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

A user-friendly, dynamic web environment for remote data browsing and analysis of multiparametric geophysical data within the MULTIMO project

NASA Astrophysics Data System (ADS)

Carniel, Roberto; Di Cecca, Mauro; Jaquet, Olivier

2006-05-01

In the framework of the EU-funded project "Multi-disciplinary monitoring, modelling and forecasting of volcanic hazard" (MULTIMO), multiparametric data have been recorded at the MULTIMO station in Montserrat. Moreover, several other long time series, recorded at Montserrat and at other volcanoes, have been acquired in order to test stochastic and deterministic methodologies under development. Creating a general framework to handle data efficiently is a considerable task even for homogeneous data. In the case of heterogeneous data, this becomes a major issue. A need for a consistent way of browsing such a heterogeneous dataset in a user-friendly way therefore arose. Additionally, a framework for applying the calculation of the developed dynamical parameters on the data series was also needed in order to easily keep these parameters under control, e.g. for monitoring, research or forecasting purposes. The solution which we present is completely based on Open Source software, including Linux operating system, MySql database management system, Apache web server, Zope application server, Scilab math engine, Plone content management framework, Unified Modelling Language. From the user point of view the main advantage is the possibility of browsing through datasets recorded on different volcanoes, with different instruments, with different sampling frequencies, stored in different formats, all via a consistent, user- friendly interface that transparently runs queries to the database, gets the data from the main storage units, generates the graphs and produces dynamically generated web pages to interact with the user. The involvement of third parties for continuing the development in the Open Source philosophy and/or extending the application fields is now sought.

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 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.

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

PubMed

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

2018-06-05

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

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/.

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

PubMed

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

2015-01-01

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

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).

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-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.

Project Assessment Skills Web Application

NASA Technical Reports Server (NTRS)

Goff, Samuel J.

2013-01-01

The purpose of this project is to utilize Ruby on Rails to create a web application that will replace a spreadsheet keeping track of training courses and tasks. The goal is to create a fast and easy to use web application that will allow users to track progress on training courses. This application will allow users to update and keep track of all of the training required of them. The training courses will be organized by group and by user, making readability easier. This will also allow group leads and administrators to get a sense of how everyone is progressing in training. Currently, updating and finding information from this spreadsheet is a long and tedious task. By upgrading to a web application, finding and updating information will be easier than ever as well as adding new training courses and tasks. Accessing this data will be much easier in that users just have to go to a website and log in with NDC credentials rather than request the relevant spreadsheet from the holder. In addition to Ruby on Rails, I will be using JavaScript, CSS, and jQuery to help add functionality and ease of use to my web application. This web application will include a number of features that will help update and track progress on training. For example, one feature will be to track progress of a whole group of users to be able to see how the group as a whole is progressing. Another feature will be to assign tasks to either a user or a group of users. All of these together will create a user friendly and functional web application.

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.

Gigwa-Genotype investigator for genome-wide analyses.

PubMed

Sempéré, Guilhem; Philippe, Florian; Dereeper, Alexis; Ruiz, Manuel; Sarah, Gautier; Larmande, Pierre

2016-06-06

Exploring the structure of genomes and analyzing their evolution is essential to understanding the ecological adaptation of organisms. However, with the large amounts of data being produced by next-generation sequencing, computational challenges arise in terms of storage, search, sharing, analysis and visualization. This is particularly true with regards to studies of genomic variation, which are currently lacking scalable and user-friendly data exploration solutions. Here we present Gigwa, a web-based tool that provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also on genotype patterns. The data storage relies on MongoDB, which offers good scalability properties. Gigwa can handle multiple databases and may be deployed in either single- or multi-user mode. In addition, it provides a wide range of popular export formats. The Gigwa application is suitable for managing large amounts of genomic variation data. Its user-friendly web interface makes such processing widely accessible. It can either be simply deployed on a workstation or be used to provide a shared data portal for a given community of researchers.

A user-friendly mathematical modelling web interface to assist local decision making in the fight against drug-resistant tuberculosis.

PubMed

Ragonnet, Romain; Trauer, James M; Denholm, Justin T; Marais, Ben J; McBryde, Emma S

2017-05-30

Multidrug-resistant and rifampicin-resistant tuberculosis (MDR/RR-TB) represent an important challenge for global tuberculosis (TB) control. The high rates of MDR/RR-TB observed among re-treatment cases can arise from diverse pathways: de novo amplification during initial treatment, inappropriate treatment of undiagnosed MDR/RR-TB, relapse despite appropriate treatment, or reinfection with MDR/RR-TB. Mathematical modelling allows quantification of the contribution made by these pathways in different settings. This information provides valuable insights for TB policy-makers, allowing better contextualised solutions. However, mathematical modelling outputs need to consider local data and be easily accessible to decision makers in order to improve their usefulness. We present a user-friendly web-based modelling interface, which can be used by people without technical knowledge. Users can input their own parameter values and produce estimates for their specific setting. This innovative tool provides easy access to mathematical modelling outputs that are highly relevant to national TB control programs. In future, the same approach could be applied to a variety of modelling applications, enhancing local decision making.

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 analyzed data, according to the user needs.

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.

E-TALEN: a web tool to design TALENs for genome engineering.

PubMed

Heigwer, Florian; Kerr, Grainne; Walther, Nike; Glaeser, Kathrin; Pelz, Oliver; Breinig, Marco; Boutros, Michael

2013-11-01

Use of transcription activator-like effector nucleases (TALENs) is a promising new technique in the field of targeted genome engineering, editing and reverse genetics. Its applications span from introducing knockout mutations to endogenous tagging of proteins and targeted excision repair. Owing to this wide range of possible applications, there is a need for fast and user-friendly TALEN design tools. We developed E-TALEN (http://www.e-talen.org), a web-based tool to design TALENs for experiments of varying scale. E-TALEN enables the design of TALENs against a single target or a large number of target genes. We significantly extended previously published design concepts to consider genomic context and different applications. E-TALEN guides the user through an end-to-end design process of de novo TALEN pairs, which are specific to a certain sequence or genomic locus. Furthermore, E-TALEN offers a functionality to predict targeting and specificity for existing TALENs. Owing to the computational complexity of many of the steps in the design of TALENs, particular emphasis has been put on the implementation of fast yet accurate algorithms. We implemented a user-friendly interface, from the input parameters to the presentation of results. An additional feature of E-TALEN is the in-built sequence and annotation database available for many organisms, including human, mouse, zebrafish, Drosophila and Arabidopsis, which can be extended in the future.

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

PubMed Central

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

2007-01-01

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

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

The GLOBE Visualization Project: Using WWW in the Classroom.

ERIC Educational Resources Information Center

de La Beaujardiere, J-F; And Others

1997-01-01

Describes a World Wide Web-based, user-friendly, language-independent graphical user interface providing access to visualizations created for GLOBE (Global Learning and Observations to Benefit the Environment), a multinational program of education and science. (DDR)

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.

WILBER and PyWEED: Event-based Seismic Data Request Tools

NASA Astrophysics Data System (ADS)

Falco, N.; Clark, A.; Trabant, C. M.

2017-12-01

WILBER and PyWEED are two user-friendly tools for requesting event-oriented seismic data. Both tools provide interactive maps and other controls for browsing and filtering event and station catalogs, and downloading data for selected event/station combinations, where the data window for each event/station pair may be defined relative to the arrival time of seismic waves from the event to that particular station. Both tools allow data to be previewed visually, and can download data in standard miniSEED, SAC, and other formats, complete with relevant metadata for performing instrument correction. WILBER is a web application requiring only a modern web browser. Once the user has selected an event, WILBER identifies all data available for that time period, and allows the user to select stations based on criteria such as the station's distance and orientation relative to the event. When the user has finalized their request, the data is collected and packaged on the IRIS server, and when it is ready the user is sent a link to download. PyWEED is a downloadable, cross-platform (Macintosh / Windows / Linux) application written in Python. PyWEED allows a user to select multiple events and stations, and will download data for each event/station combination selected. PyWEED is built around the ObsPy seismic toolkit, and allows direct interaction and control of the application through a Python interactive console.

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…

The development of a clinical outcomes survey research application: Assessment Center.

PubMed

Gershon, Richard; Rothrock, Nan E; Hanrahan, Rachel T; Jansky, Liz J; Harniss, Mark; Riley, William

2010-06-01

The National Institutes of Health sponsored Patient-Reported Outcome Measurement Information System (PROMIS) aimed to create item banks and computerized adaptive tests (CATs) across multiple domains for individuals with a range of chronic diseases. Web-based software was created to enable a researcher to create study-specific Websites that could administer PROMIS CATs and other instruments to research participants or clinical samples. This paper outlines the process used to develop a user-friendly, free, Web-based resource (Assessment Center) for storage, retrieval, organization, sharing, and administration of patient-reported outcomes (PRO) instruments. Joint Application Design (JAD) sessions were conducted with representatives from numerous institutions in order to supply a general wish list of features. Use Cases were then written to ensure that end user expectations matched programmer specifications. Program development included daily programmer "scrum" sessions, weekly Usability Acceptability Testing (UAT) and continuous Quality Assurance (QA) activities pre- and post-release. Assessment Center includes features that promote instrument development including item histories, data management, and storage of statistical analysis results. This case study of software development highlights the collection and incorporation of user input throughout the development process. Potential future applications of Assessment Center in clinical research are discussed.

DyNAVacS: an integrative tool for optimized DNA vaccine design.

PubMed

Harish, Nagarajan; Gupta, Rekha; Agarwal, Parul; Scaria, Vinod; Pillai, Beena

2006-07-01

DNA vaccines have slowly emerged as keystones in preventive immunology due to their versatility in inducing both cell-mediated as well as humoral immune responses. The design of an efficient DNA vaccine, involves choice of a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses and providing additional sequence signals for efficient translation. DyNAVacS is a web-based tool created for rapid and easy design of DNA vaccines. It follows a step-wise design flow, which guides the user through the various sequential steps in the design of the vaccine. Further, it allows restriction enzyme mapping, design of primers spanning user specified sequences and provides information regarding the vectors currently used for generation of DNA vaccines. The web version uses Apache HTTP server. The interface was written in HTML and utilizes the Common Gateway Interface scripts written in PERL for functionality. DyNAVacS is an integrated tool consisting of user-friendly programs, which require minimal information from the user. The software is available free of cost, as a web based application at URL: http://miracle.igib.res.in/dynavac/.

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 implementation. Conclusions IM proved useful to develop an intervention for targeted Ct testing among young people. We believe this to be the first web-based outreach screening strategy which combines chain referral sampling with the delivery of targeted Ct testing to high risk young people within their sexual and social networks. PMID:24148656

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 to develop an intervention for targeted Ct testing among young people. We believe this to be the first web-based outreach screening strategy which combines chain referral sampling with the delivery of targeted Ct testing to high risk young people within their sexual and social networks.

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.

Explore, Visualize, and Analyze Functional Cancer Proteomic Data Using the Cancer Proteome Atlas. | Office of Cancer Genomics

Cancer.gov

Reverse-phase protein arrays (RPPA) represent a powerful functional proteomic approach to elucidate cancer-related molecular mechanisms and to develop novel cancer therapies. To facilitate community-based investigation of the large-scale protein expression data generated by this platform, we have developed a user-friendly, open-access bioinformatic resource, The Cancer Proteome Atlas (TCPA, http://tcpaportal.org), which contains two separate web applications.

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.

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

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-25

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

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.

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

NCBI GEO: mining tens of millions of expression profiles--database and tools update.

PubMed

Barrett, Tanya; Troup, Dennis B; Wilhite, Stephen E; Ledoux, Pierre; Rudnev, Dmitry; Evangelista, Carlos; Kim, Irene F; Soboleva, Alexandra; Tomashevsky, Maxim; Edgar, Ron

2007-01-01

The Gene Expression Omnibus (GEO) repository at the National Center for Biotechnology Information (NCBI) archives and freely disseminates microarray and other forms of high-throughput data generated by the scientific community. The database has a minimum information about a microarray experiment (MIAME)-compliant infrastructure that captures fully annotated raw and processed data. Several data deposit options and formats are supported, including web forms, spreadsheets, XML and Simple Omnibus Format in Text (SOFT). In addition to data storage, a collection of user-friendly web-based interfaces and applications are available to help users effectively explore, visualize and download the thousands of experiments and tens of millions of gene expression patterns stored in GEO. This paper provides a summary of the GEO database structure and user facilities, and describes recent enhancements to database design, performance, submission format options, data query and retrieval utilities. GEO is accessible at http://www.ncbi.nlm.nih.gov/geo/

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 for the intervention to be of use to the target audience; and (2) it yields feedback on the design of the application that is broader than color and buttons, but encompasses comments on the quality of the service that the application offers.

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 clarify the needs that have to be met for the intervention to be of use to the target audience; and (2) it yields feedback on the design of the application that is broader than color and buttons, but encompasses comments on the quality of the service that the application offers. PMID:23425322

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.…

SBMLmod: a Python-based web application and web service for efficient data integration and model simulation.

PubMed

Schäuble, Sascha; Stavrum, Anne-Kristin; Bockwoldt, Mathias; Puntervoll, Pål; Heiland, Ines

2017-06-24

Systems Biology Markup Language (SBML) is the standard model representation and description language in systems biology. Enriching and analysing systems biology models by integrating the multitude of available data, increases the predictive power of these models. This may be a daunting task, which commonly requires bioinformatic competence and scripting. We present SBMLmod, a Python-based web application and service, that automates integration of high throughput data into SBML models. Subsequent steady state analysis is readily accessible via the web service COPASIWS. We illustrate the utility of SBMLmod by integrating gene expression data from different healthy tissues as well as from a cancer dataset into a previously published model of mammalian tryptophan metabolism. SBMLmod is a user-friendly platform for model modification and simulation. The web application is available at http://sbmlmod.uit.no , whereas the WSDL definition file for the web service is accessible via http://sbmlmod.uit.no/SBMLmod.wsdl . Furthermore, the entire package can be downloaded from https://github.com/MolecularBioinformatics/sbml-mod-ws . We envision that SBMLmod will make automated model modification and simulation available to a broader research community.

Using the Browser for Science: A Collaborative Toolkit for Astronomy

NASA Astrophysics Data System (ADS)

Connolly, A. J.; Smith, I.; Krughoff, K. S.; Gibson, R.

2011-07-01

Astronomical surveys have yielded hundreds of terabytes of catalogs and images that span many decades of the electromagnetic spectrum. Even when observatories provide user-friendly web interfaces, exploring these data resources remains a complex and daunting task. In contrast, gadgets and widgets have become popular in social networking (e.g. iGoogle, Facebook). They provide a simple way to make complex data easily accessible that can be customized based on the interest of the user. With ASCOT (an AStronomical COllaborative Toolkit) we expand on these concepts to provide a customizable and extensible gadget framework for use in science. Unlike iGoogle, where all of the gadgets are independent, the gadgets we develop communicate and share information, enabling users to visualize and interact with data through multiple, simultaneous views. With this approach, web-based applications for accessing and visualizing data can be generated easily and, by linking these tools together, integrated and powerful data analysis and discovery tools can be constructed.

ProteoSign: an end-user online differential proteomics statistical analysis platform.

PubMed

Efstathiou, Georgios; Antonakis, Andreas N; Pavlopoulos, Georgios A; Theodosiou, Theodosios; Divanach, Peter; Trudgian, David C; Thomas, Benjamin; Papanikolaou, Nikolas; Aivaliotis, Michalis; Acuto, Oreste; Iliopoulos, Ioannis

2017-07-03

Profiling of proteome dynamics is crucial for understanding cellular behavior in response to intrinsic and extrinsic stimuli and maintenance of homeostasis. Over the last 20 years, mass spectrometry (MS) has emerged as the most powerful tool for large-scale identification and characterization of proteins. Bottom-up proteomics, the most common MS-based proteomics approach, has always been challenging in terms of data management, processing, analysis and visualization, with modern instruments capable of producing several gigabytes of data out of a single experiment. Here, we present ProteoSign, a freely available web application, dedicated in allowing users to perform proteomics differential expression/abundance analysis in a user-friendly and self-explanatory way. Although several non-commercial standalone tools have been developed for post-quantification statistical analysis of proteomics data, most of them are not end-user appealing as they often require very stringent installation of programming environments, third-party software packages and sometimes further scripting or computer programming. To avoid this bottleneck, we have developed a user-friendly software platform accessible via a web interface in order to enable proteomics laboratories and core facilities to statistically analyse quantitative proteomics data sets in a resource-efficient manner. ProteoSign is available at http://bioinformatics.med.uoc.gr/ProteoSign and the source code at https://github.com/yorgodillo/ProteoSign. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Region Evolution eXplorer - A tool for discovering evolution trends in ontology regions.

PubMed

Christen, Victor; Hartung, Michael; Groß, Anika

2015-01-01

A large number of life science ontologies has been developed to support different application scenarios such as gene annotation or functional analysis. The continuous accumulation of new insights and knowledge affects specific portions in ontologies and thus leads to their adaptation. Therefore, it is valuable to study which ontology parts have been extensively modified or remained unchanged. Users can monitor the evolution of an ontology to improve its further development or apply the knowledge in their applications. Here we present REX (Region Evolution eXplorer) a web-based system for exploring the evolution of ontology parts (regions). REX provides an analysis platform for currently about 1,000 versions of 16 well-known life science ontologies. Interactive workflows allow an explorative analysis of changing ontology regions and can be used to study evolution trends for long-term periods. REX is a web application providing an interactive and user-friendly interface to identify (un)stable regions in large life science ontologies. It is available at http://www.izbi.de/rex.

DGIdb 3.0: a redesign and expansion of the drug-gene interaction database.

PubMed

Cotto, Kelsy C; Wagner, Alex H; Feng, Yang-Yang; Kiwala, Susanna; Coffman, Adam C; Spies, Gregory; Wollam, Alex; Spies, Nicholas C; Griffith, Obi L; Griffith, Malachi

2018-01-04

The drug-gene interaction database (DGIdb, www.dgidb.org) consolidates, organizes and presents drug-gene interactions and gene druggability information from papers, databases and web resources. DGIdb normalizes content from 30 disparate sources and allows for user-friendly advanced browsing, searching and filtering for ease of access through an intuitive web user interface, application programming interface (API) and public cloud-based server image. DGIdb v3.0 represents a major update of the database. Nine of the previously included 24 sources were updated. Six new resources were added, bringing the total number of sources to 30. These updates and additions of sources have cumulatively resulted in 56 309 interaction claims. This has also substantially expanded the comprehensive catalogue of druggable genes and anti-neoplastic drug-gene interactions included in the DGIdb. Along with these content updates, v3.0 has received a major overhaul of its codebase, including an updated user interface, preset interaction search filters, consolidation of interaction information into interaction groups, greatly improved search response times and upgrading the underlying web application framework. In addition, the expanded API features new endpoints which allow users to extract more detailed information about queried drugs, genes and drug-gene interactions, including listings of PubMed IDs, interaction type and other interaction metadata.

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.

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…

m-YouTube Mobile UI: Video Selection Based on Social Influence

NASA Astrophysics Data System (ADS)

Marcus, Aaron; Perez, Angel

The ease-of-use of Web-based video-publishing services provided by applications like YouTube has encouraged a new means of asynchronous communication, in which users can post videos not only to make them public for review and criticism, but also as a way to express moods, feelings, or intentions to an ever-growing network of friends. Following the current trend of porting Web applications onto mobile platforms, the authors sought to explore user-interface design issues of a mobile-device-based YouTube, which they call m-YouTube. They first analyzed the elements of success of the current YouTube Web site and observed its functionality. Then, they looked for unsolved issues that could give benefit through information-visualization design for small screens on mobile phones to explore a mobile version of such a product/service. The biggest challenge was to reduce the number of functions and amount information to fit into a mobile phone screen, but still be usable, useful, and appealing within the YouTube context of use and user experience. Borrowing ideas from social research in the area of social influence processes, they made design decisions aiming to help YouTube users to make the decision of what video content to watch and to increase the chances of YouTube authors being evaluated and observed by peers. The paper proposes a means to visualize large amounts of video relevant to YouTube users by using their friendship network as a relevance indicator to help in the decision-making process.

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 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 analyzed data, according to the user needs. PMID:26046471

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

PubMed

Barrett, Tanya; Edgar, Ron

2006-01-01

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

A JAVA-based multimedia tool for clinical practice guidelines.

PubMed

Maojo, V; Herrero, C; Valenzuela, F; Crespo, J; Lazaro, P; Pazos, A

1997-01-01

We have developed a specific language for the representation of Clinical Practice Guidelines (CPGs) and Windows C++ and platform independent JAVA applications for multimedia presentation and edition of electronically stored CPGs. This approach facilitates translation of guidelines and protocols from paper to computer-based flowchart representations. Users can navigate through the algorithm with a friendly user interface and access related multimedia information within the context of each clinical problem. CPGs can be stored in a computer server and distributed over the World Wide Web, facilitating dissemination, local adaptation, and use as a reference element in medical care. We have chosen the Agency for Health Care and Policy Research's heart failure guideline to demonstrate the capabilities of our tool.

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

PubMed Central

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

2016-01-01

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

Lexicon Sextant: Modeling a Mnemonic System for Customizable Browser Information Organization and Management

ERIC Educational Resources Information Center

Shen, Siu-Tsen

2016-01-01

This paper presents an ongoing study of the development of a customizable web browser information organization and management system, which the author has named Lexicon Sextant (LS). LS is a user friendly, graphical web based add-on to the latest generation of web browsers, such as Google Chrome, making it easier and more intuitive to store and…

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.

The development of a clinical outcomes survey research application: Assessment CenterSM

PubMed Central

Rothrock, Nan E.; Hanrahan, Rachel T.; Jansky, Liz J.; Harniss, Mark; Riley, William

2013-01-01

Introduction The National Institutes of Health sponsored Patient-Reported Outcome Measurement Information System (PROMIS) aimed to create item banks and computerized adaptive tests (CATs) across multiple domains for individuals with a range of chronic diseases. Purpose Web-based software was created to enable a researcher to create study-specific Websites that could administer PROMIS CATs and other instruments to research participants or clinical samples. This paper outlines the process used to develop a user-friendly, free, Web-based resource (Assessment CenterSM) for storage, retrieval, organization, sharing, and administration of patient-reported outcomes (PRO) instruments. Methods Joint Application Design (JAD) sessions were conducted with representatives from numerous institutions in order to supply a general wish list of features. Use Cases were then written to ensure that end user expectations matched programmer specifications. Program development included daily programmer “scrum” sessions, weekly Usability Acceptability Testing (UAT) and continuous Quality Assurance (QA) activities pre- and post-release. Results Assessment Center includes features that promote instrument development including item histories, data management, and storage of statistical analysis results. Conclusions This case study of software development highlights the collection and incorporation of user input throughout the development process. Potential future applications of Assessment Center in clinical research are discussed. PMID:20306332

OLSVis: an animated, interactive visual browser for bio-ontologies

PubMed Central

2012-01-01

Background More than one million terms from biomedical ontologies and controlled vocabularies are available through the Ontology Lookup Service (OLS). Although OLS provides ample possibility for querying and browsing terms, the visualization of parts of the ontology graphs is rather limited and inflexible. Results We created the OLSVis web application, a visualiser for browsing all ontologies available in the OLS database. OLSVis shows customisable subgraphs of the OLS ontologies. Subgraphs are animated via a real-time force-based layout algorithm which is fully interactive: each time the user makes a change, e.g. browsing to a new term, hiding, adding, or dragging terms, the algorithm performs smooth and only essential reorganisations of the graph. This assures an optimal viewing experience, because subsequent screen layouts are not grossly altered, and users can easily navigate through the graph. URL: http://ols.wordvis.com Conclusions The OLSVis web application provides a user-friendly tool to visualise ontologies from the OLS repository. It broadens the possibilities to investigate and select ontology subgraphs through a smooth visualisation method. PMID:22646023

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 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.

The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction.

PubMed

Salvatore, M; Shu, N; Elofsson, A

2018-01-01

SubCons is a recently developed method that predicts the subcellular localization of a protein. It combines predictions from four predictors using a Random Forest classifier. Here, we present the user-friendly web-interface implementation of SubCons. Starting from a protein sequence, the server rapidly predicts the subcellular localizations of an individual protein. In addition, the server accepts the submission of sets of proteins either by uploading the files or programmatically by using command line WSDL API scripts. This makes SubCons ideal for proteome wide analyses allowing the user to scan a whole proteome in few days. From the web page, it is also possible to download precalculated predictions for several eukaryotic organisms. To evaluate the performance of SubCons we present a benchmark of LocTree3 and SubCons using two recent mass-spectrometry based datasets of mouse and drosophila proteins. The server is available at http://subcons.bioinfo.se/. © 2017 The Protein Society.

The Anatomy of a Grid portal

NASA Astrophysics Data System (ADS)

Licari, Daniele; Calzolari, Federico

2011-12-01

In this paper we introduce a new way to deal with Grid portals referring to our implementation. L-GRID is a light portal to access the EGEE/EGI Grid infrastructure via Web, allowing users to submit their jobs from a common Web browser in a few minutes, without any knowledge about the Grid infrastructure. It provides the control over the complete lifecycle of a Grid Job, from its submission and status monitoring, to the output retrieval. The system, implemented as client-server architecture, is based on the Globus Grid middleware. The client side application is based on a java applet; the server relies on a Globus User Interface. There is no need of user registration on the server side, and the user needs only his own X.509 personal certificate. The system is user-friendly, secure (it uses SSL protocol, mechanism for dynamic delegation and identity creation in public key infrastructures), highly customizable, open source, and easy to install. The X.509 personal certificate does not get out from the local machine. It allows to reduce the time spent for the job submission, granting at the same time a higher efficiency and a better security level in proxy delegation and management.

