-logging and dynamically filled pre-formatted reports. Along with being feature-rich, SLIMS' power comes from being able to handle longitudinal data from multiple time-points and biological sources. This type of data is increasingly common from studies searching for susceptibility genes for common complex diseases that collect thousands of samples generating millions of genotypes and overwhelming amounts of data. LIMSs provide an efficient way to deal with this data while increasing accessibility and reducing laboratory errors; however, professional LIMS are often too costly to be practical. SLIMS gives labs a feasible alternative that is easily accessible, user-centrically designed and feature-rich. To facilitate system customization, and utilization for other groups, manuals have been written for users and developers. Documentation, source code and manuals are available at http://genapha.icapture.ubc.ca/SLIMS/index.jsp. SLIMS was developed using Java 1.6.0, JSPs, Hibernate 3.3.1.GA, DB2 and mySQL, Apache Tomcat 6.0.18, NetBeans IDE 6.5, Jasper Reports 3.5.1 and JasperSoft's iReport 3.5.1.

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

PubMed

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

2016-04-01

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

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

NASA Astrophysics Data System (ADS)

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

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

Web-based hydrodynamics computing

NASA Astrophysics Data System (ADS)

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

2005-01-01

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

Web-based hydrodynamics computing

NASA Astrophysics Data System (ADS)

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

2004-12-01

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

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.

Creating adaptive web recommendation system based on user behavior

NASA Astrophysics Data System (ADS)

Walek, Bogdan

2018-01-01

The paper proposes adaptive web recommendation system based on user behavior. The proposed system uses expert system to evaluating and recommending suitable items of content. Relevant items are subsequently evaluated and filtered based on history of visited items and user´s preferred categories of items. Main parts of the proposed system are presented and described. The proposed recommendation system is verified on specific example.

Science gateways for semantic-web-based life science applications.

PubMed

Ardizzone, Valeria; Bruno, Riccardo; Calanducci, Antonio; Carrubba, Carla; Fargetta, Marco; Ingrà, Elisa; Inserra, Giuseppina; La Rocca, Giuseppe; Monforte, Salvatore; Pistagna, Fabrizio; Ricceri, Rita; Rotondo, Riccardo; Scardaci, Diego; Barbera, Roberto

2012-01-01

In this paper we present the architecture of a framework for building Science Gateways supporting official standards both for user authentication and authorization and for middleware-independent job and data management. Two use cases of the customization of the Science Gateway framework for Semantic-Web-based life science applications are also described.

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

Colorado Late Cenozoic Fault and Fold Database and Internet Map Server: User-friendly technology for complex information

USGS Publications Warehouse

Morgan, K.S.; Pattyn, G.J.; Morgan, M.L.

2005-01-01

Internet mapping applications for geologic data allow simultaneous data delivery and collection, enabling quick data modification while efficiently supplying the end user with information. Utilizing Web-based technologies, the Colorado Geological Survey's Colorado Late Cenozoic Fault and Fold Database was transformed from a monothematic, nonspatial Microsoft Access database into a complex information set incorporating multiple data sources. The resulting user-friendly format supports easy analysis and browsing. The core of the application is the Microsoft Access database, which contains information compiled from available literature about faults and folds that are known or suspected to have moved during the late Cenozoic. The database contains nonspatial fields such as structure type, age, and rate of movement. Geographic locations of the fault and fold traces were compiled from previous studies at 1:250,000 scale to form a spatial database containing information such as length and strike. Integration of the two databases allowed both spatial and nonspatial information to be presented on the Internet as a single dataset (http://geosurvey.state.co.us/pubs/ceno/). The user-friendly interface enables users to view and query the data in an integrated manner, thus providing multiple ways to locate desired information. Retaining the digital data format also allows continuous data updating and quick delivery of newly acquired information. This dataset is a valuable resource to anyone interested in earthquake hazards and the activity of faults and folds in Colorado. Additional geologic hazard layers and imagery may aid in decision support and hazard evaluation. The up-to-date and customizable maps are invaluable tools for researchers or the public.

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

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

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

2008-05-04

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

Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes.

PubMed

Wick, Ryan R; Heinz, Eva; Holt, Kathryn E; Wyres, Kelly L

2018-06-01

As whole-genome sequencing becomes an established component of the microbiologist's toolbox, it is imperative that researchers, clinical microbiologists, and public health professionals have access to genomic analysis tools for the rapid extraction of epidemiologically and clinically relevant information. For the Gram-negative hospital pathogens such as Klebsiella pneumoniae , initial efforts have focused on the detection and surveillance of antimicrobial resistance genes and clones. However, with the resurgence of interest in alternative infection control strategies targeting Klebsiella surface polysaccharides, the ability to extract information about these antigens is increasingly important. Here we present Kaptive Web, an online tool for the rapid typing of Klebsiella K and O loci, which encode the polysaccharide capsule and lipopolysaccharide O antigen, respectively. Kaptive Web enables users to upload and analyze genome assemblies in a web browser. The results can be downloaded in tabular format or explored in detail via the graphical interface, making it accessible for users at all levels of computational expertise. We demonstrate Kaptive Web's utility by analyzing >500 K. pneumoniae genomes. We identify extensive K and O locus diversity among 201 genomes belonging to the carbapenemase-associated clonal group 258 (25 K and 6 O loci). The characterization of a further 309 genomes indicated that such diversity is common among the multidrug-resistant clones and that these loci represent useful epidemiological markers for strain subtyping. These findings reinforce the need for rapid, reliable, and accessible typing methods such as Kaptive Web. Kaptive Web is available for use at http://kaptive.holtlab.net/, and the source code is available at https://github.com/kelwyres/Kaptive-Web. Copyright © 2018 Wick et al.

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

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

PubMed Central

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

2016-01-01

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

Active Involvement of End Users When Developing Web-Based Mental Health Interventions.

PubMed

de Beurs, Derek; van Bruinessen, Inge; Noordman, Janneke; Friele, Roland; van Dulmen, Sandra

2017-01-01

Although many web-based mental health interventions are being released, the actual uptake by end users is limited. The marginal level of engagement of end users when developing these interventions is recognized as an important cause for uptake problems. In this paper, we offer our perceptive on how to improve user engagement. By doing so, we aim to stimulate a discourse on user involvement within the field of online mental health interventions. We shortly describe three different methods (the expert-driven method, intervention mapping, and scrum) that were currently used to develop web-based health interventions. We will focus to what extent the end user was involved in the developmental phase, and what the additional challenges were. In the final paragraph, lessons learned are summarized, and recommendations provided. Every method seems to have its trade-off: if end users are highly involved, availability of end users and means become problematic. If end users are less actively involved, the product may be less appropriate for the end user. Other challenges to consider are the funding of the more active role of technological companies, and the time it takes to process the results of shorter development cycles. Thinking about user-centered design and carefully planning, the involvement of end users should become standard in the field of web-based (mental) health. When deciding on the level of user involvement, one should balance the need for input from users with the availability of resources such as time and funding.

Sensor Network-Based and User-Friendly User Location Discovery for Future Smart Homes.

PubMed

Ahvar, Ehsan; Lee, Gyu Myoung; Han, Son N; Crespi, Noel; Khan, Imran

2016-06-27

User location is crucial context information for future smart homes where many location based services will be proposed. This location necessarily means that User Location Discovery (ULD) will play an important role in future smart homes. Concerns about privacy and the need to carry a mobile or a tag device within a smart home currently make conventional ULD systems uncomfortable for users. Future smart homes will need a ULD system to consider these challenges. This paper addresses the design of such a ULD system for context-aware services in future smart homes stressing the following challenges: (i) users' privacy; (ii) device-/tag-free; and (iii) fault tolerance and accuracy. On the other hand, emerging new technologies, such as the Internet of Things, embedded systems, intelligent devices and machine-to-machine communication, are penetrating into our daily life with more and more sensors available for use in our homes. Considering this opportunity, we propose a ULD system that is capitalizing on the prevalence of sensors for the home while satisfying the aforementioned challenges. The proposed sensor network-based and user-friendly ULD system relies on different types of inexpensive sensors, as well as a context broker with a fuzzy-based decision-maker. The context broker receives context information from different types of sensors and evaluates that data using the fuzzy set theory. We demonstrate the performance of the proposed system by illustrating a use case, utilizing both an analytical model and simulation.

Adaptive User Model for Web-Based Learning Environment.

ERIC Educational Resources Information Center

Garofalakis, John; Sirmakessis, Spiros; Sakkopoulos, Evangelos; Tsakalidis, Athanasios

This paper describes the design of an adaptive user model and its implementation in an advanced Web-based Virtual University environment that encompasses combined and synchronized adaptation between educational material and well-known communication facilities. The Virtual University environment has been implemented to support a postgraduate…

Tobacco cessation among users of telephone and web-based interventions--four states, 2011-2012.

PubMed

Puckett, Mary; Neri, Antonio; Thompson, Trevor; Underwood, J Michael; Momin, Behnoosh; Kahende, Jennifer; Zhang, Lei; Stewart, Sherri L

2015-01-02

Smoking caused an average of 480,000 deaths per year in the United States from 2005 to 2009, and three in 10 cancer deaths in the United States are tobacco related. Tobacco cessation is a high public health priority, and all states offer some form of tobacco cessation service. Quitlines provide telephone-based counseling services and are an effective intervention for tobacco cessation. In addition to telephone services, 96% of all U.S. quitlines offer Web-based cessation services. Evidence is limited on the number of tobacco users who use more than one type of service, and studies report mixed results on whether combined telephone and Web-based counseling improves long-term cessation compared with telephone alone. CDC conducted a survey of users of telephone and Web-based cessation services in four states to determine the cessation success of users of these interventions. After adjusting for multiple variables, persons who used both telephone and Web-based services were more likely to report abstinence from smoking for 30 days at follow up (odds ratio = 1.3) compared with telephone-only users and with Web-only users (odds ratio = 1.5). These findings suggest that states might consider offering both types of cessation services to increase cessation success.

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.

Terminology issues in user access to Web-based medical information.

PubMed Central

McCray, A. T.; Loane, R. F.; Browne, A. C.; Bangalore, A. K.

1999-01-01

We conducted a study of user queries to the National Library of Medicine Web site over a three month period. Our purpose was to study the nature and scope of these queries in order to understand how to improve users' access to the information they are seeking on our site. The results show that the queries are primarily medical in content (94%), with only a small percentage (5.5%) relating to library services, and with a very small percentage (.5%) not being medically relevant at all. We characterize the data set, and conclude with a discussion of our plans to develop a UMLS-based terminology server to assist NLM Web users. Images Figure 1 PMID:10566330

A Study of the Demographics of Web-Based Health-Related Social Media Users.

PubMed

Sadah, Shouq A; Shahbazi, Moloud; Wiley, Matthew T; Hristidis, Vagelis

2015-08-06

The rapid spread of Web-based social media in recent years has impacted how patients share health-related information. However, little work has studied the demographics of these users. Our aim was to study the demographics of users who participate in health-related Web-based social outlets to identify possible links to health care disparities. We analyze and compare three different types of health-related social outlets: (1) general Web-based social networks, Twitter and Google+, (2) drug review websites, and (3) health Web forums. We focus on the following demographic attributes: age, gender, ethnicity, location, and writing level. We build and evaluate domain-specific classifiers to infer missing data where possible. The estimated demographic statistics are compared against various baselines, such as Internet and social networks usage of the population. We found that (1) drug review websites and health Web forums are dominated by female users, (2) the participants of health-related social outlets are generally older with the exception of the 65+ years bracket, (3) blacks are underrepresented in health-related social networks, (4) users in areas with better access to health care participate more in Web-based health-related social outlets, and (5) the writing level of users in health-related social outlets is significantly lower than the reading level of the population. We identified interesting and actionable disparities in the participation of various demographic groups to various types of health-related social outlets. These disparities are significantly distinct from the disparities in Internet usage or general social outlets participation.

An Interactive, Web-based High Performance Modeling Environment for Computational Epidemiology.

PubMed

Deodhar, Suruchi; Bisset, Keith R; Chen, Jiangzhuo; Ma, Yifei; Marathe, Madhav V

2014-07-01

We present an integrated interactive modeling environment to support public health epidemiology. The environment combines a high resolution individual-based model with a user-friendly web-based interface that allows analysts to access the models and the analytics back-end remotely from a desktop or a mobile device. The environment is based on a loosely-coupled service-oriented-architecture that allows analysts to explore various counter factual scenarios. As the modeling tools for public health epidemiology are getting more sophisticated, it is becoming increasingly hard for non-computational scientists to effectively use the systems that incorporate such models. Thus an important design consideration for an integrated modeling environment is to improve ease of use such that experimental simulations can be driven by the users. This is achieved by designing intuitive and user-friendly interfaces that allow users to design and analyze a computational experiment and steer the experiment based on the state of the system. A key feature of a system that supports this design goal is the ability to start, stop, pause and roll-back the disease propagation and intervention application process interactively. An analyst can access the state of the system at any point in time and formulate dynamic interventions based on additional information obtained through state assessment. In addition, the environment provides automated services for experiment set-up and management, thus reducing the overall time for conducting end-to-end experimental studies. We illustrate the applicability of the system by describing computational experiments based on realistic pandemic planning scenarios. The experiments are designed to demonstrate the system's capability and enhanced user productivity.

An Interactive, Web-based High Performance Modeling Environment for Computational Epidemiology

PubMed Central

Deodhar, Suruchi; Bisset, Keith R.; Chen, Jiangzhuo; Ma, Yifei; Marathe, Madhav V.

2014-01-01

We present an integrated interactive modeling environment to support public health epidemiology. The environment combines a high resolution individual-based model with a user-friendly web-based interface that allows analysts to access the models and the analytics back-end remotely from a desktop or a mobile device. The environment is based on a loosely-coupled service-oriented-architecture that allows analysts to explore various counter factual scenarios. As the modeling tools for public health epidemiology are getting more sophisticated, it is becoming increasingly hard for non-computational scientists to effectively use the systems that incorporate such models. Thus an important design consideration for an integrated modeling environment is to improve ease of use such that experimental simulations can be driven by the users. This is achieved by designing intuitive and user-friendly interfaces that allow users to design and analyze a computational experiment and steer the experiment based on the state of the system. A key feature of a system that supports this design goal is the ability to start, stop, pause and roll-back the disease propagation and intervention application process interactively. An analyst can access the state of the system at any point in time and formulate dynamic interventions based on additional information obtained through state assessment. In addition, the environment provides automated services for experiment set-up and management, thus reducing the overall time for conducting end-to-end experimental studies. We illustrate the applicability of the system by describing computational experiments based on realistic pandemic planning scenarios. The experiments are designed to demonstrate the system's capability and enhanced user productivity. PMID:25530914

A Full-Featured User Friendly CO 2-EOR and Sequestration Planning Software

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

Savage, Bill

A Full-Featured, User Friendly CO 2-EOR and Sequestration Planning Software This project addressed the development of an integrated software solution that includes a graphical user interface, numerical simulation, visualization tools and optimization processes for reservoir simulation modeling of CO 2-EOR. The objective was to assist the industry in the development of domestic energy resources by expanding the application of CO 2-EOR technologies, and ultimately to maximize the CO 2} sequestration capacity of the U.S. The software resulted in a field-ready application for the industry to address the current CO 2-EOR technologies. The software has been made available to the publicmore » without restrictions and with user friendly operating documentation and tutorials. The software (executable only) can be downloaded from NITEC’s website at www.nitecllc.com. This integrated solution enables the design, optimization and operation of CO 2-EOR processes for small and mid-sized operators, who currently cannot afford the expensive, time intensive solutions that the major oil companies enjoy. Based on one estimate, small oil fields comprise 30% of the of total economic resource potential for the application of CO 2-EOR processes in the U.S. This corresponds to 21.7 billion barrels of incremental, technically recoverable oil using the current “best practices”, and 31.9 billion barrels using “next-generation” CO 2-EOR techniques. The project included a Case Study of a prospective CO 2-EOR candidate field in Wyoming by a small independent, Linc Energy Petroleum Wyoming, Inc. NITEC LLC has an established track record of developing innovative and user friendly software. The Principle Investigator is an experienced manager and engineer with expertise in software development, numerical techniques, and GUI applications. Unique, presently-proprietary NITEC technologies have been integrated into this application to further its ease of use and technical functionality.« less

Efficient Web Vulnerability Detection Tool for Sleeping Giant-Cross Site Request Forgery

NASA Astrophysics Data System (ADS)

Parimala, G.; Sangeetha, M.; AndalPriyadharsini, R.

2018-04-01

Now day’s web applications are very high in the rate of usage due to their user friendly environment and getting any information via internet but these web applications are affected by lot of threats. CSRF attack is one of the serious threats to web applications which is based on the vulnerabilities present in the normal web request and response of HTTP protocol. It is hard to detect but hence still it is present in most of the existing web applications. In CSRF attack, without user knowledge the unwanted actions on a reliable websites are forced to happen. So it is placed in OWASP’s top 10 Web Application attacks list. My proposed work is to do a real time scan of CSRF vulnerability attack in given URL of the web applications as well as local host address for any organization using python language. Client side detection of CSRF is depended on Form count which is presented in that given web site.

Development of a Web-Based Self-management Intervention for Intermittent Urinary Catheter Users With Spinal Cord Injury.

PubMed

Wilde, Mary H; Fairbanks, Eileen; Parshall, Robert; Zhang, Feng; Miner, Sarah; Thayer, Deborah; Harrington, Brian; Brasch, Judith; McMAHON, James M

2015-11-01

While Web-based interventions have proliferated recently, information in the literature is often lacking about how the intervention was developed. In response to that gap, this is a report of the development of a Web-based self-management intervention for intermittent urinary catheter users and pretesting with four adults with spinal cord injury living in the community. Two Web sites were created, one for recruitment and the other for the intervention itself. The intervention involved developing new Web-based technology, including an interactive urinary diary (with fluid intake/urine output and a journal), extensive catheter products information, three intervention nurse phone call consultations, and user-community discussion forums. Study participants completed an online survey and were interviewed twice about the enrollment process and their perceptions of their involvement in the intervention. Suggestions from the pretesting participants were used to revise the Web site applications prior to the next stage of research (a feasibility study). Numerous recommendations and comments were received related to content, interactivity of components, and usability. This article provides a description of how the Web sites were developed (including the technology and software programs used), issues encountered and what was done to address them, and how the Web-based intervention was modified for improvements.

ClimatePipes: User-Friendly Data Access, Manipulation, Analysis & Visualization of Community Climate Models

NASA Astrophysics Data System (ADS)

Chaudhary, A.; DeMarle, D.; Burnett, B.; Harris, C.; Silva, W.; Osmari, D.; Geveci, B.; Silva, C.; Doutriaux, C.; Williams, D. N.

2013-12-01

The impact of climate change will resonate through a broad range of fields including public health, infrastructure, water resources, and many others. Long-term coordinated planning, funding, and action are required for climate change adaptation and mitigation. Unfortunately, widespread use of climate data (simulated and observed) in non-climate science communities is impeded by factors such as large data size, lack of adequate metadata, poor documentation, and lack of sufficient computational and visualization resources. We present ClimatePipes to address many of these challenges by creating an open source platform that provides state-of-the-art, user-friendly data access, analysis, and visualization for climate and other relevant geospatial datasets, making the climate data available to non-researchers, decision-makers, and other stakeholders. The overarching goals of ClimatePipes are: - Enable users to explore real-world questions related to climate change. - Provide tools for data access, analysis, and visualization. - Facilitate collaboration by enabling users to share datasets, workflows, and visualization. ClimatePipes uses a web-based application platform for its widespread support on mainstream operating systems, ease-of-use, and inherent collaboration support. The front-end of ClimatePipes uses HTML5 (WebGL, Canvas2D, CSS3) to deliver state-of-the-art visualization and to provide a best-in-class user experience. The back-end of the ClimatePipes is built around Python using the Visualization Toolkit (VTK, http://vtk.org), Climate Data Analysis Tools (CDAT, http://uv-cdat.llnl.gov), and other climate and geospatial data processing tools such as GDAL and PROJ4. ClimatePipes web-interface to query and access data from remote sources (such as ESGF). Shown in the figure is climate data layer from ESGF on top of map data layer from OpenStreetMap. The ClimatePipes workflow editor provides flexibility and fine grained control, and uses the VisTrails (http

An Automatic Web Service Composition Framework Using QoS-Based Web Service Ranking Algorithm.

PubMed

Mallayya, Deivamani; Ramachandran, Baskaran; Viswanathan, Suganya

2015-01-01

Web service has become the technology of choice for service oriented computing to meet the interoperability demands in web applications. In the Internet era, the exponential addition of web services nominates the "quality of service" as essential parameter in discriminating the web services. In this paper, a user preference based web service ranking (UPWSR) algorithm is proposed to rank web services based on user preferences and QoS aspect of the web service. When the user's request cannot be fulfilled by a single atomic service, several existing services should be composed and delivered as a composition. The proposed framework allows the user to specify the local and global constraints for composite web services which improves flexibility. UPWSR algorithm identifies best fit services for each task in the user request and, by choosing the number of candidate services for each task, reduces the time to generate the composition plans. To tackle the problem of web service composition, QoS aware automatic web service composition (QAWSC) algorithm proposed in this paper is based on the QoS aspects of the web services and user preferences. The proposed framework allows user to provide feedback about the composite service which improves the reputation of the services.

An Automatic Web Service Composition Framework Using QoS-Based Web Service Ranking Algorithm

PubMed Central

Mallayya, Deivamani; Ramachandran, Baskaran; Viswanathan, Suganya

2015-01-01

Web service has become the technology of choice for service oriented computing to meet the interoperability demands in web applications. In the Internet era, the exponential addition of web services nominates the “quality of service” as essential parameter in discriminating the web services. In this paper, a user preference based web service ranking (UPWSR) algorithm is proposed to rank web services based on user preferences and QoS aspect of the web service. When the user's request cannot be fulfilled by a single atomic service, several existing services should be composed and delivered as a composition. The proposed framework allows the user to specify the local and global constraints for composite web services which improves flexibility. UPWSR algorithm identifies best fit services for each task in the user request and, by choosing the number of candidate services for each task, reduces the time to generate the composition plans. To tackle the problem of web service composition, QoS aware automatic web service composition (QAWSC) algorithm proposed in this paper is based on the QoS aspects of the web services and user preferences. The proposed framework allows user to provide feedback about the composite service which improves the reputation of the services. PMID:26504894

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.

Access Control of Web- and Java-Based Applications

NASA Technical Reports Server (NTRS)

Tso, Kam S.; Pajevski, Michael J.

2013-01-01

Cybersecurity has become a great concern as threats of service interruption, unauthorized access, stealing and altering of information, and spreading of viruses have become more prevalent and serious. Application layer access control of applications is a critical component in the overall security solution that also includes encryption, firewalls, virtual private networks, antivirus, and intrusion detection. An access control solution, based on an open-source access manager augmented with custom software components, was developed to provide protection to both Web-based and Javabased client and server applications. The DISA Security Service (DISA-SS) provides common access control capabilities for AMMOS software applications through a set of application programming interfaces (APIs) and network- accessible security services for authentication, single sign-on, authorization checking, and authorization policy management. The OpenAM access management technology designed for Web applications can be extended to meet the needs of Java thick clients and stand alone servers that are commonly used in the JPL AMMOS environment. The DISA-SS reusable components have greatly reduced the effort for each AMMOS subsystem to develop its own access control strategy. The novelty of this work is that it leverages an open-source access management product that was designed for Webbased applications to provide access control for Java thick clients and Java standalone servers. Thick clients and standalone servers are still commonly used in businesses and government, especially for applications that require rich graphical user interfaces and high-performance visualization that cannot be met by thin clients running on Web browsers

Sensor Network-Based and User-Friendly User Location Discovery for Future Smart Homes

PubMed Central

Ahvar, Ehsan; Lee, Gyu Myoung; Han, Son N.; Crespi, Noel; Khan, Imran

2016-01-01

User location is crucial context information for future smart homes where many location based services will be proposed. This location necessarily means that User Location Discovery (ULD) will play an important role in future smart homes. Concerns about privacy and the need to carry a mobile or a tag device within a smart home currently make conventional ULD systems uncomfortable for users. Future smart homes will need a ULD system to consider these challenges. This paper addresses the design of such a ULD system for context-aware services in future smart homes stressing the following challenges: (i) users’ privacy; (ii) device-/tag-free; and (iii) fault tolerance and accuracy. On the other hand, emerging new technologies, such as the Internet of Things, embedded systems, intelligent devices and machine-to-machine communication, are penetrating into our daily life with more and more sensors available for use in our homes. Considering this opportunity, we propose a ULD system that is capitalizing on the prevalence of sensors for the home while satisfying the aforementioned challenges. The proposed sensor network-based and user-friendly ULD system relies on different types of inexpensive sensors, as well as a context broker with a fuzzy-based decision-maker. The context broker receives context information from different types of sensors and evaluates that data using the fuzzy set theory. We demonstrate the performance of the proposed system by illustrating a use case, utilizing both an analytical model and simulation. PMID:27355951

Toward Exposing Timing-Based Probing Attacks in Web Applications †

PubMed Central

Mao, Jian; Chen, Yue; Shi, Futian; Jia, Yaoqi; Liang, Zhenkai

2017-01-01

Web applications have become the foundation of many types of systems, ranging from cloud services to Internet of Things (IoT) systems. Due to the large amount of sensitive data processed by web applications, user privacy emerges as a major concern in web security. Existing protection mechanisms in modern browsers, e.g., the same origin policy, prevent the users’ browsing information on one website from being directly accessed by another website. However, web applications executed in the same browser share the same runtime environment. Such shared states provide side channels for malicious websites to indirectly figure out the information of other origins. Timing is a classic side channel and the root cause of many recent attacks, which rely on the variations in the time taken by the systems to process different inputs. In this paper, we propose an approach to expose the timing-based probing attacks in web applications. It monitors the browser behaviors and identifies anomalous timing behaviors to detect browser probing attacks. We have prototyped our system in the Google Chrome browser and evaluated the effectiveness of our approach by using known probing techniques. We have applied our approach on a large number of top Alexa sites and reported the suspicious behavior patterns with corresponding analysis results. Our theoretical analysis illustrates that the effectiveness of the timing-based probing attacks is dramatically limited by our approach. PMID:28245610

AIRSAR Web-Based Data Processing

NASA Technical Reports Server (NTRS)

Chu, Anhua; Van Zyl, Jakob; Kim, Yunjin; Hensley, Scott; Lou, Yunling; Madsen, Soren; Chapman, Bruce; Imel, David; Durden, Stephen; Tung, Wayne

2007-01-01

The AIRSAR automated, Web-based data processing and distribution system is an integrated, end-to-end synthetic aperture radar (SAR) processing system. Designed to function under limited resources and rigorous demands, AIRSAR eliminates operational errors and provides for paperless archiving. Also, it provides a yearly tune-up of the processor on flight missions, as well as quality assurance with new radar modes and anomalous data compensation. The software fully integrates a Web-based SAR data-user request subsystem, a data processing system to automatically generate co-registered multi-frequency images from both polarimetric and interferometric data collection modes in 80/40/20 MHz bandwidth, an automated verification quality assurance subsystem, and an automatic data distribution system for use in the remote-sensor community. Features include Survey Automation Processing in which the software can automatically generate a quick-look image from an entire 90-GB SAR raw data 32-MB/s tape overnight without operator intervention. Also, the software allows product ordering and distribution via a Web-based user request system. To make AIRSAR more user friendly, it has been designed to let users search by entering the desired mission flight line (Missions Searching), or to search for any mission flight line by entering the desired latitude and longitude (Map Searching). For precision image automation processing, the software generates the products according to each data processing request stored in the database via a Queue management system. Users are able to have automatic generation of coregistered multi-frequency images as the software generates polarimetric and/or interferometric SAR data processing in ground and/or slant projection according to user processing requests for one of the 12 radar modes.

Development of a web-based intervention for the indicated prevention of depression.

PubMed

Kelders, Saskia M; Pots, Wendy T M; Oskam, Maarten Jan; Bohlmeijer, Ernst T; van Gemert-Pijnen, Julia E W C

2013-02-20

To reduce the large public health burden of the high prevalence of depression, preventive interventions targeted at people at risk are essential and can be cost-effective. Web-based interventions are able to provide this care, but there is no agreement on how to best develop these applications and often the technology is seen as a given. This seems to be one of the main reasons that web-based interventions do not reach their full potential. The current study describes the development of a web-based intervention for the indicated prevention of depression, employing the CeHRes (Center for eHealth Research and Disease Management) roadmap. The goals are to create a user-friendly application which fits the values of the stakeholders and to evaluate the process of development. The employed methods are a literature scan and discussion in the contextual inquiry; interviews, rapid prototyping and a requirement session in the value specification stage; and user-based usability evaluation, expert-based usability inspection and a requirement session in the design stage. The contextual inquiry indicated that there is a need for easily accessible interventions for the indicated prevention of depression and web-based interventions are seen as potentially meeting this need. The value specification stage yielded expected needs of potential participants, comments on the usefulness of the proposed features and comments on two proposed designs of the web-based intervention. The design stage yielded valuable comments on the system, content and service of the web-based intervention. Overall, we found that by developing the technology, we successfully (re)designed the system, content and service of the web-based intervention to match the values of stakeholders. This study has shown the importance of a structured development process of a web-based intervention for the indicated prevention of depression because: (1) it allows the development team to clarify the needs that have to be met

Development of a web-based intervention for the indicated prevention of depression

PubMed Central

2013-01-01

Background To reduce the large public health burden of the high prevalence of depression, preventive interventions targeted at people at risk are essential and can be cost-effective. Web-based interventions are able to provide this care, but there is no agreement on how to best develop these applications and often the technology is seen as a given. This seems to be one of the main reasons that web-based interventions do not reach their full potential. The current study describes the development of a web-based intervention for the indicated prevention of depression, employing the CeHRes (Center for eHealth Research and Disease Management) roadmap. The goals are to create a user-friendly application which fits the values of the stakeholders and to evaluate the process of development. Methods The employed methods are a literature scan and discussion in the contextual inquiry; interviews, rapid prototyping and a requirement session in the value specification stage; and user-based usability evaluation, expert-based usability inspection and a requirement session in the design stage. Results The contextual inquiry indicated that there is a need for easily accessible interventions for the indicated prevention of depression and web-based interventions are seen as potentially meeting this need. The value specification stage yielded expected needs of potential participants, comments on the usefulness of the proposed features and comments on two proposed designs of the web-based intervention. The design stage yielded valuable comments on the system, content and service of the web-based intervention. Conclusions Overall, we found that by developing the technology, we successfully (re)designed the system, content and service of the web-based intervention to match the values of stakeholders. This study has shown the importance of a structured development process of a web-based intervention for the indicated prevention of depression because: (1) it allows the development team to

Evaluation and comparison of classical interatomic potentials through a user-friendly interactive web-interface

NASA Astrophysics Data System (ADS)

Choudhary, Kamal; Congo, Faical Yannick P.; Liang, Tao; Becker, Chandler; Hennig, Richard G.; Tavazza, Francesca

2017-01-01

Classical empirical potentials/force-fields (FF) provide atomistic insights into material phenomena through molecular dynamics and Monte Carlo simulations. Despite their wide applicability, a systematic evaluation of materials properties using such potentials and, especially, an easy-to-use user-interface for their comparison is still lacking. To address this deficiency, we computed energetics and elastic properties of variety of materials such as metals and ceramics using a wide range of empirical potentials and compared them to density functional theory (DFT) as well as to experimental data, where available. The database currently consists of 3248 entries including energetics and elastic property calculations, and it is still increasing. We also include computational tools for convex-hull plots for DFT and FF calculations. The data covers 1471 materials and 116 force-fields. In addition, both the complete database and the software coding used in the process have been released for public use online (presently at http://www.ctcms.nist.gov/˜knc6/periodic.html) in a user-friendly way designed to enable further material design and discovery.

Evaluation and comparison of classical interatomic potentials through a user-friendly interactive web-interface

PubMed Central

Choudhary, Kamal; Congo, Faical Yannick P.; Liang, Tao; Becker, Chandler; Hennig, Richard G.; Tavazza, Francesca

2017-01-01

Classical empirical potentials/force-fields (FF) provide atomistic insights into material phenomena through molecular dynamics and Monte Carlo simulations. Despite their wide applicability, a systematic evaluation of materials properties using such potentials and, especially, an easy-to-use user-interface for their comparison is still lacking. To address this deficiency, we computed energetics and elastic properties of variety of materials such as metals and ceramics using a wide range of empirical potentials and compared them to density functional theory (DFT) as well as to experimental data, where available. The database currently consists of 3248 entries including energetics and elastic property calculations, and it is still increasing. We also include computational tools for convex-hull plots for DFT and FF calculations. The data covers 1471 materials and 116 force-fields. In addition, both the complete database and the software coding used in the process have been released for public use online (presently at http://www.ctcms.nist.gov/∼knc6/periodic.html) in a user-friendly way designed to enable further material design and discovery. PMID:28140407

Nutrient Tracking Tool - A user-friendly tool for evaluating the water and air quality and quantity as affected by various agricultural management practices

NASA Astrophysics Data System (ADS)

Saleh, A.; Niraula, R.; Gallego, O.; Osei, E.; Kannan, N.

2017-12-01

The Nutrient Tracking Tool (NTT) is a user-friendly web-based computer program that estimate nutrient (nitrogen and phosphorus) and sediment losses from fields managed under a variety of cropping patterns and management practices. The NTT includes a user-friendly web-based interface and is linked to the Agricultural Policy Environmental eXtender (APEX) model. It also accesses USDA-NRCS's Web Soil Survey to obtain field, weather, and soil information. NTT provides producers, government officials, and other users with a fast and efficient method of estimating the nutrient, sediment, and atmosphoric gases (N2o, Co2, and NH4) losses, and crop production under different conservation practices regims at the farm-level. The information obtained from NTT can help producers to determine the most cost-effective conservation practice(s) to reduce the nutrient and sediment losses while optimizing the crop production. Also, the recent version of NTT (NTTg3) has been developed for those coutries without access to national databasis, such as soils and wether. The NTTg3 also has been designed as easy to use APEX interface. NTT is currently being evaluated for trading and other programs at Cheaseapea Bay regions and numerous states in US. During this presentation the new capabilities of NTTg3 will be described and demonstrated.

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

PubMed Central

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

2016-01-01

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

Interpretation of coagulation test results using a web-based reporting system.

PubMed

Quesada, Andres E; Jabcuga, Christine E; Nguyen, Alex; Wahed, Amer; Nedelcu, Elena; Nguyen, Andy N D

2014-01-01

Web-based synoptic reporting has been successfully integrated into diverse fields of pathology, improving efficiency and reducing typographic errors. Coagulation is a challenging field for practicing pathologists and pathologists-in-training alike. To develop a Web-based program that can expedite the generation of a individualized interpretive report for a variety of coagulation tests. We developed a Web-based synoptic reporting system composed of 119 coagulation report templates and 38 thromboelastography (TEG) report templates covering a wide range of findings. Our institution implemented this reporting system in July 2011; it is currently used by pathology residents and attending pathologists. Feedback from the users of these reports have been overwhelmingly positive. Surveys note the time saved and reduced errors. Our easily accessible, user-friendly, Web-based synoptic reporting system for coagulation is a valuable asset to our laboratory services. Copyright© by the American Society for Clinical Pathology (ASCP).

Web-Based Family Life Education: Spotlight on User Experience

ERIC Educational Resources Information Center

Doty, Jennifer; Doty, Matthew; Dwrokin, Jodi

2011-01-01

Family Life Education (FLE) websites can benefit from the field of user experience, which makes technology easy to use. A heuristic evaluation of five FLE sites was performed using Neilson's heuristics, guidelines for making sites user friendly. Greater site complexity resulted in more potential user problems. Sites most frequently had problems…

Reliability and Validity of Assessing User Satisfaction With Web-Based Health Interventions.

PubMed

Boß, Leif; Lehr, Dirk; Reis, Dorota; Vis, Christiaan; Riper, Heleen; Berking, Matthias; Ebert, David Daniel

2016-08-31

The perspective of users should be taken into account in the evaluation of Web-based health interventions. Assessing the users' satisfaction with the intervention they receive could enhance the evidence for the intervention effects. Thus, there is a need for valid and reliable measures to assess satisfaction with Web-based health interventions. The objective of this study was to analyze the reliability, factorial structure, and construct validity of the Client Satisfaction Questionnaire adapted to Internet-based interventions (CSQ-I). The psychometric quality of the CSQ-I was analyzed in user samples from 2 separate randomized controlled trials evaluating Web-based health interventions, one from a depression prevention intervention (sample 1, N=174) and the other from a stress management intervention (sample 2, N=111). At first, the underlying measurement model of the CSQ-I was analyzed to determine the internal consistency. The factorial structure of the scale and the measurement invariance across groups were tested by multigroup confirmatory factor analyses. Additionally, the construct validity of the scale was examined by comparing satisfaction scores with the primary clinical outcome. Multigroup confirmatory analyses on the scale yielded a one-factorial structure with a good fit (root-mean-square error of approximation =.09, comparative fit index =.96, standardized root-mean-square residual =.05) that showed partial strong invariance across the 2 samples. The scale showed very good reliability, indicated by McDonald omegas of .95 in sample 1 and .93 in sample 2. Significant correlations with change in depressive symptoms (r=-.35, P<.001) and perceived stress (r=-.48, P<.001) demonstrated the construct validity of the scale. The proven internal consistency, factorial structure, and construct validity of the CSQ-I indicate a good overall psychometric quality of the measure to assess the user's general satisfaction with Web-based interventions for depression and

Understanding Instructional Support Needs of Emerging Internet Users for Web-Based Information Seeking

ERIC Educational Resources Information Center

Gupta, Naman K.; Penstein Rosé, Carolyn

2010-01-01

As the wealth of information available on the Web increases, Web-based information seeking becomes a more and more important skill for supporting both formal education and lifelong learning. However, Web-based information access poses hurdles that must be overcome by certain student populations, such as low English competency users, low literacy…

WE-E-BRB-11: Riview a Web-Based Viewer for Radiotherapy.

PubMed

Apte, A; Wang, Y; Deasy, J

2012-06-01

Collaborations involving radiotherapy data collection, such as the recently proposed international radiogenomics consortium, require robust, web-based tools to facilitate reviewing treatment planning information. We present the architecture and prototype characteristics for a web-based radiotherapy viewer. The web-based environment developed in this work consists of the following components: 1) Import of DICOM/RTOG data: CERR was leveraged to import DICOM/RTOG data and to convert to database friendly RT objects. 2) Extraction and Storage of RT objects: The scan and dose distributions were stored as .png files per slice and view plane. The file locations were written to the MySQL database. Structure contours and DVH curves were written to the database as numeric data. 3) Web interfaces to query, retrieve and visualize the RT objects: The Web application was developed using HTML 5 and Ruby on Rails (RoR) technology following the MVC philosophy. The open source ImageMagick library was utilized to overlay scan, dose and structures. The application allows users to (i) QA the treatment plans associated with a study, (ii) Query and Retrieve patients matching anonymized ID and study, (iii) Review up to 4 plans simultaneously in 4 window panes (iv) Plot DVH curves for the selected structures and dose distributions. A subset of data for lung cancer patients was used to prototype the system. Five user accounts were created to have access to this study. The scans, doses, structures and DVHs for 10 patients were made available via the web application. A web-based system to facilitate QA, and support Query, Retrieve and the Visualization of RT data was prototyped. The RIVIEW system was developed using open source and free technology like MySQL and RoR. We plan to extend the RIVIEW system further to be useful in clinical trial data collection, outcomes research, cohort plan review and evaluation. © 2012 American Association of Physicists in Medicine.

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

PubMed

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

2015-03-01

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

Capturing Trust in Social Web Applications

NASA Astrophysics Data System (ADS)

O'Donovan, John

The Social Web constitutes a shift in information flow from the traditional Web. Previously, content was provided by the owners of a website, for consumption by the end-user. Nowadays, these websites are being replaced by Social Web applications which are frameworks for the publication of user-provided content. Traditionally, Web content could be `trusted' to some extent based on the site it originated from. Algorithms such as Google's PageRank were (and still are) used to compute the importance of a website, based on analysis of underlying link topology. In the Social Web, analysis of link topology merely tells us about the importance of the information framework which hosts the content. Consumers of information still need to know about the importance/reliability of the content they are reading, and therefore about the reliability of the producers of that content. Research into trust and reputation of the producers of information in the Social Web is still very much in its infancy. Every day, people are forced to make trusting decisions about strangers on the Web based on a very limited amount of information. For example, purchasing a product from an eBay seller with a `reputation' of 99%, downloading a file from a peer-to-peer application such as Bit-Torrent, or allowing Amazon.com tell you what products you will like. Even something as simple as reading comments on a Web-blog requires the consumer to make a trusting decision about the quality of that information. In all of these example cases, and indeed throughout the Social Web, there is a pressing demand for increased information upon which we can make trusting decisions. This chapter examines the diversity of sources from which trust information can be harnessed within Social Web applications and discusses a high level classification of those sources. Three different techniques for harnessing and using trust from a range of sources are presented. These techniques are deployed in two sample Social Web

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.

User-Friendly Tools for Random Matrices: An Introduction

DTIC Science & Technology

2012-12-03

T 2011 , Oliveira 2010, Mackey et al . 2012, ... Joel A. Tropp, User-Friendly Tools for Random Matrices, NIPS, 3 December 2012 47 To learn more... E...the matrix product Y = AΩ 3. Construct an orthonormal basis Q for the range of Y [Ref] Halko –Martinsson–T, SIAM Rev. 2011 . Joel A. Tropp, User-Friendly...concentration inequalities...” with L. Mackey et al .. Submitted 2012. § “User-Friendly Tools for Random Matrices: An Introduction.” 2012. See also

COMPARE/Radiology, an interactive Web-based radiology teaching program evaluation of user response.

PubMed

Wagner, Matthias; Heckemann, Rolf A; Nömayr, Anton; Greess, Holger; Bautz, Werner A; Grunewald, Markus

2005-06-01

The aim of this study is to assess user benefits of COMPARE/Radiology, a highly interactive World Wide Web-based training program for radiology, as perceived by its users. COMPARE/Radiology (http://www.idr.med.uni-erlangen.de/compare.htm), an interactive training program based on 244 teaching cases, was created by the authors and made publicly available on the Internet. An anonymous survey was conducted among users to investigate the composition of the program's user base and assess the acceptance of the training program. In parallel, Web access data were collected and analyzed using descriptive statistics. The group of responding users (n = 1370) consisted of 201 preclinical medical students (14.7%), 314 clinical medical students (22.9%), 359 residents in radiology (26.2%), and 205 users of other professions (14.9%). A majority of respondents (1230; 89%) rated the interactivity of COMPARE/Radiology as good or excellent. Many respondents use COMPARE/Radiology for self-study (971; 70%) and for teaching others (600; 43%). Web access statistics show an increase in number of site visits from 1248 in December 2002 to 4651 in April 2004. Users appreciate the benefits of COMPARE/Radiology. The interactive instructional design was rated positively by responding users. The popularity of the site is growing, evidenced by the number of network accesses during the observation period.

Attitudes toward Web application supporting pharmacist-clinician comanagement of postexposure prophylaxis patients.

PubMed

Fuller, Crystal M; Turner, Alezandria K; Hernández, Diana; Rivera, Alexis V; Amesty, Silvia; Lewis, Michael D; Feldman, Stuart

2013-01-01

To qualitatively explore clinician and pharmacist attitudes toward using a Web application virtual pharmacist-clinician partnership (VPCP) to assist with comanaged care of illicit drug-using patients prescribed postexposure prophylaxis (PEP). Qualitative, descriptive, nonexperimental study. New York City (NYC) from February 2011 to March 2012. Four pharmacists and nine clinicians. In-depth interviews. Potential impact of the VPCP on pharmacist-clinician communication and potential barriers to use of the VPCP when comanaging PEP patients among pharmacists and clinicians. Pharmacists and clinicians were supportive of an interactive Web application that would expand the role of pharmacists to include assistance with PEP access and patient management. Participants noted that the VPCP would facilitate communication between pharmacists and clinicians and have potential to support adherence among patients. Pharmacists and clinicians were concerned about not having time to use the VPCP and security of patient information on the site. Pharmacist and clinician concerns informed final development of the VPCP, including creation of a user-friendly interface, linkage to users' e-mail accounts for timeline notification, and attention to security. Use of Web-based technology to support communication between pharmacists and clinicians was seen as being a potentially feasible method for improving patient care, particularly in the delivery of PEP to drug users and other high-risk groups. These findings highlight the need for further study of a technology-supported partnership, particularly for comanagement of patients who face challenges with adherence.

Development of a web application for water resources based on open source software

NASA Astrophysics Data System (ADS)

Delipetrev, Blagoj; Jonoski, Andreja; Solomatine, Dimitri P.

2014-01-01

This article presents research and development of a prototype web application for water resources using latest advancements in Information and Communication Technologies (ICT), open source software and web GIS. The web application has three web services for: (1) managing, presenting and storing of geospatial data, (2) support of water resources modeling and (3) water resources optimization. The web application is developed using several programming languages (PhP, Ajax, JavaScript, Java), libraries (OpenLayers, JQuery) and open source software components (GeoServer, PostgreSQL, PostGIS). The presented web application has several main advantages: it is available all the time, it is accessible from everywhere, it creates a real time multi-user collaboration platform, the programing languages code and components are interoperable and designed to work in a distributed computer environment, it is flexible for adding additional components and services and, it is scalable depending on the workload. The application was successfully tested on a case study with concurrent multi-users access.

Using a Java Web-based Graphical User Interface to access the SOHO Data Arch ive

NASA Astrophysics Data System (ADS)

Scholl, I.; Girard, Y.; Bykowski, A.

This paper presents the architecture of a Java web-based graphical interface dedicated to the access of the SOHO Data archive. This application allows local and remote users to search in the SOHO data catalog and retrieve the SOHO data files from the archive. It has been developed at MEDOC (Multi-Experiment Data and Operations Centre), located at the Institut d'Astrophysique Spatiale (Orsay, France), which is one of the European Archives for the SOHO data. This development is part of a joint effort between ESA, NASA and IAS in order to implement long term archive systems for the SOHO data. The software architecture is built as a client-server application using Java language and SQL above a set of components such as an HTTP server, a JDBC gateway, a RDBMS server, a data server and a Web browser. Since HTML pages and CGI scripts are not powerful enough to allow user interaction during a multi-instrument catalog search, this type of requirement enforces the choice of Java as the main language. We also discuss performance issues, security problems and portability on different Web browsers and operating syste ms.

Characterizing marijuana concentrate users: A web-based survey.

PubMed

Daniulaityte, Raminta; Lamy, Francois R; Barratt, Monica; Nahhas, Ramzi W; Martins, Silvia S; Boyer, Edward W; Sheth, Amit; Carlson, Robert G

2017-09-01

The study seeks to characterize marijuana concentrate users, describe reasons and patterns of use, perceived risk, and identify predictors of daily/near daily use. An anonymous web-based survey was conducted (April-June 2016) with 673 US-based cannabis users recruited via the Bluelight.org web-forum and included questions about marijuana concentrate use, other drugs, and socio-demographics. Multivariable logistic regression analyses were conducted to identify characteristics associated with greater odds of lifetime and daily use of marijuana concentrates. About 66% of respondents reported marijuana concentrate use. The sample was 76% male, and 87% white. Marijuana concentrate use was viewed as riskier than flower cannabis. Greater odds of marijuana concentrate use was associated with living in states with "recreational" (AOR=4.91; p=0.001) or "medical, less restrictive" marijuana policies (AOR=1.87; p=0.014), being male (AOR=2.21, p=0.002), younger (AOR=0.95, p<0.001), number of other drugs used (AOR=1.23, p<0.001), daily herbal cannabis use (AOR=4.28, p<0.001), and lower perceived risk of cannabis use (AOR=0.96, p=0.043). About 13% of marijuana concentrate users reported daily/near daily use. Greater odds of daily concentrate use was associated with being male (AOR=9.29, p=0.033), using concentrates for therapeutic purposes (AOR=7.61, p=0.001), using vape pens for marijuana concentrate administration (AOR=4.58, p=0.007), and lower perceived risk of marijuana concentrate use (AOR=0.92, p=0.017). Marijuana concentrate use was more common among male, younger and more experienced users, and those living in states with more liberal marijuana policies. Characteristics of daily users, in particular patterns of therapeutic use and utilization of different vaporization devices, warrant further research with community-recruited samples. Copyright © 2017 Elsevier B.V. All rights reserved.

Lamprey: tracking users on the World Wide Web.

PubMed

Felciano, R M; Altman, R B

1996-01-01

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

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

PubMed

Krause, Denise D

2015-11-01

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

A Web Application For Visualizing Empirical Models of the Space-Atmosphere Interface Region: AtModWeb

NASA Astrophysics Data System (ADS)

Knipp, D.; Kilcommons, L. M.; Damas, M. C.

2015-12-01

We have created a simple and user-friendly web application to visualize output from empirical atmospheric models that describe the lower atmosphere and the Space-Atmosphere Interface Region (SAIR). The Atmospheric Model Web Explorer (AtModWeb) is a lightweight, multi-user, Python-driven application which uses standard web technology (jQuery, HTML5, CSS3) to give an in-browser interface that can produce plots of modeled quantities such as temperature and individual species and total densities of neutral and ionized upper-atmosphere. Output may be displayed as: 1) a contour plot over a map projection, 2) a pseudo-color plot (heatmap) which allows visualization of a variable as a function of two spatial coordinates, or 3) a simple line plot of one spatial coordinate versus any number of desired model output variables. The application is designed around an abstraction of an empirical atmospheric model, essentially treating the model code as a black box, which makes it simple to add additional models without modifying the main body of the application. Currently implemented are the Naval Research Laboratory NRLMSISE00 model for neutral atmosphere and the International Reference Ionosphere (IRI). These models are relevant to the Low Earth Orbit environment and the SAIR. The interface is simple and usable, allowing users (students and experts) to specify time and location, and choose between historical (i.e. the values for the given date) or manual specification of whichever solar or geomagnetic activity drivers are required by the model. We present a number of use-case examples from research and education: 1) How does atmospheric density between the surface and 1000 km vary with time of day, season and solar cycle?; 2) How do ionospheric layers change with the solar cycle?; 3 How does the composition of the SAIR vary between day and night at a fixed altitude?

The ProteoRed MIAPE web toolkit: A User-friendly Framework to Connect and Share Proteomics Standards*

PubMed Central

Medina-Aunon, J. Alberto; Martínez-Bartolomé, Salvador; López-García, Miguel A.; Salazar, Emilio; Navajas, Rosana; Jones, Andrew R.; Paradela, Alberto; Albar, Juan P.

2011-01-01

The development of the HUPO-PSI's (Proteomics Standards Initiative) standard data formats and MIAPE (Minimum Information About a Proteomics Experiment) guidelines should improve proteomics data sharing within the scientific community. Proteomics journals have encouraged the use of these standards and guidelines to improve the quality of experimental reporting and ease the evaluation and publication of manuscripts. However, there is an evident lack of bioinformatics tools specifically designed to create and edit standard file formats and reports, or embed them within proteomics workflows. In this article, we describe a new web-based software suite (The ProteoRed MIAPE web toolkit) that performs several complementary roles related to proteomic data standards. First, it can verify that the reports fulfill the minimum information requirements of the corresponding MIAPE modules, highlighting inconsistencies or missing information. Second, the toolkit can convert several XML-based data standards directly into human readable MIAPE reports stored within the ProteoRed MIAPE repository. Finally, it can also perform the reverse operation, allowing users to export from MIAPE reports into XML files for computational processing, data sharing, or public database submission. The toolkit is thus the first application capable of automatically linking the PSI's MIAPE modules with the corresponding XML data exchange standards, enabling bidirectional conversions. This toolkit is freely available at http://www.proteored.org/MIAPE/. PMID:21983993

QoS prediction for web services based on user-trust propagation model

NASA Astrophysics Data System (ADS)

Thinh, Le-Van; Tu, Truong-Dinh

2017-10-01

There is an important online role for Web service providers and users; however, the rapidly growing number of service providers and users, it can create some similar functions among web services. This is an exciting area for research, and researchers seek to to propose solutions for the best service to users. Collaborative filtering (CF) algorithms are widely used in recommendation systems, although these are less effective for cold-start users. Recently, some recommender systems have been developed based on social network models, and the results show that social network models have better performance in terms of CF, especially for cold-start users. However, most social network-based recommendations do not consider the user's mood. This is a hidden source of information, and is very useful in improving prediction efficiency. In this paper, we introduce a new model called User-Trust Propagation (UTP). The model uses a combination of trust and the mood of users to predict the QoS value and matrix factorisation (MF), which is used to train the model. The experimental results show that the proposed model gives better accuracy than other models, especially for the cold-start problem.

DockingApp: a user friendly interface for facilitated docking simulations with AutoDock Vina.

PubMed

Di Muzio, Elena; Toti, Daniele; Polticelli, Fabio

2017-02-01

Molecular docking is a powerful technique that helps uncover the structural and energetic bases of the interaction between macromolecules and substrates, endogenous and exogenous ligands, and inhibitors. Moreover, this technique plays a pivotal role in accelerating the screening of large libraries of compounds for drug development purposes. The need to promote community-driven drug development efforts, especially as far as neglected diseases are concerned, calls for user-friendly tools to allow non-expert users to exploit the full potential of molecular docking. Along this path, here is described the implementation of DockingApp, a freely available, extremely user-friendly, platform-independent application for performing docking simulations and virtual screening tasks using AutoDock Vina. DockingApp sports an intuitive graphical user interface which greatly facilitates both the input phase and the analysis of the results, which can be visualized in graphical form using the embedded JMol applet. The application comes with the DrugBank set of more than 1400 ready-to-dock, FDA-approved drugs, to facilitate virtual screening and drug repurposing initiatives. Furthermore, other databases of compounds such as ZINC, available also in AutoDock format, can be readily and easily plugged in.

DockingApp: a user friendly interface for facilitated docking simulations with AutoDock Vina

NASA Astrophysics Data System (ADS)

Di Muzio, Elena; Toti, Daniele; Polticelli, Fabio

2017-02-01

Molecular docking is a powerful technique that helps uncover the structural and energetic bases of the interaction between macromolecules and substrates, endogenous and exogenous ligands, and inhibitors. Moreover, this technique plays a pivotal role in accelerating the screening of large libraries of compounds for drug development purposes. The need to promote community-driven drug development efforts, especially as far as neglected diseases are concerned, calls for user-friendly tools to allow non-expert users to exploit the full potential of molecular docking. Along this path, here is described the implementation of DockingApp, a freely available, extremely user-friendly, platform-independent application for performing docking simulations and virtual screening tasks using AutoDock Vina. DockingApp sports an intuitive graphical user interface which greatly facilitates both the input phase and the analysis of the results, which can be visualized in graphical form using the embedded JMol applet. The application comes with the DrugBank set of more than 1400 ready-to-dock, FDA-approved drugs, to facilitate virtual screening and drug repurposing initiatives. Furthermore, other databases of compounds such as ZINC, available also in AutoDock format, can be readily and easily plugged in.

PDB Editor: a user-friendly Java-based Protein Data Bank file editor with a GUI.

PubMed

Lee, Jonas; Kim, Sung Hou

2009-04-01

The Protein Data Bank file format is the format most widely used by protein crystallographers and biologists to disseminate and manipulate protein structures. Despite this, there are few user-friendly software packages available to efficiently edit and extract raw information from PDB files. This limitation often leads to many protein crystallographers wasting significant time manually editing PDB files. PDB Editor, written in Java Swing GUI, allows the user to selectively search, select, extract and edit information in parallel. Furthermore, the program is a stand-alone application written in Java which frees users from the hassles associated with platform/operating system-dependent installation and usage. PDB Editor can be downloaded from http://sourceforge.net/projects/pdbeditorjl/.

Creating Web-Based Scientific Applications Using Java Servlets

NASA Technical Reports Server (NTRS)

Palmer, Grant; Arnold, James O. (Technical Monitor)

2001-01-01

There are many advantages to developing web-based scientific applications. Any number of people can access the application concurrently. The application can be accessed from a remote location. The application becomes essentially platform-independent because it can be run from any machine that has internet access and can run a web browser. Maintenance and upgrades to the application are simplified since only one copy of the application exists in a centralized location. This paper details the creation of web-based applications using Java servlets. Java is a powerful, versatile programming language that is well suited to developing web-based programs. A Java servlet provides the interface between the central server and the remote client machines. The servlet accepts input data from the client, runs the application on the server, and sends the output back to the client machine. The type of servlet that supports the HTTP protocol will be discussed in depth. Among the topics the paper will discuss are how to write an http servlet, how the servlet can run applications written in Java and other languages, and how to set up a Java web server. The entire process will be demonstrated by building a web-based application to compute stagnation point heat transfer.

A web-based endodontic case difficulty assessment tool.

PubMed

Shah, P K; Chong, B S

2018-07-01

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

A web-server of cell type discrimination system.

PubMed

Wang, Anyou; Zhong, Yan; Wang, Yanhua; He, Qianchuan

2014-01-01

Discriminating cell types is a daily request for stem cell biologists. However, there is not a user-friendly system available to date for public users to discriminate the common cell types, embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), and somatic cells (SCs). Here, we develop WCTDS, a web-server of cell type discrimination system, to discriminate the three cell types and their subtypes like fetal versus adult SCs. WCTDS is developed as a top layer application of our recent publication regarding cell type discriminations, which employs DNA-methylation as biomarkers and machine learning models to discriminate cell types. Implemented by Django, Python, R, and Linux shell programming, run under Linux-Apache web server, and communicated through MySQL, WCTDS provides a friendly framework to efficiently receive the user input and to run mathematical models for analyzing data and then to present results to users. This framework is flexible and easy to be expended for other applications. Therefore, WCTDS works as a user-friendly framework to discriminate cell types and subtypes and it can also be expended to detect other cell types like cancer cells.

A Web-Server of Cell Type Discrimination System

PubMed Central

Zhong, Yan

2014-01-01

Discriminating cell types is a daily request for stem cell biologists. However, there is not a user-friendly system available to date for public users to discriminate the common cell types, embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), and somatic cells (SCs). Here, we develop WCTDS, a web-server of cell type discrimination system, to discriminate the three cell types and their subtypes like fetal versus adult SCs. WCTDS is developed as a top layer application of our recent publication regarding cell type discriminations, which employs DNA-methylation as biomarkers and machine learning models to discriminate cell types. Implemented by Django, Python, R, and Linux shell programming, run under Linux-Apache web server, and communicated through MySQL, WCTDS provides a friendly framework to efficiently receive the user input and to run mathematical models for analyzing data and then to present results to users. This framework is flexible and easy to be expended for other applications. Therefore, WCTDS works as a user-friendly framework to discriminate cell types and subtypes and it can also be expended to detect other cell types like cancer cells. PMID:24578634

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.

Evaluating a web-based health risk assessment with tailored feedback: what does an expert focus group yield compared to a web-based end-user survey?

PubMed

Vosbergen, Sandra; Mahieu, Guy R; Laan, Eva K; Kraaijenhagen, Roderik A; Jaspers, Monique Wm; Peek, Niels

2014-01-02

Increasingly, Web-based health applications are developed for the prevention and management of chronic diseases. However, their reach and utilization is often disappointing. Qualitative evaluations post-implementation can be used to inform the optimization process and ultimately enhance their adoption. In current practice, such evaluations are mainly performed with end-user surveys. However, a review approach by experts in a focus group may be easier to administer and might provide similar results. The aim of this study was to assess whether industrial design engineers in a focus group would address the same issues as end users in a Web-based survey when evaluating a commercial Web-based health risk assessment (HRA) with tailored feedback. Seven Dutch companies used the HRA as part of their corporate health management strategy. Employees using the HRA (N=2289) and 10 independent industrial designers were invited to participate in the study. The HRA consisted of four components: (1) an electronic health questionnaire, (2) biometric measurements, (3) laboratory evaluation, and (4) individually tailored feedback generated by decision support software. After participating in the HRA as end users, both end users and designers evaluated the program. End users completed an evaluation questionnaire that included a free-text field. Designers participated in a focus group discussion. Constructs from user satisfaction and technology acceptance theories were used to categorize and compare the remarks from both evaluations. We assessed and qualitatively analyzed 294 remarks of 189 end users and 337 remarks of 6 industrial designers, pertaining to 295 issues in total. Of those, 137 issues were addressed in the end-user survey and 148 issues in the designer focus group. Only 7.3% (10/137) of the issues addressed in the survey were also addressed in the focus group. End users made more remarks about the usefulness of the HRA and prior expectations that were not met. Designers made

Enable Web-Based Tracking and Guiding by Integrating Location-Awareness with the World Wide Web

ERIC Educational Resources Information Center

Zhou, Rui

2008-01-01

Purpose: The aim of this research is to enable web-based tracking and guiding by integrating location-awareness with the Worldwide Web so that the users can use various location-based applications without installing extra software. Design/methodology/approach: The concept of web-based tracking and guiding is introduced and the relevant issues are…

A user-centred evaluation framework for the Sealife semantic web browsers.

PubMed

Oliver, Helen; Diallo, Gayo; de Quincey, Ed; Alexopoulou, Dimitra; Habermann, Bianca; Kostkova, Patty; Schroeder, Michael; Jupp, Simon; Khelif, Khaled; Stevens, Robert; Jawaheer, Gawesh; Madle, Gemma

2009-10-01

Semantically-enriched browsing has enhanced the browsing experience by providing contextualized dynamically generated Web content, and quicker access to searched-for information. However, adoption of Semantic Web technologies is limited and user perception from the non-IT domain sceptical. Furthermore, little attention has been given to evaluating semantic browsers with real users to demonstrate the enhancements and obtain valuable feedback. The Sealife project investigates semantic browsing and its application to the life science domain. Sealife's main objective is to develop the notion of context-based information integration by extending three existing Semantic Web browsers (SWBs) to link the existing Web to the eScience infrastructure. This paper describes a user-centred evaluation framework that was developed to evaluate the Sealife SWBs that elicited feedback on users' perceptions on ease of use and information findability. Three sources of data: i) web server logs; ii) user questionnaires; and iii) semi-structured interviews were analysed and comparisons made between each browser and a control system. It was found that the evaluation framework used successfully elicited users' perceptions of the three distinct SWBs. The results indicate that the browser with the most mature and polished interface was rated higher for usability, and semantic links were used by the users of all three browsers. Confirmation or contradiction of our original hypotheses with relation to SWBs is detailed along with observations of implementation issues.

Development, Technical, and User Evaluation of a Web Mobile Application for Self-Control of Diabetes.

PubMed

Garcia-Zapirain, Begoña; de la Torre Díez, Isabel; Sainz de Abajo, Beatriz; López-Coronado, Miguel

2016-09-01

The main objective of this research was to develop and evaluate a Web-based mobile application (app) known as "Diario Diabetes" on both a technical and user level, by means of which individuals with diabetes may monitor their illness easily at any time and in any place using any device that has Internet access. The technologies used to develop the app were HTML, CSS, JavaScript, PHP, and MySQL, all of which are an open source. Once the app was developed, it was evaluated on a technical level (by measuring loading times) and on a user level, through a survey. Different loading times for the application were measured, with it being noted that under no circumstances does this exceed 2 s. Usability was evaluated by 150 users who initially used the application. A majority (71%) of users used a PC to access the app, 83% considered the app's design to be attractive, 67% considered the tasks to be very useful, and 67% found it very easy to use. Although applications exist for controlling diabetes both at mobile virtual shops or on a research level, our app may help to improve the administration of these types of patients and they are the ones who will ultimately opt for one or the other. According to the results obtained, we can state that all users would recommend the app's use to other users.

Design Options for Multimodal Web Applications

NASA Astrophysics Data System (ADS)

Stanciulescu, Adrian; Vanderdonckt, Jean

The capabilities of multimodal applications running on the web are well de-lineated since they are mainly constrained by what their underlying standard mark up language offers, as opposed to hand-made multimodal applications. As the experience in developing such multimodal web applications is growing, the need arises to identify and define major design options of such application to pave the way to a structured development life cycle. This paper provides a design space of independent design options for multimodal web applications based on three types of modalities: graphical, vocal, tactile, and combined. On the one hand, these design options may provide designers with some explicit guidance on what to decide or not for their future user interface, while exploring various design alternatives. On the other hand, these design options have been implemented as graph transformations per-formed on a user interface model represented as a graph. Thanks to a transformation engine, it allows designers to play with the different values of each design option, to preview the results of the transformation, and to obtain the corresponding code on-demand

A Web Service-Based Framework Model for People-Centric Sensing Applications Applied to Social Networking

PubMed Central

Nunes, David; Tran, Thanh-Dien; Raposo, Duarte; Pinto, André; Gomes, André; Silva, Jorge Sá

2012-01-01

As the Internet evolved, social networks (such as Facebook) have bloomed and brought together an astonishing number of users. Mashing up mobile phones and sensors with these social environments enables the creation of people-centric sensing systems which have great potential for expanding our current social networking usage. However, such systems also have many associated technical challenges, such as privacy concerns, activity detection mechanisms or intermittent connectivity, as well as limitations due to the heterogeneity of sensor nodes and networks. Considering the openness of the Web 2.0, good technical solutions for these cases consist of frameworks that expose sensing data and functionalities as common Web-Services. This paper presents our RESTful Web Service-based model for people-centric sensing frameworks, which uses sensors and mobile phones to detect users’ activities and locations, sharing this information amongst the user’s friends within a social networking site. We also present some screenshot results of our experimental prototype. PMID:22438732

AMPA: an automated web server for prediction of protein antimicrobial regions.

PubMed

Torrent, Marc; Di Tommaso, Paolo; Pulido, David; Nogués, M Victòria; Notredame, Cedric; Boix, Ester; Andreu, David

2012-01-01

AMPA is a web application for assessing the antimicrobial domains of proteins, with a focus on the design on new antimicrobial drugs. The application provides fast discovery of antimicrobial patterns in proteins that can be used to develop new peptide-based drugs against pathogens. Results are shown in a user-friendly graphical interface and can be downloaded as raw data for later examination. AMPA is freely available on the web at http://tcoffee.crg.cat/apps/ampa. The source code is also available in the web. marc.torrent@upf.edu; david.andreu@upf.edu Supplementary data are available at Bioinformatics online.