Meta-Abstract for the EnviroAtlas Poster Block at the 2013 ESRI International User Conference (7/12/13)

EPA Science Inventory

The EPA is launching a web-based mapping application—EnviroAtlas—which is designed to communicate ecosystem services, their drivers, societal benefits, and potential future status in a user-friendly manner. EnviroAtlas includes a coarse-scale national component, with...

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

PubMed

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

2014-01-01

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

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.

Write, read and answer emails with a dry 'n' wireless brain-computer interface system.

PubMed

Pinegger, Andreas; Deckert, Lisa; Halder, Sebastian; Barry, Norbert; Faller, Josef; Käthner, Ivo; Hintermüller, Christoph; Wriessnegger, Selina C; Kübler, Andrea; Müller-Putz, Gernot R

2014-01-01

Brain-computer interface (BCI) users can control very complex applications such as multimedia players or even web browsers. Therefore, different biosignal acquisition systems are available to noninvasively measure the electrical activity of the brain, the electroencephalogram (EEG). To make BCIs more practical, hardware and software are nowadays designed more user centered and user friendly. In this paper we evaluated one of the latest innovations in the area of BCI: A wireless EEG amplifier with dry electrode technology combined with a web browser which enables BCI users to use standard webmail. With this system ten volunteers performed a daily life task: Write, read and answer an email. Experimental results of this study demonstrate the power of the introduced BCI system.

The deegree framework - Spatial Data Infrastructure solution for end-users and developers

NASA Astrophysics Data System (ADS)

Kiehle, Christian; Poth, Andreas

2010-05-01

The open source software framework deegree is a comprehensive implementa­tion of standards as defined by ISO and Open Geospatial Consortium (OGC). It has been developed with two goals in mind: provide a uniform framework for implementing Spatial Data Infrastructures (SDI) and adhering to standards as strictly as possible. Although being open source software (Lesser GNU Public Li­cense, LGPL), deegree has been developed with a business model in mind: providing the general building blocks of SDIs without license fees and offer cus­tomization, consulting and tailoring by specialized companies. The core of deegree is a comprehensive Java Application Programming Inter­face (API) offering access to spatial features, analysis, metadata and coordinate reference systems. As a library, deegree can and has been integrated as a core module inside spatial information systems. It is reference implementation for several OGC standards and based on an ISO 19107 geometry model. For end users, deegree is shipped as a web application providing easy-to-set-up components for web mapping and spatial analysis. Since 2000, deegree has been the backbone of many productive SDIs, first and foremost for governmental stakeholders (e.g. Federal Agency for Cartography and Geodesy in Germany, the Ministry of Housing, Spatial Planning and the En­vironment in the Netherlands, etc.) as well as for research and development projects as an early adoption of standards, drafts and discussion papers. Be­sides mature standards like Web Map Service, Web Feature Service and Cata­logue Services, deegree also implements rather new standards like the Sensor Observation Service, the Web Processing Service and the Web Coordinate Transformation Service (WCTS). While a robust background in standardization (knowledge and implementation) is a must for consultancy, standard-compliant services and encodings alone do not provide solutions for customers. The added value is comprised by a sophistic­ated set of client software, desktop and web environments. A focus lies on different client solutions for specific standards like the Web Pro­cessing Service and the Web Coordinate Transformation Service. On the other hand, complex geoportal solutions comprised of multiple standards and en­hanced by components for user management, security and map client function­ality show the demanding requirements of real world solutions. The XPlan-GML-standard as defined by the German spatial planing authorities is a good ex­ample of how complex real-world requirements can get. XPlan-GML is intended to provide a framework for digital spatial planning documents and requires complex Geography Markup Language (GML) features along with Symbology Encoding (SE), Filter Encoding (FE), Web Map Services (WMS), Web Feature Services (WFS). This complex in­frastructure should be used by urban and spatial planners and therefore re­quires a user-friendly graphical interface hiding the complexity of the underly­ing infrastructure. Based on challenges faced within customer projects, the importance of easy to use software components is focused. SDI solution should be build upon ISO/OGC-standards, but more important, should be user-friendly and support the users in spatial data management and analysis.

The Importance of Process-Oriented Accessibility Guidelines for Web Developers.

PubMed

Steen-Hansen, Linn; Fagernes, Siri

2016-01-01

Current accessibility research shows that in the web development, the process itself may lead to inaccessible web sites and applications. Common practices typically do not allow sufficient testing. The focus is mainly on complying with minimum standards, and treating accessibility compliance as a sort of bug-fixing process, missing the user perspective. In addition, there is an alarming lack of knowledge and experience with accessibility issues. It has also been argued that bringing accessibility into the development process at all stages is the only way to achieve the highest possible level of accessibility. The work presented in this paper is based on a previous project focusing on guidelines for developing accessible rich Internet applications. The guidelines were classified as either process-oriented or technology-oriented. In this paper, we examine the process-oriented guidelines and give a practical perspective on how these guidelines will make the development process more accessibility-friendly.

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…

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).

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

PubMed

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

2018-05-01

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

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.

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

PubMed

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

2017-06-01

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

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 interpretation of RT-PCR, RNAi, gene expression microarrays, antibody-based detection, and mass spectrometry proteomics. The tools are intended for use by bench biologists as well as bioinformaticists. PMID:18638396

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/.

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

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.

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

PubMed

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

2015-03-01

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

Session management for web-based healthcare applications.

PubMed Central

Wei, L.; Sengupta, S.

1999-01-01

In health care systems, users may access multiple applications during one session of interaction with the system. However, users must sign on to each application individually, and it is difficult to maintain a common context among these applications. We are developing a session management system for web-based applications using LDAP directory service, which will allow single sign-on to multiple web-based applications, and maintain a common context among those applications for the user. This paper discusses the motivations for building this system, the system architecture, and the challenges of our approach, such as the session objects management for the user, and session security. PMID:10566511

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

PubMed Central

Barrett, Tanya; Edgar, Ron

2006-01-01

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

Services for Graduate Students: A Review of Academic Library Web Sites

ERIC Educational Resources Information Center

Rempel, Hannah Gascho

2010-01-01

A library's Web site is well recognized as the gateway to the library for the vast majority of users. Choosing the most user-friendly Web architecture to reflect the many services libraries offer is a complex process, and librarians are still experimenting to find what works best for their users. As part of a redesign of the Oregon State…

BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins.

PubMed

van Heel, Auke J; de Jong, Anne; Song, Chunxu; Viel, Jakob H; Kok, Jan; Kuipers, Oscar P

2018-05-21

Interest in secondary metabolites such as RiPPs (ribosomally synthesized and posttranslationally modified peptides) is increasing worldwide. To facilitate the research in this field we have updated our mining web server. BAGEL4 is faster than its predecessor and is now fully independent from ORF-calling. Gene clusters of interest are discovered using the core-peptide database and/or through HMM motifs that are present in associated context genes. The databases used for mining have been updated and extended with literature references and links to UniProt and NCBI. Additionally, we have included automated promoter and terminator prediction and the option to upload RNA expression data, which can be displayed along with the identified clusters. Further improvements include the annotation of the context genes, which is now based on a fast blast against the prokaryote part of the UniRef90 database, and the improved web-BLAST feature that dynamically loads structural data such as internal cross-linking from UniProt. Overall BAGEL4 provides the user with more information through a user-friendly web-interface which simplifies data evaluation. BAGEL4 is freely accessible at http://bagel4.molgenrug.nl.

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.

Optimizing real-time Web-based user interfaces for observatories

NASA Astrophysics Data System (ADS)

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

2008-08-01

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

SeaConditions: a web and mobile service for safer professional and recreational activities in the Mediterranean Sea

NASA Astrophysics Data System (ADS)

Coppini, Giovanni; Marra, Palmalisa; Lecci, Rita; Pinardi, Nadia; Cretì, Sergio; Scalas, Mario; Tedesco, Luca; D'Anca, Alessandro; Fazioli, Leopoldo; Olita, Antonio; Turrisi, Giuseppe; Palazzo, Cosimo; Aloisio, Giovanni; Fiore, Sandro; Bonaduce, Antonio; Vittal Kumkar, Yogesh; Ciliberti, Stefania Angela; Federico, Ivan; Mannarini, Gianandrea; Agostini, Paola; Bonarelli, Roberto; Martinelli, Sara; Verri, Giorgia; Lusito, Letizia; Rollo, Davide; Cavallo, Arturo; Tumolo, Antonio; Monacizzo, Tony; Spagnulo, Marco; Sorgente, Rorberto; Cucco, Andrea; Quattrocchi, Giovanni; Tonani, Marina; Drudi, Massimiliano; Nassisi, Paola; Conte, Laura; Panzera, Laura; Navarra, Antonio; Negro, Giancarlo

2017-04-01

Reliable and timely information on the environmental conditions at sea is key to the safety of professional and recreational users as well as to the optimal execution of their activities. The possibility of users obtaining environmental information in due time and with adequate accuracy in the marine and coastal environment is defined as sea situational awareness (SSA). Without adequate information on the environmental meteorological and oceanographic conditions, users have a limited capacity to respond, which has led to loss of lives and to large environmental disasters with enormous consequent damage to the economy, society and ecosystems. Within the framework of the TESSA project, new SSA services for the Mediterranean Sea have been developed. In this paper we present SeaConditions, which is a web and mobile application for the provision of meteorological and oceanographic observation and forecasting products. Model forecasts and satellite products from operational services, such as ECMWF and CMEMS, can be visualized in SeaConditions. In addition, layers of information related to bathymetry, sea level and ocean-colour data (chl a and water transparency) are displayed. Ocean forecasts at high spatial resolutions are included in the version of SeaConditions presented here. SeaConditions provides a user-friendly experience with a fluid zoom capability, facilitating the appropriate display of data with different levels of detail. SeaConditions is a single point of access to interactive maps from different geophysical fields, providing high-quality information based on advanced oceanographic models. The SeaConditions services are available through both web and mobile applications. The web application is available at www.sea-conditions.com and is accessible and compatible with present-day browsers. Interoperability with GIS software is implemented. User feedback has been collected and taken into account in order to improve the service. The SeaConditions iOS and Android apps have been downloaded by more than 105 000 users to date (May 2016), and more than 100 000 users have visited the web version.

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.

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.

Users' information-seeking behavior on a medical library Website

PubMed Central

Rozic-Hristovski, Anamarija; Hristovski, Dimitar; Todorovski, Ljupco

2002-01-01

The Central Medical Library (CMK) at the Faculty of Medicine, University of Ljubljana, Slovenia, started to build a library Website that included a guide to library services and resources in 1997. The evaluation of Website usage plays an important role in its maintenance and development. Analyzing and exploring regularities in the visitors' behavior can be used to enhance the quality and facilitate delivery of information services, identify visitors' interests, and improve the server's performance. The analysis of the CMK Website users' navigational behavior was carried out by analyzing the Web server log files. These files contained information on all user accesses to the Website and provided a great opportunity to learn more about the behavior of visitors to the Website. The majority of the available tools for Web log file analysis provide a predefined set of reports showing the access count and the transferred bytes grouped along several dimensions. In addition to the reports mentioned above, the authors wanted to be able to perform interactive exploration and ad hoc analysis and discover trends in a user-friendly way. Because of that, we developed our own solution for exploring and analyzing the Web logs based on data warehousing and online analytical processing technologies. The analytical solution we developed proved successful, so it may find further application in the field of Web log file analysis. We will apply the findings of the analysis to restructuring the CMK Website. PMID:11999179

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.

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

ModuleRole: a tool for modulization, role determination and visualization in protein-protein interaction networks.

PubMed

Li, Guipeng; Li, Ming; Zhang, Yiwei; Wang, Dong; Li, Rong; Guimerà, Roger; Gao, Juntao Tony; Zhang, Michael Q

2014-01-01

Rapidly increasing amounts of (physical and genetic) protein-protein interaction (PPI) data are produced by various high-throughput techniques, and interpretation of these data remains a major challenge. In order to gain insight into the organization and structure of the resultant large complex networks formed by interacting molecules, using simulated annealing, a method based on the node connectivity, we developed ModuleRole, a user-friendly web server tool which finds modules in PPI network and defines the roles for every node, and produces files for visualization in Cytoscape and Pajek. For given proteins, it analyzes the PPI network from BioGRID database, finds and visualizes the modules these proteins form, and then defines the role every node plays in this network, based on two topological parameters Participation Coefficient and Z-score. This is the first program which provides interactive and very friendly interface for biologists to find and visualize modules and roles of proteins in PPI network. It can be tested online at the website http://www.bioinfo.org/modulerole/index.php, which is free and open to all users and there is no login requirement, with demo data provided by "User Guide" in the menu Help. Non-server application of this program is considered for high-throughput data with more than 200 nodes or user's own interaction datasets. Users are able to bookmark the web link to the result page and access at a later time. As an interactive and highly customizable application, ModuleRole requires no expert knowledge in graph theory on the user side and can be used in both Linux and Windows system, thus a very useful tool for biologist to analyze and visualize PPI networks from databases such as BioGRID. ModuleRole is implemented in Java and C, and is freely available at http://www.bioinfo.org/modulerole/index.php. Supplementary information (user guide, demo data) is also available at this website. API for ModuleRole used for this program can be obtained upon request.

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.

The Wildland Fire Emissions Information System: Providing information for carbon cycle studies with open source geospatial tools

NASA Astrophysics Data System (ADS)

French, N. H.; Erickson, T.; McKenzie, D.

2008-12-01

A major goal of the North American Carbon Program is to resolve uncertainties in understanding and managing the carbon cycle of North America. As carbon modeling tools become more comprehensive and spatially oriented, accurate datasets to spatially quantify carbon emissions from fire are needed, and these data resources need to be accessible to users for decision-making. Under a new NASA Carbon Cycle Science project, Drs. Nancy French and Tyler Erickson, of the Michigan Technological University, Michigan Tech Research Institute (MTRI), are teaming with specialists with the USDA Forest Service Fire and Environmental Research Applications (FERA) team to provide information for mapping fire-derived carbon emissions to users. The project focus includes development of a web-based system to provide spatially resolved fire emissions estimates for North America in a user-friendly environment. The web-based Decision Support System will be based on a variety of open source technologies. The Fuel Characteristic Classification System (FCCS) raster map of fuels and MODIS-derived burned area vector maps will be processed using the Geographic Data Abstraction Library (GDAL) and OGR Simple Features Library. Tabular and spatial project data will be stored in a PostgreSQL/PostGIS, a spatially enabled relational database server. The browser-based user interface will be created using the Django web page framework to allow user input for the decision support system. The OpenLayers mapping framework will be used to provide users with interactive maps within the browser. In addition, the data products will be made available in standard open data formats such as KML, to allow for easy integration into other spatial models and data systems.

A RESTful interface to pseudonymization services in modern web applications.

PubMed

Lablans, Martin; Borg, Andreas; Ückert, Frank

2015-02-07

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

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

Social Circles: A 3D User Interface for Facebook

NASA Astrophysics Data System (ADS)

Rodrigues, Diego; Oakley, Ian

Online social network services are increasingly popular web applications which display large amounts of rich multimedia content: contacts, status updates, photos and event information. Arguing that this quantity of information overwhelms conventional user interfaces, this paper presents Social Circles, a rich interactive visualization designed to support real world users of social network services in everyday tasks such as keeping up with friends and organizing their network. It achieves this by using 3D UIs, fluid animations and a spatial metaphor to enable direct manipulation of a social network.

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

PubMed

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

2001-01-01

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

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 fingertips of users around the globe. This user-friendly and low-cost information dissemination provides global information as a basis for decision-making in a number of critical areas, including public health, energy, agriculture, weather, water, climate, natural disasters and ecosystems. GEONETCast makes available satellite images via Digital Video Broadcast (DVB) technology. An OGC WMS interface and plug-ins which convert GEONETCast data streams allow an ILWIS user to integrate various distributed data sources with data locally stored on his machine. Our paper describes a use case in which ILWIS is used with GEONETCast satellite imagery for decision making processes in Ghana. We also explain how the ILWIS software can be extended with additional functionality by means of building plug-ins and unfold our plans to implement other OGC standards, such as WCS and WPS in the same context. Especially, the latter one can be seen as a major step forward in terms of moving well-proven desktop based processing functionality to the web. This enables the embedding of ILWIS functionality in Spatial Data Infrastructures or even the execution in scalable and on-demand cloud computing environments.

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.

Life span in online communities.

PubMed

Grabowski, A; Kosiński, R A

2010-12-01

Recently online communities have attracted great interest and have become an important medium of information exchange between users. The aim of this work is to introduce a simple model of the evolution of online communities. This model describes (a) the time evolution of users' activity in a web service, e.g., the time evolution of the number of online friends or written posts, (b) the time evolution of the degree distribution of a social network, and (c) the time evolution of the number of active users of a web service. In the second part of the paper we investigate the influence of the users' lifespan (i.e., the total time in which they are active in an online community) on the process of rumor propagation in evolving social networks. Viral marketing is an important application of such method of information propagation.

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

PubMed

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

2009-01-01

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

Space Images for NASA JPL Android Version

NASA Technical Reports Server (NTRS)

Nelson, Jon D.; Gutheinz, Sandy C.; Strom, Joshua R.; Arca, Jeremy M.; Perez, Martin; Boggs, Karen; Stanboli, Alice

2013-01-01

This software addresses the demand for easily accessible NASA JPL images and videos by providing a user friendly and simple graphical user interface that can be run via the Android platform from any location where Internet connection is available. This app is complementary to the iPhone version of the application. A backend infrastructure stores, tracks, and retrieves space images from the JPL Photojournal and Institutional Communications Web server, and catalogs the information into a streamlined rating infrastructure. This system consists of four distinguishing components: image repository, database, server-side logic, and Android mobile application. The image repository contains images from various JPL flight projects. The database stores the image information as well as the user rating. The server-side logic retrieves the image information from the database and categorizes each image for display. The Android mobile application is an interfacing delivery system that retrieves the image information from the server for each Android mobile device user. Also created is a reporting and tracking system for charting and monitoring usage. Unlike other Android mobile image applications, this system uses the latest emerging technologies to produce image listings based directly on user input. This allows for countless combinations of images returned. The backend infrastructure uses industry-standard coding and database methods, enabling future software improvement and technology updates. The flexibility of the system design framework permits multiple levels of display possibilities and provides integration capabilities. Unique features of the software include image/video retrieval from a selected set of categories, image Web links that can be shared among e-mail users, sharing to Facebook/Twitter, marking as user's favorites, and image metadata searchable for instant results.

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.

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.

Development of a 3D WebGIS System for Retrieving and Visualizing CityGML Data Based on their Geometric and Semantic Characteristics by Using Free and Open Source Technology

NASA Astrophysics Data System (ADS)

Pispidikis, I.; Dimopoulou, E.

2016-10-01

CityGML is considered as an optimal standard for representing 3D city models. However, international experience has shown that visualization of the latter is quite difficult to be implemented on the web, due to the large size of data and the complexity of CityGML. As a result, in the context of this paper, a 3D WebGIS application is developed in order to successfully retrieve and visualize CityGML data in accordance with their respective geometric and semantic characteristics. Furthermore, the available web technologies and the architecture of WebGIS systems are investigated, as provided by international experience, in order to be utilized in the most appropriate way for the purposes of this paper. Specifically, a PostgreSQL/ PostGIS Database is used, in compliance with the 3DCityDB schema. At Server tier, Apache HTTP Server and GeoServer are utilized, while a Server Side programming language PHP is used. At Client tier, which implemented the interface of the application, the following technologies were used: JQuery, AJAX, JavaScript, HTML5, WebGL and Ol3-Cesium. Finally, it is worth mentioning that the application's primary objectives are a user-friendly interface and a fully open source development.

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.

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

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

PubMed Central

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

2004-01-01

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

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.

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://www.vistrails.org) workflow engine in the backend.

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…

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).

SAFOD Brittle Microstructure and Mechanics Knowledge Base (SAFOD BM2KB)

NASA Astrophysics Data System (ADS)

Babaie, H. A.; Hadizadeh, J.; di Toro, G.; Mair, K.; Kumar, A.

2008-12-01

We have developed a knowledge base to store and present the data collected by a group of investigators studying the microstructures and mechanics of brittle faulting using core samples from the SAFOD (San Andreas Fault Observatory at Depth) project. The investigations are carried out with a variety of analytical and experimental methods primarily to better understand the physics of strain localization in fault gouge. The knowledge base instantiates an specially-designed brittle rock deformation ontology developed at Georgia State University. The inference rules embedded in the semantic web languages, such as OWL, RDF, and RDFS, which are used in our ontology, allow the Pellet reasoner used in this application to derive additional truths about the ontology and knowledge of this domain. Access to the knowledge base is via a public website, which is designed to provide the knowledge acquired by all the investigators involved in the project. The stored data will be products of studies such as: experiments (e.g., high-velocity friction experiment), analyses (e.g., microstructural, chemical, mass transfer, mineralogical, surface, image, texture), microscopy (optical, HRSEM, FESEM, HRTEM]), tomography, porosity measurement, microprobe, and cathodoluminesence. Data about laboratories, experimental conditions, methods, assumptions, equipments, and mechanical properties and lithology of the studied samples will also be presented on the website per investigation. The ontology was modeled applying the UML (Unified Modeling Language) in Rational Rose, and implemented in OWL-DL (Ontology Web Language) using the Protégé ontology editor. The UML model was converted to OWL-DL by first mapping it to Ecore (.ecore) and Generator model (.genmodel) with the help of the EMF (Eclipse Modeling Framework) plugin in Eclipse. The Ecore model was then mapped to a .uml file, which later was converted into an .owl file and subsequently imported into the Protégé ontology editing environment. The web-interface was developed in java using eclipse as the IDE. The web interfaces to query and submit data were implemented applying JSP, servlets, javascript, and AJAX. The Jena API, a Java framework for building Semantic Web applications, was used to develop the web-interface. Jena provided a programmatic environment for RDF, RDFS, OWL, and SPARQL query engine. Building web applications with AJAX helps retrieving data from the server asynchronously in the background without interfering with the display and behavior of the existing page. The application was deployed on an apache tomcat server at GSU. The SAFOD BM2KB website provides user-friendly search, submit, feedback, and other services. The General Search option allows users to search the knowledge base by selecting the classes (e.g., Experiment, Surface Analysis), their respective attributes (e.g., apparatus, date performed), and the relationships to other classes (e.g., Sample, Laboratory). The Search by Sample option allows users to search the knowledge base based on sample number. The Search by Investigator lets users to search the knowledge base by choosing an investigator who is involved in this project. The website also allows users to submit new data. The Submit Data option opens a page where users can submit the SAFOD data to our knowledge base by selecting specific classes and attributes. The submitted data then become available for query as part of the knowledge base. The SAFOD BM2KB can be accessed from the main SAFOD website.

Fast Risk Assessment Software For Natural Hazard Phenomena Using Georeference Population And Infrastructure Data Bases

NASA Astrophysics Data System (ADS)

Marrero, J. M.; Pastor Paz, J. E.; Erazo, C.; Marrero, M.; Aguilar, J.; Yepes, H. A.; Estrella, C. M.; Mothes, P. A.

2015-12-01

Disaster Risk Reduction (DRR) requires an integrated multi-hazard assessment approach towards natural hazard mitigation. In the case of volcanic risk, long term hazard maps are generally developed on a basis of the most probable scenarios (likelihood of occurrence) or worst cases. However, in the short-term, expected scenarios may vary substantially depending on the monitoring data or new knowledge. In this context, the time required to obtain and process data is critical for optimum decision making. Availability of up-to-date volcanic scenarios is as crucial as it is to have this data accompanied by efficient estimations of their impact among populations and infrastructure. To address this impact estimation during volcanic crises, or other natural hazards, a web interface has been developed to execute an ANSI C application. This application allows one to compute - in a matter of seconds - the demographic and infrastructure impact that any natural hazard may cause employing an overlay-layer approach. The web interface is tailored to users involved in the volcanic crises management of Cotopaxi volcano (Ecuador). The population data base and the cartographic basis used are of public domain, published by the National Office of Statistics of Ecuador (INEC, by its Spanish acronym). To run the application and obtain results the user is expected to upload a raster file containing information related to the volcanic hazard or any other natural hazard, and determine categories to group population or infrastructure potentially affected. The results are displayed in a user-friendly report.

Global Precipitation Measurement (GPM) Mission Products and Services at the NASA Goddard Earth Sciences Data and Information Services Center (GES DISC)

NASA Technical Reports Server (NTRS)

Liu, Z.; Ostrenga, D.; Vollmer, B.; Kempler, S.; Deshong, B.; Greene, M.