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

PubMed

Verkouteren, R M; Lee, J N

2001-08-01

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

SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies

PubMed Central

Ryan, Michael C; Zeeberg, Barry R; Caplen, Natasha J; Cleland, James A; Kahn, Ari B; Liu, Hongfang; Weinstein, John N

2008-01-01

Background Over 60% of protein-coding genes in vertebrates express mRNAs that undergo alternative splicing. The resulting collection of transcript isoforms poses significant challenges for contemporary biological assays. For example, RT-PCR validation of gene expression microarray results may be unsuccessful if the two technologies target different splice variants. Effective use of sequence-based technologies requires knowledge of the specific splice variant(s) that are targeted. In addition, the critical roles of alternative splice forms in biological function and in disease suggest that assay results may be more informative if analyzed in the context of the targeted splice variant. Results A number of contemporary technologies are used for analyzing transcripts or proteins. To enable investigation of the impact of splice variation on the interpretation of data derived from those technologies, we have developed SpliceCenter. SpliceCenter is a suite of user-friendly, web-based applications that includes programs for analysis of RT-PCR primer/probe sets, effectors of RNAi, microarrays, and protein-targeting technologies. Both interactive and high-throughput implementations of the tools are provided. The interactive versions of SpliceCenter tools provide visualizations of a gene's alternative transcripts and probe target positions, enabling the user to identify which splice variants are or are not targeted. The high-throughput batch versions accept user query files and provide results in tabular form. When, for example, we used SpliceCenter's batch siRNA-Check to process the Cancer Genome Anatomy Project's large-scale shRNA library, we found that only 59% of the 50,766 shRNAs in the library target all known splice variants of the target gene, 32% target some but not all, and 9% do not target any currently annotated transcript. Conclusion SpliceCenter provides unique, user-friendly applications for assessing the impact of transcript variation on the design and

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

PubMed

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

2016-07-01

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

Fragment-based docking: development of the CHARMMing Web user interface as a platform for computer-aided drug design.

PubMed

Pevzner, Yuri; Frugier, Emilie; Schalk, Vinushka; Caflisch, Amedeo; Woodcock, H Lee

2014-09-22

Web-based user interfaces to scientific applications are important tools that allow researchers to utilize a broad range of software packages with just an Internet connection and a browser. One such interface, CHARMMing (CHARMM interface and graphics), facilitates access to the powerful and widely used molecular software package CHARMM. CHARMMing incorporates tasks such as molecular structure analysis, dynamics, multiscale modeling, and other techniques commonly used by computational life scientists. We have extended CHARMMing's capabilities to include a fragment-based docking protocol that allows users to perform molecular docking and virtual screening calculations either directly via the CHARMMing Web server or on computing resources using the self-contained job scripts generated via the Web interface. The docking protocol was evaluated by performing a series of "re-dockings" with direct comparison to top commercial docking software. Results of this evaluation showed that CHARMMing's docking implementation is comparable to many widely used software packages and validates the use of the new CHARMM generalized force field for docking and virtual screening.

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

ERIC Educational Resources Information Center

Adebiaye, Richmond

2010-01-01

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

Friendly-Sharing: Improving the Performance of City Sensoring through Contact-Based Messaging Applications

PubMed Central

Herrera-Tapia, Jorge; Hernández-Orallo, Enrique; Tomás, Andrés; Manzoni, Pietro; Tavares Calafate, Carlos; Cano, Juan-Carlos

2016-01-01

Regular citizens equipped with smart devices are being increasingly used as “sensors” by Smart Cities applications. Using contacts among users, data in the form of messages is obtained and shared. Contact-based messaging applications are based on establishing a short-range communication directly between mobile devices, and on storing the messages in these devices for subsequent delivery to cloud-based services. An effective way to increase the number of messages that can be shared is to increase the contact duration. We thus introduce the Friendly-Sharing diffusion approach, where, during a contact, the users are aware of the time needed to interchange the messages stored in their buffers, and they can thus decide to wait more time in order to increase the message sharing probability. The performance of this approach is anyway closely related to the size of the buffer in the device. We therefore compare various policies either for the message selection at forwarding times and for message dropping when the buffer is full. We evaluate our proposal with a modified version of the Opportunistic Networking Environment (ONE) simulator and using real human mobility traces. PMID:27649209

Friendly-Sharing: Improving the Performance of City Sensoring through Contact-Based Messaging Applications.

PubMed

Herrera-Tapia, Jorge; Hernández-Orallo, Enrique; Tomás, Andrés; Manzoni, Pietro; Tavares Calafate, Carlos; Cano, Juan-Carlos

2016-09-18

Regular citizens equipped with smart devices are being increasingly used as "sensors" by Smart Cities applications. Using contacts among users, data in the form of messages is obtained and shared. Contact-based messaging applications are based on establishing a short-range communication directly between mobile devices, and on storing the messages in these devices for subsequent delivery to cloud-based services. An effective way to increase the number of messages that can be shared is to increase the contact duration. We thus introduce the Friendly-Sharing diffusion approach, where, during a contact, the users are aware of the time needed to interchange the messages stored in their buffers, and they can thus decide to wait more time in order to increase the message sharing probability. The performance of this approach is anyway closely related to the size of the buffer in the device. We therefore compare various policies either for the message selection at forwarding times and for message dropping when the buffer is full. We evaluate our proposal with a modified version of the Opportunistic Networking Environment (ONE) simulator and using real human mobility traces.

CARE 3 user-friendly interface user's guide

NASA Technical Reports Server (NTRS)

Martensen, A. L.

1987-01-01

CARE 3 predicts the unreliability of highly reliable reconfigurable fault-tolerant systems that include redundant computers or computer systems. CARE3MENU is a user-friendly interface used to create an input for the CARE 3 program. The CARE3MENU interface has been designed to minimize user input errors. Although a CARE3MENU session may be successfully completed and all parameters may be within specified limits or ranges, the CARE 3 program is not guaranteed to produce meaningful results if the user incorrectly interprets the CARE 3 stochastic model. The CARE3MENU User Guide provides complete information on how to create a CARE 3 model with the interface. The CARE3MENU interface runs under the VAX/VMS operating system.

Pennsylvania StreamStats--A web-based application for obtaining water-resource-related information

USGS Publications Warehouse

Stuckey, Marla H.; Hoffman, Scott A.

2010-01-01

StreamStats is a national web-based Geographic Information System (GIS) application, developed by the U.S. Geological Survey (USGS), in cooperation with Environmental Systems Research Institute, Inc., to provide a variety of water-resource-related information. Users can easily obtain descriptive information, basin characteristics, and streamflow statistics for USGS streamgages and ungaged stream locations throughout Pennsylvania. StreamStats also allows users to search upstream and (or) downstream from user-selected points to identify locations of and obtain information for water-resource-related activities, such as dams and streamgages.

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

The iMeteo is a web-based weather visualization tool

NASA Astrophysics Data System (ADS)

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

2010-05-01

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

A User-centered Model for Web Site Design

PubMed Central

Kinzie, Mable B.; Cohn, Wendy F.; Julian, Marti F.; Knaus, William A.

2002-01-01

As the Internet continues to grow as a delivery medium for health information, the design of effective Web sites becomes increasingly important. In this paper, the authors provide an overview of one effective model for Web site design, a user-centered process that includes techniques for needs assessment, goal/task analysis, user interface design, and rapid prototyping. They detail how this approach was employed to design a family health history Web site, Health Heritage . This Web site helps patients record and maintain their family health histories in a secure, confidential manner. It also supports primary care physicians through analysis of health histories, identification of potential risks, and provision of health care recommendations. Visual examples of the design process are provided to show how the use of this model resulted in an easy-to-use Web site that is likely to meet user needs. The model is effective across diverse content arenas and is appropriate for applications in varied media. PMID:12087113

Designing Effective Web Forms for Older Web Users

ERIC Educational Resources Information Center

Li, Hui; Rau, Pei-Luen Patrick; Fujimura, Kaori; Gao, Qin; Wang, Lin

2012-01-01

This research aims to provide insight for web form design for older users. The effects of task complexity and information structure of web forms on older users' performance were examined. Forty-eight older participants with abundant computer and web experience were recruited. The results showed significant differences in task time and error rate…

A user-centred evaluation framework for the Sealife semantic web browsers

PubMed Central

Oliver, Helen; Diallo, Gayo; de Quincey, Ed; Alexopoulou, Dimitra; Habermann, Bianca; Kostkova, Patty; Schroeder, Michael; Jupp, Simon; Khelif, Khaled; Stevens, Robert; Jawaheer, Gawesh; Madle, Gemma

2009-01-01

Background Semantically-enriched browsing has enhanced the browsing experience by providing contextualised dynamically generated Web content, and quicker access to searched-for information. However, adoption of Semantic Web technologies is limited and user perception from the non-IT domain sceptical. Furthermore, little attention has been given to evaluating semantic browsers with real users to demonstrate the enhancements and obtain valuable feedback. The Sealife project investigates semantic browsing and its application to the life science domain. Sealife's main objective is to develop the notion of context-based information integration by extending three existing Semantic Web browsers (SWBs) to link the existing Web to the eScience infrastructure. Methods This paper describes a user-centred evaluation framework that was developed to evaluate the Sealife SWBs that elicited feedback on users' perceptions on ease of use and information findability. Three sources of data: i) web server logs; ii) user questionnaires; and iii) semi-structured interviews were analysed and comparisons made between each browser and a control system. Results It was found that the evaluation framework used successfully elicited users' perceptions of the three distinct SWBs. The results indicate that the browser with the most mature and polished interface was rated higher for usability, and semantic links were used by the users of all three browsers. Conclusion Confirmation or contradiction of our original hypotheses with relation to SWBs is detailed along with observations of implementation issues. PMID:19796398

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.

Evaluating a Web-Based Health Risk Assessment With Tailored Feedback: What Does an Expert Focus Group Yield Compared to a Web-Based End-User Survey?

PubMed Central

Vosbergen, Sandra; Mahieu, Guy R; Laan, Eva K; Kraaijenhagen, Roderik A; Jaspers, Monique WM

2014-01-01

Background Increasingly, Web-based health applications are developed for the prevention and management of chronic diseases. However, their reach and utilization is often disappointing. Qualitative evaluations post-implementation can be used to inform the optimization process and ultimately enhance their adoption. In current practice, such evaluations are mainly performed with end-user surveys. However, a review approach by experts in a focus group may be easier to administer and might provide similar results. Objective The aim of this study was to assess whether industrial design engineers in a focus group would address the same issues as end users in a Web-based survey when evaluating a commercial Web-based health risk assessment (HRA) with tailored feedback. Methods Seven Dutch companies used the HRA as part of their corporate health management strategy. Employees using the HRA (N=2289) and 10 independent industrial designers were invited to participate in the study. The HRA consisted of four components: (1) an electronic health questionnaire, (2) biometric measurements, (3) laboratory evaluation, and (4) individually tailored feedback generated by decision support software. After participating in the HRA as end users, both end users and designers evaluated the program. End users completed an evaluation questionnaire that included a free-text field. Designers participated in a focus group discussion. Constructs from user satisfaction and technology acceptance theories were used to categorize and compare the remarks from both evaluations. Results We assessed and qualitatively analyzed 294 remarks of 189 end users and 337 remarks of 6 industrial designers, pertaining to 295 issues in total. Of those, 137 issues were addressed in the end-user survey and 148 issues in the designer focus group. Only 7.3% (10/137) of the issues addressed in the survey were also addressed in the focus group. End users made more remarks about the usefulness of the HRA and prior

Development and utilization of a web-based application as a robust radiology teaching tool (radstax) for medical student anatomy teaching.

PubMed

Colucci, Philip G; Kostandy, Petro; Shrauner, William R; Arleo, Elizabeth; Fuortes, Michele; Griffin, Andrew S; Huang, Yun-Han; Juluru, Krishna; Tsiouris, Apostolos John

2015-02-01

Rationale and Objectives: The primary role of radiology in the preclinical setting is the use of imaging to improve students' understanding of anatomy. Many currently available Web-based anatomy programs include either suboptimal or overwhelming levels of detail for medical students.Our objective was to develop a user-friendly software program that anatomy instructors can completely tailor to match the desired level of detail for their curriculum, meets the unique needs of the first- and the second-year medical students, and is compatible with most Internet browsers and tablets.Materials and Methods: RadStax is a Web-based application developed using free, open-source, ubiquitous software. RadStax was first introduced as an interactive resource for independent study and later incorporated into lectures. First- and second-year medical students were surveyed for quantitative feedback regarding their experience.Results: RadStax was successfully introduced into our medical school curriculum. It allows the creation of learning modules with labeled multiplanar (MPR) image sets, basic anatomic information, and a self-assessment feature. The program received overwhelmingly positive feedback from students. Of 115 students surveyed, 87.0% found it highly effective as a study tool and 85.2% reported high user satisfaction with the program.Conclusions: RadStax is a novel application for instructors wishing to create an atlas of labeled MPR radiologic studies tailored to meet the specific needs their curriculum. Simple and focused, it provides an interactive experience for students similar to the practice of radiologists.This program is a robust anatomy teaching tool that effectively aids in educating the preclinical medical student.

Type 1 diabetes self-management: developing a web-based telemedicine application.

PubMed

Ayatollahi, Haleh; Hasannezhad, Mostafa; Fard, Hedieh Saneei; Haghighi, Mehran Kamkar

2016-04-01

Self-management skills are essential for patients with diabetes mellitus to minimise the risks of complications from their condition. The aim of this research was to develop a web-based application for self-management of type 1 diabetes, suitable for use by patients, their carers and physicians. The study was comprised of two phases, the first being analysis of the kind of information and capabilities required by potential users of the system. Based on the results derived from the first phase of the study, the system prototype was designed and then evaluated using the 'think aloud' method and a standard questionnaire. The application was designed for use by patients, their carers and physicians. Patients could enter the level of blood glucose, insulin and activities on a daily basis, and physicians were able to supervise a patient's health status from a distance. Users were generally satisfied with the final version of the system. People with a wide range of literacy skills were able to use the system effectively. Patients or their carers could use the web-based application as a log book by entering the level of blood glucose and insulin doses on a regular basis, and as an educational resource to improve self-management skills. Physicians could use the system at any time convenient to them to support patients by giving medical advice. Further research is needed to report the effectiveness of the system in practice.

RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps

PubMed Central

Drory Retwitzer, Matan; Polishchuk, Maya; Churkin, Elena; Kifer, Ilona; Yakhini, Zohar; Barash, Danny

2015-01-01

Searching for RNA sequence-structure patterns is becoming an essential tool for RNA practitioners. Novel discoveries of regulatory non-coding RNAs in targeted organisms and the motivation to find them across a wide range of organisms have prompted the use of computational RNA pattern matching as an enhancement to sequence similarity. State-of-the-art programs differ by the flexibility of patterns allowed as queries and by their simplicity of use. In particular—no existing method is available as a user-friendly web server. A general program that searches for RNA sequence-structure patterns is RNA Structator. However, it is not available as a web server and does not provide the option to allow flexible gap pattern representation with an upper bound of the gap length being specified at any position in the sequence. Here, we introduce RNAPattMatch, a web-based application that is user friendly and makes sequence/structure RNA queries accessible to practitioners of various background and proficiency. It also extends RNA Structator and allows a more flexible variable gaps representation, in addition to analysis of results using energy minimization methods. RNAPattMatch service is available at http://www.cs.bgu.ac.il/rnapattmatch. A standalone version of the search tool is also available to download at the site. PMID:25940619

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

Web-based auditory self-training system for adult and elderly users of hearing aids.

PubMed

Vitti, Simone Virginia; Blasca, Wanderléia Quinhoneiro; Sigulem, Daniel; Torres Pisa, Ivan

2015-01-01

Adults and elderly users of hearing aids suffer psychosocial reactions as a result of hearing loss. Auditory rehabilitation is typically carried out with support from a speech therapist, usually in a clinical center. For these cases, there is a lack of computer-based self-training tools for minimizing the psychosocial impact of hearing deficiency. To develop and evaluate a web-based auditory self-training system for adult and elderly users of hearing aids. Two modules were developed for the web system: an information module based on guidelines for using hearing aids; and an auditory training module presenting a sequence of training exercises for auditory abilities along the lines of the auditory skill steps within auditory processing. We built aweb system using PHP programming language and a MySQL database .from requirements surveyed through focus groups that were conducted by healthcare information technology experts. The web system was evaluated by speech therapists and hearing aid users. An initial sample of 150 patients at DSA/HRAC/USP was defined to apply the system with the inclusion criteria that: the individuals should be over the age of 25 years, presently have hearing impairment, be a hearing aid user, have a computer and have internet experience. They were divided into two groups: a control group (G1) and an experimental group (G2). These patients were evaluated clinically using the HHIE for adults and HHIA for elderly people, before and after system implementation. A third web group was formed with users who were invited through social networks for their opinions on using the system. A questionnaire evaluating hearing complaints was given to all three groups. The study hypothesis considered that G2 would present greater auditory perception, higher satisfaction and fewer complaints than G1 after the auditory training. It was expected that G3 would have fewer complaints regarding use and acceptance of the system. The web system, which was named Sis

Web-Based Satellite Products Database for Meteorological and Climate Applications

NASA Technical Reports Server (NTRS)

Phan, Dung; Spangenberg, Douglas A.; Palikonda, Rabindra; Khaiyer, Mandana M.; Nordeen, Michele L.; Nguyen, Louis; Minnis, Patrick

2004-01-01

The need for ready access to satellite data and associated physical parameters such as cloud properties has been steadily growing. Air traffic management, weather forecasters, energy producers, and weather and climate researchers among others can utilize more satellite information than in the past. Thus, it is essential that such data are made available in near real-time and as archival products in an easy-access and user friendly environment. A host of Internet web sites currently provide a variety of satellite products for various applications. Each site has a unique contribution with appeal to a particular segment of the public and scientific community. This is no less true for the NASA Langley's Clouds and Radiation (NLCR) website (http://www-pm.larc.nasa.gov) that has been evolving over the past 10 years to support a variety of research projects This website was originally developed to display cloud products derived from the Geostationary Operational Environmental Satellite (GOES) over the Southern Great Plains for the Atmospheric Radiation Measurement (ARM) Program. It has evolved into a site providing a comprehensive database of near real-time and historical satellite products used for meteorological, aviation, and climate studies. To encourage the user community to take advantage of the site, this paper summarizes the various products and projects supported by the website and discusses future options for new datasets.

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.

Communication and Gamification in the Web-Based Foreign Language Educational System: Web- Based Foreign Language Educational System

ERIC Educational Resources Information Center

Osipov, Ilya V.; Volinsky, Alex A.; Nikulchev, Evgeny; Prasikova, Anna Y.

2016-01-01

The paper describes development of the educational online web communication platform for teaching and learning foreign languages. The main objective was to develop a web application for teaching foreigners to understand casual fluent speech. The system is based on the time bank principle, allowing users to teach others their native language along…

MSIX - A general and user-friendly platform for RAM analysis

NASA Astrophysics Data System (ADS)

Pan, Z. J.; Blemel, Peter

The authors present a CAD (computer-aided design) platform supporting RAM (reliability, availability, and maintainability) analysis with efficient system description and alternative evaluation. The design concepts, implementation techniques, and application results are described. This platform is user-friendly because of its graphic environment, drawing facilities, object orientation, self-tutoring, and access to the operating system. The programs' independency and portability make them generally applicable to various analysis tasks.

DEIVA: a web application for interactive visual analysis of differential gene expression profiles.

PubMed

Harshbarger, Jayson; Kratz, Anton; Carninci, Piero

2017-01-07

Differential gene expression (DGE) analysis is a technique to identify statistically significant differences in RNA abundance for genes or arbitrary features between different biological states. The result of a DGE test is typically further analyzed using statistical software, spreadsheets or custom ad hoc algorithms. We identified a need for a web-based system to share DGE statistical test results, and locate and identify genes in DGE statistical test results with a very low barrier of entry. We have developed DEIVA, a free and open source, browser-based single page application (SPA) with a strong emphasis on being user friendly that enables locating and identifying single or multiple genes in an immediate, interactive, and intuitive manner. By design, DEIVA scales with very large numbers of users and datasets. Compared to existing software, DEIVA offers a unique combination of design decisions that enable inspection and analysis of DGE statistical test results with an emphasis on ease of use.

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.

Fragment-Based Docking: Development of the CHARMMing Web User Interface as a Platform for Computer-Aided Drug Design

PubMed Central

2015-01-01

Web-based user interfaces to scientific applications are important tools that allow researchers to utilize a broad range of software packages with just an Internet connection and a browser.1 One such interface, CHARMMing (CHARMM interface and graphics), facilitates access to the powerful and widely used molecular software package CHARMM. CHARMMing incorporates tasks such as molecular structure analysis, dynamics, multiscale modeling, and other techniques commonly used by computational life scientists. We have extended CHARMMing’s capabilities to include a fragment-based docking protocol that allows users to perform molecular docking and virtual screening calculations either directly via the CHARMMing Web server or on computing resources using the self-contained job scripts generated via the Web interface. The docking protocol was evaluated by performing a series of “re-dockings” with direct comparison to top commercial docking software. Results of this evaluation showed that CHARMMing’s docking implementation is comparable to many widely used software packages and validates the use of the new CHARMM generalized force field for docking and virtual screening. PMID:25151852

Documenting clinical pharmacist intervention before and after the introduction of a web-based tool.

PubMed

Nurgat, Zubeir A; Al-Jazairi, Abdulrazaq S; Abu-Shraie, Nada; Al-Jedai, Ahmed

2011-04-01

To develop a database for documenting pharmacist intervention through a web-based application. The secondary endpoint was to determine if the new, web-based application provides any benefits with regards to documentation compliance by clinical pharmacists and ease of calculating cost savings compared with our previous method of documenting pharmacist interventions. A tertiary care hospital in Saudi Arabia. The documentation of interventions using a web-based documentation application was retrospectively compared with previous methods of documentation of clinical pharmacists' interventions (multi-user PC software). The number and types of interventions recorded by pharmacists, data mining of archived data, efficiency, cost savings, and the accuracy of the data generated. The number of documented clinical interventions increased from 4,926, using the multi-user PC software, to 6,840 for the web-based application. On average, we observed 653 interventions per clinical pharmacist using the web-based application, which showed an increase compared to an average of 493 interventions using the old multi-user PC software. However, using a paired Student's t-test there was no statistical significance difference between the two means (P = 0.201). Using a χ² test, which captured management level and the type of system used, we found a strong effect of management level (P < 2.2 × 10⁻¹⁶) on the number of documented interventions. We also found a moderately significant relationship between educational level and the number of interventions documented (P = 0.045). The mean ± SD time required to document an intervention using the web-based application was 66.55 ± 8.98 s. Using the web-based application, 29.06% of documented interventions resulted in cost-savings, while using the multi-user PC software only 4.75% of interventions did so. The majority of cost savings across both platforms resulted from the discontinuation of unnecessary drugs and a change in dosage regimen

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/.

Development and Utilization of a Web-Based Application as a Robust Radiology Teaching Tool (RadStax) for Medical Student Anatomy Teaching

PubMed Central

Colucci, Philip G.; Kostandy, Petro; Shrauner, William R.; Arleo, Elizabeth; Fuortes, Michele; Griffin, Andrew S.; Huang, Yun-Han; Juluru, Krishna; Tsiouris, Apostolos John

2016-01-01

Rationale and Objectives The primary role of radiology in the preclinical setting is the use of imaging to improve students’ understanding of anatomy. Many currently available Web-based anatomy programs include either suboptimal or overwhelming levels of detail for medical students. Our objective was to develop a user-friendly software program that anatomy instructors can completely tailor to match the desired level of detail for their curriculum, meets the unique needs of the first- and the second-year medical students, and is compatible with most Internet browsers and tablets. Materials and Methods RadStax is a Web-based application developed using free, open-source, ubiquitous software. RadStax was first introduced as an interactive resource for independent study and later incorporated into lectures. First- and second-year medical students were surveyed for quantitative feedback regarding their experience. Results RadStax was successfully introduced into our medical school curriculum. It allows the creation of learning modules with labeled multiplanar (MPR) image sets, basic anatomic information, and a self-assessment feature. The program received overwhelmingly positive feedback from students. Of 115 students surveyed, 87.0% found it highly effective as a study tool and 85.2% reported high user satisfaction with the program. Conclusions RadStax is a novel application for instructors wishing to create an atlas of labeled MPR radiologic studies tailored to meet the specific needs their curriculum. Simple and focused, it provides an interactive experience for students similar to the practice of radiologists. This program is a robust anatomy teaching tool that effectively aids in educating the preclinical medical student. PMID:25964956

WebViz:A Web-based Collaborative Interactive Visualization System for large-Scale Data Sets

NASA Astrophysics Data System (ADS)

Yuen, D. A.; McArthur, E.; Weiss, R. M.; Zhou, J.; Yao, B.

2010-12-01

WebViz is a web-based application designed to conduct collaborative, interactive visualizations of large data sets for multiple users, allowing researchers situated all over the world to utilize the visualization services offered by the University of Minnesota’s Laboratory for Computational Sciences and Engineering (LCSE). This ongoing project has been built upon over the last 3 1/2 years .The motivation behind WebViz lies primarily with the need to parse through an increasing amount of data produced by the scientific community as a result of larger and faster multicore and massively parallel computers coming to the market, including the use of general purpose GPU computing. WebViz allows these large data sets to be visualized online by anyone with an account. The application allows users to save time and resources by visualizing data ‘on the fly’, wherever he or she may be located. By leveraging AJAX via the Google Web Toolkit (http://code.google.com/webtoolkit/), we are able to provide users with a remote, web portal to LCSE's (http://www.lcse.umn.edu) large-scale interactive visualization system already in place at the University of Minnesota. LCSE’s custom hierarchical volume rendering software provides high resolution visualizations on the order of 15 million pixels and has been employed for visualizing data primarily from simulations in astrophysics to geophysical fluid dynamics . In the current version of WebViz, we have implemented a highly extensible back-end framework built around HTTP "server push" technology. The web application is accessible via a variety of devices including netbooks, iPhones, and other web and javascript-enabled cell phones. Features in the current version include the ability for users to (1) securely login (2) launch multiple visualizations (3) conduct collaborative visualization sessions (4) delegate control aspects of a visualization to others and (5) engage in collaborative chats with other users within the user interface

Socio-contextual Network Mining for User Assistance in Web-based Knowledge Gathering Tasks

NASA Astrophysics Data System (ADS)

Rajendran, Balaji; Kombiah, Iyakutti

Web-based Knowledge Gathering (WKG) is a specialized and complex information seeking task carried out by many users on the web, for their various learning, and decision-making requirements. We construct a contextual semantic structure by observing the actions of the users involved in WKG task, in order to gain an understanding of their task and requirement. We also build a knowledge warehouse in the form of a master Semantic Link Network (SLX) that accommodates and assimilates all the contextual semantic structures. This master SLX, which is a socio-contextual network, is then mined to provide contextual inputs to the current users through their agents. We validated our approach through experiments and analyzed the benefits to the users in terms of resource explorations and the time saved. The results are positive enough to motivate us to implement in a larger scale.

Information-Flow-Based Access Control for Web Browsers

NASA Astrophysics Data System (ADS)

Yoshihama, Sachiko; Tateishi, Takaaki; Tabuchi, Naoshi; Matsumoto, Tsutomu

The emergence of Web 2.0 technologies such as Ajax and Mashup has revealed the weakness of the same-origin policy[1], the current de facto standard for the Web browser security model. We propose a new browser security model to allow fine-grained access control in the client-side Web applications for secure mashup and user-generated contents. We propose a browser security model that is based on information-flow-based access control (IBAC) to overcome the dynamic nature of the client-side Web applications and to accurately determine the privilege of scripts in the event-driven programming model.

Advancing the Implementation of Hydrologic Models as Web-based Applications

NASA Astrophysics Data System (ADS)

Dahal, P.; Tarboton, D. G.; Castronova, A. M.

2017-12-01

Advanced computer simulations are required to understand hydrologic phenomenon such as rainfall-runoff response, groundwater hydrology, snow hydrology, etc. Building a hydrologic model instance to simulate a watershed requires investment in data (diverse geospatial datasets such as terrain, soil) and computer resources, typically demands a wide skill set from the analyst, and the workflow involved is often difficult to reproduce. This work introduces a web-based prototype infrastructure in the form of a web application that provides researchers with easy to use access to complete hydrological modeling functionality. This includes creating the necessary geospatial and forcing data, preparing input files for a model by applying complex data preprocessing, running the model for a user defined watershed, and saving the results to a web repository. The open source Tethys Platform was used to develop the web app front-end Graphical User Interface (GUI). We used HydroDS, a webservice that provides data preparation processing capability to support backend computations used by the app. Results are saved in HydroShare, a hydrologic information system that supports the sharing of hydrologic data, model and analysis tools. The TOPographic Kinematic APproximation and Integration (TOPKAPI) model served as the example for which we developed a complete hydrologic modeling service to demonstrate the approach. The final product is a complete modeling system accessible through the web to create input files, and run the TOPKAPI hydrologic model for a watershed of interest. We are investigating similar functionality for the preparation of input to Regional Hydro-Ecological Simulation System (RHESSys). Key Words: hydrologic modeling, web services, hydrologic information system, HydroShare, HydroDS, Tethys Platform

Genetic algorithm and graph theory based matrix factorization method for online friend recommendation.

PubMed

Li, Qu; Yao, Min; Yang, Jianhua; Xu, Ning

2014-01-01

Online friend recommendation is a fast developing topic in web mining. In this paper, we used SVD matrix factorization to model user and item feature vector and used stochastic gradient descent to amend parameter and improve accuracy. To tackle cold start problem and data sparsity, we used KNN model to influence user feature vector. At the same time, we used graph theory to partition communities with fairly low time and space complexity. What is more, matrix factorization can combine online and offline recommendation. Experiments showed that the hybrid recommendation algorithm is able to recommend online friends with good accuracy.

Web3DMol: interactive protein structure visualization based on WebGL.

PubMed

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

2017-07-03

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

SIFTER search: a web server for accurate phylogeny-based protein function prediction

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

Sahraeian, Sayed M.; Luo, Kevin R.; Brenner, Steven E.

We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access tomore » precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. Lastly, the SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.« less

SIFTER search: a web server for accurate phylogeny-based protein function prediction

DOE PAGES

Sahraeian, Sayed M.; Luo, Kevin R.; Brenner, Steven E.

2015-05-15

We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access tomore » precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. Lastly, the SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.« less

PoPoolation DB: a user-friendly web-based database for the retrieval of natural polymorphisms in Drosophila.

PubMed

Pandey, Ram Vinay; Kofler, Robert; Orozco-terWengel, Pablo; Nolte, Viola; Schlötterer, Christian

2011-03-02

The enormous potential of natural variation for the functional characterization of genes has been neglected for a long time. Only since recently, functional geneticists are starting to account for natural variation in their analyses. With the new sequencing technologies it has become feasible to collect sequence information for multiple individuals on a genomic scale. In particular sequencing pooled DNA samples has been shown to provide a cost-effective approach for characterizing variation in natural populations. While a range of software tools have been developed for mapping these reads onto a reference genome and extracting SNPs, linking this information to population genetic estimators and functional information still poses a major challenge to many researchers. We developed PoPoolation DB a user-friendly integrated database. Popoolation DB links variation in natural populations with functional information, allowing a wide range of researchers to take advantage of population genetic data. PoPoolation DB provides the user with population genetic parameters (Watterson's θ or Tajima's π), Tajima's D, SNPs, allele frequencies and indels in regions of interest. The database can be queried by gene name, chromosomal position, or a user-provided query sequence or GTF file. We anticipate that PoPoolation DB will be a highly versatile tool for functional geneticists as well as evolutionary biologists. PoPoolation DB, available at http://www.popoolation.at/pgt, provides an integrated platform for researchers to investigate natural polymorphism and associated functional annotations from UCSC and Flybase genome browsers, population genetic estimators and RNA-seq information.

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

PubMed Central

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

2007-01-01

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

Design and implementation of embedded un-interruptible power supply system (EUPSS) for web-based mobile application

NASA Astrophysics Data System (ADS)

Zhang, De-gan; Zhang, Xiao-dan

2012-11-01

With the growth of the amount of information manipulated by embedded application systems, which are embedded into devices and offer access to the devices on the internet, the requirements of saving the information systemically is necessary so as to fulfil access from the client and the local processing more efficiently. For supporting mobile applications, a design and implementation solution of embedded un-interruptible power supply (UPS) system (in brief, EUPSS) is brought forward for long-distance monitoring and controlling of UPS based on Web. The implementation of system is based on ATmega161, RTL8019AS and Arm chips with TCP/IP protocol suite for communication. In the embedded UPS system, an embedded file system is designed and implemented which saves the data and index information on a serial EEPROM chip in a structured way and communicates with a microcontroller unit through I2C bus. By embedding the file system into UPS system or other information appliances, users can access and manipulate local data on the web client side. Embedded file system on chips will play a major role in the growth of IP networking. Based on our experiment tests, the mobile users can easily monitor and control UPS in different places of long-distance. The performance of EUPSS has satisfied the requirements of all kinds of Web-based mobile applications.

MAX UnMix: A web application for unmixing magnetic coercivity distributions

NASA Astrophysics Data System (ADS)

Maxbauer, Daniel P.; Feinberg, Joshua M.; Fox, David L.

2016-10-01

It is common in the fields of rock and environmental magnetism to unmix magnetic mineral components using statistical methods that decompose various types of magnetization curves (e.g., acquisition, demagnetization, or backfield). A number of programs have been developed over the past decade that are frequently used by the rock magnetic community, however many of these programs are either outdated or have obstacles inhibiting their usability. MAX UnMix is a web application (available online at http://www.irm.umn.edu/maxunmix), built using the shiny package for R studio, that can be used for unmixing coercivity distributions derived from magnetization curves. Here, we describe in detail the statistical model underpinning the MAX UnMix web application and discuss the programs functionality. MAX UnMix is an improvement over previous unmixing programs in that it is designed to be user friendly, runs as an independent website, and is platform independent.

An integrated user-friendly ArcMAP tool for bivariate statistical modeling in geoscience applications

NASA Astrophysics Data System (ADS)

Jebur, M. N.; Pradhan, B.; Shafri, H. Z. M.; Yusof, Z.; Tehrany, M. S.

2014-10-01

Modeling and classification difficulties are fundamental issues in natural hazard assessment. A geographic information system (GIS) is a domain that requires users to use various tools to perform different types of spatial modeling. Bivariate statistical analysis (BSA) assists in hazard modeling. To perform this analysis, several calculations are required and the user has to transfer data from one format to another. Most researchers perform these calculations manually by using Microsoft Excel or other programs. This process is time consuming and carries a degree of uncertainty. The lack of proper tools to implement BSA in a GIS environment prompted this study. In this paper, a user-friendly tool, BSM (bivariate statistical modeler), for BSA technique is proposed. Three popular BSA techniques such as frequency ratio, weights-of-evidence, and evidential belief function models are applied in the newly proposed ArcMAP tool. This tool is programmed in Python and is created by a simple graphical user interface, which facilitates the improvement of model performance. The proposed tool implements BSA automatically, thus allowing numerous variables to be examined. To validate the capability and accuracy of this program, a pilot test area in Malaysia is selected and all three models are tested by using the proposed program. Area under curve is used to measure the success rate and prediction rate. Results demonstrate that the proposed program executes BSA with reasonable accuracy. The proposed BSA tool can be used in numerous applications, such as natural hazard, mineral potential, hydrological, and other engineering and environmental applications.

An integrated user-friendly ArcMAP tool for bivariate statistical modelling in geoscience applications

NASA Astrophysics Data System (ADS)

Jebur, M. N.; Pradhan, B.; Shafri, H. Z. M.; Yusoff, Z. M.; Tehrany, M. S.

2015-03-01

Modelling and classification difficulties are fundamental issues in natural hazard assessment. A geographic information system (GIS) is a domain that requires users to use various tools to perform different types of spatial modelling. Bivariate statistical analysis (BSA) assists in hazard modelling. To perform this analysis, several calculations are required and the user has to transfer data from one format to another. Most researchers perform these calculations manually by using Microsoft Excel or other programs. This process is time-consuming and carries a degree of uncertainty. The lack of proper tools to implement BSA in a GIS environment prompted this study. In this paper, a user-friendly tool, bivariate statistical modeler (BSM), for BSA technique is proposed. Three popular BSA techniques, such as frequency ratio, weight-of-evidence (WoE), and evidential belief function (EBF) models, are applied in the newly proposed ArcMAP tool. This tool is programmed in Python and created by a simple graphical user interface (GUI), which facilitates the improvement of model performance. The proposed tool implements BSA automatically, thus allowing numerous variables to be examined. To validate the capability and accuracy of this program, a pilot test area in Malaysia is selected and all three models are tested by using the proposed program. Area under curve (AUC) is used to measure the success rate and prediction rate. Results demonstrate that the proposed program executes BSA with reasonable accuracy. The proposed BSA tool can be used in numerous applications, such as natural hazard, mineral potential, hydrological, and other engineering and environmental applications.

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

EPA Pesticide Factsheets

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

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

. Besides the simulation tools, a web-based data base is under development where geospatial and time series data can be stored, managed, and processed. Furthermore, a web-based information system containing user guides for the various developed tools and applications as well as basic information on MAR and related topics is published and will be regularly expanded as new tools are getting implemented. The INOWAS-DSS including its simulation tools, data base and information system provides an extensive framework to manage, plan and optimize MAR facilities. As the INOWAS-DSS is an open-source software accessible via the internet using standard web browsers, it offers new ways for data sharing and collaboration among various partners and decision makers.

Transitioning Client Based NALCOMIS to a Multi Function Web Based Application

DTIC Science & Technology

2016-09-23

NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS TRANSITIONING CLIENT- BASED NALCOMIS TO A MULTI-FUNCTION WEB- BASED APPLICATION by Aaron P...TITLE AND SUBTITLE TRANSITIONING CLIENT- BASED NALCOMIS TO A MULTI-FUNCTION WEB- BASED APPLICATION 5. FUNDING NUMBERS 6. AUTHOR(S) Aaron P. Schnetzler 7...NALCOMIS. NALCOMIS has two configurations that are used by organizational and intermediate level maintenance activi- ties, Optimized Organizational

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

PubMed

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

2012-01-01

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

Adding and Removing Web Area Users, and Changing User Roles

EPA Pesticide Factsheets

Webmasters can add users to a web area, and assign or change roles, which define the actions a user is able to take in the web area. Non-webmasters must use a request form to add users and change roles.

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.

Displaying R spatial statistics on Google dynamic maps with web applications created by Rwui.

PubMed

Newton, Richard; Deonarine, Andrew; Wernisch, Lorenz

2012-09-24

The R project includes a large variety of packages designed for spatial statistics. Google dynamic maps provide web based access to global maps and satellite imagery. We describe a method for displaying directly the spatial output from an R script on to a Google dynamic map. This is achieved by creating a Java based web application which runs the R script and then displays the results on the dynamic map. In order to make this method easy to implement by those unfamiliar with programming Java based web applications, we have added the method to the options available in the R Web User Interface (Rwui) application. Rwui is an established web application for creating web applications for running R scripts. A feature of Rwui is that all the code for the web application being created is generated automatically so that someone with no knowledge of web programming can make a fully functional web application for running an R script in a matter of minutes. Rwui can now be used to create web applications that will display the results from an R script on a Google dynamic map. Results may be displayed as discrete markers and/or as continuous overlays. In addition, users of the web application may select regions of interest on the dynamic map with mouse clicks and the coordinates of the region of interest will automatically be made available for use by the R script. This method of displaying R output on dynamic maps is designed to be of use in a number of areas. Firstly it allows statisticians, working in R and developing methods in spatial statistics, to easily visualise the results of applying their methods to real world data. Secondly, it allows researchers who are using R to study health geographics data, to display their results directly onto dynamic maps. Thirdly, by creating a web application for running an R script, a statistician can enable users entirely unfamiliar with R to run R coded statistical analyses of health geographics data. Fourthly, we envisage an

Breaking and Fixing Origin-Based Access Control in Hybrid Web/Mobile Application Frameworks.

PubMed

Georgiev, Martin; Jana, Suman; Shmatikov, Vitaly

2014-02-01

Hybrid mobile applications (apps) combine the features of Web applications and "native" mobile apps. Like Web applications, they are implemented in portable, platform-independent languages such as HTML and JavaScript. Like native apps, they have direct access to local device resources-file system, location, camera, contacts, etc. Hybrid apps are typically developed using hybrid application frameworks such as PhoneGap. The purpose of the framework is twofold. First, it provides an embedded Web browser (for example, WebView on Android) that executes the app's Web code. Second, it supplies "bridges" that allow Web code to escape the browser and access local resources on the device. We analyze the software stack created by hybrid frameworks and demonstrate that it does not properly compose the access-control policies governing Web code and local code, respectively. Web code is governed by the same origin policy, whereas local code is governed by the access-control policy of the operating system (for example, user-granted permissions in Android). The bridges added by the framework to the browser have the same local access rights as the entire application, but are not correctly protected by the same origin policy. This opens the door to fracking attacks, which allow foreign-origin Web content included into a hybrid app (e.g., ads confined in iframes) to drill through the layers and directly access device resources. Fracking vulnerabilities are generic: they affect all hybrid frameworks, all embedded Web browsers, all bridge mechanisms, and all platforms on which these frameworks are deployed. We study the prevalence of fracking vulnerabilities in free Android apps based on the PhoneGap framework. Each vulnerability exposes sensitive local resources-the ability to read and write contacts list, local files, etc.-to dozens of potentially malicious Web domains. We also analyze the defenses deployed by hybrid frameworks to prevent resource access by foreign-origin Web content

Breaking and Fixing Origin-Based Access Control in Hybrid Web/Mobile Application Frameworks

PubMed Central

Georgiev, Martin; Jana, Suman; Shmatikov, Vitaly

2014-01-01

Hybrid mobile applications (apps) combine the features of Web applications and “native” mobile apps. Like Web applications, they are implemented in portable, platform-independent languages such as HTML and JavaScript. Like native apps, they have direct access to local device resources—file system, location, camera, contacts, etc. Hybrid apps are typically developed using hybrid application frameworks such as PhoneGap. The purpose of the framework is twofold. First, it provides an embedded Web browser (for example, WebView on Android) that executes the app's Web code. Second, it supplies “bridges” that allow Web code to escape the browser and access local resources on the device. We analyze the software stack created by hybrid frameworks and demonstrate that it does not properly compose the access-control policies governing Web code and local code, respectively. Web code is governed by the same origin policy, whereas local code is governed by the access-control policy of the operating system (for example, user-granted permissions in Android). The bridges added by the framework to the browser have the same local access rights as the entire application, but are not correctly protected by the same origin policy. This opens the door to fracking attacks, which allow foreign-origin Web content included into a hybrid app (e.g., ads confined in iframes) to drill through the layers and directly access device resources. Fracking vulnerabilities are generic: they affect all hybrid frameworks, all embedded Web browsers, all bridge mechanisms, and all platforms on which these frameworks are deployed. We study the prevalence of fracking vulnerabilities in free Android apps based on the PhoneGap framework. Each vulnerability exposes sensitive local resources—the ability to read and write contacts list, local files, etc.—to dozens of potentially malicious Web domains. We also analyze the defenses deployed by hybrid frameworks to prevent resource access by foreign

Design and implementation of space physics multi-model application integration based on web

NASA Astrophysics Data System (ADS)

Jiang, Wenping; Zou, Ziming

independent modules according to different business needs is applied to solve the problem of the independence of the physical space between multiple models. The classic MVC(Model View Controller) software design pattern is concerned to build the architecture of space physics multi-model application integrated system. The JSP+servlet+javabean technology is used to integrate the web application programs of space physics multi-model. It solves the problem of multi-user requesting the same job of model computing and effectively balances each server computing tasks. In addition, we also complete follow tasks: establishing standard graphical user interface based on Java Applet application program; Designing the interface between model computing and model computing results visualization; Realizing three-dimensional network visualization without plug-ins; Using Java3D technology to achieve a three-dimensional network scene interaction; Improved ability to interact with web pages and dynamic execution capabilities, including rendering three-dimensional graphics, fonts and color control. Through the design and implementation of the SPMAIS based on Web, we provide an online computing and application runtime environment of space physics multi-model. The practical application improves that researchers could be benefit from our system in space physics research and engineering applications.

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

Pilot implementation and user preferences of a Bariatric After-care application.

PubMed

Zhang, Melvyn W B; Ho, Roger C M; Hawa, Raed; Sockalingam, Sanjeev

2015-01-01

The respective rates of obesity in Canada and the United states are estimated to be 24.1% and 34.1%. Due to the increased incidence of obesity, Bariatric surgery has been recognized as one of the treatment options. Patients who have undergone Bariatric surgery tend to need chronic long-term follow-up with a multi-disciplinary team. In the past decade, there has been massive advancement and development in Internet, Web-based and Smartphone technologies. However, there seemed to be a pacuity of applications in this area that enables post-bariatric patients to self-manage their own condition. In addition, past research have highlighted the limited evidence based with regards to currently available bariatric applications, mainly due to the lack of medical professionals involvement. Our current research objective is to illustrate the development of a Bariatric After-care smartphone application and to highlight user preferences with regards to the features integrated within the application. The Bariatric Aftercare application was developed between the months of March 2014 to April 2014. Making use of low-cost online web-based application developmental technologies, the authors embarked on the development of the web-based application. Patients who attended their routine follow-up appointments are given the links to the web-based application. They were also recruited to participate in an online user evaluation survey to identify their preferences with regards to the features integrated. Since the inception of the web-based application to date, there has been a cumulative total of 385 unique assess to the online web-based application. There is a slight change in the confidence levels of the participants with regards to using the application to help them self-manage their own condition. The majority of the users have indicated that they preferred the information pertaining to what happens during each consult with members of the multidisciplinary team and also greatly valued

Web-based spatial analysis with the ILWIS open source GIS software and satellite images from GEONETCast

NASA Astrophysics Data System (ADS)

Lemmens, R.; Maathuis, B.; Mannaerts, C.; Foerster, T.; Schaeffer, B.; Wytzisk, A.

2009-12-01

This paper involves easy accessible integrated web-based analysis of satellite images with a plug-in based open source software. The paper is targeted to both users and developers of geospatial software. Guided by a use case scenario, we describe the ILWIS software and its toolbox to access satellite images through the GEONETCast broadcasting system. The last two decades have shown a major shift from stand-alone software systems to networked ones, often client/server applications using distributed geo-(web-)services. This allows organisations to combine without much effort their own data with remotely available data and processing functionality. Key to this integrated spatial data analysis is a low-cost access to data from within a user-friendly and flexible software. Web-based open source software solutions are more often a powerful option for developing countries. The Integrated Land and Water Information System (ILWIS) is a PC-based GIS & Remote Sensing software, comprising a complete package of image processing, spatial analysis and digital mapping and was developed as commercial software from the early nineties onwards. Recent project efforts have migrated ILWIS into a modular, plug-in-based open source software, and provide web-service support for OGC-based web mapping and processing. The core objective of the ILWIS Open source project is to provide a maintainable framework for researchers and software developers to implement training components, scientific toolboxes and (web-) services. The latest plug-ins have been developed for multi-criteria decision making, water resources analysis and spatial statistics analysis. The development of this framework is done since 2007 in the context of 52°North, which is an open initiative that advances the development of cutting edge open source geospatial software, using the GPL license. GEONETCast, as part of the emerging Global Earth Observation System of Systems (GEOSS), puts essential environmental data at the

Study on online community user motif using web usage mining

NASA Astrophysics Data System (ADS)

Alphy, Meera; Sharma, Ajay

2016-04-01

The Web usage mining is the application of data mining, which is used to extract useful information from the online community. The World Wide Web contains at least 4.73 billion pages according to Indexed Web and it contains at least 228.52 million pages according Dutch Indexed web on 6th august 2015, Thursday. It’s difficult to get needed data from these billions of web pages in World Wide Web. Here is the importance of web usage mining. Personalizing the search engine helps the web user to identify the most used data in an easy way. It reduces the time consumption; automatic site search and automatic restore the useful sites. This study represents the old techniques to latest techniques used in pattern discovery and analysis in web usage mining from 1996 to 2015. Analyzing user motif helps in the improvement of business, e-commerce, personalisation and improvement of websites.

Engineering Analysis Using a Web-based Protocol

NASA Technical Reports Server (NTRS)

Schoeffler, James D.; Claus, Russell W.

2002-01-01

This paper reviews the development of a web-based framework for engineering analysis. A one-dimensional, high-speed analysis code called LAPIN was used in this study, but the approach can be generalized to any engineering analysis tool. The web-based framework enables users to store, retrieve, and execute an engineering analysis from a standard web-browser. We review the encapsulation of the engineering data into the eXtensible Markup Language (XML) and various design considerations in the storage and retrieval of application data.

Accountable Information Flow for Java-Based Web Applications

DTIC Science & Technology

2010-01-01

runtime library Swift server runtime Java servlet framework HTTP Web server Web browser Figure 2: The Swift architecture introduced an open-ended...On the server, the Java application code links against Swift’s server-side run-time library, which in turn sits on top of the standard Java servlet ...AFRL-RI-RS-TR-2010-9 Final Technical Report January 2010 ACCOUNTABLE INFORMATION FLOW FOR JAVA -BASED WEB APPLICATIONS

wHospital: a web-based application with digital signature for drugs dispensing management.

PubMed

Rossi, Lorenzo; Margola, Lorenzo; Manzelli, Vacia; Bandera, Alessandra

2006-01-01

wHospital is the result of an information technology research project, based on the utilization of a web based application for managing the hospital drugs dispensing. Part of wHospital back bone and its key distinguishing characteristic is the adoption of the digital signature system,initially deployed by the Government of Lombardia, a Northern Italy Region, throughout the distribution of smart cards to all the healthcare and hospital staffs. The developed system is a web-based application with a proposed Health Records Digital Signature (HReDS) handshake to comply with the national law and with the Joint Commission International Standards. The prototype application, for a single hospital Operative Unit (OU), has focused on data and process management, related to drug therapy. Following a multi-faceted selection process, the Infective Disease OU of the Hospital in Busto Arsizio, Lombardia, was chosen for the development and prototype implementation. The project lead time, from user requirement analysis to training and deployment was approximately 8 months. This paper highlights the applied project methodology, the system architecture, and the achieved preliminary results.

CentiServer: A Comprehensive Resource, Web-Based Application and R Package for Centrality Analysis.

PubMed

Jalili, Mahdi; Salehzadeh-Yazdi, Ali; Asgari, Yazdan; Arab, Seyed Shahriar; Yaghmaie, Marjan; Ghavamzadeh, Ardeshir; Alimoghaddam, Kamran

2015-01-01

Various disciplines are trying to solve one of the most noteworthy queries and broadly used concepts in biology, essentiality. Centrality is a primary index and a promising method for identifying essential nodes, particularly in biological networks. The newly created CentiServer is a comprehensive online resource that provides over 110 definitions of different centrality indices, their computational methods, and algorithms in the form of an encyclopedia. In addition, CentiServer allows users to calculate 55 centralities with the help of an interactive web-based application tool and provides a numerical result as a comma separated value (csv) file format or a mapped graphical format as a graph modeling language (GML) file. The standalone version of this application has been developed in the form of an R package. The web-based application (CentiServer) and R package (centiserve) are freely available at http://www.centiserver.org/.

CentiServer: A Comprehensive Resource, Web-Based Application and R Package for Centrality Analysis

PubMed Central

Jalili, Mahdi; Salehzadeh-Yazdi, Ali; Asgari, Yazdan; Arab, Seyed Shahriar; Yaghmaie, Marjan; Ghavamzadeh, Ardeshir; Alimoghaddam, Kamran

2015-01-01

Various disciplines are trying to solve one of the most noteworthy queries and broadly used concepts in biology, essentiality. Centrality is a primary index and a promising method for identifying essential nodes, particularly in biological networks. The newly created CentiServer is a comprehensive online resource that provides over 110 definitions of different centrality indices, their computational methods, and algorithms in the form of an encyclopedia. In addition, CentiServer allows users to calculate 55 centralities with the help of an interactive web-based application tool and provides a numerical result as a comma separated value (csv) file format or a mapped graphical format as a graph modeling language (GML) file. The standalone version of this application has been developed in the form of an R package. The web-based application (CentiServer) and R package (centiserve) are freely available at http://www.centiserver.org/ PMID:26571275

Bed management team with Kanban web-based application.

PubMed

Rocha, Hermano Alexandre Lima; Santos, Ana Kelly Lima da Cruz; Alcântara, Antônia Celia de Castro; Lima, Carmen Sulinete Suliano da Costa; Rocha, Sabrina Gabriele Maia Oliveira; Cardoso, Roberto Melo; Cremonin, Jair Rodrigues

2018-05-15

To measure the effectiveness of the bed management process that uses a web-based application with Kanban methodology to reduce hospitalization time of hospitalized patients. Before-after study was performed. The study was conducted between July 2013 and July 2017, at the Unimed Regional Hospital of Fortaleza, which has 300 beds, of which 60 are in the intensive care unit (ICU). It is accredited by International Society for Quality in Healthcare. Patients hospitalized in the referred period. Bed management with an application that uses color logic to signal at which stage of high flow the patients meet, in which each patient is interpreted as a card of the classical Kanban theory. It has an automatic user signaling system for process movement, and a system for monitoring and analyzing discharge forecasts. Length of hospital stay, number of customer complaints related to bed availability. After the intervention, the hospital's overall hospital stay time was reduced from 5.6 days to 4.9 days (P = 0.001). The units with the greatest reduction were the ICUs, with reduction from 6.0 days to 2.0 (P = 0.001). The relative percentage of complaints regarding bed availability in the hospital fell from 27% to 0%. We conclude that the use of an electronic tool based on Kanban methodology and accessed via the web by a bed management team is effective in reducing patients' hospital stay time.

A user-friendly SSVEP-based brain-computer interface using a time-domain classifier.

PubMed

Luo, An; Sullivan, Thomas J

2010-04-01

We introduce a user-friendly steady-state visual evoked potential (SSVEP)-based brain-computer interface (BCI) system. Single-channel EEG is recorded using a low-noise dry electrode. Compared to traditional gel-based multi-sensor EEG systems, a dry sensor proves to be more convenient, comfortable and cost effective. A hardware system was built that displays four LED light panels flashing at different frequencies and synchronizes with EEG acquisition. The visual stimuli have been carefully designed such that potential risk to photosensitive people is minimized. We describe a novel stimulus-locked inter-trace correlation (SLIC) method for SSVEP classification using EEG time-locked to stimulus onsets. We studied how the performance of the algorithm is affected by different selection of parameters. Using the SLIC method, the average light detection rate is 75.8% with very low error rates (an 8.4% false positive rate and a 1.3% misclassification rate). Compared to a traditional frequency-domain-based method, the SLIC method is more robust (resulting in less annoyance to the users) and is also suitable for irregular stimulus patterns.

Value of Information Web Application

DTIC Science & Technology

2015-04-01

their understanding of VoI attributes (source reliable, information content, and latency). The VoI web application emulates many features of a...only when using the Firefox web browser on those computers (Internet Explorer was not viable due to unchangeable user settings). During testing, the

Calypso: a user-friendly web-server for mining and visualizing microbiome-environment interactions.

PubMed

Zakrzewski, Martha; Proietti, Carla; Ellis, Jonathan J; Hasan, Shihab; Brion, Marie-Jo; Berger, Bernard; Krause, Lutz

2017-03-01

Calypso is an easy-to-use online software suite that allows non-expert users to mine, interpret and compare taxonomic information from metagenomic or 16S rDNA datasets. Calypso has a focus on multivariate statistical approaches that can identify complex environment-microbiome associations. The software enables quantitative visualizations, statistical testing, multivariate analysis, supervised learning, factor analysis, multivariable regression, network analysis and diversity estimates. Comprehensive help pages, tutorials and videos are provided via a wiki page. The web-interface is accessible via http://cgenome.net/calypso/ . The software is programmed in Java, PERL and R and the source code is available from Zenodo ( https://zenodo.org/record/50931 ). The software is freely available for non-commercial users. l.krause@uq.edu.au. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

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

PubMed

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

2010-05-01

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

Web-Based Intelligent E-Learning Systems: Technologies and Applications

ERIC Educational Resources Information Center

Ma, Zongmin

2006-01-01

Collecting and presenting the latest research and development results from the leading researchers in the field of e-learning systems, Web-Based Intelligent E-Learning Systems: Technologies and Applications provides a single record of current research and practical applications in Web-based intelligent e-learning systems. This book includes major…

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

PubMed

Bui, Thanh Quang; Pham, Hai Minh

2016-01-01

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

Web Analytics: A Picture of the Academic Library Web Site User

ERIC Educational Resources Information Center

Black, Elizabeth L.

2009-01-01

This article describes the usefulness of Web analytics for understanding the users of an academic library Web site. Using a case study, the analysis describes how Web analytics can answer questions about Web site user behavior, including when visitors come, the duration of the visit, how they get there, the technology they use, and the most…

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

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

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

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

A user-friendly tool for incremental haemodialysis prescription.

PubMed

Casino, Francesco Gaetano; Basile, Carlo

2018-01-05

There is a recently heightened interest in incremental haemodialysis (IHD), the main advantage of which could likely be a better preservation of the residual kidney function of the patients. The implementation of IHD, however, is hindered by many factors, among them, the mathematical complexity of its prescription. The aim of our study was to design a user-friendly tool for IHD prescription, consisting of only a few rows of a common spreadsheet. The keystone of our spreadsheet was the following fundamental concept: the dialysis dose to be prescribed in IHD depends only on the normalized urea clearance provided by the native kidneys (KRUn) of the patient for each frequency of treatment, according to the variable target model recently proposed by Casino and Basile (The variable target model: a paradigm shift in the incremental haemodialysis prescription. Nephrol Dial Transplant 2017; 32: 182-190). The first step was to put in sequence a series of equations in order to calculate, firstly, KRUn and, then, the key parameters to be prescribed for an adequate IHD; the second step was to compare KRUn values obtained with our spreadsheet with KRUn values obtainable with the gold standard Solute-solver (Daugirdas JT et al., Solute-solver: a web-based tool for modeling urea kinetics for a broad range of hemodialysis schedules in multiple patients. Am J Kidney Dis 2009; 54: 798-809) in a sample of 40 incident haemodialysis patients. Our spreadsheet provided excellent results. The differences with Solute-solver were clinically negligible. This was confirmed by the Bland-Altman plot built to analyse the agreement between KRUn values obtained with the two methods: the difference was 0.07 ± 0.05 mL/min/35 L. Our spreadsheet is a user-friendly tool able to provide clinically acceptable results in IHD prescription. Two immediate consequences could derive: (i) a larger dissemination of IHD might occur; and (ii) our spreadsheet could represent a useful tool for an ineludibly

User Preferences for Web-Based Module Design Layout and Design Impact on Information Recall Considering Age

ERIC Educational Resources Information Center

Pomales-García, Cristina; Rivera-Nivar, Mericia

2015-01-01

Research in design of Web-based modules should incorporate aging as an important factor given the diversity of the current workforce. This work aims to understand how Web-Based Learning modules can be designed to accommodate young (25-35 years) as well as older (55-65 years) users by: (1) identifying how information sources (instructor video,…

GEOMetaCuration: a web-based application for accurate manual curation of Gene Expression Omnibus metadata

PubMed Central

Li, Zhao; Li, Jin; Yu, Peng

2018-01-01

Abstract Metadata curation has become increasingly important for biological discovery and biomedical research because a large amount of heterogeneous biological data is currently freely available. To facilitate efficient metadata curation, we developed an easy-to-use web-based curation application, GEOMetaCuration, for curating the metadata of Gene Expression Omnibus datasets. It can eliminate mechanical operations that consume precious curation time and can help coordinate curation efforts among multiple curators. It improves the curation process by introducing various features that are critical to metadata curation, such as a back-end curation management system and a curator-friendly front-end. The application is based on a commonly used web development framework of Python/Django and is open-sourced under the GNU General Public License V3. GEOMetaCuration is expected to benefit the biocuration community and to contribute to computational generation of biological insights using large-scale biological data. An example use case can be found at the demo website: http://geometacuration.yubiolab.org. Database URL: https://bitbucket.com/yubiolab/GEOMetaCuration PMID:29688376

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

Displaying R spatial statistics on Google dynamic maps with web applications created by Rwui

PubMed Central

2012-01-01

Background The R project includes a large variety of packages designed for spatial statistics. Google dynamic maps provide web based access to global maps and satellite imagery. We describe a method for displaying directly the spatial output from an R script on to a Google dynamic map. Methods This is achieved by creating a Java based web application which runs the R script and then displays the results on the dynamic map. In order to make this method easy to implement by those unfamiliar with programming Java based web applications, we have added the method to the options available in the R Web User Interface (Rwui) application. Rwui is an established web application for creating web applications for running R scripts. A feature of Rwui is that all the code for the web application being created is generated automatically so that someone with no knowledge of web programming can make a fully functional web application for running an R script in a matter of minutes. Results Rwui can now be used to create web applications that will display the results from an R script on a Google dynamic map. Results may be displayed as discrete markers and/or as continuous overlays. In addition, users of the web application may select regions of interest on the dynamic map with mouse clicks and the coordinates of the region of interest will automatically be made available for use by the R script. Conclusions This method of displaying R output on dynamic maps is designed to be of use in a number of areas. Firstly it allows statisticians, working in R and developing methods in spatial statistics, to easily visualise the results of applying their methods to real world data. Secondly, it allows researchers who are using R to study health geographics data, to display their results directly onto dynamic maps. Thirdly, by creating a web application for running an R script, a statistician can enable users entirely unfamiliar with R to run R coded statistical analyses of health geographics

UTOPIA-User-Friendly Tools for Operating Informatics Applications.

PubMed

Pettifer, S R; Sinnott, J R; Attwood, T K

2004-01-01

Bioinformaticians routinely analyse vast amounts of information held both in large remote databases and in flat data files hosted on local machines. The contemporary toolkit available for this purpose consists of an ad hoc collection of data manipulation tools, scripting languages and visualization systems; these must often be combined in complex and bespoke ways, the result frequently being an unwieldy artefact capable of one specific task, which cannot easily be exploited or extended by other practitioners. Owing to the sizes of current databases and the scale of the analyses necessary, routine bioinformatics tasks are often automated, but many still require the unique experience and intuition of human researchers: this requires tools that support real-time interaction with complex datasets. Many existing tools have poor user interfaces and limited real-time performance when applied to realistically large datasets; much of the user's cognitive capacity is therefore focused on controlling the tool rather than on performing the research. The UTOPIA project is addressing some of these issues by building reusable software components that can be combined to make useful applications in the field of bioinformatics. Expertise in the fields of human computer interaction, high-performance rendering, and distributed systems is being guided by bioinformaticians and end-user biologists to create a toolkit that is both architecturally sound from a computing point of view, and directly addresses end-user and application-developer requirements.

StreamStats in North Carolina: a water-resources Web application

USGS Publications Warehouse

Weaver, J. Curtis; Terziotti, Silvia; Kolb, Katharine R.; Wagner, Chad R.

2012-01-01

A statewide StreamStats application for North Carolina was developed in cooperation with the North Carolina Department of Transportation following completion of a pilot application for the upper French Broad River basin in western North Carolina (Wagner and others, 2009). StreamStats for North Carolina, available at http://water.usgs.gov/osw/streamstats/north_carolina.html, is a Web-based Geographic Information System (GIS) application developed by the U.S. Geological Survey (USGS) in consultation with Environmental Systems Research Institute, Inc. (Esri) to provide access to an assortment of analytical tools that are useful for water-resources planning and management (Ries and others, 2008). The StreamStats application provides an accurate and consistent process that allows users to easily obtain streamflow statistics, basin characteristics, and descriptive information for USGS data-collection sites and user-selected ungaged sites. In the North Carolina application, users can compute 47 basin characteristics and peak-flow frequency statistics (Weaver and others, 2009; Robbins and Pope, 1996) for a delineated drainage basin. Selected streamflow statistics and basin characteristics for data-collection sites have been compiled from published reports and also are immediately accessible by querying individual sites from the web interface. Examples of basin characteristics that can be computed in StreamStats include drainage area, stream slope, mean annual precipitation, and percentage of forested area (Ries and others, 2008). Examples of streamflow statistics that were previously available only through published documents include peak-flow frequency, flow-duration, and precipitation data. These data are valuable for making decisions related to bridge design, floodplain delineation, water-supply permitting, and sustainable stream quality and ecology. The StreamStats application also allows users to identify stream reaches upstream and downstream from user-selected sites

Personalization of Rule-based Web Services.

PubMed

Choi, Okkyung; Han, Sang Yong

2008-04-04

Nowadays Web users have clearly expressed their wishes to receive personalized services directly. Personalization is the way to tailor services directly to the immediate requirements of the user. However, the current Web Services System does not provide any features supporting this such as consideration of personalization of services and intelligent matchmaking. In this research a flexible, personalized Rule-based Web Services System to address these problems and to enable efficient search, discovery and construction across general Web documents and Semantic Web documents in a Web Services System is proposed. This system utilizes matchmaking among service requesters', service providers' and users' preferences using a Rule-based Search Method, and subsequently ranks search results. A prototype of efficient Web Services search and construction for the suggested system is developed based on the current work.

A user-friendly, low-cost turbidostat with versatile growth rate estimation based on an extended Kalman filter.

PubMed

Hoffmann, Stefan A; Wohltat, Christian; Müller, Kristian M; Arndt, Katja M

2017-01-01

For various experimental applications, microbial cultures at defined, constant densities are highly advantageous over simple batch cultures. Due to high costs, however, devices for continuous culture at freely defined densities still experience limited use. We have developed a small-scale turbidostat for research purposes, which is manufactured from inexpensive components and 3D printed parts. A high degree of spatial system integration and a graphical user interface provide user-friendly operability. The used optical density feedback control allows for constant continuous culture at a wide range of densities and offers to vary culture volume and dilution rates without additional parametrization. Further, a recursive algorithm for on-line growth rate estimation has been implemented. The employed Kalman filtering approach based on a very general state model retains the flexibility of the used control type and can be easily adapted to other bioreactor designs. Within several minutes it can converge to robust, accurate growth rate estimates. This is particularly useful for directed evolution experiments or studies on metabolic challenges, as it allows direct monitoring of the population fitness.

Open-Source web-based geographical information system for health exposure assessment

PubMed Central

2012-01-01

This paper presents the design and development of an open source web-based Geographical Information System allowing users to visualise, customise and interact with spatial data within their web browser. The developed application shows that by using solely Open Source software it was possible to develop a customisable web based GIS application that provides functions necessary to convey health and environmental data to experts and non-experts alike without the requirement of proprietary software. PMID:22233606

Siberian Earth System Science Cluster - A web-based Geoportal to provide user-friendly Earth Observation Products for supporting NEESPI scientists

NASA Astrophysics Data System (ADS)

Eberle, J.; Gerlach, R.; Hese, S.; Schmullius, C.