2015-01-01

The NASA Goddard Earth Sciences (GES) Data and Information Services Center (DISC) hosts and distributes GPM data within the NASA Earth Observation System Data Information System (EOSDIS). The GES DISC is also home to the data archive for the GPM predecessor, the Tropical Rainfall Measuring Mission (TRMM). Over the past 17 years, the GES DISC has served the scientific as well as other communities with TRMM data and user-friendly services. During the GPM era, the GES DISC will continue to provide user-friendly data services and customer support to users around the world. GPM products currently and to-be available: -Level-1 GPM Microwave Imager (GMI) and partner radiometer products, DPR products -Level-2 Goddard Profiling Algorithm (GPROF) GMI and partner products, DPR products -Level-3 daily and monthly products, DPR products -Integrated Multi-satellitE Retrievals for GPM (IMERG) products (early, late, and final) A dedicated Web portal (including user guides, etc.) has been developed for GPM data (http://disc.sci.gsfc.nasa.gov/gpm). Data services that are currently and to-be available include Google-like Mirador (http://mirador.gsfc.nasa.gov/) for data search and access; data access through various Web services (e.g., OPeNDAP, GDS, WMS, WCS); conversion into various formats (e.g., netCDF, HDF, KML (for Google Earth), ASCII); exploration, visualization, and statistical online analysis through Giovanni (http://giovanni.gsfc.nasa.gov); generation of value-added products; parameter and spatial subsetting; time aggregation; regridding; data version control and provenance; documentation; science support for proper data usage, FAQ, help desk; monitoring services (e.g. Current Conditions) for applications. The United User Interface (UUI) is the next step in the evolution of the GES DISC web site. It attempts to provide seamless access to data, information and services through a single interface without sending the user to different applications or URLs (e.g., search, access, subset, Giovanni, documents).

Usability Testing, User-Centered Design, and LibGuides Subject Guides: A Case Study

ERIC Educational Resources Information Center

Sonsteby, Alec; DeJonghe, Jennifer

2013-01-01

Usability testing has become a routine way for many libraries to ensure that their Web presence is user-friendly and accessible. At the same time, popular subject guide creation systems, such as LibGuides, decentralize Web content creation and put authorship into the hands of librarians who may not be trained in user-centered design principles. At…

UManSysProp: an online facility for molecular property prediction and atmospheric aerosol calculations

NASA Astrophysics Data System (ADS)

Topping, D.; Barley, M. H.; Bane, M.; Higham, N.; Aumont, B.; McFiggans, G.

2015-11-01

In this paper we describe the development and application of a new web based facility, UManSysProp (http://umansysprop.seaes.manchester.ac.uk), for automating predictions of molecular and atmospheric aerosol properties. Current facilities include: pure component vapour pressures, critical properties and sub-cooled densities of organic molecules; activity coefficient predictions for mixed inorganic-organic liquid systems; hygroscopic growth factors and CCN activation potential of mixed inorganic/organic aerosol particles; absorptive partitioning calculations with/without a treatment of non-ideality. The aim of this new facility is to provide a single point of reference for all properties relevant to atmospheric aerosol that have been checked for applicability to atmospheric compounds where possible. The group contribution approach allows users to upload molecular information in the form of SMILES strings and UManSysProp will automatically extract the relevant information for calculations. Built using open source chemical informatics, and hosted at the University of Manchester, the facilities are provided via a browser and device-friendly web-interface, or can be accessed using the user's own code via a JSON API. In this paper we demonstrate its use with specific examples that can be simulated using the web-browser interface.

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.

TOPSAN: a dynamic web database for structural genomics.

PubMed

Ellrott, Kyle; Zmasek, Christian M; Weekes, Dana; Sri Krishna, S; Bakolitsa, Constantina; Godzik, Adam; Wooley, John

2011-01-01

The Open Protein Structure Annotation Network (TOPSAN) is a web-based collaboration platform for exploring and annotating structures determined by structural genomics efforts. Characterization of those structures presents a challenge since the majority of the proteins themselves have not yet been characterized. Responding to this challenge, the TOPSAN platform facilitates collaborative annotation and investigation via a user-friendly web-based interface pre-populated with automatically generated information. Semantic web technologies expand and enrich TOPSAN's content through links to larger sets of related databases, and thus, enable data integration from disparate sources and data mining via conventional query languages. TOPSAN can be found at http://www.topsan.org.

A web-based endodontic case difficulty assessment tool.

PubMed

Shah, P K; Chong, B S

2018-07-01

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

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.

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/.

MrGrid: A Portable Grid Based Molecular Replacement Pipeline

PubMed Central

Reboul, Cyril F.; Androulakis, Steve G.; Phan, Jennifer M. N.; Whisstock, James C.; Goscinski, Wojtek J.; Abramson, David; Buckle, Ashley M.

2010-01-01

Background The crystallographic determination of protein structures can be computationally demanding and for difficult cases can benefit from user-friendly interfaces to high-performance computing resources. Molecular replacement (MR) is a popular protein crystallographic technique that exploits the structural similarity between proteins that share some sequence similarity. But the need to trial permutations of search models, space group symmetries and other parameters makes MR time- and labour-intensive. However, MR calculations are embarrassingly parallel and thus ideally suited to distributed computing. In order to address this problem we have developed MrGrid, web-based software that allows multiple MR calculations to be executed across a grid of networked computers, allowing high-throughput MR. Methodology/Principal Findings MrGrid is a portable web based application written in Java/JSP and Ruby, and taking advantage of Apple Xgrid technology. Designed to interface with a user defined Xgrid resource the package manages the distribution of multiple MR runs to the available nodes on the Xgrid. We evaluated MrGrid using 10 different protein test cases on a network of 13 computers, and achieved an average speed up factor of 5.69. Conclusions MrGrid enables the user to retrieve and manage the results of tens to hundreds of MR calculations quickly and via a single web interface, as well as broadening the range of strategies that can be attempted. This high-throughput approach allows parameter sweeps to be performed in parallel, improving the chances of MR success. PMID:20386612

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. Data collection using the web-based application was consistently more complete when compared to the multi-user PC software. The web-based application is an efficient system for documenting pharmacist interventions. Its flexibility and accessibility, as well as its detailed report functionality is a useful tool that will hopefully encourage other primary and secondary care facilities to adopt similar applications.

UManSysProp v1.0: an online and open-source facility for molecular property prediction and atmospheric aerosol calculations

NASA Astrophysics Data System (ADS)

Topping, David; Barley, Mark; Bane, Michael K.; Higham, Nicholas; Aumont, Bernard; Dingle, Nicholas; McFiggans, Gordon

2016-03-01

In this paper we describe the development and application of a new web-based facility, UManSysProp (http://umansysprop.seaes.manchester.ac.uk), for automating predictions of molecular and atmospheric aerosol properties. Current facilities include pure component vapour pressures, critical properties, and sub-cooled densities of organic molecules; activity coefficient predictions for mixed inorganic-organic liquid systems; hygroscopic growth factors and CCN (cloud condensation nuclei) activation potential of mixed inorganic-organic aerosol particles; and absorptive partitioning calculations with/without a treatment of non-ideality. The aim of this new facility is to provide a single point of reference for all properties relevant to atmospheric aerosol that have been checked for applicability to atmospheric compounds where possible. The group contribution approach allows users to upload molecular information in the form of SMILES (Simplified Molecular Input Line Entry System) strings and UManSysProp will automatically extract the relevant information for calculations. Built using open-source chemical informatics, and hosted at the University of Manchester, the facilities are provided via a browser and device-friendly web interface, or can be accessed using the user's own code via a JSON API (application program interface). We also provide the source code for all predictive techniques provided on the site, covered by the GNU GPL (General Public License) license to encourage development of a user community. We have released this via a Github repository (doi:10.5281/zenodo.45143). In this paper we demonstrate its use with specific examples that can be simulated using the web-browser interface.

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

Krishnamurthy, Dheepak

This paper is an overview of Power System Simulation Toolbox (psst). psst is an open-source Python application for the simulation and analysis of power system models. psst simulates the wholesale market operation by solving a DC Optimal Power Flow (DCOPF), Security Constrained Unit Commitment (SCUC) and a Security Constrained Economic Dispatch (SCED). psst also includes models for the various entities in a power system such as Generator Companies (GenCos), Load Serving Entities (LSEs) and an Independent System Operator (ISO). psst features an open modular object oriented architecture that will make it useful for researchers to customize, expand, experiment beyond solvingmore » traditional problems. psst also includes a web based Graphical User Interface (GUI) that allows for user friendly interaction and for implementation on remote High Performance Computing (HPCs) clusters for parallelized operations. This paper also provides an illustrative application of psst and benchmarks with standard IEEE test cases to show the advanced features and the performance of toolbox.« less

Advanced SPARQL querying in small molecule databases.

PubMed

Galgonek, Jakub; Hurt, Tomáš; Michlíková, Vendula; Onderka, Petr; Schwarz, Jan; Vondrášek, Jiří

2016-01-01

In recent years, the Resource Description Framework (RDF) and the SPARQL query language have become more widely used in the area of cheminformatics and bioinformatics databases. These technologies allow better interoperability of various data sources and powerful searching facilities. However, we identified several deficiencies that make usage of such RDF databases restrictive or challenging for common users. We extended a SPARQL engine to be able to use special procedures inside SPARQL queries. This allows the user to work with data that cannot be simply precomputed and thus cannot be directly stored in the database. We designed an algorithm that checks a query against data ontology to identify possible user errors. This greatly improves query debugging. We also introduced an approach to visualize retrieved data in a user-friendly way, based on templates describing visualizations of resource classes. To integrate all of our approaches, we developed a simple web application. Our system was implemented successfully, and we demonstrated its usability on the ChEBI database transformed into RDF form. To demonstrate procedure call functions, we employed compound similarity searching based on OrChem. The application is publicly available at https://bioinfo.uochb.cas.cz/projects/chemRDF.

A new mobile ubiquitous computing application to control obesity: SapoFit.

PubMed

Rodrigues, Joel J P C; Lopes, Ivo M C; Silva, Bruno M C; Torre, Isabel de La

2013-01-01

The objective of this work was the proposal, design, construction and validation of a mobile health system for dietetic monitoring and assessment, called SapoFit. This application may be personalized to keep a daily personal health record of an individual's food intake and daily exercise and to share this with a social network. The initiative is a partnership with SAPO - Portugal Telecom. SapoFit uses Web services architecture, a relatively new model for distributed computing and application integration. SapoFit runs on a range of mobile platforms, and it has been implemented successfully in a range of mobile devices and has been evaluated by over 100 users. Most users strongly agree that SapoFit has an attractive design, the environment is user-friendly and intuitive, and the navigation options are clear.

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.

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.

CheD: chemical database compilation tool, Internet server, and client for SQL servers.

PubMed

Trepalin, S V; Yarkov, A V

2001-01-01

An efficient program, which runs on a personal computer, for the storage, retrieval, and processing of chemical information, is presented, The program can work both as a stand-alone application or in conjunction with a specifically written Web server application or with some standard SQL servers, e.g., Oracle, Interbase, and MS SQL. New types of data fields are introduced, e.g., arrays for spectral information storage, HTML and database links, and user-defined functions. CheD has an open architecture; thus, custom data types, controls, and services may be added. A WWW server application for chemical data retrieval features an easy and user-friendly installation on Windows NT or 95 platforms.

Leveraging Multiactions to Improve Medical Personalized Ranking for Collaborative Filtering.

PubMed

Gao, Shan; Guo, Guibing; Li, Runzhi; Wang, Zongmin

2017-01-01

Nowadays, providing high-quality recommendation services to users is an essential component in web applications, including shopping, making friends, and healthcare. This can be regarded either as a problem of estimating users' preference by exploiting explicit feedbacks (numerical ratings), or as a problem of collaborative ranking with implicit feedback (e.g., purchases, views, and clicks). Previous works for solving this issue include pointwise regression methods and pairwise ranking methods. The emerging healthcare websites and online medical databases impose a new challenge for medical service recommendation. In this paper, we develop a model, MBPR (Medical Bayesian Personalized Ranking over multiple users' actions), based on the simple observation that users tend to assign higher ranks to some kind of healthcare services that are meanwhile preferred in users' other actions. Experimental results on the real-world datasets demonstrate that MBPR achieves more accurate recommendations than several state-of-the-art methods and shows its generality and scalability via experiments on the datasets from one mobile shopping app.

Leveraging Multiactions to Improve Medical Personalized Ranking for Collaborative Filtering

PubMed Central

2017-01-01

Nowadays, providing high-quality recommendation services to users is an essential component in web applications, including shopping, making friends, and healthcare. This can be regarded either as a problem of estimating users' preference by exploiting explicit feedbacks (numerical ratings), or as a problem of collaborative ranking with implicit feedback (e.g., purchases, views, and clicks). Previous works for solving this issue include pointwise regression methods and pairwise ranking methods. The emerging healthcare websites and online medical databases impose a new challenge for medical service recommendation. In this paper, we develop a model, MBPR (Medical Bayesian Personalized Ranking over multiple users' actions), based on the simple observation that users tend to assign higher ranks to some kind of healthcare services that are meanwhile preferred in users' other actions. Experimental results on the real-world datasets demonstrate that MBPR achieves more accurate recommendations than several state-of-the-art methods and shows its generality and scalability via experiments on the datasets from one mobile shopping app. PMID:29118963

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

PubMed

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

2014-01-01

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

Enabling a systems biology knowledgebase with gaggle and firegoose

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

Baliga, Nitin S.

The overall goal of this project was to extend the existing Gaggle and Firegoose systems to develop an open-source technology that runs over the web and links desktop applications with many databases and software applications. This technology would enable researchers to incorporate workflows for data analysis that can be executed from this interface to other online applications. The four specific aims were to (1) provide one-click mapping of genes, proteins, and complexes across databases and species; (2) enable multiple simultaneous workflows; (3) expand sophisticated data analysis for online resources; and enhance open-source development of the Gaggle-Firegoose infrastructure. Gaggle is anmore » open-source Java software system that integrates existing bioinformatics programs and data sources into a user-friendly, extensible environment to allow interactive exploration, visualization, and analysis of systems biology data. Firegoose is an extension to the Mozilla Firefox web browser that enables data transfer between websites and desktop tools including Gaggle. In the last phase of this funding period, we have made substantial progress on development and application of the Gaggle integration framework. We implemented the workspace to the Network Portal. Users can capture data from Firegoose and save them to the workspace. Users can create workflows to start multiple software components programmatically and pass data between them. Results of analysis can be saved to the cloud so that they can be easily restored on any machine. We also developed the Gaggle Chrome Goose, a plugin for the Google Chrome browser in tandem with an opencpu server in the Amazon EC2 cloud. This allows users to interactively perform data analysis on a single web page using the R packages deployed on the opencpu server. The cloud-based framework facilitates collaboration between researchers from multiple organizations. We have made a number of enhancements to the cmonkey2 application to enable and improve the integration within different environments, and we have created a new tools pipeline for generating EGRIN2 models in a largely automated way.« less

WebArray: an online platform for microarray data analysis

PubMed Central

Xia, Xiaoqin; McClelland, Michael; Wang, Yipeng

2005-01-01

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

TOKEN: Trustable Keystroke-Based Authentication for Web-Based Applications on Smartphones

NASA Astrophysics Data System (ADS)

Nauman, Mohammad; Ali, Tamleek

Smartphones are increasingly being used to store personal information as well as to access sensitive data from the Internet and the cloud. Establishment of the identity of a user requesting information from smartphones is a prerequisite for secure systems in such scenarios. In the past, keystroke-based user identification has been successfully deployed on production-level mobile devices to mitigate the risks associated with naïve username/password based authentication. However, these approaches have two major limitations: they are not applicable to services where authentication occurs outside the domain of the mobile device - such as web-based services; and they often overly tax the limited computational capabilities of mobile devices. In this paper, we propose a protocol for keystroke dynamics analysis which allows web-based applications to make use of remote attestation and delegated keystroke analysis. The end result is an efficient keystroke-based user identification mechanism that strengthens traditional password protected services while mitigating the risks of user profiling by collaborating malicious web services.

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.

Developing a smartphone interface for the Florida Environmental Public Health Tracking Web portal.

PubMed

Jordan, Melissa; DuClos, Chris; Folsom, John; Thomas, Rebecca

2015-01-01

As smartphone and tablet devices continue to proliferate, it is becoming increasingly important to tailor information delivery to the mobile device. The Florida Environmental Public Health Tracking Program recognized that the mobile device user needs Web content formatted to smaller screen sizes, simplified data displays, and reduced textual information. The Florida Environmental Public Health Tracking Program developed a smartphone-friendly version of the state Web portal for easier access by mobile device users. The resulting smartphone-friendly portal combines calculated data measures such as inpatient hospitalizations and emergency department visits and presents them grouped by county, along with temporal trend graphs. An abbreviated version of the public health messaging provided on the traditional Web portal is also provided, along with social media connections. As a result of these efforts, the percentage of Web site visitors using an iPhone tripled in just 1 year.

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 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 increased and the value of using this system for other trials is reduced. Web-based central computerized systems offer time-saving, secure options for managing clinical trial data. The choice of a commercially available system or an internally developed system is determined by the requirements of the study and users. Pros and cons to both approaches were discussed. If the intention is to use the system for various trials (single and multi-center, phases I-III) across various therapeutic areas, then the overall design should be a generic structure that simplifies the general application with minimal loss of functionality.

WriteSim TCExam - An open source text simulation environment for training novice researchers in scientific writing

PubMed Central

2010-01-01

Background The ability to write clearly and effectively is of central importance to the scientific enterprise. Encouraged by the success of simulation environments in other biomedical sciences, we developed WriteSim TCExam, an open-source, Web-based, textual simulation environment for teaching effective writing techniques to novice researchers. We shortlisted and modified an existing open source application - TCExam to serve as a textual simulation environment. After testing usability internally in our team, we conducted formal field usability studies with novice researchers. These were followed by formal surveys with researchers fitting the role of administrators and users (novice researchers) Results The development process was guided by feedback from usability tests within our research team. Online surveys and formal studies, involving members of the Research on Research group and selected novice researchers, show that the application is user-friendly. Additionally it has been used to train 25 novice researchers in scientific writing to date and has generated encouraging results. Conclusion WriteSim TCExam is the first Web-based, open-source textual simulation environment designed to complement traditional scientific writing instruction. While initial reviews by students and educators have been positive, a formal study is needed to measure its benefits in comparison to standard instructional methods. PMID:20509946

Open Astronomy Catalogs API

NASA Astrophysics Data System (ADS)

Guillochon, James; Cowperthwaite, Philip S.

2018-05-01

We announce the public release of the application program interface (API) for the Open Astronomy Catalogs (OACs), the OACAPI. The OACs serve near-complete collections of supernova, tidal disruption, kilonova, and fast stars data (including photometry, spectra, radio, and X-ray observations) via a user-friendly web interface that displays the data interactively and offers full data downloads. The OACAPI, by contrast, enables users to specifically download particular pieces of the OAC dataset via a flexible programmatic syntax, either via URL GET requests, or via a module within the astroquery Python package.

SalHUD--A Graphical Interface to Public Health Data in Puerto Rico.

PubMed

Ortiz-Zuazaga, Humberto G; Arce-Corretjer, Roberto; Solá-Sloan, Juan M; Conde, José G

2015-12-22

This paper describes SalHUD, a prototype web-based application for visualizing health data from Puerto Rico. Our initial focus was to provide interactive maps displaying years of potential life lost (YPLL). The public-use mortality file for year 2008 was downloaded from the Puerto Rico Institute of Statistics website. Data was processed with R, Python and EpiInfo to calculate years of potential life lost for the leading causes of death on each of the 78 municipalities in the island. Death records were classified according to ICD-10 codes. YPLL for each municipality was integrated into AtlasPR, a D3 Javascript map library. Additional Javascript, HTML and CSS programing was required to display maps as a web-based interface. YPLL for all municipalities are displayed on a map of Puerto Rico for each of the ten leading causes of death and for all causes combined, so users may dynamically explore the impact of premature mortality. This work is the first step in providing the general public in Puerto Rico with user-friendly, interactive, visual access to public health data that is usually published in numerical, text-based media.

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.

Online promotion a must for hospital marketing professionals. Employ tactics to ensure your Web site is working to build your brand.

PubMed

Anderson, Eric

2007-01-01

Maintaining an online presence and more effectively executing Web-based marketing strategies can help you better target consumers and increase brand recognition, says Eric Anderson, director of agency services at interactive marketing agency White Horse in Portland, OR. With consumers heading to the Internet for health information now more than ever, it's in your best interest to not only have a well-designed, user-friendly Web site, but also to take advantage of the Internet's capabilities with blogs and microsites.

A repository based on a dynamically extensible data model supporting multidisciplinary research in neuroscience.

PubMed

Corradi, Luca; Porro, Ivan; Schenone, Andrea; Momeni, Parastoo; Ferrari, Raffaele; Nobili, Flavio; Ferrara, Michela; Arnulfo, Gabriele; Fato, Marco M

2012-10-08

Robust, extensible and distributed databases integrating clinical, imaging and molecular data represent a substantial challenge for modern neuroscience. It is even more difficult to provide extensible software environments able to effectively target the rapidly changing data requirements and structures of research experiments. There is an increasing request from the neuroscience community for software tools addressing technical challenges about: (i) supporting researchers in the medical field to carry out data analysis using integrated bioinformatics services and tools; (ii) handling multimodal/multiscale data and metadata, enabling the injection of several different data types according to structured schemas; (iii) providing high extensibility, in order to address different requirements deriving from a large variety of applications simply through a user runtime configuration. A dynamically extensible data structure supporting collaborative multidisciplinary research projects in neuroscience has been defined and implemented. We have considered extensibility issues from two different points of view. First, the improvement of data flexibility has been taken into account. This has been done through the development of a methodology for the dynamic creation and use of data types and related metadata, based on the definition of "meta" data model. This way, users are not constrainted to a set of predefined data and the model can be easily extensible and applicable to different contexts. Second, users have been enabled to easily customize and extend the experimental procedures in order to track each step of acquisition or analysis. This has been achieved through a process-event data structure, a multipurpose taxonomic schema composed by two generic main objects: events and processes. Then, a repository has been built based on such data model and structure, and deployed on distributed resources thanks to a Grid-based approach. Finally, data integration aspects have been addressed by providing the repository application with an efficient dynamic interface designed to enable the user to both easily query the data depending on defined datatypes and view all the data of every patient in an integrated and simple way. The results of our work have been twofold. First, a dynamically extensible data model has been implemented and tested based on a "meta" data-model enabling users to define their own data types independently from the application context. This data model has allowed users to dynamically include additional data types without the need of rebuilding the underlying database. Then a complex process-event data structure has been built, based on this data model, describing patient-centered diagnostic processes and merging information from data and metadata. Second, a repository implementing such a data structure has been deployed on a distributed Data Grid in order to provide scalability both in terms of data input and data storage and to exploit distributed data and computational approaches in order to share resources more efficiently. Moreover, data managing has been made possible through a friendly web interface. The driving principle of not being forced to preconfigured data types has been satisfied. It is up to users to dynamically configure the data model for the given experiment or data acquisition program, thus making it potentially suitable for customized applications. Based on such repository, data managing has been made possible through a friendly web interface. The driving principle of not being forced to preconfigured data types has been satisfied. It is up to users to dynamically configure the data model for the given experiment or data acquisition program, thus making it potentially suitable for customized applications.

A repository based on a dynamically extensible data model supporting multidisciplinary research in neuroscience

PubMed Central

2012-01-01

Background Robust, extensible and distributed databases integrating clinical, imaging and molecular data represent a substantial challenge for modern neuroscience. It is even more difficult to provide extensible software environments able to effectively target the rapidly changing data requirements and structures of research experiments. There is an increasing request from the neuroscience community for software tools addressing technical challenges about: (i) supporting researchers in the medical field to carry out data analysis using integrated bioinformatics services and tools; (ii) handling multimodal/multiscale data and metadata, enabling the injection of several different data types according to structured schemas; (iii) providing high extensibility, in order to address different requirements deriving from a large variety of applications simply through a user runtime configuration. Methods A dynamically extensible data structure supporting collaborative multidisciplinary research projects in neuroscience has been defined and implemented. We have considered extensibility issues from two different points of view. First, the improvement of data flexibility has been taken into account. This has been done through the development of a methodology for the dynamic creation and use of data types and related metadata, based on the definition of “meta” data model. This way, users are not constrainted to a set of predefined data and the model can be easily extensible and applicable to different contexts. Second, users have been enabled to easily customize and extend the experimental procedures in order to track each step of acquisition or analysis. This has been achieved through a process-event data structure, a multipurpose taxonomic schema composed by two generic main objects: events and processes. Then, a repository has been built based on such data model and structure, and deployed on distributed resources thanks to a Grid-based approach. Finally, data integration aspects have been addressed by providing the repository application with an efficient dynamic interface designed to enable the user to both easily query the data depending on defined datatypes and view all the data of every patient in an integrated and simple way. Results The results of our work have been twofold. First, a dynamically extensible data model has been implemented and tested based on a “meta” data-model enabling users to define their own data types independently from the application context. This data model has allowed users to dynamically include additional data types without the need of rebuilding the underlying database. Then a complex process-event data structure has been built, based on this data model, describing patient-centered diagnostic processes and merging information from data and metadata. Second, a repository implementing such a data structure has been deployed on a distributed Data Grid in order to provide scalability both in terms of data input and data storage and to exploit distributed data and computational approaches in order to share resources more efficiently. Moreover, data managing has been made possible through a friendly web interface. The driving principle of not being forced to preconfigured data types has been satisfied. It is up to users to dynamically configure the data model for the given experiment or data acquisition program, thus making it potentially suitable for customized applications. Conclusions Based on such repository, data managing has been made possible through a friendly web interface. The driving principle of not being forced to preconfigured data types has been satisfied. It is up to users to dynamically configure the data model for the given experiment or data acquisition program, thus making it potentially suitable for customized applications. PMID:23043673

TopoCad - A unified system for geospatial data and services

NASA Astrophysics Data System (ADS)

Felus, Y. A.; Sagi, Y.; Regev, R.; Keinan, E.

2013-10-01

"E-government" is a leading trend in public sector activities in recent years. The Survey of Israel set as a vision to provide all of its services and datasets online. The TopoCad system is the latest software tool developed in order to unify a number of services and databases into one on-line and user friendly system. The TopoCad system is based on Web 1.0 technology; hence the customer is only a consumer of data. All data and services are accessible for the surveyors and geo-information professional in an easy and comfortable way. The future lies in Web 2.0 and Web 3.0 technologies through which professionals can upload their own data for quality control and future assimilation with the national database. A key issue in the development of this complex system was to implement a simple and easy (comfortable) user experience (UX). The user interface employs natural language dialog box in order to understand the user requirements. The system then links spatial data with alpha-numeric data in a flawless manner. The operation of the TopoCad requires no user guide or training. It is intuitive and self-taught. The system utilizes semantic engines and machine understanding technologies to link records from diverse databases in a meaningful way. Thus, the next generation of TopoCad will include five main modules: users and projects information, coordinates transformations and calculations services, geospatial data quality control, linking governmental systems and databases, smart forms and applications. The article describes the first stage of the TopoCad system and gives an overview of its future development.

ProtDec-LTR2.0: an improved method for protein remote homology detection by combining pseudo protein and supervised Learning to Rank.

PubMed

Chen, Junjie; Guo, Mingyue; Li, Shumin; Liu, Bin

2017-11-01

As one of the most important tasks in protein sequence analysis, protein remote homology detection is critical for both basic research and practical applications. Here, we present an effective web server for protein remote homology detection called ProtDec-LTR2.0 by combining ProtDec-Learning to Rank (LTR) and pseudo protein representation. Experimental results showed that the detection performance is obviously improved. The web server provides a user-friendly interface to explore the sequence and structure information of candidate proteins and find their conserved domains by launching a multiple sequence alignment tool. The web server is free and open to all users with no login requirement at http://bioinformatics.hitsz.edu.cn/ProtDec-LTR2.0/. bliu@hit.edu.cn. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

An advanced web query interface for biological databases

PubMed Central

Latendresse, Mario; Karp, Peter D.

2010-01-01

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

Web-based hydrodynamics computing

NASA Astrophysics Data System (ADS)

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

2005-01-01

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

Web-based hydrodynamics computing

NASA Astrophysics Data System (ADS)

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

2004-12-01

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

Web 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.

OPACs in the Clouds

ERIC Educational Resources Information Center

Webb, Paula L.; Nero, Muriel D.

2009-01-01

In today's world of instant everything, everyone has been exposed to some form of Web 2.0 technology, and higher education is not exempt from its long reach. Libraries of all types are incorporating Web 2.0 features to attract users as well as to showcase library services. The Online Public Access Catalog (OPAC) has become more user-friendly with…

AGORA : Organellar genome annotation from the amino acid and nucleotide references.

PubMed

Jung, Jaehee; Kim, Jong Im; Jeong, Young-Sik; Yi, Gangman

2018-03-29

Next-generation sequencing (NGS) technologies have led to the accumulation of highthroughput sequence data from various organisms in biology. To apply gene annotation of organellar genomes for various organisms, more optimized tools for functional gene annotation are required. Almost all gene annotation tools are mainly focused on the chloroplast genome of land plants or the mitochondrial genome of animals.We have developed a web application AGORA for the fast, user-friendly, and improved annotations of organellar genomes. AGORA annotates genes based on a BLAST-based homology search and clustering with selected reference sequences from the NCBI database or user-defined uploaded data. AGORA can annotate the functional genes in almost all mitochondrion and plastid genomes of eukaryotes. The gene annotation of a genome with an exon-intron structure within a gene or inverted repeat region is also available. It provides information of start and end positions of each gene, BLAST results compared with the reference sequence, and visualization of gene map by OGDRAW. Users can freely use the software, and the accessible URL is https://bigdata.dongguk.edu/gene_project/AGORA/.The main module of the tool is implemented by the python and php, and the web page is built by the HTML and CSS to support all browsers. gangman@dongguk.edu.

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…

An Earthquake Information Service with Free and Open Source Tools

NASA Astrophysics Data System (ADS)

Schroeder, M.; Stender, V.; Jüngling, S.

2015-12-01

At the GFZ German Research Centre for Geosciences in Potsdam, the working group Earthquakes and Volcano Physics examines the spatiotemporal behavior of earthquakes. In this context also the hazards of volcanic eruptions and tsunamis are explored. The aim is to collect related information after the occurrence of such extreme event and make them available for science and partly to the public as quickly as possible. However, the overall objective of this research is to reduce the geological risks that emanate from such natural hazards. In order to meet the stated objectives and to get a quick overview about the seismicity of a particular region and to compare the situation to historical events, a comprehensive visualization was desired. Based on the web-accessible data from the famous GFZ GEOFON network a user-friendly web mapping application was realized. Further, this web service integrates historical and current earthquake information from the USGS earthquake database, and more historical events from various other catalogues like Pacheco, International Seismological Centre (ISC) and more. This compilation of sources is unique in Earth sciences. Additionally, information about historical and current occurrences of volcanic eruptions and tsunamis are also retrievable. Another special feature in the application is the containment of times via a time shifting tool. Users can interactively vary the visualization by moving the time slider. Furthermore, the application was realized by using the newest JavaScript libraries which enables the application to run in all sizes of displays and devices. Our contribution will present the making of, the architecture behind, and few examples of the look and feel of this application.

PathScore: a web tool for identifying altered pathways in cancer data.

PubMed

Gaffney, Stephen G; Townsend, Jeffrey P

2016-12-01

PathScore quantifies the level of enrichment of somatic mutations within curated pathways, applying a novel approach that identifies pathways enriched across patients. The application provides several user-friendly, interactive graphic interfaces for data exploration, including tools for comparing pathway effect sizes, significance, gene-set overlap and enrichment differences between projects. Web application available at pathscore.publichealth.yale.edu. Site implemented in Python and MySQL, with all major browsers supported. Source code available at: github.com/sggaffney/pathscore with a GPLv3 license. stephen.gaffney@yale.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

BRepertoire: a user-friendly web server for analysing antibody repertoire data.

PubMed

Margreitter, Christian; Lu, Hui-Chun; Townsend, Catherine; Stewart, Alexander; Dunn-Walters, Deborah K; Fraternali, Franca

2018-04-14

Antibody repertoire analysis by high throughput sequencing is now widely used, but a persisting challenge is enabling immunologists to explore their data to discover discriminating repertoire features for their own particular investigations. Computational methods are necessary for large-scale evaluation of antibody properties. We have developed BRepertoire, a suite of user-friendly web-based software tools for large-scale statistical analyses of repertoire data. The software is able to use data preprocessed by IMGT, and performs statistical and comparative analyses with versatile plotting options. BRepertoire has been designed to operate in various modes, for example analysing sequence-specific V(D)J gene usage, discerning physico-chemical properties of the CDR regions and clustering of clonotypes. Those analyses are performed on the fly by a number of R packages and are deployed by a shiny web platform. The user can download the analysed data in different table formats and save the generated plots as image files ready for publication. We believe BRepertoire to be a versatile analytical tool that complements experimental studies of immune repertoires. To illustrate the server's functionality, we show use cases including differential gene usage in a vaccination dataset and analysis of CDR3H properties in old and young individuals. The server is accessible under http://mabra.biomed.kcl.ac.uk/BRepertoire.

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.

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

TrustRank: a Cold-Start tolerant recommender system

NASA Astrophysics Data System (ADS)

Zou, Haitao; Gong, Zhiguo; Zhang, Nan; Zhao, Wei; Guo, Jingzhi

2015-02-01

The explosive growth of the World Wide Web leads to the fast advancing development of e-commerce techniques. Recommender systems, which use personalised information filtering techniques to generate a set of items suitable to a given user, have received considerable attention. User- and item-based algorithms are two popular techniques for the design of recommender systems. These two algorithms are known to have Cold-Start problems, i.e., they are unable to effectively handle Cold-Start users who have an extremely limited number of purchase records. In this paper, we develop TrustRank, a novel recommender system which handles the Cold-Start problem by leveraging the user-trust networks which are commonly available for e-commerce applications. A user-trust network is formed by friendships or trust relationships that users specify among them. While it is straightforward to conjecture that a user-trust network is helpful for improving the accuracy of recommendations, a key challenge for using user-trust network to facilitate Cold-Start users is that these users also tend to have a very limited number of trust relationships. To address this challenge, we propose a pre-processing propagation of the Cold-Start users' trust network. In particular, by applying the personalised PageRank algorithm, we expand the friends of a given user to include others with similar purchase records to his/her original friends. To make this propagation algorithm scalable to a large amount of users, as required by real-world recommender systems, we devise an iterative computation algorithm of the original personalised TrustRank which can incrementally compute trust vectors for Cold-Start users. We conduct extensive experiments to demonstrate the consistently improvement provided by our proposed algorithm over the existing recommender algorithms on the accuracy of recommendations for Cold-Start users.

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.

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.

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.

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.

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

PubMed

Li, Yan; Andrade, Jorge

2017-01-01

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

Lynx: a database and knowledge extraction engine for integrative medicine

PubMed Central

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

2014-01-01

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

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…

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.

Framework to parameterize and validate APEX to support deployment of the nutrient tracking tool

USDA-ARS?s Scientific Manuscript database

The Agricultural Policy Environmental eXtender (APEX) model is the scientific basis for the Nutrient Tracking Tool (NTT). NTT is an enhanced version of the Nitrogen Trading Tool, a user-friendly web-based computer program originally developed by the USDA. NTT was developed to estimate reductions in...

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

CovalentDock Cloud: a web server for automated covalent docking.

PubMed

Ouyang, Xuchang; Zhou, Shuo; Ge, Zemei; Li, Runtao; Kwoh, Chee Keong

2013-07-01

Covalent binding is an important mechanism for many drugs to gain its function. We developed a computational algorithm to model this chemical event and extended it to a web server, the CovalentDock Cloud, to make it accessible directly online without any local installation and configuration. It provides a simple yet user-friendly web interface to perform covalent docking experiments and analysis online. The web server accepts the structures of both the ligand and the receptor uploaded by the user or retrieved from online databases with valid access id. It identifies the potential covalent binding patterns, carries out the covalent docking experiments and provides visualization of the result for user analysis. This web server is free and open to all users at http://docking.sce.ntu.edu.sg/.

CovalentDock Cloud: a web server for automated covalent docking

PubMed Central

Ouyang, Xuchang; Zhou, Shuo; Ge, Zemei; Li, Runtao; Kwoh, Chee Keong

2013-01-01

Covalent binding is an important mechanism for many drugs to gain its function. We developed a computational algorithm to model this chemical event and extended it to a web server, the CovalentDock Cloud, to make it accessible directly online without any local installation and configuration. It provides a simple yet user-friendly web interface to perform covalent docking experiments and analysis online. The web server accepts the structures of both the ligand and the receptor uploaded by the user or retrieved from online databases with valid access id. It identifies the potential covalent binding patterns, carries out the covalent docking experiments and provides visualization of the result for user analysis. This web server is free and open to all users at http://docking.sce.ntu.edu.sg/. PMID:23677616

Dcs Data Viewer, an Application that Accesses ATLAS DCS Historical Data

NASA Astrophysics Data System (ADS)

Tsarouchas, C.; Schlenker, S.; Dimitrov, G.; Jahn, G.

2014-06-01

The ATLAS experiment at CERN is one of the four Large Hadron Collider experiments. The Detector Control System (DCS) of ATLAS is responsible for the supervision of the detector equipment, the reading of operational parameters, the propagation of the alarms and the archiving of important operational data in a relational database (DB). DCS Data Viewer (DDV) is an application that provides access to the ATLAS DCS historical data through a web interface. Its design is structured using a client-server architecture. The pythonic server connects to the DB and fetches the data by using optimized SQL requests. It communicates with the outside world, by accepting HTTP requests and it can be used stand alone. The client is an AJAX (Asynchronous JavaScript and XML) interactive web application developed under the Google Web Toolkit (GWT) framework. Its web interface is user friendly, platform and browser independent. The selection of metadata is done via a column-tree view or with a powerful search engine. The final visualization of the data is done using java applets or java script applications as plugins. The default output is a value-over-time chart, but other types of outputs like tables, ascii or ROOT files are supported too. Excessive access or malicious use of the database is prevented by a dedicated protection mechanism, allowing the exposure of the tool to hundreds of inexperienced users. The current configuration of the client and of the outputs can be saved in an XML file. Protection against web security attacks is foreseen and authentication constrains have been taken into account, allowing the exposure of the tool to hundreds of users world wide. Due to its flexible interface and its generic and modular approach, DDV could be easily used for other experiment control systems.

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.

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.

Sharing on Web 3d Models of Ancient Theatres. a Methodological Workflow

NASA Astrophysics Data System (ADS)

Scianna, A.; La Guardia, M.; Scaduto, M. L.

2016-06-01

In the last few years, the need to share on the Web the knowledge of Cultural Heritage (CH) through navigable 3D models has increased. This need requires the availability of Web-based virtual reality systems and 3D WEBGIS. In order to make the information available to all stakeholders, these instruments should be powerful and at the same time very user-friendly. However, research and experiments carried out so far show that a standardized methodology doesn't exist. All this is due both to complexity and dimensions of geometric models to be published, on the one hand, and to excessive costs of hardware and software tools, on the other. In light of this background, the paper describes a methodological approach for creating 3D models of CH, freely exportable on the Web, based on HTML5 and free and open source software. HTML5, supporting the WebGL standard, allows the exploration of 3D spatial models using most used Web browsers like Chrome, Firefox, Safari, Internet Explorer. The methodological workflow here described has been tested for the construction of a multimedia geo-spatial platform developed for three-dimensional exploration and documentation of the ancient theatres of Segesta and of Carthage, and the surrounding landscapes. The experimental application has allowed us to explore the potential and limitations of sharing on the Web of 3D CH models based on WebGL standard. Sharing capabilities could be extended defining suitable geospatial Web-services based on capabilities of HTML5 and WebGL technology.

Earth Science Computational Architecture for Multi-disciplinary Investigations

NASA Astrophysics Data System (ADS)

Parker, J. W.; Blom, R.; Gurrola, E.; Katz, D.; Lyzenga, G.; Norton, C.

2005-12-01

Understanding the processes underlying Earth's deformation and mass transport requires a non-traditional, integrated, interdisciplinary, approach dependent on multiple space and ground based data sets, modeling, and computational tools. Currently, details of geophysical data acquisition, analysis, and modeling largely limit research to discipline domain experts. Interdisciplinary research requires a new computational architecture that is optimized to perform complex data processing of multiple solid Earth science data types in a user-friendly environment. A web-based computational framework is being developed and integrated with applications for automatic interferometric radar processing, and models for high-resolution deformation & gravity, forward models of viscoelastic mass loading over short wavelengths & complex time histories, forward-inverse codes for characterizing surface loading-response over time scales of days to tens of thousands of years, and inversion of combined space magnetic & gravity fields to constrain deep crustal and mantle properties. This framework combines an adaptation of the QuakeSim distributed services methodology with the Pyre framework for multiphysics development. The system uses a three-tier architecture, with a middle tier server that manages user projects, available resources, and security. This ensures scalability to very large networks of collaborators. Users log into a web page and have a personal project area, persistently maintained between connections, for each application. Upon selection of an application and host from a list of available entities, inputs may be uploaded or constructed from web forms and available data archives, including gravity, GPS and imaging radar data. The user is notified of job completion and directed to results posted via URLs. Interdisciplinary work is supported through easy availability of all applications via common browsers, application tutorials and reference guides, and worked examples with visual response. At the platform level, multi-physics application development and workflow are available in the enriched environment of the Pyre framework. Advantages for combining separate expert domains include: multiple application components efficiently interact through Python shared libraries, investigators may nimbly swap models and try new parameter values, and a rich array of common tools are inherent in the Pyre system. The first four specific investigations to use this framework are: Gulf Coast subsidence: understanding of partitioning between compaction, subsidence and growth faulting; Gravity & deformation of a layered spherical earth model due to large earthquakes; Rift setting of Lake Vostok, Antarctica; and global ice mass changes.

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

PubMed Central

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

2015-01-01

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

A 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

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?

Written online situational feedback via mobile phone to support self-management of chronic widespread pain: a usability study of a Web-based intervention

PubMed Central

2011-01-01

Background This pretrial study aimed to develop and test the usability of a four-week Internet intervention delivered by a Web-enabled mobile phone to support self-management of chronic widespread pain. Methods The intervention included daily online entries and individualized written feedback, grounded in a mindfulness-based cognitive behavioral approach. The participants registered activities, emotions and pain cognitions three times daily using the mobile device. The therapist had immediate access to this information through a secure Web site. The situational information was used to formulate and send a personalized text message to the participant with the aim of stimulating effective self-management of the current situation. Six women participated and evaluated the experience. Results The intervention was rated as supportive, meaningful and user-friendly by the majority of the women. The response rate to the daily registration entries was high and technical problems were few. Conclusion The results indicate a feasible intervention. Web-applications are fast becoming standard features of mobile phones and interventions of this kind can therefore be more available than before. Trial registration number ClinicalTrials.gov: NCT01236209 PMID:21352516

Data in the Classroom: New Tools for Engaging Students with Data

NASA Astrophysics Data System (ADS)

Dean, A.; Pisut, D.

2017-12-01

The ability to understand and analyze data effectively can increase students ability to understand current and historical global change. Since 2009, NOAA Data in the Classroom Project has been offering formal education resources and tools aimed at helping teachers to build data and environmental literacy in their classrooms. Currently, NOAA is modernizing its Data in the Classroom resources using a web application within Esri's web-based GIS platform, Story Maps. Story Maps have been used for a wide variety of purposes, including teaching and instruction, for more than a decade. This technology can help to engage students in a story, like El Niño, while harnessing the power of data - using maps, data visualizations and data query tools. The aim is to create an effective education tool that allows students access to user-friendly, relevant data sets from NOAA, ultimately providing the opportunity to explore dynamic Earth processes and understand the impact of environmental events on a regional or global scale. This presentation will include demonstrations of the recently launched web-based curricular modules, highlighting the Esri web technology used to build and distribute each module and the interactive data tools that are unique to this project.

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/.

Facilitating Scientific Collaboration and Education with Easy Access Web Maps Using the AGAP Antarctic Geophysical Data

NASA Astrophysics Data System (ADS)

Abdi, A.

2012-12-01

Science and science education benefit from easy access to data yet often geophysical data sets are large, complex and difficult to share. The difficulty in sharing data and imagery easily inhibits both collaboration and the use of real data in educational applications. The dissemination of data products through web maps serves a very efficient and user-friendly method for students, the public and the science community to gain insights and understanding from data. Few research groups provide direct access to their data, let alone map-based visualizations. By building upon current GIS infrastructure with web mapping technologies, like ArcGIS Server, scientific groups, institutions and agencies can enhance the value of their GIS investments. The advantages of web maps to serve data products are many; existing web-mapping technology allows complex GIS analysis to be shared across the Internet, and can be easily scaled from a few users to millions. This poster highlights the features of an interactive web map developed at the Polar Geophysics Group at the Lamont-Doherty Earth Observatory of Columbia University that provides a visual representation of, and access to, data products that resulted from the group's recently concluded AGAP project (http://pgg.ldeo.columbia.edu). The AGAP project collected more than 120,000 line km of new aerogeophysical data using two Twin Otter aircrafts. Data included ice penetrating radar, magnetometer, gravimeter and laser altimeter measurements. The web map is based upon ArcGIS Viewer for Flex, which is a configurable client application built on the ArcGIS API for Flex that works seamlessly with ArcGIS Server 10. The application can serve a variety of raster and vector file formats through the Data Interoperability for Server, which eliminates data sharing barriers across numerous file formats. The ability of the application to serve large datasets is only hindered by the availability of appropriate hardware. ArcGIS is a proprietary product, but there are a few data portals in the earth sciences that have a map interface using open access products such as MapServer and OpenLayers, the most notable being the NASA IceBridge Data Portal. Indeed, with the widespread availability of web mapping technology, the scientific community should advance towards this direction when disseminating their data.

iScreen: world's first cloud-computing web server for virtual screening and de novo drug design based on TCM database@Taiwan

NASA Astrophysics Data System (ADS)

Tsai, Tsung-Ying; Chang, Kai-Wei; Chen, Calvin Yu-Chian

2011-06-01

The rapidly advancing researches on traditional Chinese medicine (TCM) have greatly intrigued pharmaceutical industries worldwide. To take initiative in the next generation of drug development, we constructed a cloud-computing system for TCM intelligent screening system (iScreen) based on TCM Database@Taiwan. iScreen is compacted web server for TCM docking and followed by customized de novo drug design. We further implemented a protein preparation tool that both extract protein of interest from a raw input file and estimate the size of ligand bind site. In addition, iScreen is designed in user-friendly graphic interface for users who have less experience with the command line systems. For customized docking, multiple docking services, including standard, in-water, pH environment, and flexible docking modes are implemented. Users can download first 200 TCM compounds of best docking results. For TCM de novo drug design, iScreen provides multiple molecular descriptors for a user's interest. iScreen is the world's first web server that employs world's largest TCM database for virtual screening and de novo drug design. We believe our web server can lead TCM research to a new era of drug development. The TCM docking and screening server is available at http://iScreen.cmu.edu.tw/.

iScreen: world's first cloud-computing web server for virtual screening and de novo drug design based on TCM database@Taiwan.

PubMed

Tsai, Tsung-Ying; Chang, Kai-Wei; Chen, Calvin Yu-Chian

2011-06-01

The rapidly advancing researches on traditional Chinese medicine (TCM) have greatly intrigued pharmaceutical industries worldwide. To take initiative in the next generation of drug development, we constructed a cloud-computing system for TCM intelligent screening system (iScreen) based on TCM Database@Taiwan. iScreen is compacted web server for TCM docking and followed by customized de novo drug design. We further implemented a protein preparation tool that both extract protein of interest from a raw input file and estimate the size of ligand bind site. In addition, iScreen is designed in user-friendly graphic interface for users who have less experience with the command line systems. For customized docking, multiple docking services, including standard, in-water, pH environment, and flexible docking modes are implemented. Users can download first 200 TCM compounds of best docking results. For TCM de novo drug design, iScreen provides multiple molecular descriptors for a user's interest. iScreen is the world's first web server that employs world's largest TCM database for virtual screening and de novo drug design. We believe our web server can lead TCM research to a new era of drug development. The TCM docking and screening server is available at http://iScreen.cmu.edu.tw/.

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 .

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.

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

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

PubMed

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

2015-01-01

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

An intelligent tool for activity data collection.

PubMed

Sarkar, A M Jehad

2011-01-01

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

National Geothermal Data System: Open Access to Geoscience Data, Maps, and Documents

NASA Astrophysics Data System (ADS)

Caudill, C. M.; Richard, S. M.; Musil, L.; Sonnenschein, A.; Good, J.

2014-12-01

The U.S. National Geothermal Data System (NGDS) provides free open access to millions of geoscience data records, publications, maps, and reports via distributed web services to propel geothermal research, development, and production. NGDS is built on the US Geoscience Information Network (USGIN) data integration framework, which is a joint undertaking of the USGS and the Association of American State Geologists (AASG), and is compliant with international standards and protocols. NGDS currently serves geoscience information from 60+ data providers in all 50 states. Free and open source software is used in this federated system where data owners maintain control of their data. This interactive online system makes geoscience data easily discoverable, accessible, and interoperable at no cost to users. The dynamic project site http://geothermaldata.org serves as the information source and gateway to the system, allowing data and applications discovery and availability of the system's data feed. It also provides access to NGDS specifications and the free and open source code base (on GitHub), a map-centric and library style search interface, other software applications utilizing NGDS services, NGDS tutorials (via YouTube and USGIN site), and user-created tools and scripts. The user-friendly map-centric web-based application has been created to support finding, visualizing, mapping, and acquisition of data based on topic, location, time, provider, or key words. Geographic datasets visualized through the map interface also allow users to inspect the details of individual GIS data points (e.g. wells, geologic units, etc.). In addition, the interface provides the information necessary for users to access the GIS data from third party software applications such as GoogleEarth, UDig, and ArcGIS. A redistributable, free and open source software package called GINstack (USGIN software stack) was also created to give data providers a simple way to release data using interoperable and shareable standards, upload data and documents, and expose those data as a node in the NGDS or any larger data system through a CSW endpoint. The easy-to-use interface is supported by back-end software including Postgres, GeoServer, and custom CKAN extensions among others.

Technobabble: Photoshop 6 Converges Web, Print Photograph-Editing Capabilities.

ERIC Educational Resources Information Center

Communication: Journalism Education Today, 2001

2001-01-01

Discusses the newly-released Adobe Photoshop 6, and its use in student publications. Notes its refined text-handling capabilities, a more user-friendly interface, integrated vector functions, easier preparation of Web images, and new and more powerful layer functions. (SR)

Promoting Teacher Adoption of GIS Using Teacher-Centered and Teacher-Friendly Design

ERIC Educational Resources Information Center

Hong, Jung Eun

2014-01-01

This article reports the results of a case study that employed user-centered design to develop training tutorials for helping middle school social studies teachers use Web-based GIS in their classrooms. This study placed teachers in the center of the design process in planning, designing, and developing the tutorials. This article describes how…

OpenGL in Multi-User Web-Based Applications

NASA Astrophysics Data System (ADS)

Szostek, K.; Piórkowski, A.