2012-04-01

To provide earth observation products in the area of Siberia, the Siberian Earth System Science Cluster (SIB-ESS-C) was established as a spatial data infrastructure at the University of Jena (Germany), Department for Earth Observation. This spatial data infrastructure implements standards published by the Open Geospatial Consortium (OGC) and the International Organizsation for Standardization (ISO) for data discovery, data access, data processing and data analysis. The objective of SIB-ESS-C is to faciliate environmental research and Earth system science in Siberia. The region for this project covers the entire Asian part of the Russian Federation approximately between 58°E - 170°W and 48°N - 80°N. To provide discovery, access and analysis services a webportal was published for searching and visualisation of available data. This webportal is based on current web technologies like AJAX, Drupal Content Management System as backend software and a user-friendly surface with Drag-n-Drop and further mouse events. To have a wide range of regular updated earth observation products, some products from sensor MODIS at the satellites Aqua and Terra were processed. A direct connection to NASA archive servers makes it possible to download MODIS Level 3 and 4 products and integrate it in the SIB-ESS-C infrastructure. These data can be downloaded in a file format called Hierarchical Data Format (HDF). For visualisation and further analysis, this data is reprojected, converted to GeoTIFF and global products clipped to the project area. All these steps are implemented as an automatic process chain. If new MODIS data is available within the infrastructure this process chain is executed. With the link to a MODIS catalogue system, the system gets new data daily. With the implemented analysis processes, timeseries data can be analysed, for example to plot a trend or different time series against one another. Scientists working in this area and working with MODIS data can make use

De-MA: a web Database for electron Microprobe Analyses to assist EMP lab manager and users

NASA Astrophysics Data System (ADS)

Allaz, J. M.

2012-12-01

Lab managers and users of electron microprobe (EMP) facilities require comprehensive, yet flexible documentation structures, as well as an efficient scheduling mechanism. A single on-line database system for managing reservations, and providing information on standards, quantitative and qualitative setups (element mapping, etc.), and X-ray data has been developed for this purpose. This system is particularly useful in multi-user facilities where experience ranges from beginners to the highly experienced. New users and occasional facility users will find these tools extremely useful in developing and maintaining high quality, reproducible, and efficient analyses. This user-friendly database is available through the web, and uses MySQL as a database and PHP/HTML as script language (dynamic website). The database includes several tables for standards information, X-ray lines, X-ray element mapping, PHA, element setups, and agenda. It is configurable for up to five different EMPs in a single lab, each of them having up to five spectrometers and as many diffraction crystals as required. The installation should be done on a web server supporting PHP/MySQL, although installation on a personal computer is possible using third-party freeware to create a local Apache server, and to enable PHP/MySQL. Since it is web-based, any user outside the EMP lab can access this database anytime through any web browser and on any operating system. The access can be secured using a general password protection (e.g. htaccess). The web interface consists of 6 main menus. (1) "Standards" lists standards defined in the database, and displays detailed information on each (e.g. material type, name, reference, comments, and analyses). Images such as EDS spectra or BSE can be associated with a standard. (2) "Analyses" lists typical setups to use for quantitative analyses, allows calculation of mineral composition based on a mineral formula, or calculation of mineral formula based on a fixed

SynergyFinder: a web application for analyzing drug combination dose-response matrix data.

PubMed

Ianevski, Aleksandr; He, Liye; Aittokallio, Tero; Tang, Jing

2017-08-01

Rational design of drug combinations has become a promising strategy to tackle the drug sensitivity and resistance problem in cancer treatment. To systematically evaluate the pre-clinical significance of pairwise drug combinations, functional screening assays that probe combination effects in a dose-response matrix assay are commonly used. To facilitate the analysis of such drug combination experiments, we implemented a web application that uses key functions of R-package SynergyFinder, and provides not only the flexibility of using multiple synergy scoring models, but also a user-friendly interface for visualizing the drug combination landscapes in an interactive manner. The SynergyFinder web application is freely accessible at https://synergyfinder.fimm.fi ; The R-package and its source-code are freely available at http://bioconductor.org/packages/release/bioc/html/synergyfinder.html . jing.tang@helsinki.fi. © The Author(s) 2017. Published by Oxford University Press.

Mendel,MD: A user-friendly open-source web tool for analyzing WES and WGS in the diagnosis of patients with Mendelian disorders

PubMed Central

D. Linhares, Natália; Pena, Sérgio D. J.

2017-01-01

Whole exome and whole genome sequencing have both become widely adopted methods for investigating and diagnosing human Mendelian disorders. As pangenomic agnostic tests, they are capable of more accurate and agile diagnosis compared to traditional sequencing methods. This article describes new software called Mendel,MD, which combines multiple types of filter options and makes use of regularly updated databases to facilitate exome and genome annotation, the filtering process and the selection of candidate genes and variants for experimental validation and possible diagnosis. This tool offers a user-friendly interface, and leads clinicians through simple steps by limiting the number of candidates to achieve a final diagnosis of a medical genetics case. A useful innovation is the “1-click” method, which enables listing all the relevant variants in genes present at OMIM for perusal by clinicians. Mendel,MD was experimentally validated using clinical cases from the literature and was tested by students at the Universidade Federal de Minas Gerais, at GENE–Núcleo de Genética Médica in Brazil and at the Children’s University Hospital in Dublin, Ireland. We show in this article how it can simplify and increase the speed of identifying the culprit mutation in each of the clinical cases that were received for further investigation. Mendel,MD proved to be a reliable web-based tool, being open-source and time efficient for identifying the culprit mutation in different clinical cases of patients with Mendelian Disorders. It is also freely accessible for academic users on the following URL: https://mendelmd.org. PMID:28594829

The value of Web-based library services at Cedars-Sinai Health System.

PubMed

Halub, L P

1999-07-01

Cedars-Sinai Medical Library/Information Center has maintained Web-based services since 1995 on the Cedars-Sinai Health System network. In that time, the librarians have found the provision of Web-based services to be a very worthwhile endeavor. Library users value the services that they access from their desktops because the services save time. They also appreciate being able to access services at their convenience, without restriction by the library's hours of operation. The library values its Web site because it brings increased visibility within the health system, and it enables library staff to expand services when budget restrictions have forced reduced hours of operation. In creating and maintaining the information center Web site, the librarians have learned the following lessons: consider the design carefully; offer what services you can, but weigh the advantages of providing the services against the time required to maintain them; make the content as accessible as possible; promote your Web site; and make friends in other departments, especially information services.

FluDetWeb: an interactive web-based system for the early detection of the onset of influenza epidemics.

PubMed

Conesa, David; López-Quílez, Antonio; Martínez-Beneito, Miguel Angel; Miralles, María Teresa; Verdejo, Francisco

2009-07-29

The early identification of influenza outbreaks has became a priority in public health practice. A large variety of statistical algorithms for the automated monitoring of influenza surveillance have been proposed, but most of them require not only a lot of computational effort but also operation of sometimes not-so-friendly software. In this paper, we introduce FluDetWeb, an implementation of a prospective influenza surveillance methodology based on a client-server architecture with a thin (web-based) client application design. Users can introduce and edit their own data consisting of a series of weekly influenza incidence rates. The system returns the probability of being in an epidemic phase (via e-mail if desired). When the probability is greater than 0.5, it also returns the probability of an increase in the incidence rate during the following week. The system also provides two complementary graphs. This system has been implemented using statistical free-software (R and WinBUGS), a web server environment for Java code (Tomcat) and a software module created by us (Rdp) responsible for managing internal tasks; the software package MySQL has been used to construct the database management system. The implementation is available on-line from: http://www.geeitema.org/meviepi/fludetweb/. The ease of use of FluDetWeb and its on-line availability can make it a valuable tool for public health practitioners who want to obtain information about the probability that their system is in an epidemic phase. Moreover, the architecture described can also be useful for developers of systems based on computationally intensive methods.

A user-friendly, open-source tool to project impact and cost of diagnostic tests for tuberculosis

PubMed Central

Dowdy, David W; Andrews, Jason R; Dodd, Peter J; Gilman, Robert H

2014-01-01

Most models of infectious diseases, including tuberculosis (TB), do not provide results customized to local conditions. We created a dynamic transmission model to project TB incidence, TB mortality, multidrug-resistant (MDR) TB prevalence, and incremental costs over 5 years after scale-up of nine alternative diagnostic strategies. A corresponding web-based interface allows users to specify local costs and epidemiology. In settings with little capacity for up-front investment, same-day microscopy had the greatest impact on TB incidence and became cost-saving within 5 years if delivered at $10/test. With greater initial investment, population-level scale-up of Xpert MTB/RIF or microcolony-based culture often averted 10 times more TB cases than narrowly-targeted strategies, at minimal incremental long-term cost. Xpert for smear-positive TB had reasonable impact on MDR-TB incidence, but at substantial price and little impact on overall TB incidence and mortality. This user-friendly modeling framework improves decision-makers' ability to evaluate the local impact of TB diagnostic strategies. DOI: http://dx.doi.org/10.7554/eLife.02565.001 PMID:24898755

Reliability and Validity of Assessing User Satisfaction With Web-Based Health Interventions

PubMed Central

Lehr, Dirk; Reis, Dorota; Vis, Christiaan; Riper, Heleen; Berking, Matthias; Ebert, David Daniel

2016-01-01

Background The perspective of users should be taken into account in the evaluation of Web-based health interventions. Assessing the users’ satisfaction with the intervention they receive could enhance the evidence for the intervention effects. Thus, there is a need for valid and reliable measures to assess satisfaction with Web-based health interventions. Objective The objective of this study was to analyze the reliability, factorial structure, and construct validity of the Client Satisfaction Questionnaire adapted to Internet-based interventions (CSQ-I). Methods The psychometric quality of the CSQ-I was analyzed in user samples from 2 separate randomized controlled trials evaluating Web-based health interventions, one from a depression prevention intervention (sample 1, N=174) and the other from a stress management intervention (sample 2, N=111). At first, the underlying measurement model of the CSQ-I was analyzed to determine the internal consistency. The factorial structure of the scale and the measurement invariance across groups were tested by multigroup confirmatory factor analyses. Additionally, the construct validity of the scale was examined by comparing satisfaction scores with the primary clinical outcome. Results Multigroup confirmatory analyses on the scale yielded a one-factorial structure with a good fit (root-mean-square error of approximation =.09, comparative fit index =.96, standardized root-mean-square residual =.05) that showed partial strong invariance across the 2 samples. The scale showed very good reliability, indicated by McDonald omegas of .95 in sample 1 and .93 in sample 2. Significant correlations with change in depressive symptoms (r=−.35, P<.001) and perceived stress (r=−.48, P<.001) demonstrated the construct validity of the scale. Conclusions The proven internal consistency, factorial structure, and construct validity of the CSQ-I indicate a good overall psychometric quality of the measure to assess the user’s general

A web-based platform to support an evidence-based mental health intervention: lessons from the CBITS web site.

PubMed

Vona, Pamela; Wilmoth, Pete; Jaycox, Lisa H; McMillen, Janey S; Kataoka, Sheryl H; Wong, Marleen; DeRosier, Melissa E; Langley, Audra K; Kaufman, Joshua; Tang, Lingqi; Stein, Bradley D

2014-11-01

To explore the role of Web-based platforms in behavioral health, the study examined usage of a Web site for supporting training and implementation of an evidence-based intervention. Using data from an online registration survey and Google Analytics, the investigators examined user characteristics and Web site utilization. Site engagement was substantial across user groups. Visit duration differed by registrants' characteristics. Less experienced clinicians spent more time on the Web site. The training section accounted for most page views across user groups. Individuals previously trained in the Cognitive-Behavioral Intervention for Trauma in Schools intervention viewed more implementation assistance and online community pages than did other user groups. Web-based platforms have the potential to support training and implementation of evidence-based interventions for clinicians of varying levels of experience and may facilitate more rapid dissemination. Web-based platforms may be promising for trauma-related interventions, because training and implementation support should be readily available after a traumatic event.

Web Services Provide Access to SCEC Scientific Research Application Software

NASA Astrophysics Data System (ADS)

Gupta, N.; Gupta, V.; Okaya, D.; Kamb, L.; Maechling, P.

2003-12-01

Web services offer scientific communities a new paradigm for sharing research codes and communicating results. While there are formal technical definitions of what constitutes a web service, for a user community such as the Southern California Earthquake Center (SCEC), we may conceptually consider a web service to be functionality provided on-demand by an application which is run on a remote computer located elsewhere on the Internet. The value of a web service is that it can (1) run a scientific code without the user needing to install and learn the intricacies of running the code; (2) provide the technical framework which allows a user's computer to talk to the remote computer which performs the service; (3) provide the computational resources to run the code; and (4) bundle several analysis steps and provide the end results in digital or (post-processed) graphical form. Within an NSF-sponsored ITR project coordinated by SCEC, we are constructing web services using architectural protocols and programming languages (e.g., Java). However, because the SCEC community has a rich pool of scientific research software (written in traditional languages such as C and FORTRAN), we also emphasize making existing scientific codes available by constructing web service frameworks which wrap around and directly run these codes. In doing so we attempt to broaden community usage of these codes. Web service wrapping of a scientific code can be done using a "web servlet" construction or by using a SOAP/WSDL-based framework. This latter approach is widely adopted in IT circles although it is subject to rapid evolution. Our wrapping framework attempts to "honor" the original codes with as little modification as is possible. For versatility we identify three methods of user access: (A) a web-based GUI (written in HTML and/or Java applets); (B) a Linux/OSX/UNIX command line "initiator" utility (shell-scriptable); and (C) direct access from within any Java application (and with the

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

PubMed

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

2018-05-18

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

DecoFungi: a web application for automatic characterisation of dye decolorisation in fungal strains.

PubMed

Domínguez, César; Heras, Jónathan; Mata, Eloy; Pascual, Vico

2018-02-27

Fungi have diverse biotechnological applications in, among others, agriculture, bioenergy generation, or remediation of polluted soil and water. In this context, culture media based on color change in response to degradation of dyes are particularly relevant; but measuring dye decolorisation of fungal strains mainly relies on a visual and semiquantitative classification of color intensity changes. Such a classification is a subjective, time-consuming and difficult to reproduce process. DecoFungi is the first, at least up to the best of our knowledge, application to automatically characterise dye decolorisation level of fungal strains from images of inoculated plates. In order to deal with this task, DecoFungi employs a deep-learning model, accessible through a user-friendly web interface, with an accuracy of 96.5%. DecoFungi is an easy to use system for characterising dye decolorisation level of fungal strains from images of inoculated plates.

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.

ST Spot Detector: a web-based application for automatic spot and tissue detection for spatial Transcriptomics image datasets.

PubMed

Wong, Kim; Navarro, José Fernández; Bergenstråhle, Ludvig; Ståhl, Patrik L; Lundeberg, Joakim

2018-06-01

Spatial Transcriptomics (ST) is a method which combines high resolution tissue imaging with high troughput transcriptome sequencing data. This data must be aligned with the images for correct visualization, a process that involves several manual steps. Here we present ST Spot Detector, a web tool that automates and facilitates this alignment through a user friendly interface. jose.fernandez.navarro@scilifelab.se. Supplementary data are available at Bioinformatics online.

Web data mining

NASA Astrophysics Data System (ADS)

Wibonele, Kasanda J.; Zhang, Yanqing

2002-03-01

A web data mining system using granular computing and ASP programming is proposed. This is a web based application, which allows web users to submit survey data for many different companies. This survey is a collection of questions that will help these companies develop and improve their business and customer service with their clients by analyzing survey data. This web application allows users to submit data anywhere. All the survey data is collected into a database for further analysis. An administrator of this web application can login to the system and view all the data submitted. This web application resides on a web server, and the database resides on the MS SQL server.

Responding to User's Expectation in the Library: Innovative Web 2.0 Applications at JUIT Library: A Case Study

ERIC Educational Resources Information Center

Ram, Shri; Anbu K., John Paul; Kataria, Sanjay

2011-01-01

Purpose: This paper seeks to provide an insight into the implementation of some of the innovative Web 2.0 applications at Jaypee University of Information Technology with the aim of exploring the expectations of the users and their awareness and usage of such applications. Design/methodology/approach: The study was undertaken at the Learning…

[A web-based integrated clinical database for laryngeal cancer].

PubMed

E, Qimin; Liu, Jialin; Li, Yong; Liang, Chuanyu

2014-08-01

To establish an integrated database for laryngeal cancer, and to provide an information platform for laryngeal cancer in clinical and fundamental researches. This database also meet the needs of clinical and scientific use. Under the guidance of clinical expert, we have constructed a web-based integrated clinical database for laryngeal carcinoma on the basis of clinical data standards, Apache+PHP+MySQL technology, laryngeal cancer specialist characteristics and tumor genetic information. A Web-based integrated clinical database for laryngeal carcinoma had been developed. This database had a user-friendly interface and the data could be entered and queried conveniently. In addition, this system utilized the clinical data standards and exchanged information with existing electronic medical records system to avoid the Information Silo. Furthermore, the forms of database was integrated with laryngeal cancer specialist characteristics and tumor genetic information. The Web-based integrated clinical database for laryngeal carcinoma has comprehensive specialist information, strong expandability, high feasibility of technique and conforms to the clinical characteristics of laryngeal cancer specialties. Using the clinical data standards and structured handling clinical data, the database can be able to meet the needs of scientific research better and facilitate information exchange, and the information collected and input about the tumor sufferers are very informative. In addition, the user can utilize the Internet to realize the convenient, swift visit and manipulation on the database.

Software-supported USER cloning strategies for site-directed mutagenesis and DNA assembly.

PubMed

Genee, Hans Jasper; Bonde, Mads Tvillinggaard; Bagger, Frederik Otzen; Jespersen, Jakob Berg; Sommer, Morten O A; Wernersson, Rasmus; Olsen, Lars Rønn

2015-03-20

USER cloning is a fast and versatile method for engineering of plasmid DNA. We have developed a user friendly Web server tool that automates the design of optimal PCR primers for several distinct USER cloning-based applications. Our Web server, named AMUSER (Automated DNA Modifications with USER cloning), facilitates DNA assembly and introduction of virtually any type of site-directed mutagenesis by designing optimal PCR primers for the desired genetic changes. To demonstrate the utility, we designed primers for a simultaneous two-position site-directed mutagenesis of green fluorescent protein (GFP) to yellow fluorescent protein (YFP), which in a single step reaction resulted in a 94% cloning efficiency. AMUSER also supports degenerate nucleotide primers, single insert combinatorial assembly, and flexible parameters for PCR amplification. AMUSER is freely available online at http://www.cbs.dtu.dk/services/AMUSER/.

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

NASA Astrophysics Data System (ADS)

Sundaravel, A.; Wilkinson, D. C.

2010-12-01

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

The use of Graphic User Interface for development of a user-friendly CRS-Stack software

NASA Astrophysics Data System (ADS)

Sule, Rachmat; Prayudhatama, Dythia; Perkasa, Muhammad D.; Hendriyana, Andri; Fatkhan; Sardjito; Adriansyah

2017-04-01

The development of a user-friendly Common Reflection Surface (CRS) Stack software that has been built by implementing Graphical User Interface (GUI) is described in this paper. The original CRS-Stack software developed by WIT Consortium is compiled in the unix/linux environment, which is not a user-friendly software, so that a user must write the commands and parameters manually in a script file. Due to this limitation, the CRS-Stack become a non popular method, although applying this method is actually a promising way in order to obtain better seismic sections, which have better reflector continuity and S/N ratio. After obtaining successful results that have been tested by using several seismic data belong to oil companies in Indonesia, it comes to an idea to develop a user-friendly software in our own laboratory. Graphical User Interface (GUI) is a type of user interface that allows people to interact with computer programs in a better way. Rather than typing commands and module parameters, GUI allows the users to use computer programs in much simple and easy. Thus, GUI can transform the text-based interface into graphical icons and visual indicators. The use of complicated seismic unix shell script can be avoided. The Java Swing GUI library is used to develop this CRS-Stack GUI. Every shell script that represents each seismic process is invoked from Java environment. Besides developing interactive GUI to perform CRS-Stack processing, this CRS-Stack GUI is design to help geophysicists to manage a project with complex seismic processing procedures. The CRS-Stack GUI software is composed by input directory, operators, and output directory, which are defined as a seismic data processing workflow. The CRS-Stack processing workflow involves four steps; i.e. automatic CMP stack, initial CRS-Stack, optimized CRS-Stack, and CRS-Stack Supergather. Those operations are visualized in an informative flowchart with self explanatory system to guide the user inputting the

BIOSMILE web search: a web application for annotating biomedical entities and relations.

PubMed

Dai, Hong-Jie; Huang, Chi-Hsin; Lin, Ryan T K; Tsai, Richard Tzong-Han; Hsu, Wen-Lian

2008-07-01

BIOSMILE web search (BWS), a web-based NCBI-PubMed search application, which can analyze articles for selected biomedical verbs and give users relational information, such as subject, object, location, manner, time, etc. After receiving keyword query input, BWS retrieves matching PubMed abstracts and lists them along with snippets by order of relevancy to protein-protein interaction. Users can then select articles for further analysis, and BWS will find and mark up biomedical relations in the text. The analysis results can be viewed in the abstract text or in table form. To date, BWS has been field tested by over 30 biologists and questionnaires have shown that subjects are highly satisfied with its capabilities and usability. BWS is accessible free of charge at http://bioservices.cse.yzu.edu.tw/BWS.

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.

Prototype development of a web-based participative decision support platform in risk management

NASA Astrophysics Data System (ADS)

Aye, Zar Chi; Olyazadeh, Roya; Jaboyedoff, Michel; Derron, Marc-Henri

2014-05-01

This paper discusses the proposed background architecture and prototype development of an internet-based decision support system (DSS) in the field of natural hazards and risk management using open-source geospatial software and web technologies. It is based on a three-tier, client-server architecture with the support of boundless (opengeo) framework and its client side SDK application environment using customized gxp components and data utility classes. The main purpose of the system is to integrate the workflow of risk management systematically with the diverse involvement of stakeholders from different organizations dealing with natural hazards and risk for evaluation of management measures through the active online participation approach. It aims to develop an adaptive user friendly, web-based environment that allows the users to set up risk management strategies based on actual context and data by integrating web-GIS and DSS functionality associated with process flow and other visualization tools. Web-GIS interface has been integrated within the DSS to deliver maps and provide certain geo-processing capabilities on the web, which can be easily accessible and shared by different organizations located in case study sites of the project. This platform could be envisaged not only as a common web-based platform for the centralized sharing of data such as hazard maps, elements at risk maps and additional information but also to ensure an integrated platform of risk management where the users could upload data, analyze risk and identify possible alternative scenarios for risk reduction especially for floods and landslides, either quantitatively or qualitatively depending on the risk information provided by the stakeholders in case study regions. The level of involvement, access to and interaction with the provided functionality of the system varies depending on the roles and responsibilities of the stakeholders, for example, only the experts (planners, geological

75 FR 75170 - APHIS User Fee Web Site

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-02

...] APHIS User Fee Web Site AGENCY: Animal and Plant Health Inspection Service, USDA. ACTION: Notice... recover the costs of providing certain services. This notice announces the availability of a Web site that contains information about the Agency's user fees. ADDRESSES: The Agency's user fee Web site is located at...

Effects of User and System Characteristics on Perceived Usefulness and Perceived Ease of Use of the Web-Based Classroom Response System

ERIC Educational Resources Information Center

Ke, Chih-Horng; Sun, Huey-Min; Yang, Yuan-Chi; Sun, Huey-Min

2012-01-01

This study explores the effect of user and system characteristics on our proposed web-based classroom response system (CRS) by a longitudinal design. The results of research are expected to understand the important factors of user and system characteristics in the web-based CRS. The proposed system can supply interactive teaching contents,…

A Multi-Channel Approach for Collaborative Web-Based Learning

ERIC Educational Resources Information Center

Azeta, A. A.

2008-01-01

This paper describes an architectural framework and a prototype implementation of a web-based multi-channel e-Learning application that allows students, lecturers and the research communities to collaborate irrespective of the communication device a user is carrying. The application was developed based on the concept of "right once run on any…

A user-friendly LabVIEW software platform for grating based X-ray phase-contrast imaging.

PubMed

Wang, Shenghao; Han, Huajie; Gao, Kun; Wang, Zhili; Zhang, Can; Yang, Meng; Wu, Zhao; Wu, Ziyu

2015-01-01

X-ray phase-contrast imaging can provide greatly improved contrast over conventional absorption-based imaging for weakly absorbing samples, such as biological soft tissues and fibre composites. In this study, we introduced an easy and fast way to develop a user-friendly software platform dedicated to the new grating-based X-ray phase-contrast imaging setup at the National Synchrotron Radiation Laboratory of the University of Science and Technology of China. The control of 21 motorized stages, of a piezoelectric stage and of an X-ray tube are achieved with this software, it also covers image acquisition with a flat panel detector for automatic phase stepping scan. Moreover, a data post-processing module for signals retrieval and other custom features are in principle available. With a seamless integration of all the necessary functions in one software package, this platform greatly facilitate users' activities during experimental runs with this grating based X-ray phase contrast imaging setup.

GOssTo: a stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology.

PubMed

Caniza, Horacio; Romero, Alfonso E; Heron, Samuel; Yang, Haixuan; Devoto, Alessandra; Frasca, Marco; Mesiti, Marco; Valentini, Giorgio; Paccanaro, Alberto

2014-08-01

We present GOssTo, the Gene Ontology semantic similarity Tool, a user-friendly software system for calculating semantic similarities between gene products according to the Gene Ontology. GOssTo is bundled with six semantic similarity measures, including both term- and graph-based measures, and has extension capabilities to allow the user to add new similarities. Importantly, for any measure, GOssTo can also calculate the Random Walk Contribution that has been shown to greatly improve the accuracy of similarity measures. GOssTo is very fast, easy to use, and it allows the calculation of similarities on a genomic scale in a few minutes on a regular desktop machine. alberto@cs.rhul.ac.uk GOssTo is available both as a stand-alone application running on GNU/Linux, Windows and MacOS from www.paccanarolab.org/gossto and as a web application from www.paccanarolab.org/gosstoweb. The stand-alone application features a simple and concise command line interface for easy integration into high-throughput data processing pipelines. © The Author 2014. Published by Oxford University Press.

A web-based clinical trial management system for a sham-controlled multicenter clinical trial in depression.

PubMed

Durkalski, Valerie; Wenle Zhao; Dillon, Catherine; Kim, Jaemyung

2010-04-01

Clinical trial investigators and sponsors invest vast amounts of resources and energy into conducting trials and often face daily challenges with data management, project management, and data quality control. Rather than waiting months for study progress reports, investigators need the ability to use real-time data for the coordination and management of study activities across all study team members including site investigators, oversight committees, data and safety monitoring boards, and medical safety monitors. Web-based data management systems are beginning to meet this need but what distinguishes one system from the other are user needs/requirements and cost. To illustrate the development and implementation of a web-based data and project management system for a multicenter clinical trial designed to test the superiority of repeated transcranial magnetic stimulation versus sham for the treatment of patients with major depression. The authors discuss the reasons for not using a commercially available system for this study and describe the approach to developing their own web-based system for the OPT-TMS study. Timelines, effort, system architecture, and lessons learned are shared with the hope that this information will direct clinical trial researchers and software developers towards more efficient, user-friendly systems. The developers use a combination of generic and custom application code to allow for the flexibility to adapt the system to the needs of the study. Features of the system include: central participant registration and randomization; secure data entry at the site; participant progress/study calendar; safety data reporting; device accounting; monitor verification; and user-configurable generic reports and built-in customized reports. Hard coding was more time-efficient to address project-specific issues compared with the effort of creating a generic code application. As a consequence of this strategy, the required maintenance of the system is

Open Source Web-Based Solutions for Disseminating and Analyzing Flood Hazard Information at the Community Level

NASA Astrophysics Data System (ADS)

Santillan, M. M.-M.; Santillan, J. R.; Morales, E. M. O.

2017-09-01

We discuss in this paper the development, including the features and functionalities, of an open source web-based flood hazard information dissemination and analytical system called "Flood EViDEns". Flood EViDEns is short for "Flood Event Visualization and Damage Estimations", an application that was developed by the Caraga State University to address the needs of local disaster managers in the Caraga Region in Mindanao, Philippines in accessing timely and relevant flood hazard information before, during and after the occurrence of flood disasters at the community (i.e., barangay and household) level. The web application made use of various free/open source web mapping and visualization technologies (GeoServer, GeoDjango, OpenLayers, Bootstrap), various geospatial datasets including LiDAR-derived elevation and information products, hydro-meteorological data, and flood simulation models to visualize various scenarios of flooding and its associated damages to infrastructures. The Flood EViDEns application facilitates the release and utilization of this flood-related information through a user-friendly front end interface consisting of web map and tables. A public version of the application can be accessed at http://121.97.192.11:8082/. The application is currently expanded to cover additional sites in Mindanao, Philippines through the "Geo-informatics for the Systematic Assessment of Flood Effects and Risks for a Resilient Mindanao" or the "Geo-SAFER Mindanao" Program.

Quora.com: Another Place for Users to Ask Questions

ERIC Educational Resources Information Center

Ovadia, Steven

2011-01-01

Quora (www.quora.com) is a contemporary, web-based take on reference. Users post questions within Quora and other users answer the questions. Users can vote for and against answers (or not vote at all). It is users asking questions of friends and strangers and then sorting through the results. If the model sounds familiar, it's because it is.…

Internet-based peer support for Ménière's disease: a summary of web-based data collection, impact evaluation, and user evaluation.

PubMed

Pyykkő, Ilmari; Manchaiah, Vinaya; Levo, Hilla; Kentala, Erna; Juhola, Martti

2017-07-01

This paper presents a summary of web-based data collection, impact evaluation, and user evaluations of an Internet-based peer support program for Ménière's disease (MD). The program is written in html-form. The data are stored in a MySQL database and uses machine learning in the diagnosis of MD. The program works interactively with the user and assesses the participant's disorder profile in various dimensions (i.e., symptoms, impact, personal traits, and positive attitude). The inference engine uses a database to compare the impact with 50 referents, and provides regular feedback to the user. Data were analysed using descriptive statistics and regression analysis. The impact evaluation was based on 740 cases and the user evaluation on a sample of 75 cases of MD respectively. The web-based system was useful in data collection and impact evaluation of people with MD. Among those with a recent onset of MD, 78% rated the program as useful or very useful, whereas those with chronic MD rated the program 55%. We suggest that a web-based data collection and impact evaluation for peer support can be helpful while formulating the rehabilitation goals of building the self-confidence needed for coping and increasing social participation.

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

NASA Astrophysics Data System (ADS)

Hošek, Petr; Spiwok, Vojtěch

2016-01-01

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

The new ALICE DQM client: a web access to ROOT-based objects

NASA Astrophysics Data System (ADS)

von Haller, B.; Carena, F.; Carena, W.; Chapeland, S.; Chibante Barroso, V.; Costa, F.; Delort, C.; Dénes, E.; Diviá, R.; Fuchs, U.; Niedziela, J.; Simonetti, G.; Soós, C.; Telesca, A.; Vande Vyvre, P.; Wegrzynek, A.

2015-12-01

A Large Ion Collider Experiment (ALICE) is the heavy-ion detector designed to study the physics of strongly interacting matter and the quark-gluon plasma at the CERN Large Hadron Collider (LHC). The online Data Quality Monitoring (DQM) plays an essential role in the experiment operation by providing shifters with immediate feedback on the data being recorded in order to quickly identify and overcome problems. An immediate access to the DQM results is needed not only by shifters in the control room but also by detector experts worldwide. As a consequence, a new web application has been developed to dynamically display and manipulate the ROOT-based objects produced by the DQM system in a flexible and user friendly interface. The architecture and design of the tool, its main features and the technologies that were used, both on the server and the client side, are described. In particular, we detail how we took advantage of the most recent ROOT JavaScript I/O and web server library to give interactive access to ROOT objects stored in a database. We describe as well the use of modern web techniques and packages such as AJAX, DHTMLX and jQuery, which has been instrumental in the successful implementation of a reactive and efficient application. We finally present the resulting application and how code quality was ensured. We conclude with a roadmap for future technical and functional developments.

Pregnancy eHealth and mHealth: user proportions and characteristics of pregnant women using Web-based information sources-a cross-sectional study.

PubMed

Wallwiener, Stephanie; Müller, Mitho; Doster, Anne; Laserer, Wolfgang; Reck, Corinna; Pauluschke-Fröhlich, Jan; Brucker, Sara Y; Wallwiener, Christian W; Wallwiener, Markus

2016-11-01

To analyze the current proportions and characteristics of women using Internet (eHealth) and smartphone (mHealth) based sources of information during pregnancy and to investigate the influence, this information-seeking behavior has on decision-making. A cross-sectional study was conducted at two major German university hospitals. Questionnaires covering socio-demographic data, medical data and details of Internet, and smartphone application use were administered to 220 pregnant women. Data analysis utilized descriptive statistics and multiple regression analysis. 50.7 % of pregnant women were online information seekers. 22.4 % used an mHealth pregnancy application. Women using eHealth information showed no specific profile, while women using mHealth applications proved to be younger, were more likely to be in their first pregnancy, felt less healthy, and were more likely to be influenced by the retrieved information. Stepwise backward regression analysis explained 25.8 % of the variance of mHealth use. 80.5 % of cases were classified correctly by the identified predictors. All types of Web-based information correlated significantly with decision-making during pregnancy. Pregnant women frequently use the Internet and smartphone applications as a source of information. While Web usage was a common phenomenon, this study revealed specific characteristics of mHealth users during pregnancy. Improved, medically accurate smartphone applications might provide a way to specifically target the mHealth user group. As user influenceability was of major relevance to all types of information, all medical content should be carefully reviewed by a multidisciplinary board of medical specialists.