In this article construction and potential of OpenGL multi-user web-based application are presented. The most common technologies like: .NET ASP, Java and Mono were used with specific OpenGL libraries to visualize tree-dimensional medical data. The most important conclusion of this work is that server side applications can easily take advantage of fast GPU and produce efficient results of advanced computation just like the visualization.

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

Evaluation of Story Maps to Enhance Public Engagement and Communication at Legacy Management Sites – 17334

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

Castillo, Darina; Carpenter, Cliff; Linard, Joshua

Story Maps are being used in both public and private sectors to convey information to stakeholders, create enterprise platforms, and assist in decision making. Story Maps are web applications that combine maps, narrative text, images, and multimedia content to provide information. These applications provide a user-friendly platform to share the remarkable history of our sites, the complexity of their contamination and remediation, successes we achieve in our LTS&M activities, and even the challenges we face as we aim to fulfill our mission.

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, improving the ease of navigation, and balancing a "low prevalence of use, yet high impact" message. A total of 9138 users visited the website in the 3 months immediately post launch, and over 25,000 hard-copy Cracks in the Ice booklets and flyers were distributed across Australia. Of these resources, 60.93% (15,525/25,480) were distributed to relevant organizations and mailing list subscribers, and 39.07% (9955/25,480) were ordered directly by individuals, services, and community groups via the Cracks in the Ice website. The codevelopment process resulted in an engaging Web-based resource for the Australian community to access up-to-date and evidence-based resources about crystal methamphetamine. The Cracks in the Ice Community Toolkit provides much-needed information and support for individuals, families, and communities. ©Katrina Elizabeth Champion, Cath Chapman, Nicola Clare Newton, Mary-Ellen Brierley, Lexine Stapinski, Frances Kay-Lambkin, Jack Nagle, Maree Teesson. Originally published in JMIR Mental Health (http://mental.jmir.org), 20.03.2018.

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

Life span in online communities

NASA Astrophysics Data System (ADS)

Grabowski, A.; Kosiński, R. A.

2010-12-01

Recently online communities have attracted great interest and have become an important medium of information exchange between users. The aim of this work is to introduce a simple model of the evolution of online communities. This model describes (a) the time evolution of users’ activity in a web service, e.g., the time evolution of the number of online friends or written posts, (b) the time evolution of the degree distribution of a social network, and (c) the time evolution of the number of active users of a web service. In the second part of the paper we investigate the influence of the users’ lifespan (i.e., the total time in which they are active in an online community) on the process of rumor propagation in evolving social networks. Viral marketing is an important application of such method of information propagation.

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

PubMed

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

2016-01-01

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

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

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.

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.

[HyperPsych--resources for medicine and psychology on the World Wide Web].

PubMed

Laszig, P

1997-07-01

Progress in the research of interactive communication technology and the acceleration of processing and transmitting information have promoted the development of computer networks allowing global access to scientific information and services. The recently most well-known net is the internet. Based on its integrative structure as a communication-directed as well as an information-directed medium, the internet helps researchers design scientific research. Especially medicine and psychology as information-dependent scientific disciplines may profit by using this technological offer. As a method to coordinate to the vast amount of medical and psychological data around the globe and to communicate with researchers world-wide, it enhances innovative possibilities for research, diagnosis and therapy. Currently, the World Wide Web is regarded as the most user-friendly and practical of all the internet resources. Based on a systematic introduction to the applications of the WWW, this article discusses relevant resources, points out possibilities and limits of network-supported scientific research and proposes many uses of this new medium.

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.

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

PubMed

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

2016-11-18

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

SMPBS: Web server for computing biomolecular electrostatics using finite element solvers of size modified Poisson-Boltzmann equation.

PubMed

Xie, Yang; Ying, Jinyong; Xie, Dexuan

2017-03-30

SMPBS (Size Modified Poisson-Boltzmann Solvers) is a web server for computing biomolecular electrostatics using finite element solvers of the size modified Poisson-Boltzmann equation (SMPBE). SMPBE not only reflects ionic size effects but also includes the classic Poisson-Boltzmann equation (PBE) as a special case. Thus, its web server is expected to have a broader range of applications than a PBE web server. SMPBS is designed with a dynamic, mobile-friendly user interface, and features easily accessible help text, asynchronous data submission, and an interactive, hardware-accelerated molecular visualization viewer based on the 3Dmol.js library. In particular, the viewer allows computed electrostatics to be directly mapped onto an irregular triangular mesh of a molecular surface. Due to this functionality and the fast SMPBE finite element solvers, the web server is very efficient in the calculation and visualization of electrostatics. In addition, SMPBE is reconstructed using a new objective electrostatic free energy, clearly showing that the electrostatics and ionic concentrations predicted by SMPBE are optimal in the sense of minimizing the objective electrostatic free energy. SMPBS is available at the URL: smpbs.math.uwm.edu © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Web-based metabolic network visualization with a zooming user interface

PubMed Central

2011-01-01

Background Displaying complex metabolic-map diagrams, for Web browsers, and allowing users to interact with them for querying and overlaying expression data over them is challenging. Description We present a Web-based metabolic-map diagram, which can be interactively explored by the user, called the Cellular Overview. The main characteristic of this application is the zooming user interface enabling the user to focus on appropriate granularities of the network at will. Various searching commands are available to visually highlight sets of reactions, pathways, enzymes, metabolites, and so on. Expression data from single or multiple experiments can be overlaid on the diagram, which we call the Omics Viewer capability. The application provides Web services to highlight the diagram and to invoke the Omics Viewer. This application is entirely written in JavaScript for the client browsers and connect to a Pathway Tools Web server to retrieve data and diagrams. It uses the OpenLayers library to display tiled diagrams. Conclusions This new online tool is capable of displaying large and complex metabolic-map diagrams in a very interactive manner. This application is available as part of the Pathway Tools software that powers multiple metabolic databases including Biocyc.org: The Cellular Overview is accessible under the Tools menu. PMID:21595965

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.

TRFolder-W: a web server for telomerase RNA structure prediction in yeast genomes.

PubMed

Zhang, Dong; Xue, Xingran; Malmberg, Russell L; Cai, Liming

2012-10-15

TRFolder-W is a web server capable of predicting core structures of telomerase RNA (TR) in yeast genomes. TRFolder is a command-line Python toolkit for TR-specific structure prediction. We developed a web-version built on the django web framework, leveraging the work done previously, to include enhancements to increase flexibility of usage. To date, there are five core sub-structures commonly found in TR of fungal species, which are the template region, downstream pseudoknot, boundary element, core-closing stem and triple helix. The aim of TRFolder-W is to use the five core structures as fundamental units to predict potential TR genes for yeast, and to provide a user-friendly interface. Moreover, the application of TRFolder-W can be extended to predict the characteristic structure on species other than fungal species. The web server TRFolder-W is available at http://rna-informatics.uga.edu/?f=software&p=TRFolder-w.

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, leading us to believe that such guidelines need to be adapted for this user group. As web applications proliferate, it is important to ensure those who are most vulnerable-who have the least knowledge and the lowest literacy, health literacy, and computer proficiency-can access, understand, and use them. In order for the investment in public reporting to produce value, consumer-facing web applications need to be designed to address end users' unique strengths and limitations. Our findings may help others to build consumer-facing tools or technology targeted to a predominantly older population. We encourage others designing consumer-facing web technologies to critically evaluate their assumptions about user interface design, particularly if they are designing tools for older adults, and to test products with their end users.

Little Boy Blue Goes High-Tech: Providing Customers with Topic-Driven Content

ERIC Educational Resources Information Center

King, David

2005-01-01

In an attempt to make the Kansas City Public Library's Web site more user friendly, the Web team took an opportunity to completely redesign the site. This article describes the techniques that the team used to organize and design the new Web site. By adopting a guided approach to the Internet, they were able to streamline their Web links and…

SCENERY: a web application for (causal) network reconstruction from cytometry data

PubMed Central

Papoutsoglou, Georgios; Athineou, Giorgos; Lagani, Vincenzo; Xanthopoulos, Iordanis; Schmidt, Angelika; Éliás, Szabolcs; Tegnér, Jesper

2017-01-01

Abstract Flow and mass cytometry technologies can probe proteins as biological markers in thousands of individual cells simultaneously, providing unprecedented opportunities for reconstructing networks of protein interactions through machine learning algorithms. The network reconstruction (NR) problem has been well-studied by the machine learning community. However, the potentials of available methods remain largely unknown to the cytometry community, mainly due to their intrinsic complexity and the lack of comprehensive, powerful and easy-to-use NR software implementations specific for cytometry data. To bridge this gap, we present Single CEll NEtwork Reconstruction sYstem (SCENERY), a web server featuring several standard and advanced cytometry data analysis methods coupled with NR algorithms in a user-friendly, on-line environment. In SCENERY, users may upload their data and set their own study design. The server offers several data analysis options categorized into three classes of methods: data (pre)processing, statistical analysis and NR. The server also provides interactive visualization and download of results as ready-to-publish images or multimedia reports. Its core is modular and based on the widely-used and robust R platform allowing power users to extend its functionalities by submitting their own NR methods. SCENERY is available at scenery.csd.uoc.gr or http://mensxmachina.org/en/software/. PMID:28525568

ToxRefDB - Release user-friendly web-based tool for mining ToxRefDB

EPA Science Inventory

The updated URL link is for a table of NCCT ToxCast public datasets. The next to last row of the table has the link for the US EPA ToxCast ToxRefDB Data Release October 2014. ToxRefDB provides detailed chemical toxicity data in a publically accessible searchable format. ToxRefD...

Software applications for flux balance analysis.

PubMed

Lakshmanan, Meiyappan; Koh, Geoffrey; Chung, Bevan K S; Lee, Dong-Yup

2014-01-01

Flux balance analysis (FBA) is a widely used computational method for characterizing and engineering intrinsic cellular metabolism. The increasing number of its successful applications and growing popularity are possibly attributable to the availability of specific software tools for FBA. Each tool has its unique features and limitations with respect to operational environment, user-interface and supported analysis algorithms. Presented herein is an in-depth evaluation of currently available FBA applications, focusing mainly on usability, functionality, graphical representation and inter-operability. Overall, most of the applications are able to perform basic features of model creation and FBA simulation. COBRA toolbox, OptFlux and FASIMU are versatile to support advanced in silico algorithms to identify environmental and genetic targets for strain design. SurreyFBA, WEbcoli, Acorn, FAME, GEMSiRV and MetaFluxNet are the distinct tools which provide the user friendly interfaces in model handling. In terms of software architecture, FBA-SimVis and OptFlux have the flexible environments as they enable the plug-in/add-on feature to aid prospective functional extensions. Notably, an increasing trend towards the implementation of more tailored e-services such as central model repository and assistance to collaborative efforts was observed among the web-based applications with the help of advanced web-technologies. Furthermore, most recent applications such as the Model SEED, FAME, MetaFlux and MicrobesFlux have even included several routines to facilitate the reconstruction of genome-scale metabolic models. Finally, a brief discussion on the future directions of FBA applications was made for the benefit of potential tool developers.

Cross-Dataset Analysis and Visualization Driven by Expressive Web Services

NASA Astrophysics Data System (ADS)

Alexandru Dumitru, Mircea; Catalin Merticariu, Vlad

2015-04-01

The deluge of data that is hitting us every day from satellite and airborne sensors is changing the workflow of environmental data analysts and modelers. Web geo-services play now a fundamental role, and are no longer needed to preliminary download and store the data, but rather they interact in real-time with GIS applications. Due to the very large amount of data that is curated and made available by web services, it is crucial to deploy smart solutions for optimizing network bandwidth, reducing duplication of data and moving the processing closer to the data. In this context we have created a visualization application for analysis and cross-comparison of aerosol optical thickness datasets. The application aims to help researchers identify and visualize discrepancies between datasets coming from various sources, having different spatial and time resolutions. It also acts as a proof of concept for integration of OGC Web Services under a user-friendly interface that provides beautiful visualizations of the explored data. The tool was built on top of the World Wind engine, a Java based virtual globe built by NASA and the open source community. For data retrieval and processing we exploited the OGC Web Coverage Service potential: the most exciting aspect being its processing extension, a.k.a. the OGC Web Coverage Processing Service (WCPS) standard. A WCPS-compliant service allows a client to execute a processing query on any coverage offered by the server. By exploiting a full grammar, several different kinds of information can be retrieved from one or more datasets together: scalar condensers, cross-sectional profiles, comparison maps and plots, etc. This combination of technology made the application versatile and portable. As the processing is done on the server-side, we ensured that the minimal amount of data is transferred and that the processing is done on a fully-capable server, leaving the client hardware resources to be used for rendering the visualization. The application offers a set of features to visualize and cross-compare the datasets. Users can select a region of interest in space and time on which an aerosol map layer is plotted. Hovmoeller time-latitude and time-longitude profiles can be displayed by selecting orthogonal cross-sections on the globe. Statistics about the selected dataset are also displayed in different text and plot formats. The datasets can also be cross-compared either by using the delta map tool or the merged map tool. For more advanced users, a WCPS query console is also offered allowing users to process their data with ad-hoc queries and then choose how to display the results. Overall, the user has a rich set of tools that can be used to visualize and cross-compare the aerosol datasets. With our application we have shown how the NASA WorldWind framework can be used to display results processed efficiently - and entirely - on the server side using the expressiveness of the OGC WCPS web-service. The application serves not only as a proof of concept of a new paradigm in working with large geospatial data but also as an useful tool for environmental data analysts.

GeoChronos: An On-line Collaborative Platform for Earth Observation Scientists

NASA Astrophysics Data System (ADS)

Gamon, J. A.; Kiddle, C.; Curry, R.; Markatchev, N.; Zonta-Pastorello, G., Jr.; Rivard, B.; Sanchez-Azofeifa, G. A.; Simmonds, R.; Tan, T.

2009-12-01

Recent advances in cyberinfrastructure are offering new solutions to the growing challenges of managing and sharing large data volumes. Web 2.0 and social networking technologies, provide the means for scientists to collaborate and share information more effectively. Cloud computing technologies can provide scientists with transparent and on-demand access to applications served over the Internet in a dynamic and scalable manner. Semantic Web technologies allow for data to be linked together in a manner understandable by machines, enabling greater automation. Combining all of these technologies together can enable the creation of very powerful platforms. GeoChronos (http://geochronos.org/), part of a CANARIE Network Enabled Platforms project, is an online collaborative platform that incorporates these technologies to enable members of the earth observation science community to share data and scientific applications and to collaborate more effectively. The GeoChronos portal is built on an open source social networking platform called Elgg. Elgg provides a full set of social networking functionalities similar to Facebook including blogs, tags, media/document sharing, wikis, friends/contacts, groups, discussions, message boards, calendars, status, activity feeds and more. An underlying cloud computing infrastructure enables scientists to access dynamically provisioned applications via the portal for visualizing and analyzing data. Users are able to access and run the applications from any computer that has a Web browser and Internet connectivity and do not need to manage and maintain the applications themselves. Semantic Web Technologies, such as the Resource Description Framework (RDF) are being employed for relating and linking together spectral, satellite, meteorological and other data. Social networking functionality plays an integral part in facilitating the sharing of data and applications. Examples of recent GeoChronos users during the early testing phase have included the IAI International Wireless Sensor Networking Summer School at the University of Alberta, and the IAI Tropi-Dry community. Current GeoChronos activities include the development of a web-based spectral library and related analytical and visualization tools, in collaboration with members of the SpecNet community. The GeoChronos portal will be open to all members of the earth observation science community when the project nears completion at the end of 2010.

Java Web Simulation (JWS); a web based database of kinetic models.

PubMed

Snoep, J L; Olivier, B G

2002-01-01

Software to make a database of kinetic models accessible via the internet has been developed and a core database has been set up at http://jjj.biochem.sun.ac.za/. This repository of models, available to everyone with internet access, opens a whole new way in which we can make our models public. Via the database, a user can change enzyme parameters and run time simulations or steady state analyses. The interface is user friendly and no additional software is necessary. The database currently contains 10 models, but since the generation of the program code to include new models has largely been automated the addition of new models is straightforward and people are invited to submit their models to be included in the database.

Smart roadside initiative : user manual.

DOT National Transportation Integrated Search

2015-09-01

This document provides the user instructions for the Smart Roadside Initiative (SRI) applications including mobile and web-based SRI applications. These applications include smartphone-enabled information exchange and notification, and software compo...

Service Incentive: Towards an SOA-Friendly Acquisition Process

DTIC Science & Technology

2010-11-01

cell) 17000 Commerce Parkway, Suite A Mt. Laurel, NJ 08054 arlene.minkiewicz@pricesystems.com 1. McGovern, J, et. al., Java Based Web Applications...Web Services”, Dec 2004, available at <https://www.sdn.sap.com/irj/ servlet /prt/portal/prtroot/docs/library/ uuid/512de490-0201-0010-ffb4

The Xeno-glycomics database (XDB): a relational database of qualitative and quantitative pig glycome repertoire.

PubMed

Park, Hae-Min; Park, Ju-Hyeong; Kim, Yoon-Woo; Kim, Kyoung-Jin; Jeong, Hee-Jin; Jang, Kyoung-Soon; Kim, Byung-Gee; Kim, Yun-Gon

2013-11-15

In recent years, the improvement of mass spectrometry-based glycomics techniques (i.e. highly sensitive, quantitative and high-throughput analytical tools) has enabled us to obtain a large dataset of glycans. Here we present a database named Xeno-glycomics database (XDB) that contains cell- or tissue-specific pig glycomes analyzed with mass spectrometry-based techniques, including a comprehensive pig glycan information on chemical structures, mass values, types and relative quantities. It was designed as a user-friendly web-based interface that allows users to query the database according to pig tissue/cell types or glycan masses. This database will contribute in providing qualitative and quantitative information on glycomes characterized from various pig cells/organs in xenotransplantation and might eventually provide new targets in the α1,3-galactosyltransferase gene-knock out pigs era. The database can be accessed on the web at http://bioinformatics.snu.ac.kr/xdb.

FGMReview: design of a knowledge management tool on female genital mutilation.

PubMed

Martínez Pérez, Guillermo; Turetsky, Risa

2015-11-01

Web-based literature search engines may not be user-friendly for some readers searching for information on female genital mutilation. This is a traditional practice that has no health benefits, and about 140 million girls and women worldwide have undergone it. In 2012, the website FGMReview was created with the aim to offer a user-friendly, accessible, scalable, and innovative knowledge management tool specialized in female genital mutilation. The design of this website was guided by a conceptual model based on the use of benchmarking techniques and requirements engineering, an area of knowledge from the computer informatics field, influenced by the Transcultural Nursing model. The purpose of this article is to describe this conceptual model. Nurses and other health care providers can use this conceptual model to guide their methodological approach to design and launch other eHealth projects. © The Author(s) 2014.

Design and implementation of a secure and user-friendly broker platform supporting the end-to-end provisioning of e-homecare services.

PubMed

Van Hoecke, Sofie; Steurbaut, Kristof; Taveirne, Kristof; De Turck, Filip; Dhoedt, Bart

2010-01-01

We designed a broker platform for e-homecare services using web service technology. The broker allows efficient data communication and guarantees quality requirements such as security, availability and cost-efficiency by dynamic selection of services, minimizing user interactions and simplifying authentication through a single user sign-on. A prototype was implemented, with several e-homecare services (alarm, telemonitoring, audio diary and video-chat). It was evaluated by patients with diabetes and multiple sclerosis. The patients found that the start-up time and overhead imposed by the platform was satisfactory. Having all e-homecare services integrated into a single application, which required only one login, resulted in a high quality of experience for the patients.

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.

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

Interactive Voice/Web Response System in clinical research

PubMed Central

Ruikar, Vrishabhsagar

2016-01-01

Emerging technologies in computer and telecommunication industry has eased the access to computer through telephone. An Interactive Voice/Web Response System (IxRS) is one of the user friendly systems for end users, with complex and tailored programs at its backend. The backend programs are specially tailored for easy understanding of users. Clinical research industry has experienced revolution in methodologies of data capture with time. Different systems have evolved toward emerging modern technologies and tools in couple of decades from past, for example, Electronic Data Capture, IxRS, electronic patient reported outcomes, etc. PMID:26952178

Interactive Voice/Web Response System in clinical research.

PubMed

Ruikar, Vrishabhsagar

2016-01-01

Emerging technologies in computer and telecommunication industry has eased the access to computer through telephone. An Interactive Voice/Web Response System (IxRS) is one of the user friendly systems for end users, with complex and tailored programs at its backend. The backend programs are specially tailored for easy understanding of users. Clinical research industry has experienced revolution in methodologies of data capture with time. Different systems have evolved toward emerging modern technologies and tools in couple of decades from past, for example, Electronic Data Capture, IxRS, electronic patient reported outcomes, etc.

lncRNATargets: A platform for lncRNA target prediction based on nucleic acid thermodynamics.

PubMed

Hu, Ruifeng; Sun, Xiaobo

2016-08-01

Many studies have supported that long noncoding RNAs (lncRNAs) perform various functions in various critical biological processes. Advanced experimental and computational technologies allow access to more information on lncRNAs. Determining the functions and action mechanisms of these RNAs on a large scale is urgently needed. We provided lncRNATargets, which is a web-based platform for lncRNA target prediction based on nucleic acid thermodynamics. The nearest-neighbor (NN) model was used to calculate binging-free energy. The main principle of NN model for nucleic acid assumes that identity and orientation of neighbor base pairs determine stability of a given base pair. lncRNATargets features the following options: setting of a specific temperature that allow use not only for human but also for other animals or plants; processing all lncRNAs in high throughput without RNA size limitation that is superior to any other existing tool; and web-based, user-friendly interface, and colored result displays that allow easy access for nonskilled computer operators and provide better understanding of results. This technique could provide accurate calculation on the binding-free energy of lncRNA-target dimers to predict if these structures are well targeted together. lncRNATargets provides high accuracy calculations, and this user-friendly program is available for free at http://www.herbbol.org:8001/lrt/ .

Real-Time fMRI Pattern Decoding and Neurofeedback Using FRIEND: An FSL-Integrated BCI Toolbox

PubMed Central

Sato, João R.; Basilio, Rodrigo; Paiva, Fernando F.; Garrido, Griselda J.; Bramati, Ivanei E.; Bado, Patricia; Tovar-Moll, Fernanda; Zahn, Roland; Moll, Jorge

2013-01-01

The demonstration that humans can learn to modulate their own brain activity based on feedback of neurophysiological signals opened up exciting opportunities for fundamental and applied neuroscience. Although EEG-based neurofeedback has been long employed both in experimental and clinical investigation, functional MRI (fMRI)-based neurofeedback emerged as a promising method, given its superior spatial resolution and ability to gauge deep cortical and subcortical brain regions. In combination with improved computational approaches, such as pattern recognition analysis (e.g., Support Vector Machines, SVM), fMRI neurofeedback and brain decoding represent key innovations in the field of neuromodulation and functional plasticity. Expansion in this field and its applications critically depend on the existence of freely available, integrated and user-friendly tools for the neuroimaging research community. Here, we introduce FRIEND, a graphic-oriented user-friendly interface package for fMRI neurofeedback and real-time multivoxel pattern decoding. The package integrates routines for image preprocessing in real-time, ROI-based feedback (single-ROI BOLD level and functional connectivity) and brain decoding-based feedback using SVM. FRIEND delivers an intuitive graphic interface with flexible processing pipelines involving optimized procedures embedding widely validated packages, such as FSL and libSVM. In addition, a user-defined visual neurofeedback module allows users to easily design and run fMRI neurofeedback experiments using ROI-based or multivariate classification approaches. FRIEND is open-source and free for non-commercial use. Processing tutorials and extensive documentation are available. PMID:24312569

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.

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

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 data. Fourthly, we envisage an educational role for such applications. PMID:22998945

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 educational role for such applications.

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 services, etc.) can have access to the alternative definition component to formulate the risk reduction measures. The development of such a participative platform would finally lead to an integrated risk management approach highlighting the needs to deal with involved experts and civil society in the decision-making process for evaluation of risk management measures through the active participation approach. The system will be applied and evaluated in four case study areas of the CHANGES project in Europe: Romania, North Eastern Italy, French Alps and Poland. However, the framework of the system is designed in a generic way so as to be applicable in other regions to achieve the high adaptability and flexibility of the system. The research has been undertaken as a part of the CHANGES project funded by the European Commission's 7th framework program.

Engaging Stakeholders in the Development of an eHealth Intervention for Cancer Symptom Management for Rural Residents.

PubMed

Gilbertson-White, Stephanie; Yeung, Chi W; Saeidzadeh, Seyedehtanaz; Tykol, Hannah; Vikas, Praveen; Cannon, Ashley

2018-04-25

Late-stage cancer diagnoses disproportionately occur in rural residents, frequently resulting in increased need for symptom management support with minimal access to these services. Oncology Associated Symptoms and Individualized Strategies (OASIS) is an eHealth symptom self-management intervention that was developed to provide cancer symptom self-management support and address this disparity. To engage stakeholders about the symptom management needs and concerns of patients with advanced cancer living in rural areas. A 3-phased, mixed-methods design was used to (1) assess stakeholder needs and opinions; (2) develop a symptom self-management website; and (3) obtain usability feedback from potential users. Interviews with stakeholders (patients and clinic staff) from rural areas using a descriptive qualitative approach were analyzed; cross-cutting themes were identified; a symptom management web application was developed; and stakeholders completed a 12-item usability survey about the web application. Patients (n = 16) and clinical staff (n = 10) participated in phase 1. Three major themes were identified: "symptom experience," "symptom management," and "technology." Through an iterative process using these results and evidence from the literature, the OASIS web application was developed. Usability testing with N = 126 stakeholders demonstrated that the web application is easy to use, contains relevant content, and has pleasing graphics. No differences were found among patients, family/friends, and staff. Both frequent and infrequent internet users positively evaluated the web application.  CONCLUSIONS: Rural stakeholders report significant symptom management needs, are interested in eHealth technologies, and perceived OASIS positively. Future research is needed to evaluate the feasibility, acceptability, and efficacy of OASIS. © 2018 National Rural Health Association.

A Novel Web Application to Analyze and Visualize Extreme Heat Events

NASA Astrophysics Data System (ADS)

Li, G.; Jones, H.; Trtanj, J.

2016-12-01

Extreme heat is the leading cause of weather-related deaths in the United States annually and is expected to increase with our warming climate. However, most of these deaths are preventable with proper tools and services to inform the public about heat waves. In this project, we have investigated the key indicators of a heat wave, the vulnerable populations, and the data visualization strategies of how those populations most effectively absorb heat wave data. A map-based web app has been created that allows users to search and visualize historical heat waves in the United States incorporating these strategies. This app utilizes daily maximum temperature data from NOAA Global Historical Climatology Network which contains about 2.7 million data points from over 7,000 stations per year. The point data are spatially aggregated into county-level data using county geometry from US Census Bureau and stored in Postgres database with PostGIS spatial capability. GeoServer, a powerful map server, is used to serve the image and data layers (WMS and WFS). The JavaScript-based web-mapping platform Leaflet is used to display the temperature layers. A number of functions have been implemented for the search and display. Users can search for extreme heat events by county or by date. The "by date" option allows a user to select a date and a Tmax threshold which then highlights all of the areas on the map that meet those date and temperature parameters. The "by county" option allows the user to select a county on the map which then retrieves a list of heat wave dates and daily Tmax measurements. This visualization is clean, user-friendly, and novel because while this sort of time, space, and temperature measurements can be found by querying meteorological datasets, there does not exist a tool that neatly packages this information together in an easily accessible and non-technical manner, especially in a time where climate change urges a better understanding of heat waves.

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 the feature with regards to the ability to re-schedule their appointments. The vast majority also found the additional resources to be helpful. This is one of the first studies to demonstrate the potential use of smartphone innovations in Bariatric After-care self-management. The current study has shown that users are generally receptive towards such an innovative implementation and has also highlighted some of their preferences with regards to such a self-management application for self-management of their health condition post bariatric surgery. In addition, the authors have also managed to demonstrate how clinicians could be involved in the formulation of a bariatric care application, which has an evidence base.

Effective electron-density map improvement and structure validation on a Linux multi-CPU web cluster: The TB Structural Genomics Consortium Bias Removal Web Service.

PubMed

Reddy, Vinod; Swanson, Stanley M; Segelke, Brent; Kantardjieff, Katherine A; Sacchettini, James C; Rupp, Bernhard

2003-12-01

Anticipating a continuing increase in the number of structures solved by molecular replacement in high-throughput crystallography and drug-discovery programs, a user-friendly web service for automated molecular replacement, map improvement, bias removal and real-space correlation structure validation has been implemented. The service is based on an efficient bias-removal protocol, Shake&wARP, and implemented using EPMR and the CCP4 suite of programs, combined with various shell scripts and Fortran90 routines. The service returns improved maps, converted data files and real-space correlation and B-factor plots. User data are uploaded through a web interface and the CPU-intensive iteration cycles are executed on a low-cost Linux multi-CPU cluster using the Condor job-queuing package. Examples of map improvement at various resolutions are provided and include model completion and reconstruction of absent parts, sequence correction, and ligand validation in drug-target structures.

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

PubMed

Tsukamoto, Takafumi; Yasunaga, Takuo

2014-11-01

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

Client-Side Event Processing for Personalized Web Advertisement

NASA Astrophysics Data System (ADS)

Stühmer, Roland; Anicic, Darko; Sen, Sinan; Ma, Jun; Schmidt, Kay-Uwe; Stojanovic, Nenad

The market for Web advertisement is continuously growing and correspondingly, the number of approaches that can be used for realizing Web advertisement are increasing. However, current approaches fail to generate very personalized ads for a current Web user that is visiting a particular Web content. They mainly try to develop a profile based on the content of that Web page or on a long-term user's profile, by not taking into account current user's preferences. We argue that by discovering a user's interest from his current Web behavior we can support the process of ad generation, especially the relevance of an ad for the user. In this paper we present the conceptual architecture and implementation of such an approach. The approach is based on the extraction of simple events from the user interaction with a Web page and their combination in order to discover the user's interests. We use semantic technologies in order to build such an interpretation out of many simple events. We present results from preliminary evaluation studies. The main contribution of the paper is a very efficient, semantic-based client-side architecture for generating and combining Web events. The architecture ensures the agility of the whole advertisement system, by complexly processing events on the client. In general, this work contributes to the realization of new, event-driven applications for the (Semantic) Web.

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.

WEB-GIS Decision Support System for CO2 storage

NASA Astrophysics Data System (ADS)

Gaitanaru, Dragos; Leonard, Anghel; Radu Gogu, Constantin; Le Guen, Yvi; Scradeanu, Daniel; Pagnejer, Mihaela

2013-04-01

Environmental decision support systems (DSS) paradigm evolves and changes as more knowledge and technology become available to the environmental community. Geographic Information Systems (GIS) can be used to extract, assess and disseminate some types of information, which are otherwise difficult to access by traditional methods. In the same time, with the help of the Internet and accompanying tools, creating and publishing online interactive maps has become easier and rich with options. The Decision Support System (MDSS) developed for the MUSTANG (A MUltiple Space and Time scale Approach for the quaNtification of deep saline formations for CO2 storaGe) project is a user friendly web based application that uses the GIS capabilities. MDSS can be exploited by the experts for CO2 injection and storage in deep saline aquifers. The main objective of the MDSS is to help the experts to take decisions based large structured types of data and information. In order to achieve this objective the MDSS has a geospatial objected-orientated database structure for a wide variety of data and information. The entire application is based on several principles leading to a series of capabilities and specific characteristics: (i) Open-Source - the entire platform (MDSS) is based on open-source technologies - (1) database engine, (2) application server, (3) geospatial server, (4) user interfaces, (5) add-ons, etc. (ii) Multiple database connections - MDSS is capable to connect to different databases that are located on different server machines. (iii)Desktop user experience - MDSS architecture and design follows the structure of a desktop software. (iv)Communication - the server side and the desktop are bound together by series functions that allows the user to upload, use, modify and download data within the application. The architecture of the system involves one database and a modular application composed by: (1) a visualization module, (2) an analysis module, (3) a guidelines module, and (4) a risk assessment module. The Database component is build by using the PostgreSQL and PostGIS open source technology. The visualization module allows the user to view data of CO2 injection sites in different ways: (1) geospatial visualization, (2) table view, (3) 3D visualization. The analysis module will allow the user to perform certain analysis like Injectivity, Containment and Capacity analysis. The Risk Assessment module focus on the site risk matrix approach. The Guidelines module contains the methodologies of CO2 injection and storage into deep saline aquifers guidelines.

The Water SWITCH-ON Spatial Information Platform (SIP)

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

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.

Grid-based HPC astrophysical applications at INAF Catania.

NASA Astrophysics Data System (ADS)

Costa, A.; Calanducci, A.; Becciani, U.; Capuzzo Dolcetta, R.

The research activity on grid area at INAF Catania has been devoted to two main goals: the integration of a multiprocessor supercomputer (IBM SP4) within INFN-GRID middleware and the developing of a web-portal, Astrocomp-G, for the submission of astrophysical jobs into the grid infrastructure. Most of the actual grid implementation infrastructure is based on common hardware, i.e. i386 architecture machines (Intel Celeron, Pentium III, IV, Amd Duron, Athlon) using Linux RedHat OS. We were the first institute to integrate a totally different machine, an IBM SP with RISC architecture and AIX OS, as a powerful Worker Node inside a grid infrastructure. We identified and ported to AIX OS the grid components dealing with job monitoring and execution and properly tuned the Computing Element to delivery jobs into this special Worker Node. For testing purpose we used MARA, an astrophysical application for the analysis of light curve sequences. Astrocomp-G is a user-friendly front end to our grid site. Users who want to submit the astrophysical applications already available in the portal need to own a valid personal X509 certificate in addiction to a username and password released by the grid portal web master. The personal X509 certificate is a prerequisite for the creation of a short or long-term proxy certificate that allows the grid infrastructure services to identify clearly whether the owner of the job has the permissions to use resources and data. X509 and proxy certificates are part of GSI (Grid Security Infrastructure), a standard security tool adopted by all major grid sites around the world.

Kwf-Grid workflow management system for Earth science applications

NASA Astrophysics Data System (ADS)

Tran, V.; Hluchy, L.

2009-04-01

In this paper, we present workflow management tool for Earth science applications in EGEE. The workflow management tool was originally developed within K-wf Grid project for GT4 middleware and has many advanced features like semi-automatic workflow composition, user-friendly GUI for managing workflows, knowledge management. In EGEE, we are porting the workflow management tool to gLite middleware for Earth science applications K-wf Grid workflow management system was developed within "Knowledge-based Workflow System for Grid Applications" under the 6th Framework Programme. The workflow mangement system intended to - semi-automatically compose a workflow of Grid services, - execute the composed workflow application in a Grid computing environment, - monitor the performance of the Grid infrastructure and the Grid applications, - analyze the resulting monitoring information, - capture the knowledge that is contained in the information by means of intelligent agents, - and finally to reuse the joined knowledge gathered from all participating users in a collaborative way in order to efficiently construct workflows for new Grid applications. Kwf Grid workflow engines can support different types of jobs (e.g. GRAM job, web services) in a workflow. New class of gLite job has been added to the system, allows system to manage and execute gLite jobs in EGEE infrastructure. The GUI has been adapted to the requirements of EGEE users, new credential management servlet is added to portal. Porting K-wf Grid workflow management system to gLite would allow EGEE users to use the system and benefit from its avanced features. The system is primarly tested and evaluated with applications from ES clusters.

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…

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

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

How to Create a Web-Ready PDF

EPA Pesticide Factsheets

Making EPA's PDF documents accessible (by Section 508 standards) and user-friendly includes steps such as adding bookmarks, using electronic conversion rather than scanning pages, and adding metadata.

Image processing and applications based on visualizing navigation service

NASA Astrophysics Data System (ADS)

Hwang, Chyi-Wen

2015-07-01

When facing the "overabundant" of semantic web information, in this paper, the researcher proposes the hierarchical classification and visualizing RIA (Rich Internet Application) navigation system: Concept Map (CM) + Semantic Structure (SS) + the Knowledge on Demand (KOD) service. The aim of the Multimedia processing and empirical applications testing, was to investigating the utility and usability of this visualizing navigation strategy in web communication design, into whether it enables the user to retrieve and construct their personal knowledge or not. Furthermore, based on the segment markets theory in the Marketing model, to propose a User Interface (UI) classification strategy and formulate a set of hypermedia design principles for further UI strategy and e-learning resources in semantic web communication. These research findings: (1) Irrespective of whether the simple declarative knowledge or the complex declarative knowledge model is used, the "CM + SS + KOD navigation system" has a better cognition effect than the "Non CM + SS + KOD navigation system". However, for the" No web design experience user", the navigation system does not have an obvious cognition effect. (2) The essential of classification in semantic web communication design: Different groups of user have a diversity of preference needs and different cognitive styles in the CM + SS + KOD navigation system.

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 of the web application. These features are all in addition to a full range of essential visualization functions including 3-D camera and object orientation, position manipulation, time-stepping control, and custom color/alpha mapping.

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.

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps

PubMed Central

2013-01-01

Background Molecular biology knowledge can be formalized and systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist an increasing number of maps of molecular interactions containing detailed and step-wise description of various cell mechanisms. It is difficult to explore these large maps, to organize discussion of their content and to maintain them. Several efforts were recently made to combine these capabilities together in one environment, and NaviCell is one of them. Results NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. It is characterized by a combination of three essential features: (1) efficient map browsing based on Google Maps; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of interest in the context of signaling pathways and crosstalk between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell greatly facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive and user-friendly fashion due to an imbedded blogging system. Conclusions NaviCell provides user-friendly exploration of large-scale maps of molecular interactions, thanks to Google Maps and WordPress interfaces, with which many users are already familiar. Semantic zooming which is used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization readable. In addition, NaviCell provides a framework for community-based curation of maps. PMID:24099179

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps.

PubMed

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

2013-10-07

Molecular biology knowledge can be formalized and systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist an increasing number of maps of molecular interactions containing detailed and step-wise description of various cell mechanisms. It is difficult to explore these large maps, to organize discussion of their content and to maintain them. Several efforts were recently made to combine these capabilities together in one environment, and NaviCell is one of them. NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. It is characterized by a combination of three essential features: (1) efficient map browsing based on Google Maps; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of interest in the context of signaling pathways and crosstalk between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell greatly facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive and user-friendly fashion due to an imbedded blogging system. NaviCell provides user-friendly exploration of large-scale maps of molecular interactions, thanks to Google Maps and WordPress interfaces, with which many users are already familiar. Semantic zooming which is used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization readable. In addition, NaviCell provides a framework for community-based curation of maps.

Use of XML and Java for collaborative petroleum reservoir modeling on the Internet

NASA Astrophysics Data System (ADS)

Victorine, John; Watney, W. Lynn; Bhattacharya, Saibal

2005-11-01

The GEMINI (Geo-Engineering Modeling through INternet Informatics) is a public-domain, web-based freeware that is made up of an integrated suite of 14 Java-based software tools to accomplish on-line, real-time geologic and engineering reservoir modeling. GEMINI facilitates distant collaborations for small company and academic clients, negotiating analyses of both single and multiple wells. The system operates on a single server and an enterprise database. External data sets must be uploaded into this database. Feedback from GEMINI users provided the impetus to develop Stand Alone Web Start Applications of GEMINI modules that reside in and operate from the user's PC. In this version, the GEMINI modules run as applets, which may reside in local user PCs, on the server, or Java Web Start. In this enhanced version, XML-based data handling procedures are used to access data from remote and local databases and save results for later access and analyses. The XML data handling process also integrates different stand-alone GEMINI modules enabling the user(s) to access multiple databases. It provides flexibility to the user to customize analytical approach, database location, and level of collaboration. An example integrated field-study using GEMINI modules and Stand Alone Web Start Applications is provided to demonstrate the versatile applicability of this freeware for cost-effective reservoir modeling.

Use of XML and Java for collaborative petroleum reservoir modeling on the Internet

USGS Publications Warehouse

Victorine, J.; Watney, W.L.; Bhattacharya, S.

2005-01-01

The GEMINI (Geo-Engineering Modeling through INternet Informatics) is a public-domain, web-based freeware that is made up of an integrated suite of 14 Java-based software tools to accomplish on-line, real-time geologic and engineering reservoir modeling. GEMINI facilitates distant collaborations for small company and academic clients, negotiating analyses of both single and multiple wells. The system operates on a single server and an enterprise database. External data sets must be uploaded into this database. Feedback from GEMINI users provided the impetus to develop Stand Alone Web Start Applications of GEMINI modules that reside in and operate from the user's PC. In this version, the GEMINI modules run as applets, which may reside in local user PCs, on the server, or Java Web Start. In this enhanced version, XML-based data handling procedures are used to access data from remote and local databases and save results for later access and analyses. The XML data handling process also integrates different stand-alone GEMINI modules enabling the user(s) to access multiple databases. It provides flexibility to the user to customize analytical approach, database location, and level of collaboration. An example integrated field-study using GEMINI modules and Stand Alone Web Start Applications is provided to demonstrate the versatile applicability of this freeware for cost-effective reservoir modeling. ?? 2005 Elsevier Ltd. All rights reserved.

Brain-controlled applications using dynamic P300 speller matrices.

PubMed

Halder, Sebastian; Pinegger, Andreas; Käthner, Ivo; Wriessnegger, Selina C; Faller, Josef; Pires Antunes, João B; Müller-Putz, Gernot R; Kübler, Andrea

2015-01-01

Access to the world wide web and multimedia content is an important aspect of life. We present a web browser and a multimedia user interface adapted for control with a brain-computer interface (BCI) which can be used by severely motor impaired persons. The web browser dynamically determines the most efficient P300 BCI matrix size to select the links on the current website. This enables control of the web browser with fewer commands and smaller matrices. The multimedia player was based on an existing software. Both applications were evaluated with a sample of ten healthy participants and three end-users. All participants used a visual P300 BCI with face-stimuli for control. The healthy participants completed the multimedia player task with 90% accuracy and the web browsing task with 85% accuracy. The end-users completed the tasks with 62% and 58% accuracy. All healthy participants and two out of three end-users reported that they felt to be in control of the system. In this study we presented a multimedia application and an efficient web browser implemented for control with a BCI. Both applications provide access to important areas of modern information retrieval and entertainment. Copyright © 2014 Elsevier B.V. All rights reserved.

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. The framework built provides a flexible and robust informatics infrastructure by separating the modules of functionality through an ontological model for vector-borne disease. The VBD‒AIR tool is designed as an evidence base for visualizing the risks of vector-borne disease by air travel for a wide range of users, including planners and decisions makers based in state and local government, and in particular, those at international and domestic airports tasked with planning for health risks and allocating limited resources. PMID:22892045

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 and robust informatics infrastructure by separating the modules of functionality through an ontological model for vector-borne disease. The VBD‒AIR tool is designed as an evidence base for visualizing the risks of vector-borne disease by air travel for a wide range of users, including planners and decisions makers based in state and local government, and in particular, those at international and domestic airports tasked with planning for health risks and allocating limited resources.

Hospital Web site 'tops' in Louisiana. Hospital PR, marketing group cites East Jefferson General Hospital.

PubMed

Rees, Tom

2002-01-01

East Jefferson General Hospital in Metairie, La., launched a new Web site in October 2001. Its user-friendly home page offers links to hospital services, medical staff, and employer information. Its jobline is a powerful tool for recruitment. The site was awarded the 2002 Pelican Award for Best Consumer Web site by the Louisiana Society for Hospital Public Relations & Marketing.

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

NASA Astrophysics Data System (ADS)

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

2011-03-01

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

MyGeneFriends: A Social Network Linking Genes, Genetic Diseases, and Researchers.

PubMed

Allot, Alexis; Chennen, Kirsley; Nevers, Yannis; Poidevin, Laetitia; Kress, Arnaud; Ripp, Raymond; Thompson, Julie Dawn; Poch, Olivier; Lecompte, Odile

2017-06-16

The constant and massive increase of biological data offers unprecedented opportunities to decipher the function and evolution of genes and their roles in human diseases. However, the multiplicity of sources and flow of data mean that efficient access to useful information and knowledge production has become a major challenge. This challenge can be addressed by taking inspiration from Web 2.0 and particularly social networks, which are at the forefront of big data exploration and human-data interaction. MyGeneFriends is a Web platform inspired by social networks, devoted to genetic disease analysis, and organized around three types of proactive agents: genes, humans, and genetic diseases. The aim of this study was to improve exploration and exploitation of biological, postgenomic era big data. MyGeneFriends leverages conventions popularized by top social networks (Facebook, LinkedIn, etc), such as networks of friends, profile pages, friendship recommendations, affinity scores, news feeds, content recommendation, and data visualization. MyGeneFriends provides simple and intuitive interactions with data through evaluation and visualization of connections (friendships) between genes, humans, and diseases. The platform suggests new friends and publications and allows agents to follow the activity of their friends. It dynamically personalizes information depending on the user's specific interests and provides an efficient way to share information with collaborators. Furthermore, the user's behavior itself generates new information that constitutes an added value integrated in the network, which can be used to discover new connections between biological agents. We have developed MyGeneFriends, a Web platform leveraging conventions from popular social networks to redefine the relationship between humans and biological big data and improve human processing of biomedical data. MyGeneFriends is available at lbgi.fr/mygenefriends. ©Alexis Allot, Kirsley Chennen, Yannis Nevers, Laetitia Poidevin, Arnaud Kress, Raymond Ripp, Julie Dawn Thompson, Olivier Poch, Odile Lecompte. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 16.06.2017.

Recommendations from Friends Anytime and Anywhere: Toward a Model of Contextual Offer and Consumption Values

PubMed Central

Shen, Xiao-Liang; Wang, Nan

2013-01-01

Abstract The ubiquity and portability of mobile devices provide additional opportunities for information retrieval. People can easily access mobile applications anytime and anywhere when they need to acquire specific context-aware recommendations (contextual offer) from their friends. This study, thus, represents an initial attempt to understand users' acceptance of a mobile-based social reviews platform, where recommendations from friends can be obtained with mobile devices. Based on the consumption value theory, a theoretical model is proposed and empirically examined using survey data from 218 mobile users. The findings demonstrate that contextual offers based on users' profiles, access time, and geographic positions significantly predict their value perceptions (utilitarian, hedonic, and social), which, in turn, affect their intention to use a mobile social reviews platform. This study is also believed to provide some useful insights to both research and practice. PMID:23530548

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

ERIC Educational Resources Information Center

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

2008-01-01

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

Cancer patients’ experiences of using an Interactive Health Communication Application (IHCA)

PubMed Central

Grimsbø, Gro H.; Engelsrud, Gunn H.; Ruland, Cornelia M.

2012-01-01

Interactive Health Communication Applications (IHCAs) are increasingly used in health care. Studies document that IHCAs provide patients with knowledge and social support, enhance self- efficacy and can improve behavioural and clinical outcomes. However, research exploring patients’ experiences of using IHCAs has been scarce. The aim of this study was to explore cancer patients’ perspectives and experiences related to the use of an IHCA called WebChoice in their homes. Qualitative interviews were conducted with infrequent, medium and frequent IHCA users—six women and four men with breast and prostate cancer. The interviews were transcribed and analyzed inspired by interactionistic perspectives. We found that some patients’ perceived WebChoice as a “friend,” others as a “stranger.” Access to WebChoice stimulated particularly high frequency users to position themselves as “information seeking agents,” assuming an active patient role. However, to position oneself as an “active patient” was ambiguous and emotional. Feelings of “calmness”, “normalization of symptoms”, feelings of “being part of a community”, feeling “upset” and “vulnerable”, as well as “feeling supported” were identified. Interaction with WebChoice implied for some users an increased focus on illness. Our findings indicate that the interaction between patients and an IHCA such as WebChoice occurs in a variety of ways, some of which are ambivalent or conflicting. Particularly for frequent and medium frequency users, it offers support, but may at the same time reinforce an element of uncertainty in their life. Such insights should be taken into consideration in the future development of IHCAs in healthcare in general and in particular for implementation into patients’ private sphere. PMID:22582085

From Web 2.0 to Teacher 2.0

ERIC Educational Resources Information Center

Thomas, David A.; Li, Qing

2008-01-01

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

SETAC Short Course: Introduction to interspecies toxicity extrapolation using EPA’s Web-ICE tool

EPA Science Inventory

The Web-ICE tool is a user friendly interface that contains modules to predict acute toxicity to over 500 species of aquatic (algae, invertebrates, fish) and terrestrial (birds and mammals) taxa. The tool contains a suite of over 3000 ICE models developed from a database of over ...

WMI2, the Student's On-Line Symbolic Calculator

ERIC Educational Resources Information Center

Kovacs, Zoltan

2011-01-01

Student activities focused on discovering mathematics play an important role in the teaching and learning process. WebMathematics Interactive (WMI2) was developed to offer a fast and user-friendly on-line web interface to enhance the quality of both theoretical and applied mathematics courses. For the teacher, in the classroom, it provides…

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

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.

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

Development and implementation of an Integrated Water Resources Management System (IWRMS)

NASA Astrophysics Data System (ADS)

Flügel, W.-A.; Busch, C.

2011-04-01

One of the innovative objectives in the EC project BRAHMATWINN was the development of a stakeholder oriented Integrated Water Resources Management System (IWRMS). The toolset integrates the findings of the project and presents it in a user friendly way for decision support in sustainable integrated water resources management (IWRM) in river basins. IWRMS is a framework, which integrates different types of basin information and which supports the development of IWRM options for climate change mitigation. It is based on the River Basin Information System (RBIS) data models and delivers a graphical user interface for stakeholders. A special interface was developed for the integration of the enhanced DANUBIA model input and the NetSyMod model with its Mulino decision support system (mulino mDss) component. The web based IWRMS contains and combines different types of data and methods to provide river basin data and information for decision support. IWRMS is based on a three tier software framework which uses (i) html/javascript at the client tier, (ii) PHP programming language to realize the application tier, and (iii) a postgresql/postgis database tier to manage and storage all data, except the DANUBIA modelling raw data, which are file based and registered in the database tier. All three tiers can reside on one or different computers and are adapted to the local hardware infrastructure. IWRMS as well as RBIS are based on Open Source Software (OSS) components and flexible and time saving access to that database is guaranteed by web-based interfaces for data visualization and retrieval. The IWRMS is accessible via the BRAHMATWINN homepage: http://www.brahmatwinn.uni-jena.de and a user manual for the RBIS is available for download as well.