Demographic-Based Content Analysis of Web-Based Health-Related Social Media.

PubMed

Sadah, Shouq A; Shahbazi, Moloud; Wiley, Matthew T; Hristidis, Vagelis

2016-06-13

An increasing number of patients from diverse demographic groups share and search for health-related information on Web-based social media. However, little is known about the content of the posted information with respect to the users' demographics. The aims of this study were to analyze the content of Web-based health-related social media based on users' demographics to identify which health topics are discussed in which social media by which demographic groups and to help guide educational and research activities. We analyze 3 different types of health-related social media: (1) general Web-based social networks Twitter and Google+; (2) drug review websites; and (3) health Web forums, with a total of about 6 million users and 20 million posts. We analyzed the content of these posts based on the demographic group of their authors, in terms of sentiment and emotion, top distinctive terms, and top medical concepts. The results of this study are: (1) Pregnancy is the dominant topic for female users in drug review websites and health Web forums, whereas for male users, it is cardiac problems, HIV, and back pain, but this is not the case for Twitter; (2) younger users (0-17 years) mainly talk about attention-deficit hyperactivity disorder (ADHD) and depression-related drugs, users aged 35-44 years discuss about multiple sclerosis (MS) drugs, and middle-aged users (45-64 years) talk about alcohol and smoking; (3) users from the Northeast United States talk about physical disorders, whereas users from the West United States talk about mental disorders and addictive behaviors; (4) Users with higher writing level express less anger in their posts. We studied the popular topics and the sentiment based on users' demographics in Web-based health-related social media. Our results provide valuable information, which can help create targeted and effective educational campaigns and guide experts to reach the right users on Web-based social chatter.

Development and preliminary testing of a web-based, self-help application for disaster-affected families

PubMed Central

Yuen, Erica K; Gros, Kirstin; Welsh, Kyleen E; McCauley, Jenna; Resnick, Heidi S; Danielson, Carla K; Price, Matthew; Ruggiero, Kenneth J

2015-01-01

Technology-based self-help interventions have the potential to increase access to evidence-based mental healthcare, especially for families affected by natural disasters. However, development of these interventions is a complex process and poses unique challenges. Usability testing, which assesses the ability of individuals to use an application successfully, can have a significant impact on the quality of a self-help intervention. This article describes (a) the development of a novel web-based multi-module self-help intervention for disaster-affected adolescents and their parents and (b) a mixed-methods formal usability study to evaluate user response. A total of 24 adolescents were observed, videotaped, and interviewed as they used the depressed mood component of the self-help intervention. Quantitative results indicated an above-average user experience, and qualitative analysis identified 120 unique usability issues. We discuss the challenges of developing self-help applications, including design considerations and the value of usability testing in technology-based interventions, as well as our plan for widespread dissemination. PMID:25933798

User-friendly cognitive training for the elderly: a technical report.

PubMed

Boquete, Luciano; Rodríguez-Ascariz, José Manuel; Amo-Usanos, Carlos; Martínez-Arribas, Alejandro; Amo-Usanos, Javier; Otón, Salvador

2011-01-01

This article presents a system that implements a cognitive training program in users' homes. The system comprises various applications designed to create a daily brain-fitness regime. The proposed mental training system uses television and a remote control specially designed for the elderly. This system integrates Java applications to promote brain-fitness training in three areas: arithmetic, memory, and idea association. The system comprises the following: Standard television set, simplified wireless remote control, black box (system's core hardware and software), brain-fitness games (language Java), and Wi-Fi-enabled Internet-connected router. All data from the user training sessions are monitored through a control center. This control center analyzes the evolution of the user and the proper performance of the system during the test. The implemented system has been tested by six healthy volunteers. The results for this user group demonstrated the accessibility and usability of the system in a controlled real environment. The impressions of the users were very favorable, and they reported high adaptability to the system. The mean score for usability and accessibility assigned by the users was 3.56 out of 5 points. The operation stress test (over 200 h) was successful. The proposed system was used to implement a cognitive training program in users' homes, which was developed to be a low-cost tool with a high degree of user interactivity. The results of this preliminary study indicate that this user-friendly system could be adopted as a form of cognitive training for the elderly.

Web 2.0 Applications in China

NASA Astrophysics Data System (ADS)

Zhai, Dongsheng; Liu, Chen

Since 2005, the term Web 2.0 has gradually become a hot topic on the Internet. Web 2.0 lets users create web contents as distinct from webmasters or web coders. Web 2.0 has come to our work, our life and even has become an indispensable part of our web-life. Its applications have already been widespread in many fields on the Internet. So far, China has about 137 million netizens [1], therefore its Web 2.0 market is so attractive that many sources of venture capital flow into the Chinese Web 2.0 market and there are also a lot of new Web 2.0 companies in China. However, the development of Web 2.0 in China is accompanied by some problems and obstacles. In this paper, we will mainly discuss Web 2.0 applications in China, with their current problems and future development trends.

Ontology-Based Administration of Web Directories

NASA Astrophysics Data System (ADS)

Horvat, Marko; Gledec, Gordan; Bogunović, Nikola

Administration of a Web directory and maintenance of its content and the associated structure is a delicate and labor intensive task performed exclusively by human domain experts. Subsequently there is an imminent risk of a directory structures becoming unbalanced, uneven and difficult to use to all except for a few users proficient with the particular Web directory and its domain. These problems emphasize the need to establish two important issues: i) generic and objective measures of Web directories structure quality, and ii) mechanism for fully automated development of a Web directory's structure. In this paper we demonstrate how to formally and fully integrate Web directories with the Semantic Web vision. We propose a set of criteria for evaluation of a Web directory's structure quality. Some criterion functions are based on heuristics while others require the application of ontologies. We also suggest an ontology-based algorithm for construction of Web directories. By using ontologies to describe the semantics of Web resources and Web directories' categories it is possible to define algorithms that can build or rearrange the structure of a Web directory. Assessment procedures can provide feedback and help steer the ontology-based construction process. The issues raised in the article can be equally applied to new and existing Web directories.

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.

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

DTIC Science & Technology

2016-05-01

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

FluDetWeb: an interactive web-based system for the early detection of the onset of influenza epidemics

PubMed Central

2009-01-01

Background The early identification of influenza outbreaks has became a priority in public health practice. A large variety of statistical algorithms for the automated monitoring of influenza surveillance have been proposed, but most of them require not only a lot of computational effort but also operation of sometimes not-so-friendly software. Results In this paper, we introduce FluDetWeb, an implementation of a prospective influenza surveillance methodology based on a client-server architecture with a thin (web-based) client application design. Users can introduce and edit their own data consisting of a series of weekly influenza incidence rates. The system returns the probability of being in an epidemic phase (via e-mail if desired). When the probability is greater than 0.5, it also returns the probability of an increase in the incidence rate during the following week. The system also provides two complementary graphs. This system has been implemented using statistical free-software (ℝ and WinBUGS), a web server environment for Java code (Tomcat) and a software module created by us (Rdp) responsible for managing internal tasks; the software package MySQL has been used to construct the database management system. The implementation is available on-line from: http://www.geeitema.org/meviepi/fludetweb/. Conclusion The ease of use of FluDetWeb and its on-line availability can make it a valuable tool for public health practitioners who want to obtain information about the probability that their system is in an epidemic phase. Moreover, the architecture described can also be useful for developers of systems based on computationally intensive methods. PMID:19640304

Is Accessibility an Issue in the Knowledge Society? Modern Web Applications in the Light of Accessibility

NASA Astrophysics Data System (ADS)

Bártek, Luděk; Ošlejšek, Radek; Pitner, Tomáš

Recent development in Web shows a significant trend towards more user participation, massive use of new devices including portables, and high interactivity. The user participation goes hand in hand with inclusion of all potential user groups - also with special needs. However, we claim that albeit all the effort towards accessibility, it has not yet found an appopriate reflection among stakeholders of the "Top Web Applications" nor their users. This leads to undesired causes - the business-driven Web without all user participation is not a really democratic medium and, actually, does not comply with the original characteristics of Web 2.0. The paper tries to identify perspectives of further development including standardization processes and technical obstacles behind. It also shows ways and techniques to cope with the challenge based on our own research and development in accessible graphics and dialog-based systems.

User Driven Image Stacking for ODI Data and Beyond via a Highly Customizable Web Interface

NASA Astrophysics Data System (ADS)

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

2015-09-01

While some astronomical archives have begun serving standard calibrated data products, the process of producing stacked images remains a challenge left to the end-user. The benefits of astronomical image stacking are well established, and dither patterns are recommended for almost all observing targets. Some archives automatically produce stacks of limited scientific usefulness without any fine-grained user or operator configurability. In this paper, we present PPA Stack, a web based stacking framework within the ODI - Portal, Pipeline, and Archive system. PPA Stack offers a web user interface with built-in heuristics (based on pointing, filter, and other metadata information) to pre-sort images into a set of likely stacks while still allowing the user or operator complete control over the images and parameters for each of the stacks they wish to produce. The user interface, designed using AngularJS, provides multiple views of the input dataset and parameters, all of which are synchronized in real time. A backend consisting of a Python application optimized for ODI data, wrapped around the SWarp software, handles the execution of stacking workflow jobs on Indiana University's Big Red II supercomputer, and the subsequent ingestion of the combined images back into the PPA archive. PPA Stack is designed to enable seamless integration of other stacking applications in the future, so users can select the most appropriate option for their science.

Using SAHRIS a web-based application for creating heritage cases and permit applications

NASA Astrophysics Data System (ADS)

Mlungwana, N.

2015-08-01

Since the inception of the South African Heritage Resources Information System (SAHRIS) in 2012, creating heritage cases and permit applications has been streamlined, and interaction with South African Heritage Authorities has been simplified. SAHRIS facilitates applications for development cases and mining applications that trigger the South African National Heritage Resources Act (Act 25 of 1999) and is able to differentiate between cases that require comment only, where the heritage process is subsidiary to environmental or mining law (Section 38(8)), and those where the heritage authority is the deciding authority (Section 38(1)). The system further facilitates cases related to site and object management, as well as permit applications for excavation, invasive research techniques and export of materials for research abroad in the case of archaeological or palaeontological specimens, or for sale or exhibition in the case of heritage objects. The integrated, easy to use, online system has removed the need for applicants to print out forms, take documents from one government department to the next for approval and other time-consuming processes that accompany paper-based systems. SAHRIS is a user friendly application that makes it easy for applicants to make their submissions, but also allows applicants to track the progress of their cases with the relevant heritage authority, which allows for better response rates and turnaround times from the authorities, while also ensuring transparency and good governance practice.

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.

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.

The value of Web-based library services at Cedars-Sinai Health System.

PubMed Central

Halub, L P

1999-01-01

Cedars-Sinai Medical Library/Information Center has maintained Web-based services since 1995 on the Cedars-Sinai Health System network. In that time, the librarians have found the provision of Web-based services to be a very worthwhile endeavor. Library users value the services that they access from their desktops because the services save time. They also appreciate being able to access services at their convenience, without restriction by the library's hours of operation. The library values its Web site because it brings increased visibility within the health system, and it enables library staff to expand services when budget restrictions have forced reduced hours of operation. In creating and maintaining the information center Web site, the librarians have learned the following lessons: consider the design carefully; offer what services you can, but weigh the advantages of providing the services against the time required to maintain them; make the content as accessible as possible; promote your Web site; and make friends in other departments, especially information services. PMID:10427423

Demographic-Based Content Analysis of Web-Based Health-Related Social Media

PubMed Central

Shahbazi, Moloud; Wiley, Matthew T; Hristidis, Vagelis

2016-01-01

Background An increasing number of patients from diverse demographic groups share and search for health-related information on Web-based social media. However, little is known about the content of the posted information with respect to the users’ demographics. Objective The aims of this study were to analyze the content of Web-based health-related social media based on users’ demographics to identify which health topics are discussed in which social media by which demographic groups and to help guide educational and research activities. Methods We analyze 3 different types of health-related social media: (1) general Web-based social networks Twitter and Google+; (2) drug review websites; and (3) health Web forums, with a total of about 6 million users and 20 million posts. We analyzed the content of these posts based on the demographic group of their authors, in terms of sentiment and emotion, top distinctive terms, and top medical concepts. Results The results of this study are: (1) Pregnancy is the dominant topic for female users in drug review websites and health Web forums, whereas for male users, it is cardiac problems, HIV, and back pain, but this is not the case for Twitter; (2) younger users (0-17 years) mainly talk about attention-deficit hyperactivity disorder (ADHD) and depression-related drugs, users aged 35-44 years discuss about multiple sclerosis (MS) drugs, and middle-aged users (45-64 years) talk about alcohol and smoking; (3) users from the Northeast United States talk about physical disorders, whereas users from the West United States talk about mental disorders and addictive behaviors; (4) Users with higher writing level express less anger in their posts. Conclusion We studied the popular topics and the sentiment based on users' demographics in Web-based health-related social media. Our results provide valuable information, which can help create targeted and effective educational campaigns and guide experts to reach the right users on Web-based

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

PubMed

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

2016-11-01

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

Utilization of a Web-Based vs Integrated Phone/Web Cessation Program Among 140,000 Tobacco Users: An Evaluation Across 10 Free State Quitlines

PubMed Central

Vickerman, Katrina A; Kellogg, Elizabeth S; Zbikowski, Susan M

2015-01-01

Background Phone-based tobacco cessation program effectiveness has been established and randomized controlled trials have provided some support for Web-based services. Relatively little is known about who selects different treatment modalities and how they engage with treatments in a real-world setting. Objective This paper describes the characteristics, Web utilization patterns, and return rates of tobacco users who self-selected into a Web-based (Web-Only) versus integrated phone/Web (Phone/Web) cessation program. Methods We examined the demographics, baseline tobacco use, Web utilization patterns, and return rates of 141,429 adult tobacco users who self-selected into a Web-Only or integrated Phone/Web cessation program through 1 of 10 state quitlines from August 2012 through July 2013. For each state, registrants were only included from the timeframe in which both programs were offered to all enrollees. Utilization data were limited to site interactions occurring within 6 months after registration. Results Most participants selected the Phone/Web program (113,019/141,429, 79.91%). After enrollment in Web services, Web-Only were more likely to log in compared to Phone/Web (21,832/28,410, 76.85% vs 23,920/56,892, 42.04%; P<.001), but less likely to return after their initial log-in (8766/21,832, 40.15% vs 13,966/23,920, 58.39%; P<.001). In bivariate and multivariable analyses, those who chose Web-Only were younger, healthier, more highly educated, more likely to be uninsured or commercially insured, more likely to be white non-Hispanic and less likely to be black non-Hispanic, less likely to be highly nicotine-addicted, and more likely to have started their program enrollment online (all P<.001). Among both program populations, participants were more likely to return to Web services if they were women, older, more highly educated, or were sent nicotine replacement therapy (NRT) through their quitline (all P<.001). Phone/Web were also more likely to return if they

Utilization of a Web-based vs integrated phone/Web cessation program among 140,000 tobacco users: an evaluation across 10 free state quitlines.

PubMed

Nash, Chelsea M; Vickerman, Katrina A; Kellogg, Elizabeth S; Zbikowski, Susan M

2015-02-04

Phone-based tobacco cessation program effectiveness has been established and randomized controlled trials have provided some support for Web-based services. Relatively little is known about who selects different treatment modalities and how they engage with treatments in a real-world setting. This paper describes the characteristics, Web utilization patterns, and return rates of tobacco users who self-selected into a Web-based (Web-Only) versus integrated phone/Web (Phone/Web) cessation program. We examined the demographics, baseline tobacco use, Web utilization patterns, and return rates of 141,429 adult tobacco users who self-selected into a Web-Only or integrated Phone/Web cessation program through 1 of 10 state quitlines from August 2012 through July 2013. For each state, registrants were only included from the timeframe in which both programs were offered to all enrollees. Utilization data were limited to site interactions occurring within 6 months after registration. Most participants selected the Phone/Web program (113,019/141,429, 79.91%). After enrollment in Web services, Web-Only were more likely to log in compared to Phone/Web (21,832/28,410, 76.85% vs 23,920/56,892, 42.04%; P<.001), but less likely to return after their initial log-in (8766/21,832, 40.15% vs 13,966/23,920, 58.39%; P<.001). In bivariate and multivariable analyses, those who chose Web-Only were younger, healthier, more highly educated, more likely to be uninsured or commercially insured, more likely to be white non-Hispanic and less likely to be black non-Hispanic, less likely to be highly nicotine-addicted, and more likely to have started their program enrollment online (all P<.001). Among both program populations, participants were more likely to return to Web services if they were women, older, more highly educated, or were sent nicotine replacement therapy (NRT) through their quitline (all P<.001). Phone/Web were also more likely to return if they had completed a coaching call

StreamStats: A water resources web application

USGS Publications Warehouse

Ries, Kernell G.; Guthrie, John G.; Rea, Alan H.; Steeves, Peter A.; Stewart, David W.

2008-01-01

. Streamflow measurements are collected systematically over a period of years at partial-record stations to estimate peak-flow or low-flow statistics. Streamflow measurements usually are collected at miscellaneous-measurement stations for specific hydrologic studies with various objectives.StreamStats is a Web-based Geographic Information System (GIS) application that was created by the USGS, in cooperation with Environmental Systems Research Institute, Inc. (ESRI)1, to provide users with access to an assortment of analytical tools that are useful for water-resources planning and management. StreamStats functionality is based on ESRI’s ArcHydro Data Model and Tools, described on the Web at http://resources.arcgis.com/en/communities/hydro/01vn0000000s000000.htm. StreamStats allows users to easily obtain streamflow statistics, basin characteristics, and descriptive information for USGS data-collection stations and user-selected ungaged sites. It also allows users to identify stream reaches that are upstream and downstream from user-selected sites, and to identify and obtain information for locations along the streams where activities that may affect streamflow conditions are occurring. This functionality can be accessed through a map-based user interface that appears in the user’s Web browser, or individual functions can be requested remotely as Web services by other Web or desktop computer applications. StreamStats can perform these analyses much faster than historically used manual techniques.StreamStats was designed so that each state would be implemented as a separate application, with a reliance on local partnerships to fund the individual applications, and a goal of eventual full national implementation. Idaho became the first state to implement StreamStats in 2003. By mid-2008, 14 states had applications available to the public, and 18 other states were in various stages of implementation.

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

USGS Publications Warehouse

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

2009-01-01

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

Applicability of the "Emotiv EEG Neuroheadset" as a user-friendly input interface.

PubMed

Boutani, Hidenori; Ohsuga, Mieko

2013-01-01

We aimed to develop an input interface by using the P3 component of visual event-related potentials (ERPs). When using electroencephalography (EEG) in daily applications, coping with ocular-motor artifacts and ensuring that the equipment is user-friendly are both important. To address the first issue, we applied a previously proposed method that applies an unmixing matrix to acquire independent components (ICs) obtained from another dataset. For the second issue, we introduced a 14-channel EEG commercial headset called the "Emotiv EEG Neuroheadset". An advantage of the Emotiv headset is that users can put it on by themselves within 1 min without any specific skills. However, only a few studies have investigated whether EEG and ERP signals are accurately measured by Emotiv. Additionally, no electrodes of the Emotiv headset are located over the centroparietal area of the head where P3 components are reported to show large amplitudes. Therefore, we first demonstrated that the P3 components obtained by the headset and by commercial plate electrodes and a multipurpose bioelectric amplifier during an oddball task were comparable. Next, we confirmed that eye-blink and ocular movement components could be decomposed by independent component analysis (ICA) using the 14-channel signals measured by the headset. We also demonstrated that artifacts could be removed with an unmixing matrix, as long as the matrix was obtained from the same person, even if they were measured on different days. Finally, we confirmed that the fluctuation of the sampling frequency of the Emotiv headset was not a major problem.

Development of a Web-Based Distributed Interactive Simulation (DIS) Environment Using JavaScript

DTIC Science & Technology

2014-09-01

scripting that let users change or interact with web content depending on user input, which is in contrast with server-side scripts such as PHP, Java and...transfer, DIS usually broadcasts or multicasts its PDUs based on UDP socket. 3. JavaScript JavaScript is the scripting language of the web, and all...IDE) for developing desktop, mobile and web applications with JAVA , C++, HTML5, JavaScript and more. b. Framework The DIS implementation of

A web-based program for informal caregivers of persons with Alzheimer's disease: an iterative user-centered design.

PubMed

Cristancho-Lacroix, Victoria; Moulin, Florence; Wrobel, Jérémy; Batrancourt, Bénédicte; Plichart, Matthieu; De Rotrou, Jocelyne; Cantegreil-Kallen, Inge; Rigaud, Anne-Sophie

2014-09-15

Web-based programs have been developed for informal caregivers of people with Alzheimer's disease (PWAD). However, these programs can prove difficult to adopt, especially for older people, who are less familiar with the Internet than other populations. Despite the fundamental role of usability testing in promoting caregivers' correct use and adoption of these programs, to our knowledge, this is the first study describing this process before evaluating a program for caregivers of PWAD in a randomized clinical trial. The objective of the study was to describe the development process of a fully automated Web-based program for caregivers of PWAD, aiming to reduce caregivers' stress, and based on the user-centered design approach. There were 49 participants (12 health care professionals, 6 caregivers, and 31 healthy older adults) that were involved in a double iterative design allowing for the adaptation of program content and for the enhancement of website usability. This process included three component parts: (1) project team workshops, (2) a proof of concept, and (3) two usability tests. The usability tests were based on a mixed methodology using behavioral analysis, semistructured interviews, and a usability questionnaire. The user-centered design approach provided valuable guidelines to adapt the content and design of the program, and to improve website usability. The professionals, caregivers (mainly spouses), and older adults considered that our project met the needs of isolated caregivers. Participants underlined that contact between caregivers would be desirable. During usability observations, the mistakes of users were also due to ergonomics issues from Internet browsers and computer interfaces. Moreover, negative self-stereotyping was evidenced, when comparing interviews and results of behavioral analysis. Face-to-face psycho-educational programs may be used as a basis for Web-based programs. Nevertheless, a user-centered design approach involving targeted

Taking advantage of Google's Web-based applications and services.

PubMed

Brigham, Tara J

2014-01-01

Google is a company that is constantly expanding and growing its services and products. While most librarians possess a "love/hate" relationship with Google, there are a number of reasons you should consider exploring some of the tools Google has created and made freely available. Applications and services such as Google Docs, Slides, and Google+ are functional and dynamic without the cost of comparable products. This column will address some of the issues users should be aware of before signing up to use Google's tools, and a description of some of Google's Web applications and services, plus how they can be useful to librarians in health care.

Specification Patent Management for Web Application Platform Ecosystem

NASA Astrophysics Data System (ADS)

Fukami, Yoshiaki; Isshiki, Masao; Takeda, Hideaki; Ohmukai, Ikki; Kokuryo, Jiro

Diversified usage of web applications has encouraged disintegration of web platform into management of identification and applications. Users make use of various kinds of data linked to their identity with multiple applications on certain social web platforms such as Facebook or MySpace. There has emerged competition among web application platforms. Platformers can design relationship with developers by controlling patent of their own specification and adopt open technologies developed external organizations. Platformers choose a way to open according to feature of the specification and their position. Patent management of specification come to be a key success factor to build competitive web application platforms. Each way to attract external developers such as standardization, open source has not discussed and analyzed all together.

GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms.

PubMed

Moraes, João P A; Pappa, Gisele L; Pires, Douglas E V; Izidoro, Sandro C

2017-07-03

Enzyme active sites are important and conserved functional regions of proteins whose identification can be an invaluable step toward protein function prediction. Most of the existing methods for this task are based on active site similarity and present limitations including performing only exact matches on template residues, template size restraints, despite not being capable of finding inter-domain active sites. To fill this gap, we proposed GASS-WEB, a user-friendly web server that uses GASS (Genetic Active Site Search), a method based on an evolutionary algorithm to search for similar active sites in proteins. GASS-WEB can be used under two different scenarios: (i) given a protein of interest, to match a set of specific active site templates; or (ii) given an active site template, looking for it in a database of protein structures. The method has shown to be very effective on a range of experiments and was able to correctly identify >90% of the catalogued active sites from the Catalytic Site Atlas. It also managed to achieve a Matthew correlation coefficient of 0.63 using the Critical Assessment of protein Structure Prediction (CASP 10) dataset. In our analysis, GASS was ranking fourth among 18 methods. GASS-WEB is freely available at http://gass.unifei.edu.br/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

A Service Oriented Web Application for Learner Knowledge Representation, Management and Sharing Conforming to IMS LIP

ERIC Educational Resources Information Center

Lazarinis, Fotis

2014-01-01

iLM is a Web based application for representation, management and sharing of IMS LIP conformant user profiles. The tool is developed using a service oriented architecture with emphasis on the easy data sharing. Data elicitation from user profiles is based on the utilization of XQuery scripts and sharing with other applications is achieved through…

A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal.

PubMed

Eijssen, Lars M T; Goelela, Varshna S; Kelder, Thomas; Adriaens, Michiel E; Evelo, Chris T; Radonjic, Marijana

2015-06-30

Illumina whole-genome expression bead arrays are a widely used platform for transcriptomics. Most of the tools available for the analysis of the resulting data are not easily applicable by less experienced users. ArrayAnalysis.org provides researchers with an easy-to-use and comprehensive interface to the functionality of R and Bioconductor packages for microarray data analysis. As a modular open source project, it allows developers to contribute modules that provide support for additional types of data or extend workflows. To enable data analysis of Illumina bead arrays for a broad user community, we have developed a module for ArrayAnalysis.org that provides a free and user-friendly web interface for quality control and pre-processing for these arrays. This module can be used together with existing modules for statistical and pathway analysis to provide a full workflow for Illumina gene expression data analysis. The module accepts data exported from Illumina's GenomeStudio, and provides the user with quality control plots and normalized data. The outputs are directly linked to the existing statistics module of ArrayAnalysis.org, but can also be downloaded for further downstream analysis in third-party tools. The Illumina bead arrays analysis module is available at http://www.arrayanalysis.org . A user guide, a tutorial demonstrating the analysis of an example dataset, and R scripts are available. The module can be used as a starting point for statistical evaluation and pathway analysis provided on the website or to generate processed input data for a broad range of applications in life sciences research.

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.

Towards pathogenomics: a web-based resource for pathogenicity islands

PubMed Central

Yoon, Sung Ho; Park, Young-Kyu; Lee, Soohyun; Choi, Doil; Oh, Tae Kwang; Hur, Cheol-Goo; Kim, Jihyun F.

2007-01-01

Pathogenicity islands (PAIs) are genetic elements whose products are essential to the process of disease development. They have been horizontally (laterally) transferred from other microbes and are important in evolution of pathogenesis. In this study, a comprehensive database and search engines specialized for PAIs were established. The pathogenicity island database (PAIDB) is a comprehensive relational database of all the reported PAIs and potential PAI regions which were predicted by a method that combines feature-based analysis and similarity-based analysis. Also, using the PAI Finder search application, a multi-sequence query can be analyzed onsite for the presence of potential PAIs. As of April 2006, PAIDB contains 112 types of PAIs and 889 GenBank accessions containing either partial or all PAI loci previously reported in the literature, which are present in 497 strains of pathogenic bacteria. The database also offers 310 candidate PAIs predicted from 118 sequenced prokaryotic genomes. With the increasing number of prokaryotic genomes without functional inference and sequenced genetic regions of suspected involvement in diseases, this web-based, user-friendly resource has the potential to be of significant use in pathogenomics. PAIDB is freely accessible at . PMID:17090594

The heat-transfer method: a versatile low-cost, label-free, fast, and user-friendly readout platform for biosensor applications.

PubMed

van Grinsven, Bart; Eersels, Kasper; Peeters, Marloes; Losada-Pérez, Patricia; Vandenryt, Thijs; Cleij, Thomas J; Wagner, Patrick

2014-08-27

In recent years, biosensors have become increasingly important in various scientific domains including medicine, biology, and pharmacology, resulting in an increased demand for fast and effective readout techniques. In this Spotlight on Applications, we report on the recently developed heat-transfer method (HTM) and illustrate the use of the technique by zooming in on four established bio(mimetic) sensor applications: (i) mutation analysis in DNA sequences, (ii) cancer cell identification through surface-imprinted polymers, (iii) detection of neurotransmitters with molecularly imprinted polymers, and (iv) phase-transition analysis in lipid vesicle layers. The methodology is based on changes in heat-transfer resistance at a functionalized solid-liquid interface. To this extent, the device applies a temperature gradient over this interface and monitors the temperature underneath and above the functionalized chip in time. The heat-transfer resistance can be obtained by dividing this temperature gradient by the power needed to achieve a programmed temperature. The low-cost, fast, label-free and user-friendly nature of the technology in combination with a high degree of specificity, selectivity, and sensitivity makes HTM a promising sensor technology.

Enhancing Web applications in radiology with Java: estimating MR imaging relaxation times.

PubMed

Dagher, A P; Fitzpatrick, M; Flanders, A E; Eng, J

1998-01-01

Java is a relatively new programming language that has been used to develop a World Wide Web-based tool for estimating magnetic resonance (MR) imaging relaxation times, thereby demonstrating how Java may be used for Web-based radiology applications beyond improving the user interface of teaching files. A standard processing algorithm coded with Java is downloaded along with the hypertext markup language (HTML) document. The user (client) selects the desired pulse sequence and inputs data obtained from a region of interest on the MR images. The algorithm is used to modify selected MR imaging parameters in an equation that models the phenomenon being evaluated. MR imaging relaxation times are estimated, and confidence intervals and a P value expressing the accuracy of the final results are calculated. Design features such as simplicity, object-oriented programming, and security restrictions allow Java to expand the capabilities of HTML by offering a more versatile user interface that includes dynamic annotations and graphics. Java also allows the client to perform more sophisticated information processing and computation than is usually associated with Web applications. Java is likely to become a standard programming option, and the development of stand-alone Java applications may become more common as Java is integrated into future versions of computer operating systems.

A Web-based vital sign telemonitor and recorder for telemedicine applications.

PubMed

Mendoza, Patricia; Gonzalez, Perla; Villanueva, Brenda; Haltiwanger, Emily; Nazeran, Homer

2004-01-01

We describe a vital sign telemonitor (VST) that acquires, records, displays, and provides readings such as: electrocardiograms (ECGs), temperature (T), and oxygen saturation (SaO2) over the Internet to any site. The design of this system consisted of three parts: sensors, analog signal processing circuits, and a user-friendly graphical user interface (GUI). The first part involved selection of appropriate sensors. For ECG, disposable Ag/AgCl electrodes; for temperature, LM35 precision temperature sensor; and for SaO2 the Nonin Oximetry Development Kit equipped with a finger clip were selected. The second part consisted of processing the analog signals obtained from these sensors. This was achieved by implementing suitable amplifiers and filters for the vital signs. The final part focused on development of a GUI to display the vital signs in the LabVIEW environment. From these measurements, important values such as heart rate (HR), beat-to-beat (RR) intervals, SaO2 percentages, and T in both degrees Celsius and Fahrenheit were calculated The GUI could be accessed through the Internet in a Web-page facilitating the possibility of real-time patient telemonitoring. The final system was completed and tested on volunteers with satisfactory results.

The Design of Modular Web-Based Collaboration

NASA Astrophysics Data System (ADS)

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

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

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.

User experience integrated life-style cloud-based medical application.

PubMed

Serban, Alexandru; Lupşe, Oana Sorina; Stoicu-Tivadar, Lăcrămioara

2015-01-01

Having a modern application capable to automatically collect and process data from users, based on information and lifestyle answers is one of current challenges for researchers and medical science. The purpose of the current study is to integrate user experience design (UXD) in a cloud-based medical application to improve patient safety, quality of care and organizational efficiency. The process consists of collecting traditional and new data from patients and users using online questionnaires. A questionnaire dynamically asks questions about the user's current diet and lifestyle. After the user will introduce the data, the application will formulate a presumptive nutritional plan and will suggest different medical recommendations regarding a healthy lifestyle, and calculates a risk factor for diseases. This software application, by design and usability will be an efficient tool dedicated for fitness, nutrition and health professionals.

Earthdata User Interface Patterns: Building Usable Web Interfaces Through a Shared UI Pattern Library

NASA Astrophysics Data System (ADS)

Siarto, J.

2014-12-01

As more Earth science software tools and services move to the web--the design and usability of those tools become ever more important. A good user interface is becoming expected and users are becoming increasingly intolerant of websites and web applications that work against them. The Earthdata UI Pattern Library attempts to give these scientists and developers the design tools they need to make usable, compelling user interfaces without the associated overhead of using a full design team. Patterns are tested and functional user interface elements targeted specifically at the Earth science community and will include web layouts, buttons, tables, typography, iconography, mapping and visualization/graphing widgets. These UI elements have emerged as the result of extensive user testing, research and software development within the NASA Earthdata team over the past year.

Development and evaluation of a web-based application for digital findings and documentation in physiotherapy education.

PubMed

Spieler, Bernadette; Burgsteiner, Harald; Messer-Misak, Karin; Gödl-Purrer, Barbara; Salchinger, Beate

2015-01-01

Findings in physiotherapy have standardized approaches in treatment, but there is also a significant margin of differences in how to implement these standards. Clinical decisions require experience and continuous learning processes to consolidate personal values and opinions and studies suggest that lecturers can influence students positively. Recently, the study course of Physiotherapy at the University of Applied Science in Graz has offered a paper based finding document. This document supported decisions through the adaption of the clinical reasoning process. The document was the starting point for our learning application called "EasyAssess", a Java based web-application for a digital findings documentation. A central point of our work was to ensure efficiency, effectiveness and usability of the web-application through usability tests utilized by both students and lecturers. Results show that our application fulfills the previously defined requirements and can be efficiently used in daily routine largely because of its simple user interface and its modest design. Due to the close cooperation with the study course Physiotherapy, the application has incorporated the various needs of the target audiences and confirmed the usefulness of our application.