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

PubMed

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

2018-04-05

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

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.

Search Engines: Gateway to a New ``Panopticon''?

NASA Astrophysics Data System (ADS)

Kosta, Eleni; Kalloniatis, Christos; Mitrou, Lilian; Kavakli, Evangelia

Nowadays, Internet users are depending on various search engines in order to be able to find requested information on the Web. Although most users feel that they are and remain anonymous when they place their search queries, reality proves otherwise. The increasing importance of search engines for the location of the desired information on the Internet usually leads to considerable inroads into the privacy of users. The scope of this paper is to study the main privacy issues with regard to search engines, such as the anonymisation of search logs and their retention period, and to examine the applicability of the European data protection legislation to non-EU search engine providers. Ixquick, a privacy-friendly meta search engine will be presented as an alternative to privacy intrusive existing practices of search engines.

78 FR 56266 - Consent Based Social Security Number Verification (CBSV) Service

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-12

... developed CBSV as a user- friendly, internet-based application with safeguards that protect the public's information. In addition to the benefit of providing high volume, centralized SSN verification services to users in a secure manner, CBSV provides us with cost and workload management benefits. New Information...

Application of crowdsourced hail data and damage information for hail risk assessment in the province of Styria, Austria

NASA Astrophysics Data System (ADS)

Tani, Satyanarayana; Rechberger, Andreas; Süsser Rechberger, Barbara; Teschl, Reinhard; Paulitsch, Helmut

2017-04-01

Hail storm damage is a major concern to the farmers in the province of Styria, Austria. Each year severe hail storms are causing damages to crops, resulting in losses of millions of euros. High spatial and timely ground truth information of the hail event and crop damage measurements are essential for better hail risk assessment. Usually, hail pad networks and visual damage surveys are used to collect the hail data and corresponding damage information. However, these hail pad networks are expensive and need laborious maintenance. The traditional crop damage assessment approaches are very labour-intensive and time-consuming. The advancements in information and communication technology (ICT) and the power of citizen based crowdsourcing data, will help to overcome these problems and ultimately provide a platform for data collection. A user-friendly and bilingual web interface was developed to collect hail data and crop damage information in the province of Styria, Austria. The dynamic web interface was developed using HTML5, JavaScript, and PHP7 combined with a MySQL database back-end. OpenStreetMap was integrated into the web interface and tile server optimised for an easy identification of geolocation information. The user needs an internet connection to transfer the data through smartphone or computer. Crowdsourced data will be quality tested and evaluated with 3D single polarisation C-band weather radar data to remove potential false reports. Further, the relationship between the reported hail events and radar-based hail detection algorithms (Waldvogel and Auer) and derived hail signature information intended for crop hail risk assessment will be investigated. The details about the web interface tool, application and verification methods to collect, analyse, and integrate different data sets are given. Further, the high spatial risk assessment information is communicated to support risk management policy.

75 FR 44020 - Biweekly Notice; Applications and Amendments to Facility Operating Licenses Involving No...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-27

... representative, already holds an NRC- issued digital ID certificate). Based upon this information, the Secretary... online, Web-based submission form. In order to serve documents through EIE, users will be required to install a Web browser plug-in from the NRC Web site. Further information on the Web- based submission form...

Using the World Wide Web and Creating Home Pages. A How-To-Do-It Manual. How-To-Do-It Manuals for Librarieans, Number 67.

ERIC Educational Resources Information Center

Metz, Ray E.; Junion-Metz, Gail

This book provides basic information about the World Wide Web and serves as a guide to the tools and techniques needed to browse the Web, integrate it into library services, or build an attractive, user-friendly home page for the library. Chapter 1 provides an overview of Web basics and chapter 2 discusses some of the big issues related to…

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

PubMed

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

2013-07-01

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

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

PubMed Central

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

2013-01-01

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

SCENERY: a web application for (causal) network reconstruction from cytometry data.

PubMed

Papoutsoglou, Georgios; Athineou, Giorgos; Lagani, Vincenzo; Xanthopoulos, Iordanis; Schmidt, Angelika; Éliás, Szabolcs; Tegnér, Jesper; Tsamardinos, Ioannis

2017-07-03

Flow and mass cytometry technologies can probe proteins as biological markers in thousands of individual cells simultaneously, providing unprecedented opportunities for reconstructing networks of protein interactions through machine learning algorithms. The network reconstruction (NR) problem has been well-studied by the machine learning community. However, the potentials of available methods remain largely unknown to the cytometry community, mainly due to their intrinsic complexity and the lack of comprehensive, powerful and easy-to-use NR software implementations specific for cytometry data. To bridge this gap, we present Single CEll NEtwork Reconstruction sYstem (SCENERY), a web server featuring several standard and advanced cytometry data analysis methods coupled with NR algorithms in a user-friendly, on-line environment. In SCENERY, users may upload their data and set their own study design. The server offers several data analysis options categorized into three classes of methods: data (pre)processing, statistical analysis and NR. The server also provides interactive visualization and download of results as ready-to-publish images or multimedia reports. Its core is modular and based on the widely-used and robust R platform allowing power users to extend its functionalities by submitting their own NR methods. SCENERY is available at scenery.csd.uoc.gr or http://mensxmachina.org/en/software/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

NASA Astrophysics Data System (ADS)

Sundaravel, A.; Wilkinson, D. C.

2010-12-01

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

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.

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.

PELE web server: atomistic study of biomolecular systems at your fingertips.

PubMed

Madadkar-Sobhani, Armin; Guallar, Victor

2013-07-01

PELE, Protein Energy Landscape Exploration, our novel technology based on protein structure prediction algorithms and a Monte Carlo sampling, is capable of modelling the all-atom protein-ligand dynamical interactions in an efficient and fast manner, with two orders of magnitude reduced computational cost when compared with traditional molecular dynamics techniques. PELE's heuristic approach generates trial moves based on protein and ligand perturbations followed by side chain sampling and global/local minimization. The collection of accepted steps forms a stochastic trajectory. Furthermore, several processors may be run in parallel towards a collective goal or defining several independent trajectories; the whole procedure has been parallelized using the Message Passing Interface. Here, we introduce the PELE web server, designed to make the whole process of running simulations easier and more practical by minimizing input file demand, providing user-friendly interface and producing abstract outputs (e.g. interactive graphs and tables). The web server has been implemented in C++ using Wt (http://www.webtoolkit.eu) and MySQL (http://www.mysql.com). The PELE web server, accessible at http://pele.bsc.es, is free and open to all users with no login requirement.

Development of a Web Based Simulating System for Earthquake Modeling on the Grid

NASA Astrophysics Data System (ADS)

Seber, D.; Youn, C.; Kaiser, T.

2007-12-01

Existing cyberinfrastructure-based information, data and computational networks now allow development of state- of-the-art, user-friendly simulation environments that democratize access to high-end computational environments and provide new research opportunities for many research and educational communities. Within the Geosciences cyberinfrastructure network, GEON, we have developed the SYNSEIS (SYNthetic SEISmogram) toolkit to enable efficient computations of 2D and 3D seismic waveforms for a variety of research purposes especially for helping to analyze the EarthScope's USArray seismic data in a speedy and efficient environment. The underlying simulation software in SYNSEIS is a finite difference code, E3D, developed by LLNL (S. Larsen). The code is embedded within the SYNSEIS portlet environment and it is used by our toolkit to simulate seismic waveforms of earthquakes at regional distances (<1000km). Architecturally, SYNSEIS uses both Web Service and Grid computing resources in a portal-based work environment and has a built in access mechanism to connect to national supercomputer centers as well as to a dedicated, small-scale compute cluster for its runs. Even though Grid computing is well-established in many computing communities, its use among domain scientists still is not trivial because of multiple levels of complexities encountered. We grid-enabled E3D using our own dialect XML inputs that include geological models that are accessible through standard Web services within the GEON network. The XML inputs for this application contain structural geometries, source parameters, seismic velocity, density, attenuation values, number of time steps to compute, and number of stations. By enabling a portal based access to a such computational environment coupled with its dynamic user interface we enable a large user community to take advantage of such high end calculations in their research and educational activities. Our system can be used to promote an efficient and effective modeling environment to help scientists as well as educators in their daily activities and speed up the scientific discovery process.

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…

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.

Clinicians' expectations of Web 2.0 as a mechanism for knowledge transfer of stroke best practices.

PubMed

David, Isabelle; Poissant, Lise; Rochette, Annie

2012-09-13

Health professionals are increasingly encouraged to adopt an evidence-based practice to ensure greater efficiency of their services. To promote this practice, several strategies exist: distribution of educational materials, local consensus processes, educational outreach visits, local opinion leaders, and reminders. Despite these strategies, gaps continue to be observed between practice and scientific evidence. Therefore, it is important to implement innovative knowledge transfer strategies that will change health professionals' practices. Through its interactive capacities, Web 2.0 applications are worth exploring. As an example, virtual communities of practice have already begun to influence professional practice. This study was initially developed to help design a Web 2.0 platform for health professionals working with stroke patients. The aim was to gain a better understanding of professionals' perceptions of Web 2.0 before the development of the platform. A qualitative study following a phenomenological approach was chosen. We conducted individual semi-structured interviews with clinicians and managers. Interview transcripts were subjected to a content analysis. Twenty-four female clinicians and managers in Quebec, Canada, aged 28-66 participated. Most participants identified knowledge transfer as the most useful outcome of a Web 2.0 platform. Respondents also expressed their need for a user-friendly platform. Accessibility to a computer and the Internet, features of the Web 2.0 platform, user support, technology skills, and previous technological experience were found to influence perceived ease of use and usefulness. Our results show that the perceived lack of time of health professionals has an influence on perceived behavioral intention to use it despite favorable perception of the usefulness of the Web 2.0 platform. In conclusion, female health professionals in Quebec believe that Web 2.0 may be a useful mechanism for knowledge transfer. However, lack of time and lack of technological skills may limit their use of a future Web 2.0 platform. Further studies are required with other populations and in other regions to confirm these findings.

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.

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 amount of oxygen, or of cation (using an analysis in element or oxide weight-%); this latter includes re-calculation of H2O/CO2 based on stoichiometry, and oxygen correction for F and Cl. Another option offers a list of any available standards and possible peak or background interferences for a series of elements. (3) "X-ray maps" lists the different setups recommended for element mapping using WDS, and a map calculator to facilitate maps setups and to estimate the total mapping time. (4) "X-ray data" lists all x-ray lines for a specific element (K, L, M, absorption edges, and satellite peaks) in term of energy, wavelength and peak position. A check for possible interferences on peak or background is also possible. Theoretical x-ray peak positions for each crystal are calculated based on the 2d spacing of each crystal and the wavelength of each line. (5) "Agenda" menu displays the reservation dates for each month and for each EMP lab defined. It also offers a reservation request option, this request being sent by email to the EMP manager for approval. (6) Finally, "Admin" is password restricted, and contains all necessary options to manage the database through user-friendly forms. The installation of this database is made easy and knowledge of HTML, PHP, or MySQL is unnecessary to install, configure, manage, or use it. A working database is accessible at http://cub.geoloweb.ch.

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

Increasing information accessibility for patients in obstetrics-gynecology domain.

PubMed

Crişan-Vida, Mihaela; Stoicu-Tivadar, Lăcrămioara

2014-01-01

It is important for the patient to have access to personal medical information in order to manage information for increased quality of medical care and life. The paper presents a module added to an Obstetrics-Gynaecology Department information system (OGD IS) supporting patient empowerment. The patient is accessing the system easily using laptops or mobile devices. The application accessed by the patient is web-based, implemented in Visual Studio. NET, using ASP.NET pages and C# language, and the application is published in the Windows Azure cloud. The solution is user friendly using familiar devices and is ubiquitous using the cloud solution. A module for translating medical terms in colloquial ones is integrated in the system. For certain situations the patient will get information related to life style influencing health status as how and what to eat or what type of exercise it is recommended.

Forecasting and visualization of wildfires in a 3D geographical information system

NASA Astrophysics Data System (ADS)

Castrillón, M.; Jorge, P. A.; López, I. J.; Macías, A.; Martín, D.; Nebot, R. J.; Sabbagh, I.; Quintana, F. M.; Sánchez, J.; Sánchez, A. J.; Suárez, J. P.; Trujillo, A.

2011-03-01

This paper describes a wildfire forecasting application based on a 3D virtual environment and a fire simulation engine. A novel open-source framework is presented for the development of 3D graphics applications over large geographic areas, offering high performance 3D visualization and powerful interaction tools for the Geographic Information Systems (GIS) community. The application includes a remote module that allows simultaneous connections of several users for monitoring a real wildfire event. The system is able to make a realistic composition of what is really happening in the area of the wildfire with dynamic 3D objects and location of human and material resources in real time, providing a new perspective to analyze the wildfire information. The user is enabled to simulate and visualize the propagation of a fire on the terrain integrating at the same time spatial information on topography and vegetation types with weather and wind data. The application communicates with a remote web service that is in charge of the simulation task. The user may specify several parameters through a friendly interface before the application sends the information to the remote server responsible of carrying out the wildfire forecasting using the FARSITE simulation model. During the process, the server connects to different external resources to obtain up-to-date meteorological data. The client application implements a realistic 3D visualization of the fire evolution on the landscape. A Level Of Detail (LOD) strategy contributes to improve the performance of the visualization system.

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…

Biblio-MetReS: A bibliometric network reconstruction application and server

PubMed Central

2011-01-01

Background Reconstruction of genes and/or protein networks from automated analysis of the literature is one of the current targets of text mining in biomedical research. Some user-friendly tools already perform this analysis on precompiled databases of abstracts of scientific papers. Other tools allow expert users to elaborate and analyze the full content of a corpus of scientific documents. However, to our knowledge, no user friendly tool that simultaneously analyzes the latest set of scientific documents available on line and reconstructs the set of genes referenced in those documents is available. Results This article presents such a tool, Biblio-MetReS, and compares its functioning and results to those of other user-friendly applications (iHOP, STRING) that are widely used. Under similar conditions, Biblio-MetReS creates networks that are comparable to those of other user friendly tools. Furthermore, analysis of full text documents provides more complete reconstructions than those that result from using only the abstract of the document. Conclusions Literature-based automated network reconstruction is still far from providing complete reconstructions of molecular networks. However, its value as an auxiliary tool is high and it will increase as standards for reporting biological entities and relationships become more widely accepted and enforced. Biblio-MetReS is an application that can be downloaded from http://metres.udl.cat/. It provides an easy to use environment for researchers to reconstruct their networks of interest from an always up to date set of scientific documents. PMID:21975133

Browser-Based Online Applications: Something for Everyone!

ERIC Educational Resources Information Center

Descy, Don E.

2007-01-01

Just as many people log onto a Web mail site (Gmail, Yahoo, MSN, etc.) to read, write and store their email, there are Web sites out there with word processing, database, and a myriad of other software applications that are not downloadable but used on the site through a Web browser. The user does not have to download the applications to a…

Monitoring Receptivity to Online Health Messages by Tracking Daily Web Traffic Engagement Patterns: A Review of More than 13 Million US Web Exposures over 1,235 Days.

PubMed

Seeman, Neil; Seeman, Bob

2017-01-01

Reaching the recipient of online health messages is necessary to Web-based health promotion applications. To measure willingness to adhere to a health-related Web message, we explored the frequency with which more than 13 million Web users ignored or opted to receive a random inbound message. The findings suggest declining curiosity among Web users about online messages, and that certain days may be more propitious than others for communicating with users. This approach can be modified to gather more granular insights into how messages, including timing and design features, can be tailored to promote improved public health messaging.

A safety app to respond to dating violence for college women and their friends: the MyPlan study randomized controlled trial protocol.

PubMed

Glass, Nancy; Clough, Amber; Case, James; Hanson, Ginger; Barnes-Hoyt, Jamie; Waterbury, Amy; Alhusen, Jeanne; Ehrensaft, Miriam; Grace, Karen Trister; Perrin, Nancy

2015-09-08

Research demonstrates high rates of physical and sexual victimization of women by intimate partners on college campuses (Black et al. 2001). College women in abusive relationships must weigh complex factors (health, academics, economics, and social stigma) during critical decision-making regarding the relationship. Rather than access formal support systems (e.g., campus security, administrators, counselors), research indicates abused college women most often turn to informal networks; specifically friends (Perspect Psychiatr Care 41:162-171, 2005), who often lack the knowledge or resources to provide effective support (Nurs Res 54(4):235-242, 2005). Decision aids have been shown to assist with health-related decisions by improving knowledge, creating realistic expectations, and resolving decisional conflict (Cochrane Database Syst Rev 1:1-332, 2014). This study is a randomized controlled trial testing the effectiveness of an interactive safety decision aid web-based and smartphone application (App) for abused college women and their friends. Three hundred female college students experiencing abuse and three hundred friends of female college students experiencing abuse will be recruited in Maryland and Oregon and randomized to either the intervention safety decision aid, accessible by website or smartphone App, or a usual safety planning control website/App. The intervention App allows users to enter information on: a) relationship health; b) safety priorities; and c) severity of violence/danger in relationship. The App uses this information to provide personalized safety planning information and resources. Self-reported outcome measures for abused college women on safety seeking behaviors, decisional conflict, IPV exposure and mental health will be collected at baseline, six, and 12-months post-baseline via the study App/website. Outcomes measured for friends are IPV awareness, confidence to intervene, supportive behaviors and decisional conflict. Protocols for safely recruiting, retaining and collecting data from abused women via web/App are discussed. This trial may provide important information on the impact of an App and web-based safety planning tool on college women's decisional conflict and safety behavior use when making difficult safety decisions. This study is the first, to our knowledge, to test an intervention that engages friends of abused college women. The trial may also inform researchers on the feasibility of safely conducting research with abused women using online recruitment and enrollment methods and collecting data via an App or website. Clinicaltrials.gov ID: NCT02236663.

Generalized Intelligent Framework for Tutoring (GIFT) Cloud/Virtual Open Campus Quick Start Guide (Revision 1)

DTIC Science & Technology

2017-06-01

for GIFT Cloud, the web -based application version of the Generalized Intelligent Framework for Tutoring (GIFT). GIFT is a modular, open-source...external applications. GIFT is available to users with a GIFT Account at no cost. GIFT Cloud is an implementation of GIFT. This web -based application...section. Approved for public release; distribution is unlimited. 3 3. Requirements for GIFT Cloud GIFT Cloud is accessed via a web browser

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.

MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes.

PubMed

Vařeková, Radka Svobodová; Jaiswal, Deepti; Sehnal, David; Ionescu, Crina-Maria; Geidl, Stanislav; Pravda, Lukáš; Horský, Vladimír; Wimmerová, Michaela; Koča, Jaroslav

2014-07-01

Structure validation has become a major issue in the structural biology community, and an essential step is checking the ligand structure. This paper introduces MotiveValidator, a web-based application for the validation of ligands and residues in PDB or PDBx/mmCIF format files provided by the user. Specifically, MotiveValidator is able to evaluate in a straightforward manner whether the ligand or residue being studied has a correct annotation (3-letter code), i.e. if it has the same topology and stereochemistry as the model ligand or residue with this annotation. If not, MotiveValidator explicitly describes the differences. MotiveValidator offers a user-friendly, interactive and platform-independent environment for validating structures obtained by any type of experiment. The results of the validation are presented in both tabular and graphical form, facilitating their interpretation. MotiveValidator can process thousands of ligands or residues in a single validation run that takes no more than a few minutes. MotiveValidator can be used for testing single structures, or the analysis of large sets of ligands or fragments prepared for binding site analysis, docking or virtual screening. MotiveValidator is freely available via the Internet at http://ncbr.muni.cz/MotiveValidator. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Investigating health information needs of community radio stations and applying the World Wide Web to disseminate audio products.

PubMed

Snyders, Janus; van Wyk, Elmarie; van Zyl, Hendra

2010-01-01

The Web and Media Technologies Platform (WMTP) of the South African Medical Research Council (MRC) conducted a pilot project amongst community radio stations in South Africa. Based on previous research done in Africa WMTP investigated the following research question: How reliable is the content of health information broadcast by community radio stations? The main objectives of the project were to determine the 1) intervals of health slots on community radio stations, 2) sources used by community radio stations for health slots, 3) type of audio products needed for health slots, and 4) to develop a user friendly Web site in response to the stations' needs for easy access to audio material on health information.

Development and Validation of an Interactive Internet Platform for Older People: The Healthy Ageing Through Internet Counselling in the Elderly Study.

PubMed

Jongstra, Susan; Beishuizen, Cathrien; Andrieu, Sandrine; Barbera, Mariagnese; van Dorp, Matthijs; van de Groep, Bram; Guillemont, Juliette; Mangialasche, Francesca; van Middelaar, Tessa; Moll van Charante, Eric; Soininen, Hilkka; Kivipelto, Miia; Richard, Edo

2017-02-01

A myriad of Web-based applications on self-management have been developed, but few focus on older people. In the face of global aging, older people form an important target population for cardiovascular prevention. This article describes the full development of an interactive Internet platform for older people, which was designed for the Healthy Ageing Through Internet Counselling in the Elderly (HATICE) study. We provide recommendations to design senior-friendly Web-based applications for a new approach to multicomponent cardiovascular prevention. The development of the platform followed five phases: (1) conceptual framework; (2) platform concept and functional design; (3) platform building (software and content); (4) testing and pilot study; and (5) final product. We performed a meta-analysis, reviewed guidelines for cardiovascular diseases, and consulted end users, experts, and software developers to create the platform concept and content. The software was built in iterative cycles. In the pilot study, 41 people aged ≥65 years used the platform for 8 weeks. Participants used the interactive features of the platform and appreciated the coach support. During all phases adjustments were made to incorporate all improvements from the previous phases. The final platform is a personal, secured, and interactive platform supported by a coach. When carefully designed, an interactive Internet platform is acceptable and feasible for use by older people with basic computer skills. To improve acceptability by older people, we recommend involving the end users in the process of development, to personalize the platform and to combine the application with human support. The interactive HATICE platform will be tested for efficacy in a multinational randomized controlled trial (ISRCTN48151589).

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.

An HTML5-Based Pure Website Solution for Rapidly Viewing and Processing Large-Scale 3D Medical Volume Reconstruction on Mobile Internet

PubMed Central

Chen, Xin; Zhang, Ye; Zhang, Jingna; Li, Ying; Mo, Xuemei; Chen, Wei

2017-01-01

This study aimed to propose a pure web-based solution to serve users to access large-scale 3D medical volume anywhere with good user experience and complete details. A novel solution of the Master-Slave interaction mode was proposed, which absorbed advantages of remote volume rendering and surface rendering. On server side, we designed a message-responding mechanism to listen to interactive requests from clients (Slave model) and to guide Master volume rendering. On client side, we used HTML5 to normalize user-interactive behaviors on Slave model and enhance the accuracy of behavior request and user-friendly experience. The results showed that more than four independent tasks (each with a data size of 249.4 MB) could be simultaneously carried out with a 100-KBps client bandwidth (extreme test); the first loading time was <12 s, and the response time of each behavior request for final high quality image remained at approximately 1 s, while the peak value of bandwidth was <50-KBps. Meanwhile, the FPS value for each client was ≥40. This solution could serve the users by rapidly accessing the application via one URL hyperlink without special software and hardware requirement in a diversified network environment and could be easily integrated into other telemedical systems seamlessly. PMID:28638406

An HTML5-Based Pure Website Solution for Rapidly Viewing and Processing Large-Scale 3D Medical Volume Reconstruction on Mobile Internet.

PubMed

Qiao, Liang; Chen, Xin; Zhang, Ye; Zhang, Jingna; Wu, Yi; Li, Ying; Mo, Xuemei; Chen, Wei; Xie, Bing; Qiu, Mingguo

2017-01-01

This study aimed to propose a pure web-based solution to serve users to access large-scale 3D medical volume anywhere with good user experience and complete details. A novel solution of the Master-Slave interaction mode was proposed, which absorbed advantages of remote volume rendering and surface rendering. On server side, we designed a message-responding mechanism to listen to interactive requests from clients ( Slave model) and to guide Master volume rendering. On client side, we used HTML5 to normalize user-interactive behaviors on Slave model and enhance the accuracy of behavior request and user-friendly experience. The results showed that more than four independent tasks (each with a data size of 249.4 MB) could be simultaneously carried out with a 100-KBps client bandwidth (extreme test); the first loading time was <12 s, and the response time of each behavior request for final high quality image remained at approximately 1 s, while the peak value of bandwidth was <50-KBps. Meanwhile, the FPS value for each client was ≥40. This solution could serve the users by rapidly accessing the application via one URL hyperlink without special software and hardware requirement in a diversified network environment and could be easily integrated into other telemedical systems seamlessly.

CALIL.JP, a new web service that provides one-stop searching of Japan-wide libraries' collections

NASA Astrophysics Data System (ADS)

Yoshimoto, Ryuuji

Calil.JP is a new free online service that enables federated searching, marshalling and integration of Web-OPAC data on the collections of libraries from around Japan. It offers the search results through user-friendly interface. Developed with a concept of accelerating discovery of fun-to-read books and motivating users to head for libraries, Calil was initially designed mainly for public library users. It now extends to cover university libraries and special libraries. This article presents the Calil's basic capabilities, concept, progress made thus far, and plan for further development as viewed from an engineering development manager.