User-Friendly Data Servers for Climate Studies at the Asia-Pacific Data-Research Center (APDRC)

NASA Astrophysics Data System (ADS)

Yuan, G.; Shen, Y.; Zhang, Y.; Merrill, R.; Waseda, T.; Mitsudera, H.; Hacker, P.

2002-12-01

, SODA, WOCE-Satellite, TMI, GPI and GSSTF products through the CAS. The APDRC is also running an EPIC server developed by PMEL/NOAA. EPIC is a web-based, data search and display system suited for in situ (station versus gridded) data. The process of locating and selecting individual station data from large collections (millions of profiles or time series, etc.) of in situ data is a major challenge. Serving in situ data on the Internet faces two problems: the irregularity of data formats; and the large quantity of data files. To solve the first problem, we have converted the in situ data into netCDF data format. The second problem was solved by using the EPIC server, which allows users to easily subset the files using a friendly graphical interface. Furthermore, we enhanced the capability of EPIC and configured OPeNDAP into EPIC to serve the numerous in situ data files and to export them to users through two different options: 1) an OPeNDAP pointer file of user-selected data files; and 2) a data package that includes meta-information (e.g., location, time, cruise no, etc.), a local pointer file, and the data files that the user selected. Option 1) is for those who do not want to download the selected data but want to use their own application software (such as GrADS, Matlab and Ferret) for access and analysis; option 2) is for users who want to store the data on their own system (e.g. laptops before going for a cruise) for subsequent analysis. Currently, WOCE CTD and bottle data, the WOCE current meter data, and some Argo float data are being served on the EPIC server.

AMBIT RESTful web services: an implementation of the OpenTox application programming interface.

PubMed

Jeliazkova, Nina; Jeliazkov, Vedrin

2011-05-16

allows researchers to setup an arbitrary number of service instances for specific purposes and at suitable locations. These services could be used as a distributed framework for processing of resource-intensive tasks and data sharing or in a fully independent way, according to the specific needs. The advantage of exposing the functionality via the OpenTox API is seamless interoperability, not only within a single web application, but also in a network of distributed services. Last, but not least, the services provide a basis for building web mashups, end user applications with friendly GUIs, as well as embedding the functionalities in existing workflow systems.

AMBIT RESTful web services: an implementation of the OpenTox application programming interface

PubMed Central

2011-01-01

allows researchers to setup an arbitrary number of service instances for specific purposes and at suitable locations. These services could be used as a distributed framework for processing of resource-intensive tasks and data sharing or in a fully independent way, according to the specific needs. The advantage of exposing the functionality via the OpenTox API is seamless interoperability, not only within a single web application, but also in a network of distributed services. Last, but not least, the services provide a basis for building web mashups, end user applications with friendly GUIs, as well as embedding the functionalities in existing workflow systems. PMID:21575202

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

Bias Correction of Satellite Precipitation Products (SPPs) using a User-friendly Tool: A Step in Enhancing Technical Capacity

NASA Astrophysics Data System (ADS)

Rushi, B. R.; Ellenburg, W. L.; Adams, E. C.; Flores, A.; Limaye, A. S.; Valdés-Pineda, R.; Roy, T.; Valdés, J. B.; Mithieu, F.; Omondi, S.

2017-12-01

SERVIR, a joint NASA-USAID initiative, works to build capacity in Earth observation technologies in developing countries for improved environmental decision making in the arena of: weather and climate, water and disasters, food security and land use/land cover. SERVIR partners with leading regional organizations in Eastern and Southern Africa, Hindu Kush-Himalaya, Mekong region, and West Africa to achieve its objectives. SERVIR develops hydrological applications to address specific needs articulated by key stakeholders and daily rainfall estimates are a vital input for these applications. Satellite-derived rainfall is subjected to systemic biases which need to be corrected before it can be used for any hydrologic application such as real-time or seasonal forecasting. SERVIR and the SWAAT team at the University of Arizona, have co-developed an open-source and user friendly tool of rainfall bias correction approaches for SPPs. Bias correction tools were developed based on Linear Scaling and Quantile Mapping techniques. A set of SPPs, such as PERSIANN-CCS, TMPA-RT, and CMORPH, are bias corrected using Climate Hazards Group InfraRed Precipitation with Station (CHIRPS) data which incorporates ground based precipitation observations. This bias correction tools also contains a component, which is included to improve monthly mean of CHIRPS using precipitation products of the Global Surface Summary of the Day (GSOD) database developed by the National Climatic Data Center (NCDC). This tool takes input from command-line which makes it user-friendly and applicable in any operating platform without prior programming skills. This presentation will focus on this bias-correction tool for SPPs, including application scenarios.

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.

Development and preliminary testing of a web-based, self-help application for disaster-affected families.

PubMed

Yuen, Erica K; Gros, Kirstin; Welsh, Kyleen E; McCauley, Jenna; Resnick, Heidi S; Danielson, Carla K; Price, Matthew; Ruggiero, Kenneth J

2016-09-01

Technology-based self-help interventions have the potential to increase access to evidence-based mental healthcare, especially for families affected by natural disasters. However, development of these interventions is a complex process and poses unique challenges. Usability testing, which assesses the ability of individuals to use an application successfully, can have a significant impact on the quality of a self-help intervention. This article describes (a) the development of a novel web-based multi-module self-help intervention for disaster-affected adolescents and their parents and (b) a mixed-methods formal usability study to evaluate user response. A total of 24 adolescents were observed, videotaped, and interviewed as they used the depressed mood component of the self-help intervention. Quantitative results indicated an above-average user experience, and qualitative analysis identified 120 unique usability issues. We discuss the challenges of developing self-help applications, including design considerations and the value of usability testing in technology-based interventions, as well as our plan for widespread dissemination. © The Author(s) 2015.

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

Spontaneous diffusion of an effective skin cancer prevention program through Web-based access to program materials.

PubMed

Hall, Dawn M; Escoffery, Cam; Nehl, Eric; Glanz, Karen

2010-11-01

Little information exists about the diffusion of evidence-based interventions, a process that can occur naturally in organized networks with established communication channels. This article describes the diffusion of an effective skin cancer prevention program called Pool Cool through available Web-based program materials. We used self-administered surveys to collect information from program users about access to and use of Web-based program materials. We analyzed the content of e-mails sent to the official Pool Cool Web site to obtain qualitative information about spontaneous diffusion. Program users were dispersed throughout the United States, most often learning about the program through a Web site (32%), publication (26%), or colleague (19%). Most respondents (86%) reported that their pool provided educational activities at swimming lessons. The Leader's Guide (59%) and lesson cards (50%) were the most commonly downloaded materials, and most respondents reported using these core items sometimes, often, or always. Aluminum sun-safety signs were the least frequently used materials. A limited budget was the most commonly noted obstacle to sun-safety efforts at the pool (85%). Factors supporting sun safety at the pool centered around risk management (85%) and health of the pool staff (78%). Diffusion promotes the use of evidence-based health programs and can occur with and without systematic efforts. Strategies such as providing well-packaged, user-friendly program materials at low or no cost and strategic advertisement of the availability of program materials may increase program use and exposure. Furthermore, highlighting the benefits of the program can motivate potential program users.

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

Web application for detailed real-time database transaction monitoring for CMS condition data

NASA Astrophysics Data System (ADS)

de Gruttola, Michele; Di Guida, Salvatore; Innocente, Vincenzo; Pierro, Antonio

2012-12-01

In the upcoming LHC era, database have become an essential part for the experiments collecting data from LHC, in order to safely store, and consistently retrieve, a wide amount of data, which are produced by different sources. In the CMS experiment at CERN, all this information is stored in ORACLE databases, allocated in several servers, both inside and outside the CERN network. In this scenario, the task of monitoring different databases is a crucial database administration issue, since different information may be required depending on different users' tasks such as data transfer, inspection, planning and security issues. We present here a web application based on Python web framework and Python modules for data mining purposes. To customize the GUI we record traces of user interactions that are used to build use case models. In addition the application detects errors in database transactions (for example identify any mistake made by user, application failure, unexpected network shutdown or Structured Query Language (SQL) statement error) and provides warning messages from the different users' perspectives. Finally, in order to fullfill the requirements of the CMS experiment community, and to meet the new development in many Web client tools, our application was further developed, and new features were deployed.

A digital atlas of breast histopathology: an application of web based virtual microscopy

PubMed Central

Lundin, M; Lundin, J; Helin, H; Isola, J

2004-01-01

Aims: To develop an educationally useful atlas of breast histopathology, using advanced web based virtual microscopy technology. Methods: By using a robotic microscope and software adopted and modified from the aerial and satellite imaging industry, a virtual microscopy system was developed that allows fully automated slide scanning and image distribution via the internet. More than 150 slides were scanned at high resolution with an oil immersion ×40 objective (numerical aperture, 1.3) and archived on an image server residing in a high speed university network. Results: A publicly available website was constructed, http://www.webmicroscope.net/breastatlas, which features a comprehensive virtual slide atlas of breast histopathology according to the World Health Organisation 2003 classification. Users can view any part of an entire specimen at any magnification within a standard web browser. The virtual slides are supplemented with concise textual descriptions, but can also be viewed without diagnostic information for self assessment of histopathology skills. Conclusions: Using the technology described here, it is feasible to develop clinically and educationally useful virtual microscopy applications. Web based virtual microscopy will probably become widely used at all levels in pathology teaching. PMID:15563669

Web-based Collaboration and Visualization in the ANDRILL Program

NASA Astrophysics Data System (ADS)

Reed, J.; Rack, F. R.; Huffman, L. T.; Cattadori, M.

2009-12-01

ANDRILL has embraced the web as a platform for facilitating collaboration and communicating science with educators, students and researchers alike. Two recent ANDRILL education and outreach projects, Project Circle 2008 and the Climate Change Student Summit, brought together classrooms from around the world to participate in cutting edge science. A large component of each project was the online collaboration achieved through project websites, blogs, and the GroupHub--a secure online environment where students could meet to send messages, exchange presentations and pictures, and even chat live. These technologies enabled students from different countries and time zones to connect and participate in a shared 'conversation' about climate change research. ANDRILL has also developed several interactive, web-based visualizations to make scientific drilling data more engaging and accessible to the science community and the public. Each visualization is designed around three core concepts that enable the Web 2.0 platform, namely, that they are: (1) customizable - a user can customize the visualization to display the exact data she is interested in; (2) linkable - each view in the visualization has a distinct URL that the user can share with her friends via sites like Facebook and Twitter; and (3) mashable - the user can take the visualization, mash it up with data from other sites or her own research, and embed it in her blog or website. The web offers an ideal environment for visualization and collaboration because it requires no special software and works across all computer platforms, which allows organizations and research projects to engage much larger audiences. In this presentation we will describe past challenges and successes, as well as future plans.

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 .

Integrating geo web services for a user driven exploratory analysis

NASA Astrophysics Data System (ADS)

Moncrieff, Simon; Turdukulov, Ulanbek; Gulland, Elizabeth-Kate

2016-04-01

In data exploration, several online data sources may need to be dynamically aggregated or summarised over spatial region, time interval, or set of attributes. With respect to thematic data, web services are mainly used to present results leading to a supplier driven service model limiting the exploration of the data. In this paper we propose a user need driven service model based on geo web processing services. The aim of the framework is to provide a method for the scalable and interactive access to various geographic data sources on the web. The architecture combines a data query, processing technique and visualisation methodology to rapidly integrate and visually summarise properties of a dataset. We illustrate the environment on a health related use case that derives Age Standardised Rate - a dynamic index that needs integration of the existing interoperable web services of demographic data in conjunction with standalone non-spatial secure database servers used in health research. Although the example is specific to the health field, the architecture and the proposed approach are relevant and applicable to other fields that require integration and visualisation of geo datasets from various web services and thus, we believe is generic in its approach.

Envisioning Advanced User Interfaces for E-Government Applications: A Case Study

NASA Astrophysics Data System (ADS)

Calvary, Gaëlle; Serna, Audrey; Coutaz, Joëlle; Scapin, Dominique; Pontico, Florence; Winckler, Marco

The increasing use of the Web as a software platform together with the advance of technology has promoted Web applications as a starting point for improving communication between citizens and administration. Currently, several e-government Web portals propose applications for accessing information regarding healthcare, taxation, registration, housing, agriculture, education, and social services, which otherwise may be difficult to obtain. However, the adoption of services provided to citizens depends upon how such applications comply with the users' needs. Unfortunately, building an e-government website doesn't guarantee that all citizens who come to use it can access its contents. These services need to be accessible to all citizens/customers equally to ensure wider reach and subsequent adoption of the e-government services. User disabilities, computer or language illiteracy (e.g., foreign language), flexibility on information access (e.g., user remotely located in rural areas, homeless, mobile users), and ensuring user privacy on sensitive data are some of the barriers that must be taken into account when designing the User Interface (UI) of e-government applications.

A Web-Based Resource for Investigating Environmental Change: The Emigrant Pass Observatory

ERIC Educational Resources Information Center

Davis, Michael G.; Chapman, David S.

2012-01-01

We present a user-friendly, data-driven Web site (http://thermal.gg.utah.edu/facilities/epo/) for a geothermal, climate change observatory that is educational for the general public, students, and researchers alike. The Emigrant Pass Observatory (EPO), located in the Grouse Creek Mountains in northwestern Utah, gathers both meteorological data…

Web-based training for primary healthcare workers in rural China: a qualitative exploration of stakeholders' perceptions.

PubMed

Zhang, Zhixia; Zhan, Xingxin; Li, Yingxue; Hu, Rong; Yan, Weirong

2015-01-01

Equitable access to basic public health services is a priority in China. However, primary healthcare workers' competence to deliver public health services is relatively poor because they lack professional training. Since the availability of web-based training has increased in China, the current study explored stakeholders' perceptions of a web-based training program on basic public health services to understand their thoughts, experiences, and attitudes about it. Six focus group discussions with primary healthcare workers and three with directors of township hospitals, county-level Health Bureaus, and county-level Centers for Disease Control and Prevention were conducted in Yichang City during 2013. Semi-structured topic guides were used to facilitate qualitative data collection. Audio recordings of the sessions were transcribed verbatim and theme analysis was performed. Most of the study's participants, especially the village doctors, had insufficient knowledge of basic public health services. The existing training program for primary healthcare workers consisted of ineffective traditional face-to-face sessions and often posed accessibility problems for the trainees. Most of the study's participants had a positive attitude about web-based learning and expressed a strong desire to receive this novel training approach because of its flexibility and convenience. The perceived barriers to utilizing the web-based training method included poor computer literacy, lack of personal interaction, inadequate infrastructure, and lack of time and motivation. The facilitators of this approach included the training content applicability, the user-friendly and interactive learning format, and policy support. Web-based training on basic public health services is a promising option in rural China. The findings of the study will contribute knowledge to implementation of web-based training in similar settings.

New-generation bar adsorptive microextraction (BAμE) devices for a better eco-user-friendly analytical approach-Application for the determination of antidepressant pharmaceuticals in biological fluids.

PubMed

Ide, A H; Nogueira, J M F

2018-05-10

The present contribution aims to design new-generation bar adsorptive microextraction (BAμE) devices that promote an innovative and much better user-friendly analytical approach. The novel BAμE devices were lab-made prepared having smaller dimensions by using flexible nylon-based supports (7.5 × 1.0 mm) coated with convenient sorbents (≈ 0.5 mg). This novel advance allows effective microextraction and back-extraction ('only single liquid desorption step') stages as well as interfacing enhancement with the instrumental systems dedicated for routine analysis. To evaluate the achievements of these improvements, four antidepressant agents (bupropion, citalopram, amitriptyline and trazodone) were used as model compounds in aqueous media combined with liquid chromatography (LC) systems. By using an N-vinylpyrrolidone based-polymer phase good selectivity and efficiency were obtained. Assays performed on 25 mL spiked aqueous samples, yielded average recoveries in between 67.8 ± 12.4% (bupropion) and 88.3 ± 12.1% (citalopram), under optimized experimental conditions. The analytical performance also showed convenient precision (RSD < 12%) and detection limits (50 ng L -1 ), as well as linear dynamic ranges (160-2000 ng L -1 ) with suitable determination coefficients (r 2  > 0.9820). The application of the proposed analytical approach on biological fluids showed negligible matrix effects by using the standard addition methodology. From the data obtained, the new-generation BAμE devices presented herein provide an innovative and robust analytical cycle, are simple to prepare, cost-effective, user-friendly and compatible with the current LC autosampler systems. Furthermore, the novel devices were designed to be disposable and used together with negligible amounts of organic solvents (100 μL) during back-extraction, in compliance with the green analytical chemistry principles. In short, the new-generation BAμE devices showed to be

Design and Development of a Web-Based Self-Monitoring System to Support Wellness Coaching.

PubMed

Zarei, Reza; Kuo, Alex

2017-01-01

We analyzed, designed and deployed a web-based, self-monitoring system to support wellness coaching. A wellness coach can plan for clients' exercise and diet through the system and is able to monitor the changes in body dimensions and body composition that the client reports. The system can also visualize the client's data in form of graphs for both the client and the coach. Both parties can also communicate through the messaging feature embedded in the application. A reminder system is also incorporated into the system and sends reminder messages to the clients when their reporting is due. The web-based self-monitoring application uses Oracle 11g XE as the backend database and Application Express 4.2 as user interface development tool. The system allowed users to access, update and modify data through web browser anytime, anywhere, and on any device.

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…

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.

Hazardous Waste Generator Regulations: A User-Friendly Reference Document

EPA Pesticide Factsheets

User-friendly reference to assist EPA and state staff, industrial facilities generating and managing hazardous wastes as well as the general public, in locating and understanding RCRA hazardous waste generator regulations.

3D-Lab: a collaborative web-based platform for molecular modeling.

PubMed

Grebner, Christoph; Norrby, Magnus; Enström, Jonatan; Nilsson, Ingemar; Hogner, Anders; Henriksson, Jonas; Westin, Johan; Faramarzi, Farzad; Werner, Philip; Boström, Jonas

2016-09-01

The use of 3D information has shown impact in numerous applications in drug design. However, it is often under-utilized and traditionally limited to specialists. We want to change that, and present an approach making 3D information and molecular modeling accessible and easy-to-use 'for the people'. A user-friendly and collaborative web-based platform (3D-Lab) for 3D modeling, including a blazingly fast virtual screening capability, was developed. 3D-Lab provides an interface to automatic molecular modeling, like conformer generation, ligand alignments, molecular dockings and simple quantum chemistry protocols. 3D-Lab is designed to be modular, and to facilitate sharing of 3D-information to promote interactions between drug designers. Recent enhancements to our open-source virtual reality tool Molecular Rift are described. The integrated drug-design platform allows drug designers to instantaneously access 3D information and readily apply advanced and automated 3D molecular modeling tasks, with the aim to improve decision-making in drug design projects.

[Development and application of a web-based expert system using artificial intelligence for management of mental health by Korean emigrants].

PubMed

Bae, Jeongyee

2013-04-01

The purpose of this project was to develop an international web-based expert system using principals of artificial intelligence and user-centered design for management of mental health by Korean emigrants. Using this system, anyone can access the system via computer access to the web. Our design process utilized principles of user-centered design with 4 phases: needs assessment, analysis, design/development/testing, and application release. A survey was done with 3,235 Korean emigrants. Focus group interviews were also conducted. Survey and analysis results guided the design of the web-based expert system. With this system, anyone can check their mental health status by themselves using a personal computer. The system analyzes facts based on answers to automated questions, and suggests solutions accordingly. A history tracking mechanism enables monitoring and future analysis. In addition, this system will include intervention programs to promote mental health status. This system is interactive and accessible to anyone in the world. It is expected that this management system will contribute to Korean emigrants' mental health promotion and allow researchers and professionals to share information on mental health.

ALPHACAL: A new user-friendly tool for the calibration of alpha-particle sources.

PubMed

Timón, A Fernández; Vargas, M Jurado; Gallardo, P Álvarez; Sánchez-Oro, J; Peralta, L

2018-05-01

In this work, we present and describe the program ALPHACAL, specifically developed for the calibration of alpha-particle sources. It is therefore more user-friendly and less time-consuming than multipurpose codes developed for a wide range of applications. The program is based on the recently developed code AlfaMC, which simulates specifically the transport of alpha particles. Both cylindrical and point sources mounted on the surface of polished backings can be simulated, as is the convention in experimental measurements of alpha-particle sources. In addition to the efficiency calculation and determination of the backscattering coefficient, some additional tools are available to the user, like the visualization of energy spectrum, use of energy cut-off or low-energy tail corrections. ALPHACAL has been implemented in C++ language using QT library, so it is available for Windows, MacOs and Linux platforms. It is free and can be provided under request to the authors. Copyright © 2018 Elsevier Ltd. All rights reserved.

Analysing trends and forecasting malaria epidemics in Madagascar using a sentinel surveillance network: a web-based application.

PubMed

Girond, Florian; Randrianasolo, Laurence; Randriamampionona, Lea; Rakotomanana, Fanjasoa; Randrianarivelojosia, Milijaona; Ratsitorahina, Maherisoa; Brou, Télesphore Yao; Herbreteau, Vincent; Mangeas, Morgan; Zigiumugabe, Sixte; Hedje, Judith; Rogier, Christophe; Piola, Patrice

2017-02-13

The use of a malaria early warning system (MEWS) to trigger prompt public health interventions is a key step in adding value to the epidemiological data routinely collected by sentinel surveillance systems. This study describes a system using various epidemic thresholds and a forecasting component with the support of new technologies to improve the performance of a sentinel MEWS. Malaria-related data from 21 sentinel sites collected by Short Message Service are automatically analysed to detect malaria trends and malaria outbreak alerts with automated feedback reports. Roll Back Malaria partners can, through a user-friendly web-based tool, visualize potential outbreaks and generate a forecasting model. The system already demonstrated its ability to detect malaria outbreaks in Madagascar in 2014. This approach aims to maximize the usefulness of a sentinel surveillance system to predict and detect epidemics in limited-resource environments.

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

PubMed

Schweiger, Dominik; Trajanoski, Zlatko; Pabinger, Stephan

2014-08-15

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

Application of Mobile Agents in Web-Based Learning Environment.

ERIC Educational Resources Information Center

Hong Hong, Kinshuk; He, Xiaoqin; Patel, Ashok; Jesshope, Chris

Web-based learning environments are strongly driven by the information revolution and the Internet, but they have a number of common deficiencies, such as slow access, no adaptivity to the individual student, limitation by bandwidth, and more. This paper outlines the benefits of mobile agents technology, and describes its application in Web-based…

Web-Based Software for Managing Research

NASA Technical Reports Server (NTRS)

Hoadley, Sherwood T.; Ingraldi, Anthony M.; Gough, Kerry M.; Fox, Charles; Cronin, Catherine K.; Hagemann, Andrew G.; Kemmerly, Guy T.; Goodman, Wesley L.

2007-01-01

aeroCOMPASS is a software system, originally designed to aid in the management of wind tunnels at Langley Research Center, that could be adapted to provide similar aid to other enterprises in which research is performed in common laboratory facilities by users who may be geographically dispersed. Included in aeroCOMPASS is Web-interface software that provides a single, convenient portal to a set of project- and test-related software tools and other application programs. The heart of aeroCOMPASS is a user-oriented document-management software subsystem that enables geographically dispersed users to easily share and manage a variety of documents. A principle of "write once, read many" is implemented throughout aeroCOMPASS to eliminate the need for multiple entry of the same information. The Web framework of aeroCOMPASS provides links to client-side application programs that are fully integrated with databases and server-side application programs. Other subsystems of aeroCOMPASS include ones for reserving hardware, tracking of requests and feedback from users, generating interactive notes, administration of a customer-satisfaction questionnaire, managing execution of tests, managing archives of metadata about tests, planning tests, and providing online help and instruction for users.

Effective Filtering of Query Results on Updated User Behavioral Profiles in Web Mining

PubMed Central

Sadesh, S.; Suganthe, R. C.

2015-01-01

Web with tremendous volume of information retrieves result for user related queries. With the rapid growth of web page recommendation, results retrieved based on data mining techniques did not offer higher performance filtering rate because relationships between user profile and queries were not analyzed in an extensive manner. At the same time, existing user profile based prediction in web data mining is not exhaustive in producing personalized result rate. To improve the query result rate on dynamics of user behavior over time, Hamilton Filtered Regime Switching User Query Probability (HFRS-UQP) framework is proposed. HFRS-UQP framework is split into two processes, where filtering and switching are carried out. The data mining based filtering in our research work uses the Hamilton Filtering framework to filter user result based on personalized information on automatic updated profiles through search engine. Maximized result is fetched, that is, filtered out with respect to user behavior profiles. The switching performs accurate filtering updated profiles using regime switching. The updating in profile change (i.e., switches) regime in HFRS-UQP framework identifies the second- and higher-order association of query result on the updated profiles. Experiment is conducted on factors such as personalized information search retrieval rate, filtering efficiency, and precision ratio. PMID:26221626

A Web-Based Earth-Systems Knowledge Portal and Collaboration Platform

NASA Astrophysics Data System (ADS)

D'Agnese, F. A.; Turner, A. K.

2010-12-01

technical platform that is accessed through a flexible series of knowledge portal and collaboration environment styles reflecting the information needs and user expectations of a diverse community of users. Recent investigations have defined the information needs and expectations of the major end-users and also have reviewed and assessed a wide variety of modern web-based technologies. Combining these efforts produced design specifications and recommendations for the selection and integration of web- and client-based tools. When fully developed, the resulting platform will: -Support new, advanced information systems and decision environments that take full advantage of multiple data sources and platforms; -Provide a distribution network tailored to the timely delivery of products to a broad range of users that are needed to support applications in disaster management, resource management, energy, and urban sustainability; -Establish new integrated multiple-user requirements and knowledge databases that support researchers and promote infusion of successful technologies into existing processes; and -Develop new decision support strategies and presentation methodologies for applied earth science applications to reduce risk, cost, and time.

A Web-Based Toolkit to Provide Evidence-Based Resources About Crystal Methamphetamine for the Australian Community: Collaborative Development of Cracks in the Ice.

PubMed

Champion, Katrina Elizabeth; Chapman, Cath; Newton, Nicola Clare; Brierley, Mary-Ellen; Stapinski, Lexine; Kay-Lambkin, Frances; Nagle, Jack; Teesson, Maree

2018-03-20

The use of crystal methamphetamine (ice) and the associated harms for individuals, families, and communities across Australia has been the subject of growing concern in recent years. The provision of easily accessible, evidence-based, and up-to-date information and resources about crystal methamphetamine for the community is a critical component of an effective public health response. This paper aims to describe the codevelopment process of the Web-based Cracks in the Ice Community Toolkit, which was developed to improve access to evidence-based information and resources about crystal methamphetamine for the Australian community. Development of the Cracks in the Ice Community Toolkit was conducted in collaboration with community members across Australia and with experts working in the addiction field. The iterative process involved the following: (1) consultation with end users, including community members, crystal methamphetamine users, families and friends of someone using crystal methamphetamine, health professionals, and teachers (n=451) via a cross-sectional Web-based survey to understand information needs; (2) content and Web development; and (3) user testing of a beta version of the Web-based toolkit among end users (n=41) and experts (n=10) to evaluate the toolkit's acceptability, relevance, and appeal. Initial end user consultation indicated that the most commonly endorsed reasons for visiting a website about crystal methamphetamine were "to get information for myself" (185/451, 41.0%) and "to find out how to help a friend or a family member" (136/451, 30.2%). Community consultation also revealed the need for simple information about crystal methamphetamine, including what it is, its effects, and when and where to seek help or support. Feedback on a beta version of the toolkit was positive in terms of content, readability, layout, look, and feel. Commonly identified areas for improvement related to increasing the level of engagement and personal connection

GeoSymbio: a hybrid, cloud-based web application of global geospatial bioinformatics and ecoinformatics for Symbiodinium-host symbioses.

PubMed

Franklin, Erik C; Stat, Michael; Pochon, Xavier; Putnam, Hollie M; Gates, Ruth D

2012-03-01

The genus Symbiodinium encompasses a group of unicellular, photosynthetic dinoflagellates that are found free living or in hospite with a wide range of marine invertebrate hosts including scleractinian corals. We present GeoSymbio, a hybrid web application that provides an online, easy to use and freely accessible interface for users to discover, explore and utilize global geospatial bioinformatic and ecoinformatic data on Symbiodinium-host symbioses. The novelty of this application lies in the combination of a variety of query and visualization tools, including dynamic searchable maps, data tables with filter and grouping functions, and interactive charts that summarize the data. Importantly, this application is hosted remotely or 'in the cloud' using Google Apps, and therefore does not require any specialty GIS, web programming or data programming expertise from the user. The current version of the application utilizes Symbiodinium data based on the ITS2 genetic marker from PCR-based techniques, including denaturing gradient gel electrophoresis, sequencing and cloning of specimens collected during 1982-2010. All data elements of the application are also downloadable as spatial files, tables and nucleic acid sequence files in common formats for desktop analysis. The application provides a unique tool set to facilitate research on the basic biology of Symbiodinium and expedite new insights into their ecology, biogeography and evolution in the face of a changing global climate. GeoSymbio can be accessed at https://sites.google.com/site/geosymbio/. © 2011 Blackwell Publishing Ltd.

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.

Factors Influencing the Use of a Web-Based Application for Supporting the Self-Care of Patients with Type 2 Diabetes: A Longitudinal Study

PubMed Central

van Gemert-Pijnen, Julia EWC; Kelders, Saskia M; Brandenburg, Bart J; Seydel, Erwin R

2011-01-01

Background The take-up of eHealth applications in general is still rather low and user attrition is often high. Only limited information is available about the use of eHealth technologies among specific patient groups. Objective The aim of this study was to explore the factors that influence the initial and long-term use of a Web-based application (DiabetesCoach) for supporting the self-care of patients with type 2 diabetes. Methods A mixed-methods research design was used for a process analysis of the actual usage of the Web application over a 2-year period and to identify user profiles. Research instruments included log files, interviews, usability tests, and a survey. Results The DiabetesCoach was predominantly used for interactive features like online monitoring, personal data, and patient–nurse email contact. It was the continuous, personal feedback that particularly appealed to the patients; they felt more closely monitored by their nurse and encouraged to play a more active role in self-managing their disease. Despite the positive outcomes, usage of the Web application was hindered by low enrollment and nonusage attrition. The main barrier to enrollment had to do with a lack of access to the Internet (146/226, 65%). Although 68% (34/50) of the enrollees were continuous users, of whom 32% (16/50) could be defined as hardcore users (highly active), the remaining 32% (16/50) did not continue using the Web application for the full duration of the study period. Barriers to long-term use were primarily due to poor user-friendliness of the Web application (the absence of “push” factors or reminders) and selection of the “wrong” users; the well-regulated patients were not the ones who could benefit the most from system use because of a ceiling effect. Patients with a greater need for care seemed to be more engaged in long-term use; highly active users were significantly more often medication users than low/inactive users (P = .005) and had a longer

Factors influencing the use of a Web-based application for supporting the self-care of patients with type 2 diabetes: a longitudinal study.

PubMed

Nijland, Nicol; van Gemert-Pijnen, Julia E W C; Kelders, Saskia M; Brandenburg, Bart J; Seydel, Erwin R

2011-09-30

The take-up of eHealth applications in general is still rather low and user attrition is often high. Only limited information is available about the use of eHealth technologies among specific patient groups. The aim of this study was to explore the factors that influence the initial and long-term use of a Web-based application (DiabetesCoach) for supporting the self-care of patients with type 2 diabetes. A mixed-methods research design was used for a process analysis of the actual usage of the Web application over a 2-year period and to identify user profiles. Research instruments included log files, interviews, usability tests, and a survey. The DiabetesCoach was predominantly used for interactive features like online monitoring, personal data, and patient-nurse email contact. It was the continuous, personal feedback that particularly appealed to the patients; they felt more closely monitored by their nurse and encouraged to play a more active role in self-managing their disease. Despite the positive outcomes, usage of the Web application was hindered by low enrollment and nonusage attrition. The main barrier to enrollment had to do with a lack of access to the Internet (146/226, 65%). Although 68% (34/50) of the enrollees were continuous users, of whom 32% (16/50) could be defined as hardcore users (highly active), the remaining 32% (16/50) did not continue using the Web application for the full duration of the study period. Barriers to long-term use were primarily due to poor user-friendliness of the Web application (the absence of "push" factors or reminders) and selection of the "wrong" users; the well-regulated patients were not the ones who could benefit the most from system use because of a ceiling effect. Patients with a greater need for care seemed to be more engaged in long-term use; highly active users were significantly more often medication users than low/inactive users (P = .005) and had a longer diabetes duration (P = .03). Innovations in health

Investigation and Implementation of a Tree Transformation System for User Friendly Programming.

DTIC Science & Technology

1984-12-01

systems have become an important area of research because of theiL direct impact on all areas of computer science such as software engineering ...RD-i52 716 INVESTIGTIN AND IMPLEMENTATION OF A TREE I/2TRANSFORMATION SYSTEM FOR USER FRIENDLY PROGRAMMING (U) NAVAL POSTGRADUATE SCHOOL MONTEREY CA...Implementation of a Master’s Thesis Tree Transformation System for User December 1984 Friendly Programming 6. PERFORMING ORG. REPORT NUMBER 7. AU~THOR(s) S

WebGIS based on semantic grid model and web services

NASA Astrophysics Data System (ADS)

Zhang, WangFei; Yue, CaiRong; Gao, JianGuo

2009-10-01

As the combination point of the network technology and GIS technology, WebGIS has got the fast development in recent years. With the restriction of Web and the characteristics of GIS, traditional WebGIS has some prominent problems existing in development. For example, it can't accomplish the interoperability of heterogeneous spatial databases; it can't accomplish the data access of cross-platform. With the appearance of Web Service and Grid technology, there appeared great change in field of WebGIS. Web Service provided an interface which can give information of different site the ability of data sharing and inter communication. The goal of Grid technology was to make the internet to a large and super computer, with this computer we can efficiently implement the overall sharing of computing resources, storage resource, data resource, information resource, knowledge resources and experts resources. But to WebGIS, we only implement the physically connection of data and information and these is far from the enough. Because of the different understanding of the world, following different professional regulations, different policies and different habits, the experts in different field will get different end when they observed the same geographic phenomenon and the semantic heterogeneity produced. Since these there are large differences to the same concept in different field. If we use the WebGIS without considering of the semantic heterogeneity, we will answer the questions users proposed wrongly or we can't answer the questions users proposed. To solve this problem, this paper put forward and experienced an effective method of combing semantic grid and Web Services technology to develop WebGIS. In this paper, we studied the method to construct ontology and the method to combine Grid technology and Web Services and with the detailed analysis of computing characteristics and application model in the distribution of data, we designed the WebGIS query system driven by

CoP Sensing Framework on Web-Based Environment

NASA Astrophysics Data System (ADS)

Mustapha, S. M. F. D. Syed

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

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

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

The utilization of oncology web-based resources in Spanish-speaking Internet users.

PubMed

Simone, Charles B; Hampshire, Margaret K; Vachani, Carolyn; Metz, James M

2012-12-01

There currently are few web-based resources written in Spanish providing oncology-specific information. This study examines utilization of Spanish-language oncology web-based resources and evaluates oncology-related Internet browsing practices of Spanish-speaking patients. OncoLink (http://www.oncolink.org) is the oldest and among the largest Internet-based cancer information resources. In September 2005, OncoLink pioneered OncoLink en español (OEE) (http://es.oncolink.org), a Spanish translation of OncoLink. Internet utilization data on these sites for 2006 to 2007 were compared. Visits to OncoLink rose from 4,440,843 in 2006 to 5,125,952 in 2007. OEE had 204,578 unique visitors and 240,442 visits in 2006, and 351,228 visitors and 412,153 visits in 2007. Although there was no time predilection for viewing OncoLink, less relative browsing on OEE was conducted during weekends and early morning hours. Although OncoLink readers searched for information on the most common cancers in the United States, OEE readers most often search for gastric, vaginal, osteosarcoma, leukemia, penile, cervical, and testicular malignancies. Average visit duration on OEE was shorter, and fewer readers surveyed OEE more than 15 minutes (4.5% vs. 14.9%, P < 0.001). Spanish-speaking users of web-based oncology resources are increasingly using the Internet to supplement their cancer knowledge. Limited available resources written in Spanish contribute to disparities in information access and disease outcomes. Spanish-speaking oncology readers differ from English-speaking readers in day and time of Internet browsing, visit duration, Internet search patterns, and types of cancers searched. By acknowledging these differences, content of web-based oncology resources can be developed to best target the needs of Spanish-speaking viewers.

The Utilization of Oncology Web-based Resources in Spanish-speaking Internet Users

PubMed Central

Simone, Charles B.; Hampshire, Margaret K.; Vachani, Carolyn; Metz, James M.

2011-01-01

Objectives: There currently are few web-based resources written in Spanish providing oncology-specific information. This study examines utilization of Spanish-language oncology web-based resources and evaluates oncology-related Internet browsing practices of Spanish-speaking patients. Methods: OncoLink (http://www.oncolink.org) is the oldest and among the largest Internet-based cancer information resources. In 9/2005, OncoLink pioneered OncoLink en español (OEE) (http://es.oncolink.org), a Spanish translation of OncoLink. Internet utilization data on these sites for 2006-2007 were compared. Results: Visits to OncoLink rose from 4,440,843 in 2006 to 5,125,952 in 2007. OEE had 204,578 unique visitors and 240,442 visits in 2006, and 351,228 visitors and 412,153 visits in 2007. While there was no time predilection for viewing OncoLink, less relative browsing on OEE was conducted during weekends and early morning hours. While OncoLink readers searched for information on the most common cancers in the United States, OEE readers most often search for gastric, vaginal, osteosarcoma, leukemia, penile, cervical, and testicular malignancies. Average visit duration on OEE was shorter, and fewer readers surveyed OEE >15 minutes (4.5% vs. 14.9%, p<0.001). Conclusions: Spanish-speaking users of web-based oncology resources are increasingly using the Internet to supplement their cancer knowledge. Limited available resources written in Spanish contribute to disparities in information access and disease outcomes. Spanish-speaking oncology readers differ from English-speaking readers in day and time of Internet browsing, visit duration, Internet search patterns, and types of cancers searched. By acknowledging these differences, content of web-based oncology resources can be developed to best target the needs of Spanish-speaking viewers. PMID:21654312

Automatic and continuous landslide monitoring: the Rotolon Web-based platform

NASA Astrophysics Data System (ADS)

Frigerio, Simone; Schenato, Luca; Mantovani, Matteo; Bossi, Giulia; Marcato, Gianluca; Cavalli, Marco; Pasuto, Alessandro

2013-04-01

Mount Rotolon (Eastern Italian Alps) is affected by a complex landslide that, since 1985, is threatening the nearby village of Recoaro Terme. The first written proof of a landslide occurrence dated back to 1798. After the last re-activation on November 2010 (637 mm of intense rainfall recorded in the 12 days prior the event), a mass of approximately 320.000 m3 detached from the south flank of Mount Rotolon and evolved into a fast debris flow that ran for about 3 km along the stream bed. A real-time monitoring system was required to detect early indication of rapid movements, potentially saving lives and property. A web-based platform for automatic and continuous monitoring was designed as a first step in the implementation of an early-warning system. Measurements collected by the automated geotechnical and topographic instrumentation, deployed over the landslide body, are gathered in a central box station. After the calibration process, they are transmitted by web services on a local server, where graphs, maps, reports and alert announcement are automatically generated and updated. All the processed information are available by web browser with different access rights. The web environment provides the following advantages: 1) data is collected from different data sources and matched on a single server-side frame 2) a remote user-interface allows regular technical maintenance and direct access to the instruments 3) data management system is synchronized and automatically tested 4) a graphical user interface on browser provides a user-friendly tool for decision-makers to interact with a system continuously updated. On this site two monitoring systems are actually on course: 1) GB-InSAR radar interferometer (University of Florence - Department of Earth Science) and 2) Automated Total Station (ATS) combined with extensometers network in a Web-based solution (CNR-IRPI Padova). This work deals with details on methodology, services and techniques adopted for the second

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

gemcWeb: A Cloud Based Nuclear Physics Simulation Software

NASA Astrophysics Data System (ADS)

Markelon, Sam

2017-09-01

gemcWeb allows users to run nuclear physics simulations from the web. Being completely device agnostic, scientists can run simulations from anywhere with an Internet connection. Having a full user system, gemcWeb allows users to revisit and revise their projects, and share configurations and results with collaborators. gemcWeb is based on simulation software gemc, which is based on standard GEant4. gemcWeb requires no C++, gemc, or GEant4 knowledge. Using a simple but powerful GUI allows users to configure their project from geometries and configurations stored on the deployment server. Simulations are then run on the server, with results being posted to the user, and then securely stored. Python based and open-source, the main version of gemcWeb is hosted internally at Jefferson National Labratory and used by the CLAS12 and Electron-Ion Collider Project groups. However, as the software is open-source, and hosted as a GitHub repository, an instance can be deployed on the open web, or any institution's intra-net. An instance can be configured to host experiments specific to an institution, and the code base can be modified by any individual or group. Special thanks to: Maurizio Ungaro, PhD., creator of gemc; Markus Diefenthaler, PhD., advisor; and Kyungseon Joo, PhD., advisor.

eLearning in education and advanced training in neuroradiology: introduction of a web-based teaching and learning application.

PubMed

Zajaczek, J E W; Götz, F; Kupka, T; Behrends, M; Haubitz, B; Donnerstag, F; Rodt, T; Walter, G F; Matthies, H K; Becker, H

2006-09-01

New information technologies offer the possibility of major improvements in the professional education and advanced training of physicians. The web-based, multimedia teaching and learning application Schoolbook has been created and utilized for neuroradiology. Schoolbook is technically based as a content management system and is realized in a LAMP environment. The content is generated with the help of the developed system and stored in a database. The layout is defined by a PHP application, and the webpages are generated from the system. Schoolbook is realized as an authoring tool so that it can be integrated into daily practice. This enables the teacher to autonomously process the content into the web-based application which is used for lectures, seminars and self-study. A multimedia case library is the central building block of Schoolbook for neuroradiology, whereby the learner is provided with original diagnostic and therapeutic data from numerous individual cases. The user can put individual emphasis on key learning points as there are various ways to work with the case histories. Besides the case-based way of teaching and learning, a systematically structured way of dealing with the content is available. eLearning offers various opportunities for teaching and learning in academic and scientific as well as in economic contexts. Web-based applications such as Schoolbook may be beneficial not only for basic university education but also for the realization of international educational programmes such as the European Master of Medical Science with a major in neuroradiology.

A novel web-enabled healthcare solution on health vault system.

PubMed

Liao, Lingxia; Chen, Min; Rodrigues, Joel J P C; Lai, Xiaorong; Vuong, Son

2012-06-01

Complicated Electronic Medical Records (EMR) systems have created problems in systems regarding an easy implementation and interoperability for a Web-enabled Healthcare Solution, which is normally provided by an independent healthcare giver with limited IT knowledge and interests. An EMR system with well-designed and user-friendly interface, such as Microsoft HealthVault System used as the back-end platform of a Web-enabled healthcare application will be an approach to deal with these problems. This paper analyzes the patient oriented Web-enabled healthcare service application as the new trend to delivery healthcare from hospital/clinic-centric to patient-centric, the current e-healthcare applications, and the main backend EMR systems. Then, we present a novel web-enabled healthcare solution based on Microsoft HealthVault EMR system to meet customers' needs, such as, low total cost, easily development and maintenance, and good interoperability. A sample system is given to show how the solution can be fulfilled, evaluated, and validated. We expect that this paper will provide a deep understanding of the available EMR systems, leading to insights for new solutions and approaches driven to next generation EMR systems.

SSE Announcement - New GIS Web Mapping Applications and Services

Atmospheric Science Data Center

2016-06-30

Dear SSE Users, We are excited to announce SSE-GIS v1.0.3 is now available! If you haven’t already noticed the link to the new SSE-GIS web application on the SSE homepage entitled “GIS Web Mapping ...

SCHeMA web-based observation data information system

NASA Astrophysics Data System (ADS)

Novellino, Antonio; Benedetti, Giacomo; D'Angelo, Paolo; Confalonieri, Fabio; Massa, Francesco; Povero, Paolo; Tercier-Waeber, Marie-Louise

2016-04-01

It is well recognized that the need of sharing ocean data among non-specialized users is constantly increasing. Initiatives that are built upon international standards will contribute to simplify data processing and dissemination, improve user-accessibility also through web browsers, facilitate the sharing of information across the integrated network of ocean observing systems; and ultimately provide a better understanding of the ocean functioning. The SCHeMA (Integrated in Situ Chemical MApping probe) Project is developing an open and modular sensing solution for autonomous in situ high resolution mapping of a wide range of anthropogenic and natural chemical compounds coupled to master bio-physicochemical parameters (www.schema-ocean.eu). The SCHeMA web system is designed to ensure user-friendly data discovery, access and download as well as interoperability with other projects through a dedicated interface that implements the Global Earth Observation System of Systems - Common Infrastructure (GCI) recommendations and the international Open Geospatial Consortium - Sensor Web Enablement (OGC-SWE) standards. This approach will insure data accessibility in compliance with major European Directives and recommendations. Being modular, the system allows the plug-and-play of commercially available probes as well as new sensor probess under development within the project. The access to the network of monitoring probes is provided via a web-based system interface that, being implemented as a SOS (Sensor Observation Service), is providing standard interoperability and access tosensor observations systems through O&M standard - as well as sensor descriptions - encoded in Sensor Model Language (SensorML). The use of common vocabularies in all metadatabases and data formats, to describe data in an already harmonized and common standard is a prerequisite towards consistency and interoperability. Therefore, the SCHeMA SOS has adopted the SeaVox common vocabularies populated by

Robust image obfuscation for privacy protection in Web 2.0 applications

NASA Astrophysics Data System (ADS)

Poller, Andreas; Steinebach, Martin; Liu, Huajian

2012-03-01

We present two approaches to robust image obfuscation based on permutation of image regions and channel intensity modulation. The proposed concept of robust image obfuscation is a step towards end-to-end security in Web 2.0 applications. It helps to protect the privacy of the users against threats caused by internet bots and web applications that extract biometric and other features from images for data-linkage purposes. The approaches described in this paper consider that images uploaded to Web 2.0 applications pass several transformations, such as scaling and JPEG compression, until the receiver downloads them. In contrast to existing approaches, our focus is on usability, therefore the primary goal is not a maximum of security but an acceptable trade-off between security and resulting image quality.

U.S. Geological Survey (USGS) Earthquake Web Applications

NASA Astrophysics Data System (ADS)

Fee, J.; Martinez, E.

2015-12-01

USGS Earthquake web applications provide access to earthquake information from USGS and other Advanced National Seismic System (ANSS) contributors. One of the primary goals of these applications is to provide a consistent experience for accessing both near-real time information as soon as it is available and historic information after it is thoroughly reviewed. Millions of people use these applications every month including people who feel an earthquake, emergency responders looking for the latest information about a recent event, and scientists researching historic earthquakes and their effects. Information from multiple catalogs and contributors is combined by the ANSS Comprehensive Catalog into one composite catalog, identifying the most preferred information from any source for each event. A web service and near-real time feeds provide access to all contributed data, and are used by a number of users and software packages. The Latest Earthquakes application displays summaries of many events, either near-real time feeds or custom searches, and the Event Page application shows detailed information for each event. Because all data is accessed through the web service, it can also be downloaded by users. The applications are maintained as open source projects on github, and use mobile-first and responsive-web-design approaches to work well on both mobile devices and desktop computers. http://earthquake.usgs.gov/earthquakes/map/

A user friendly system for ultrasound carotid intima-media thickness image interpretation

NASA Astrophysics Data System (ADS)

Zhu, Xiangjun; Kendall, Christopher B.; Hurst, R. Todd; Liang, Jianming

2011-03-01

Assessment of Carotid Intima-Media Thickness (CIMT) by B-mode ultrasound is a technically mature and reproducible technology. Given the high morbidity, mortality and the large societal burden associated with CV diseases, as a safe yet inexpensive tool, CIMT is increasingly utilized for cardiovascular (CV) risk stratification. However, CIMT requires a precise measure of the thickness of the intima and media layers of the carotid artery that can be tedious, time consuming, and demand specialized expertise and experience. To this end, we have developed a highly user-friendly system for semiautomatic CIMT image interpretation. Our contribution is the application of active contour models (snake models) with hard constraints, leading to an accurate, adaptive and user-friendly border detection algorithm. A comparison study with the CIMT measurement software in Siemens Syngo® Arterial Health Package shows that our system gives a small bias in mean (0.049 +/-0.051mm) and maximum (0.010 +/- 0.083 mm) CIMT measures and offers a higher reproducibility (average correlation coefficients were 0.948 and 0.844 in mean and maximum CIMT respectively (P <0.001)). This superior performance is attributed to our novel interface design for hard constraints in the snake models.

Web-Based Training for Primary Healthcare Workers in Rural China: A Qualitative Exploration of Stakeholders’ Perceptions

PubMed Central

Zhang, Zhixia; Zhan, Xingxin; Li, Yingxue; Hu, Rong; Yan, Weirong

2015-01-01

Background Equitable access to basic public health services is a priority in China. However, primary healthcare workers’ competence to deliver public health services is relatively poor because they lack professional training. Since the availability of web-based training has increased in China, the current study explored stakeholders’ perceptions of a web-based training program on basic public health services to understand their thoughts, experiences, and attitudes about it. Methods Six focus group discussions with primary healthcare workers and three with directors of township hospitals, county-level Health Bureaus, and county-level Centers for Disease Control and Prevention were conducted in Yichang City during 2013. Semi-structured topic guides were used to facilitate qualitative data collection. Audio recordings of the sessions were transcribed verbatim and theme analysis was performed. Results Most of the study’s participants, especially the village doctors, had insufficient knowledge of basic public health services. The existing training program for primary healthcare workers consisted of ineffective traditional face-to-face sessions and often posed accessibility problems for the trainees. Most of the study’s participants had a positive attitude about web-based learning and expressed a strong desire to receive this novel training approach because of its flexibility and convenience. The perceived barriers to utilizing the web-based training method included poor computer literacy, lack of personal interaction, inadequate infrastructure, and lack of time and motivation. The facilitators of this approach included the training content applicability, the user-friendly and interactive learning format, and policy support. Conclusions Web-based training on basic public health services is a promising option in rural China. The findings of the study will contribute knowledge to implementation of web-based training in similar settings. PMID:25961727

A web-based application for initial screening of living kidney donors: development, implementation and evaluation.

PubMed

Moore, D R; Feurer, I D; Zavala, E Y; Shaffer, D; Karp, S; Hoy, H; Moore, D E

2013-02-01

Most centers utilize phone or written surveys to screen candidates who self-refer to be living kidney donors. To increase efficiency and reduce resource utilization, we developed a web-based application to screen kidney donor candidates. The aim of this study was to evaluate the use of this web-based application. Method and time of referral were tabulated and descriptive statistics summarized demographic characteristics. Time series analyses evaluated use over time. Between January 1, 2011 and March 31, 2012, 1200 candidates self-referred to be living kidney donors at our center. Eight hundred one candidates (67%) completed the web-based survey and 399 (33%) completed a phone survey. Thirty-nine percent of donors accessed the application on nights and weekends. Postimplementation of the web-based application, there was a statistically significant increase (p < 0.001) in the number of self-referrals via the web-based application as opposed to telephone contact. Also, there was a significant increase (p = 0.025) in the total number of self-referrals post-implementation from 61 to 116 per month. An interactive web-based application is an effective strategy for the initial screening of donor candidates. The web-based application increased the ability to interface with donors, process them efficiently and ultimately increased donor self-referral at our center. © Copyright 2012 The American Society of Transplantation and the American Society of Transplant Surgeons.

Web-based Data Exploration, Exploitation and Visualization Tools for Satellite Sensor VIS/IR Calibration Applications

NASA Astrophysics Data System (ADS)

Gopalan, A.; Doelling, D. R.; Scarino, B. R.; Chee, T.; Haney, C.; Bhatt, R.

2016-12-01

The CERES calibration group at NASA/LaRC has developed and deployed a suite of online data exploration and visualization tools targeted towards a range of spaceborne VIS/IR imager calibration applications for the Earth Science community. These web-based tools are driven by the open-source R (Language for Statistical Computing and Visualization) with a web interface for the user to customize the results according to their application. The tool contains a library of geostationary and sun-synchronous imager spectral response functions (SRF), incoming solar spectra, SCIAMACHY and Hyperion Earth reflected visible hyper-spectral data, and IASI IR hyper-spectral data. The suite of six specific web-based tools was designed to provide critical information necessary for sensor cross-calibration. One of the challenges of sensor cross-calibration is accounting for spectral band differences and may introduce biases if not handled properly. The spectral band adjustment factors (SBAF) are a function of the earth target, atmospheric and cloud conditions or scene type and angular conditions, when obtaining sensor radiance pairs. The SBAF will need to be customized for each inter-calibration target and sensor pair. The advantages of having a community open source tool are: 1) only one archive of SCIAMACHY, Hyperion, and IASI datasets needs to be maintained, which is on the order of 50TB. 2) the framework will allow easy incorporation of new satellite SRFs and hyper-spectral datasets and associated coincident atmospheric and cloud properties, such as PW. 3) web tool or SBAF algorithm improvements or suggestions when incorporated can benefit the community at large. 4) The customization effort is on the user rather than on the host. In this paper we discuss each of these tools in detail and explore the variety of advanced options that can be used to constrain the results along with specific use cases to highlight the value-added by these datasets.

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.

Depressive symptoms and web user experience

PubMed Central

Thielsch, Carolin

2018-01-01

Background Depression, as one of the most prevalent mental disorders, is expected to become a leading cause of disability. While evidence-based treatments are not always easily accessible, Internet-based information and self-help appears as a promising approach to improve the strained supply situation by avoiding barriers of traditional offline treatment. User experience in the domain of mental problems therefore emerges as an important research topic. The aim of our study is to investigate the impact of depressive symptoms on subjective and objective measures of web user experience. Method In this two-part online study (Ntotal = 721) we investigate the relationship between depressive symptoms of web users and basic website characteristics (i.e., content, subjective and objective usability, aesthetics). Participants completed search and memory tasks on different fully-functional websites. In addition, they were asked to evaluate the given websites with standardized measures and were screened for symptoms of depression using the PHQ-9. We used structural equation modeling (SEM) to determine whether depression severity affects users’ perception of and performance in using information websites. Results We found significant associations between depressive symptoms and subjective user experience, specifically of website content, usability, and aesthetics, as well as an effect of content perception on the overall appraisal of a website in terms of the intention to visit it again. Small yet significant negative effects of depression severity on all named subjective website evaluations were revealed, leading to an indirect negative effect on the intention to revisit a website via impaired content perceptions. However, objective task performance was not influenced by depressiveness of users. Discussion Depression emerges as capable of altering the subjective perception of a website to some extend with respect to the main features content, usability, and aesthetics. The

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.

Creating the User-Friendly Library by Evaluating Patron Perception of Signage.

ERIC Educational Resources Information Center

Bosman, Ellen; Rusinek, Carol

1997-01-01

Librarians at Indiana University Northwest Library surveyed patrons on how to make the library's collection and services more accessible by improving signage. Examines the effectiveness of signage to instruct users, reduce difficulties and fears, ameliorate negative experiences, and contribute to a user-friendly environment. (AEF)

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-01-01

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

Web-based GIS: the vector-borne disease airline importation risk (VBD-AIR) tool

PubMed Central

2012-01-01

Background Over the past century, the size and complexity of the air travel network has increased dramatically. Nowadays, there are 29.6 million scheduled flights per year and around 2.7 billion passengers are transported annually. The rapid expansion of the network increasingly connects regions of endemic vector-borne disease with the rest of the world, resulting in challenges to health systems worldwide in terms of vector-borne pathogen importation and disease vector invasion events. Here we describe the development of a user-friendly Web-based GIS tool: the Vector-Borne Disease Airline Importation Risk Tool (VBD-AIR), to help better define the roles of airports and airlines in the transmission and spread of vector-borne diseases. Methods Spatial datasets on modeled global disease and vector distributions, as well as climatic and air network traffic data were assembled. These were combined to derive relative risk metrics via air travel for imported infections, imported vectors and onward transmission, and incorporated into a three-tier server architecture in a Model-View-Controller framework with distributed GIS components. A user-friendly web-portal was built that enables dynamic querying of the spatial databases to provide relevant information. Results The VBD-AIR tool constructed enables the user to explore the interrelationships among modeled global distributions of vector-borne infectious diseases (malaria. dengue, yellow fever and chikungunya) and international air service routes to quantify seasonally changing risks of vector and vector-borne disease importation and spread by air travel, forming an evidence base to help plan mitigation strategies. The VBD-AIR tool is available at http://www.vbd-air.com. Conclusions VBD-AIR supports a data flow that generates analytical results from disparate but complementary datasets into an organized cartographical presentation on a web map for the assessment of vector-borne disease movements on the air travel network

Web-based GIS: the vector-borne disease airline importation risk (VBD-AIR) tool.

PubMed

Huang, Zhuojie; Das, Anirrudha; Qiu, Youliang; Tatem, Andrew J

2012-08-14

Over the past century, the size and complexity of the air travel network has increased dramatically. Nowadays, there are 29.6 million scheduled flights per year and around 2.7 billion passengers are transported annually. The rapid expansion of the network increasingly connects regions of endemic vector-borne disease with the rest of the world, resulting in challenges to health systems worldwide in terms of vector-borne pathogen importation and disease vector invasion events. Here we describe the development of a user-friendly Web-based GIS tool: the Vector-Borne Disease Airline Importation Risk Tool (VBD-AIR), to help better define the roles of airports and airlines in the transmission and spread of vector-borne diseases. Spatial datasets on modeled global disease and vector distributions, as well as climatic and air network traffic data were assembled. These were combined to derive relative risk metrics via air travel for imported infections, imported vectors and onward transmission, and incorporated into a three-tier server architecture in a Model-View-Controller framework with distributed GIS components. A user-friendly web-portal was built that enables dynamic querying of the spatial databases to provide relevant information. The VBD-AIR tool constructed enables the user to explore the interrelationships among modeled global distributions of vector-borne infectious diseases (malaria. dengue, yellow fever and chikungunya) and international air service routes to quantify seasonally changing risks of vector and vector-borne disease importation and spread by air travel, forming an evidence base to help plan mitigation strategies. The VBD-AIR tool is available at http://www.vbd-air.com. VBD-AIR supports a data flow that generates analytical results from disparate but complementary datasets into an organized cartographical presentation on a web map for the assessment of vector-borne disease movements on the air travel network. The framework built provides a flexible

GrTEdb: the first web-based database of transposable elements in cotton (Gossypium raimondii).

PubMed

Xu, Zhenzhen; Liu, Jing; Ni, Wanchao; Peng, Zhen; Guo, Yue; Ye, Wuwei; Huang, Fang; Zhang, Xianggui; Xu, Peng; Guo, Qi; Shen, Xinlian; Du, Jianchang

2017-01-01

Although several diploid and tetroploid Gossypium species genomes have been sequenced, the well annotated web-based transposable elements (TEs) database is lacking. To better understand the roles of TEs in structural, functional and evolutionary dynamics of the cotton genome, a comprehensive, specific, and user-friendly web-based database, Gossypium raimondii transposable elements database (GrTEdb), was constructed. A total of 14 332 TEs were structurally annotated and clearly categorized in G. raimondii genome, and these elements have been classified into seven distinct superfamilies based on the order of protein-coding domains, structures and/or sequence similarity, including 2929 Copia-like elements, 10 368 Gypsy-like elements, 299 L1 , 12 Mutators , 435 PIF-Harbingers , 275 CACTAs and 14 Helitrons . Meanwhile, the web-based sequence browsing, searching, downloading and blast tool were implemented to help users easily and effectively to annotate the TEs or TE fragments in genomic sequences from G. raimondii and other closely related Gossypium species. GrTEdb provides resources and information related with TEs in G. raimondii , and will facilitate gene and genome analyses within or across Gossypium species, evaluating the impact of TEs on their host genomes, and investigating the potential interaction between TEs and protein-coding genes in Gossypium species. http://www.grtedb.org/. © The Author(s) 2017. Published by Oxford University Press.

Global Location-Based Access to Web Applications Using Atom-Based Automatic Update

NASA Astrophysics Data System (ADS)

Singh, Kulwinder; Park, Dong-Won

We propose an architecture which enables people to enquire about information available in directory services by voice using regular phones. We implement a Virtual User Agent (VUA) which mediates between the human user and a business directory service. The system enables the user to search for the nearest clinic, gas station by price, motel by price, food / coffee, banks/ATM etc. and fix an appointment, or automatically establish a call between the user and the business party if the user prefers. The user also has an option to receive appointment confirmation by phone, SMS, or e-mail. The VUA is accessible by a toll free DID (Direct Inward Dialing) number using a phone by anyone, anywhere, anytime. We use the Euclidean formula for distance measurement. Since, shorter geodesic distances (on the Earth’s surface) correspond to shorter Euclidean distances (measured by a straight line through the Earth). Our proposed architecture uses Atom XML syndication format protocol for data integration, VoiceXML for creating the voice user interface (VUI) and CCXML for controlling the call components. We also provide an efficient algorithm for parsing Atom feeds which provide data to the system. Moreover, we describe a cost-effective way for providing global access to the VUA based on Asterisk (an open source IP-PBX). We also provide some information on how our system can be integrated with GPS for locating the user coordinates and therefore efficiently and spontaneously enhancing the system response. Additionally, the system has a mechanism for validating the phone numbers in its database, and it updates the number and other information such as daily price of gas, motel etc. automatically using an Atom-based feed. Currently, the commercial directory services (Example 411) do not have facilities to update the listing in the database automatically, so that why callers most of the times get out-of-date phone numbers or other information. Our system can be integrated very easily

SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments.

PubMed

Ajawatanawong, Pravech; Atkinson, Gemma C; Watson-Haigh, Nathan S; Mackenzie, Bryony; Baldauf, Sandra L

2012-07-01

Analyses of multiple sequence alignments generally focus on well-defined conserved sequence blocks, while the rest of the alignment is largely ignored or discarded. This is especially true in phylogenomics, where large multigene datasets are produced through automated pipelines. However, some of the most powerful phylogenetic markers have been found in the variable length regions of multiple alignments, particularly insertions/deletions (indels) in protein sequences. We have developed Sequence Feature and Indel Region Extractor (SeqFIRE) to enable the automated identification and extraction of indels from protein sequence alignments. The program can also extract conserved blocks and identify fast evolving sites using a combination of conservation and entropy. All major variables can be adjusted by the user, allowing them to identify the sets of variables most suited to a particular analysis or dataset. Thus, all major tasks in preparing an alignment for further analysis are combined in a single flexible and user-friendly program. The output includes a numbered list of indels, alignments in NEXUS format with indels annotated or removed and indel-only matrices. SeqFIRE is a user-friendly web application, freely available online at www.seqfire.org/.

IFIS Model-Plus: A Web-Based GUI for Visualization, Comparison and Evaluation of Distributed Flood Forecasts and Hindcasts

NASA Astrophysics Data System (ADS)

Krajewski, W. F.; Della Libera Zanchetta, A.; Mantilla, R.; Demir, I.

2017-12-01

This work explores the use of hydroinformatics tools to provide an user friendly and accessible interface for executing and assessing the output of realtime flood forecasts using distributed hydrological models. The main result is the implementation of a web system that uses an Iowa Flood Information System (IFIS)-based environment for graphical displays of rainfall-runoff simulation results for both real-time and past storm events. It communicates with ASYNCH ODE solver to perform large-scale distributed hydrological modeling based on segmentation of the terrain into hillslope-link hydrologic units. The cyber-platform also allows hindcast of model performance by testing multiple model configurations and assumptions of vertical flows in the soils. The scope of the currently implemented system is the entire set of contributing watersheds for the territory of the state of Iowa. The interface provides resources for visualization of animated maps for different water-related modeled states of the environment, including flood-waves propagation with classification of flood magnitude, runoff generation, surface soil moisture and total water column in the soil. Additional tools for comparing different model configurations and performing model evaluation by comparing to observed variables at monitored sites are also available. The user friendly interface has been published to the web under the URL http://ifis.iowafloodcenter.org/ifis/sc/modelplus/.

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

NASA Astrophysics Data System (ADS)

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

2011-06-01

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

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.

User Requirements Based Development of a Web Portal for Chronic Patients.

PubMed

Kopanitsa, Georgy

2017-01-01

In the current study, we tried to identify practices that help overcoming data entering and operational barriers, and involve patients and doctors in the development process to improve the acceptance of Web portals for chronic patients. This paper presents a follow up project implementing a Web portal for chronic patients considering previously studied barriers and opportunities. The following methods were applied to facilitate the acceptance of the portal: 1) a joint use case definition and discussion session before starting the development; 2) involvement of the users in prototyping the portal; 3) training of doctors and patients together before the implementation. During the first week of the portal's operation we have measured the number of data transactions and the number of active users to compare it with previous experience. The first weeks of operating the portal, we could observe an active contribution of doctors and patients, who submitted vital signs data and recommendations to the portal.

SimArray: a user-friendly and user-configurable microarray design tool

PubMed Central

Auburn, Richard P; Russell, Roslin R; Fischer, Bettina; Meadows, Lisa A; Sevillano Matilla, Santiago; Russell, Steven

2006-01-01

Background Microarrays were first developed to assess gene expression but are now also used to map protein-binding sites and to assess allelic variation between individuals. Regardless of the intended application, efficient production and appropriate array design are key determinants of experimental success. Inefficient production can make larger-scale studies prohibitively expensive, whereas poor array design makes normalisation and data analysis problematic. Results We have developed a user-friendly tool, SimArray, which generates a randomised spot layout, computes a maximum meta-grid area, and estimates the print time, in response to user-specified design decisions. Selected parameters include: the number of probes to be printed; the microtitre plate format; the printing pin configuration, and the achievable spot density. SimArray is compatible with all current robotic spotters that employ 96-, 384- or 1536-well microtitre plates, and can be configured to reflect most production environments. Print time and maximum meta-grid area estimates facilitate evaluation of each array design for its suitability. Randomisation of the spot layout facilitates correction of systematic biases by normalisation. Conclusion SimArray is intended to help both established researchers and those new to the microarray field to develop microarray designs with randomised spot layouts that are compatible with their specific production environment. SimArray is an open-source program and is available from . PMID:16509966