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.

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

Crowdsourcing engagement and applications for communities within crisis events

NASA Astrophysics Data System (ADS)

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

2017-04-01

Civil protection attitude is a changing pattern within natural hazards, deploying responsibilities from central government to local authorities. The competence of volunteers and the awareness and involvement of local inhabitants are key points for prevention and preparedness. Citizens and volunteers become first actors of civil protection, toward context-specific strategies of surveillance and territorial surveys. The crowd-mapping technology includes a mobile solution tested insight trained communities, as participation within disaster response. The platform includes also a user-friendly dashboard for data gathering and analysis in multi-hazard realities, tested with pilot case studies. Usability and gradual innovation of platform are continuous granted by cloud dataset and bugfixing controls. The first module focuses on flood processes gathering data from local and trained population, for awareness and long-term preparedness. The second module integrates field survey of several volunteers within rescue squads, combining geolocations and comparing dataset collected in pre-emergency steps in urban case studies. The results include an easy-to-use data interface for crisis management, a tested support within crisis combined with personal awareness, continuously updated and customized. The development provides a version for Android 4.0 onward, the web application combines a cloud architecture with a relational database and web services, integrated with SDK cloud notification. The wireframes planned two accesses for a Citizens Kit and a Volunteers Kit, synchronized with a common dashboard. The follow up includes the integration between mobile solutions with sensors for dynamic update and data export for GIS analysis. The location-based services uses location data to monitor parameters and control features within natural hazard. A human sensor network is the aim, integrating sensor measurements with external observation as baseline of future modelling. Point data like humidity, temperature and pressure are geolocated and real-time. Human sensors reveal a massive approach of crowdsourcing, and user-friendly dashboards appears as solid control of data management to support resilience and quality of risk assessment.

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

PubMed

Muin, Michael; Fontelo, Paul

2006-11-03

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

PomBase: a comprehensive online resource for fission yeast

PubMed Central

Wood, Valerie; Harris, Midori A.; McDowall, Mark D.; Rutherford, Kim; Vaughan, Brendan W.; Staines, Daniel M.; Aslett, Martin; Lock, Antonia; Bähler, Jürg; Kersey, Paul J.; Oliver, Stephen G.

2012-01-01

PomBase (www.pombase.org) is a new model organism database established to provide access to comprehensive, accurate, and up-to-date molecular data and biological information for the fission yeast Schizosaccharomyces pombe to effectively support both exploratory and hypothesis-driven research. PomBase encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets, and supports sophisticated user-defined queries. The implementation of PomBase integrates a Chado relational database that houses manually curated data with Ensembl software that supports sequence-based annotation and web access. PomBase will provide user-friendly tools to promote curation by experts within the fission yeast community. This will make a key contribution to shaping its content and ensuring its comprehensiveness and long-term relevance. PMID:22039153

BioTextQuest: a web-based biomedical text mining suite for concept discovery.

PubMed

Papanikolaou, Nikolas; Pafilis, Evangelos; Nikolaou, Stavros; Ouzounis, Christos A; Iliopoulos, Ioannis; Promponas, Vasilis J

2011-12-01

BioTextQuest combines automated discovery of significant terms in article clusters with structured knowledge annotation, via Named Entity Recognition services, offering interactive user-friendly visualization. A tag-cloud-based illustration of terms labeling each document cluster are semantically annotated according to the biological entity, and a list of document titles enable users to simultaneously compare terms and documents of each cluster, facilitating concept association and hypothesis generation. BioTextQuest allows customization of analysis parameters, e.g. clustering/stemming algorithms, exclusion of documents/significant terms, to better match the biological question addressed. http://biotextquest.biol.ucy.ac.cy vprobon@ucy.ac.cy; iliopj@med.uoc.gr Supplementary data are available at Bioinformatics online.

Flow Regime Based Climatologies of Lightning Probabilities for Spaceports and Airports

NASA Technical Reports Server (NTRS)

Bauman, William H., III; Volmer, Matthew; Sharp, David; Spratt, Scott; Lafosse, Richard A.

2007-01-01

Objective: provide forecasters with a "first guess" climatological lightning probability tool (1) Focus on Space Shuttle landings and NWS T AFs (2) Four circles around sites: 5-, 10-, 20- and 30 n mi (4) Three time intervals: hourly, every 3 hr and every 6 hr It is based on: (1) NLDN gridded data (2) Flow regime (3) Warm season months of May-Sep for years 1989-2004 Gridded data and available code yields squares, not circles Over 850 spread sheets converted into manageable user-friendly web-based GUI

Online Statistical Modeling (Regression Analysis) for Independent Responses

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

Web tools for effective retrieval, visualization, and evaluation of cardiology medical images and records

NASA Astrophysics Data System (ADS)

Masseroli, Marco; Pinciroli, Francesco

2000-12-01

To provide easy retrieval, integration and evaluation of multimodal cardiology images and data in a web browser environment, distributed application technologies and java programming were used to implement a client-server architecture based on software agents. The server side manages secure connections and queries to heterogeneous remote databases and file systems containing patient personal and clinical data. The client side is a Java applet running in a web browser and providing a friendly medical user interface to perform queries on patient and medical test dat and integrate and visualize properly the various query results. A set of tools based on Java Advanced Imaging API enables to process and analyze the retrieved cardiology images, and quantify their features in different regions of interest. The platform-independence Java technology makes the developed prototype easy to be managed in a centralized form and provided in each site where an intranet or internet connection can be located. Giving the healthcare providers effective tools for querying, visualizing and evaluating comprehensively cardiology medical images and records in all locations where they can need them- i.e. emergency, operating theaters, ward, or even outpatient clinics- the developed prototype represents an important aid in providing more efficient diagnoses and medical treatments.

Improvements to the User Interface for LHCb's Software continuous integration system.

NASA Astrophysics Data System (ADS)

Clemencic, M.; Couturier, B.; Kyriazi, S.

2015-12-01

The purpose of this paper is to identify a set of steps leading to an improved interface for LHCb's Nightly Builds Dashboard. The goal is to have an efficient application that meets the needs of both the project developers, by providing them with a user friendly interface, as well as those of the computing team supporting the system, by providing them with a dashboard allowing for better monitoring of the build job themselves. In line with what is already used by LHCb, the web interface has been implemented with the Flask Python framework for future maintainability and code clarity. The Database chosen to host the data is the schema-less CouchDB[7], serving the purpose of flexibility in document form changes. To improve the user experience, we use JavaScript libraries such as JQuery[11].

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.

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.

75 FR 25853 - Agency Information Collection Activities; Submission to OMB for Review and Approval; Comment...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-10

....gov , to submit or view public comments, access the index listing of the contents of the docket, and...:8080/glas/login.htm . The Web-site will contain a user-friendly data entry interface for recipients to... series of screens containing pull-down menus and text boxes, where users can enter project specific...

Adopting and adapting a commercial view of web services for the Navy

NASA Astrophysics Data System (ADS)

Warner, Elizabeth; Ladner, Roy; Katikaneni, Uday; Petry, Fred

2005-05-01

Web Services are being adopted as the enabling technology to provide net-centric capabilities for many Department of Defense operations. The Navy Enterprise Portal, for example, is Web Services-based, and the Department of the Navy is promulgating guidance for developing Web Services. Web Services, however, only constitute a baseline specification that provides the foundation on which users, under current approaches, write specialized applications in order to retrieve data over the Internet. Application development may increase dramatically as the number of different available Web Services increases. Reasons for specialized application development include XML schema versioning differences, adoption/use of diverse business rules, security access issues, and time/parameter naming constraints, among others. We are currently developing for the US Navy a system which will improve delivery of timely and relevant meteorological and oceanographic (MetOc) data to the warfighter. Our objective is to develop an Advanced MetOc Broker (AMB) that leverages Web Services technology to identify, retrieve and integrate relevant MetOc data in an automated manner. The AMB will utilize a Mediator, which will be developed by applying ontological research and schema matching techniques to MetOc forms of data. The AMB, using the Mediator, will support a new, advanced approach to the use of Web Services; namely, the automated identification, retrieval and integration of MetOc data. Systems based on this approach will then not require extensive end-user application development for each Web Service from which data can be retrieved. Users anywhere on the globe will be able to receive timely environmental data that fits their particular needs.

iMetaLab 1.0: A web platform for metaproteomics data analysis.

PubMed

Liao, Bo; Ning, Zhibin; Cheng, Kai; Zhang, Xu; Li, Leyuan; Mayne, Janice; Figeys, Daniel

2018-06-15

The human gut microbiota, a complex, dynamic and biodiverse community, has been increasingly shown to influence many aspects of health and disease. Metaproteomic analysis has proven to be a powerful approach to study the functionality of the microbiota. However, the processing and analyses of metaproteomic mass spectrometry (MS) data remains a daunting task in metaproteomics data analysis. We developed iMetaLab, a web based platform to provide a user-friendly and comprehensive data analysis pipeline with a focus on lowering the technical barrier for metaproteomics data analysis. iMetaLab is freely available through at http://imetalab.ca. Supplementary data are available at Bioinformatics online.

Prototype of a Mobile Social Network for Education Using Dynamic Web Service

ERIC Educational Resources Information Center

Hoentsch, Sandra Costa Pinto; Carvalho, Felipe Oliveira; Santos, Luiz Marcus Monteiro de Almeida; Ribeiro, Admilson de Ribamar Lima

2012-01-01

This article presents the proposal of a social network site SocialNetLab that belongs to the Department of Computing-Federal University of Sergipe and which aims to locate and notify users of a nearby friend independently of the location technology available in the equipment through dynamic Web Service; to serve as a laboratory for research in…

PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization.

PubMed

Dogrusoz, U; Erson, E Z; Giral, E; Demir, E; Babur, O; Cetintas, A; Colak, R

2006-02-01

Patikaweb provides a Web interface for retrieving and analyzing biological pathways in the Patika database, which contains data integrated from various prominent public pathway databases. It features a user-friendly interface, dynamic visualization and automated layout, advanced graph-theoretic queries for extracting biologically important phenomena, local persistence capability and exporting facilities to various pathway exchange formats.

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.

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.

High-performance web viewer for cardiac images

NASA Astrophysics Data System (ADS)

dos Santos, Marcelo; Furuie, Sergio S.

2004-04-01

With the advent of the digital devices for medical diagnosis the use of the regular films in radiology has decreased. Thus, the management and handling of medical images in digital format has become an important and critical task. In Cardiology, for example, the main difficulty is to display dynamic images with the appropriated color palette and frame rate used on acquisition process by Cath, Angio and Echo systems. In addition, other difficulty is handling large images in memory by any existing personal computer, including thin clients. In this work we present a web-based application that carries out these tasks with robustness and excellent performance, without burdening the server and network. This application provides near-diagnostic quality display of cardiac images stored as DICOM 3.0 files via a web browser and provides a set of resources that allows the viewing of still and dynamic images. It can access image files from the local disks, or network connection. Its features include: allows real-time playback, dynamic thumbnails image viewing during loading, access to patient database information, image processing tools, linear and angular measurements, on-screen annotations, image printing and exporting DICOM images to other image formats, and many others, all characterized by a pleasant user-friendly interface, inside a Web browser by means of a Java application. This approach offers some advantages over the most of medical images viewers, such as: facility of installation, integration with other systems by means of public and standardized interfaces, platform independence, efficient manipulation and display of medical images, all with high performance.

Web N.0, the New Development Trend of Internet

NASA Astrophysics Data System (ADS)

Sun, Zhiguo; Wang, Wensheng

This article analyzes the Internet basic theory, the network foundation environment and the user behavior change and so on, Which analyzes the development tendency of existing partial Internet products in the future Internet environment. The article also hot on the concept of cloud computing, Demonstrates the relation between Cloud Computing and Web 2.0 from the angle of Cloud-based end-user applications, The possibly killing application in the future was discussed.

RSRE: RNA structural robustness evaluator

PubMed Central

Shu, Wenjie; Zheng, Zhiqiang; Wang, Shengqi

2007-01-01

Biological robustness, defined as the ability to maintain stable functioning in the face of various perturbations, is an important and fundamental topic in current biology, and has become a focus of numerous studies in recent years. Although structural robustness has been explored in several types of RNA molecules, the origins of robustness are still controversial. Computational analysis results are needed to make up for the lack of evidence of robustness in natural biological systems. The RNA structural robustness evaluator (RSRE) web server presented here provides a freely available online tool to quantitatively evaluate the structural robustness of RNA based on the widely accepted definition of neutrality. Several classical structure comparison methods are employed; five randomization methods are implemented to generate control sequences; sub-optimal predicted structures can be optionally utilized to mitigate the uncertainty of secondary structure prediction. With a user-friendly interface, the web application is easy to use. Intuitive illustrations are provided along with the original computational results to facilitate analysis. The RSRE will be helpful in the wide exploration of RNA structural robustness and will catalyze our understanding of RNA evolution. The RSRE web server is freely available at http://biosrv1.bmi.ac.cn/RSRE/ or http://biotech.bmi.ac.cn/RSRE/. PMID:17567615

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

PubMed

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

2017-01-20

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

A Lexical-Ontological Resource for Consumer Healthcare

NASA Astrophysics Data System (ADS)

Cardillo, Elena; Serafini, Luciano; Tamilin, Andrei

In Consumer Healthcare Informatics it is still difficult for laypeople to find, understand and act on health information, due to the persistent communication gap between specialized medical terminology and that used by healthcare consumers. Furthermore, existing clinically-oriented terminologies cannot provide sufficient support when integrated into consumer-oriented applications, so there is a need to create consumer-friendly terminologies reflecting the different ways healthcare consumers express and think about health topics. Following this direction, this work suggests a way to support the design of an ontology-based system that mitigates this gap, using knowledge engineering and semantic web technologies. The system is based on the development of a consumer-oriented medical terminology that will be integrated with other medical domain ontologies and terminologies into a medical ontology repository. This will support consumer-oriented healthcare systems, such as Personal Health Records, by providing many knowledge services to help users in accessing and managing their healthcare data.

A Lexical-Ontological Resource for Consumer Heathcare

NASA Astrophysics Data System (ADS)

Cardillo, Elena

In Consumer Healthcare Informatics it is still difficult for laypersons to understand and act on health information, due to the persistent communication gap between specialized medical terminology and that used by healthcare consumers. Furthermore, existing clinically-oriented terminologies cannot provide sufficient support when integrated into consumer-oriented applications, so there is a need to create consumer-friendly terminologies reflecting the different ways healthcare consumers express and think about health topics. Following this direction, this work suggests a way to support the design of an ontology-based system that mitigates this gap, using knowledge engineering and Semantic Web technologies. The system is based on the development of a consumer-oriented medical terminology which will be integrated with other existing domain ontologies/terminologies into a medical ontology repository. This will support consumer-oriented healthcare systems by providing many knowledge services to help users in accessing and managing their healthcare data.

[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.

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.

Optimizing the Information Presentation on Mining Potential by using Web Services Technology with Restful Protocol

NASA Astrophysics Data System (ADS)

Abdillah, T.; Dai, R.; Setiawan, E.

2018-02-01

This study aims to develop the application of Web Services technology with RestFul Protocol to optimize the information presentation on mining potential. This study used User Interface Design approach for the information accuracy and relevance as well as the Web Service for the reliability in presenting the information. The results show that: the information accuracy and relevance regarding mining potential can be seen from the achievement of User Interface implementation in the application that is based on the following rules: The consideration of the appropriate colours and objects, the easiness of using the navigation, and users’ interaction with the applications that employs symbols and languages understood by the users; the information accuracy and relevance related to mining potential can be observed by the information presented by using charts and Tool Tip Text to help the users understand the provided chart/figure; the reliability of the information presentation is evident by the results of Web Services testing in Figure 4.5.6. This study finds out that User Interface Design and Web Services approaches (for the access of different Platform apps) are able to optimize the presentation. The results of this study can be used as a reference for software developers and Provincial Government of Gorontalo.

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 applications—a recommender system and an online auction. In all cases, it is shown that harnessing an increased amount of information upon which to make trust decisions greatly enhances the user experience with the Social Web application.

DISTING: A web application for fast algorithmic computation of alternative indistinguishable linear compartmental models.

PubMed

Davidson, Natalie R; Godfrey, Keith R; Alquaddoomi, Faisal; Nola, David; DiStefano, Joseph J

2017-05-01

We describe and illustrate use of DISTING, a novel web application for computing alternative structurally identifiable linear compartmental models that are input-output indistinguishable from a postulated linear compartmental model. Several computer packages are available for analysing the structural identifiability of such models, but DISTING is the first to be made available for assessing indistinguishability. The computational algorithms embedded in DISTING are based on advanced versions of established geometric and algebraic properties of linear compartmental models, embedded in a user-friendly graphic model user interface. Novel computational tools greatly speed up the overall procedure. These include algorithms for Jacobian matrix reduction, submatrix rank reduction, and parallelization of candidate rank computations in symbolic matrix analysis. The application of DISTING to three postulated models with respectively two, three and four compartments is given. The 2-compartment example is used to illustrate the indistinguishability problem; the original (unidentifiable) model is found to have two structurally identifiable models that are indistinguishable from it. The 3-compartment example has three structurally identifiable indistinguishable models. It is found from DISTING that the four-compartment example has five structurally identifiable models indistinguishable from the original postulated model. This example shows that care is needed when dealing with models that have two or more compartments which are neither perturbed nor observed, because the numbering of these compartments may be arbitrary. DISTING is universally and freely available via the Internet. It is easy to use and circumvents tedious and complicated algebraic analysis previously done by hand. Copyright © 2017 Elsevier B.V. All rights reserved.

Interactive, Secure Web-enabled Aircraft Engine Simulation Using XML Databinding Integration

NASA Technical Reports Server (NTRS)

Lin, Risheng; Afjeh, Abdollah A.

2003-01-01

This paper discusses the detailed design of an XML databinding framework for aircraft engine simulation. The framework provides an object interface to access and use engine data. while at the same time preserving the meaning of the original data. The Language independent representation of engine component data enables users to move around XML data using HTTP through disparate networks. The application of this framework is demonstrated via a web-based turbofan propulsion system simulation using the World Wide Web (WWW). A Java Servlet based web component architecture is used for rendering XML engine data into HTML format and dealing with input events from the user, which allows users to interact with simulation data from a web browser. The simulation data can also be saved to a local disk for archiving or to restart the simulation at a later time.

NABIC marker database: A molecular markers information network of agricultural crops.

PubMed

Kim, Chang-Kug; Seol, Young-Joo; Lee, Dong-Jun; Jeong, In-Seon; Yoon, Ung-Han; Lee, Gang-Seob; Hahn, Jang-Ho; Park, Dong-Suk

2013-01-01

In 2013, National Agricultural Biotechnology Information Center (NABIC) reconstructs a molecular marker database for useful genetic resources. The web-based marker database consists of three major functional categories: map viewer, RSN marker and gene annotation. It provides 7250 marker locations, 3301 RSN marker property, 3280 molecular marker annotation information in agricultural plants. The individual molecular marker provides information such as marker name, expressed sequence tag number, gene definition and general marker information. This updated marker-based database provides useful information through a user-friendly web interface that assisted in tracing any new structures of the chromosomes and gene positional functions using specific molecular markers. The database is available for free at http://nabic.rda.go.kr/gere/rice/molecularMarkers/

Smart "geomorphological" map browsing - a tale about geomorphological maps and the internet

NASA Astrophysics Data System (ADS)

Geilhausen, M.; Otto, J.-C.

2012-04-01

With the digital production of geomorphological maps, the dissemination of research outputs now extends beyond simple paper products. Internet technologies can contribute to both, the dissemination of geomorphological maps and access to geomorphologic data and help to make geomorphological knowledge available to a greater public. Indeed, many national geological surveys employ end-to-end digital workflows from data capture in the field to final map production and dissemination. This paper deals with the potential of web mapping applications and interactive, portable georeferenced PDF maps for the distribution of geomorphological information. Web mapping applications such as Google Maps have become very popular and widespread and increased the interest and access to mapping. They link the Internet with GIS technology and are a common way of presenting dynamic maps online. The GIS processing is performed online and maps are visualised in interactive web viewers characterised by different capabilities such as zooming, panning or adding further thematic layers, with the map refreshed after each task. Depending on the system architecture and the components used, advanced symbology, map overlays from different applications and sources and their integration into a Desktop GIS are possible. This interoperability is achieved through the use of international open standards that include mechanisms for the integration and visualisation of information from multiple sources. The portable document format (PDF) is commonly used for printing and is a standard format that can be processed by many graphic software and printers without loss of information. A GeoPDF enables the sharing of geospatial maps and data in PDF documents. Multiple, independent map frames with individual spatial reference systems are possible within a GeoPDF, for example, for map overlays or insets. Geospatial functionality of a GeoPDF includes scalable map display, layer visibility control, access to attribute data, coordinate queries and spatial measurements. The full functionality of GeoPDFs requires free and user-friendly plug-ins for PDF readers and GIS software. A GeoPDF enables fundamental GIS functionality turning the formerly static PDF map into an interactive, portable georeferenced PDF map. GeoPDFs are easy to create and provide an interesting and valuable way to disseminate geomorphological maps. Our motivation to engage with the online distribution of geomorphological maps originates in the increasing number of web mapping applications available today indicating that the Internet has become a medium for displaying geographical information in rich forms and user-friendly interfaces. So, why not use the Internet to distribute geomorphological maps and enhance their practical application? Web mapping and dynamic PDF maps can play a key role in the movement towards a global dissemination of geomorphological information. This will be exemplified by live demonstrations of i.) existing geomorphological WebGIS applications, ii.) data merging from various sources using web map services, and iii.) free to download GeoPDF maps during the presentations.

A Web-Based Psychoeducational Intervention for Adolescent Depression: Design and Development of MoodHwb

PubMed Central

Thapar, Anita; Rice, Frances; Beeching, Harriet; Cichosz, Rachel; Mars, Becky; Smith, Daniel J; Merry, Sally; Stallard, Paul; Jones, Ian; Thapar, Ajay K; Simpson, Sharon A

2018-01-01

Background Depression is common in adolescence and leads to distress and impairment in individuals, families and carers. Treatment and prevention guidelines highlight the key role of information and evidence-based psychosocial interventions not only for individuals but also for their families and carers. Engaging young people in prevention and early intervention programs is a challenge, and early treatment and prevention of adolescent depression is a major public health concern. There has been growing interest in psychoeducational interventions to provide accurate information about health issues and to enhance and develop self-management skills. However, for adolescents with, or at high risk of depression, there is a lack of engaging Web-based psychoeducation programs that have been developed with user input and in line with research guidelines and targeted at both the individual and their family or carer. There are also few studies published on the process of development of Web-based psychoeducational interventions. Objective The aim of this study was to describe the process underlying the design and development of MoodHwb (HwbHwyliau in Welsh): a Web-based psychoeducation multimedia program for young people with, or at high risk of, depression and their families, carers, friends, and professionals. Methods The initial prototype was informed by (1) a systematic review of psychoeducational interventions for adolescent depression; (2) findings from semistructured interviews and focus groups conducted with adolescents (with depressive symptoms or at high risk), parents or carers, and professionals working with young people; and (3) workshops and discussions with a multimedia company and experts (in clinical, research, and multimedia work). Twelve interviews were completed (four each with young people, parents or carers, and professionals) and six focus groups (three with young people, one with parents and carers, one with professionals, and one with academics). Results Key themes from the interviews and focus groups were: aims of the program, design and content issues, and integration and context of the program. The prototype was designed to be person-centered, multiplatform, engaging, interactive, and bilingual. It included mood-monitoring and goal-setting components and was available as a Web-based program and an app for mobile technologies. Conclusions MoodHwb is a Web-based psychoeducational intervention developed for young people with, or at high risk of, depression and their families and carers. It was developed with user input using qualitative methods as well as user-centered design and educational and psychological theory. Further research is needed to evaluate the effectiveness of the program in a randomized controlled trial. If found to be effective, it could be implemented in health, education, youth and social services, and charities, to not only help young people but also families, carers, friends, and professionals involved in their care. PMID:29449202

KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems

PubMed Central

2014-01-01

Background The kinetic modeling of biological systems is mainly composed of three steps that proceed iteratively: model building, simulation and analysis. In the first step, it is usually required to set initial metabolite concentrations, and to assign kinetic rate laws, along with estimating parameter values using kinetic data through optimization when these are not known. Although the rapid development of high-throughput methods has generated much omics data, experimentalists present only a summary of obtained results for publication, the experimental data files are not usually submitted to any public repository, or simply not available at all. In order to automatize as much as possible the steps of building kinetic models, there is a growing requirement in the systems biology community for easily exchanging data in combination with models, which represents the main motivation of KiMoSys development. Description KiMoSys is a user-friendly platform that includes a public data repository of published experimental data, containing concentration data of metabolites and enzymes and flux data. It was designed to ensure data management, storage and sharing for a wider systems biology community. This community repository offers a web-based interface and upload facility to turn available data into publicly accessible, centralized and structured-format data files. Moreover, it compiles and integrates available kinetic models associated with the data. KiMoSys also integrates some tools to facilitate the kinetic model construction process of large-scale metabolic networks, especially when the systems biologists perform computational research. Conclusions KiMoSys is a web-based system that integrates a public data and associated model(s) repository with computational tools, providing the systems biology community with a novel application facilitating data storage and sharing, thus supporting construction of ODE-based kinetic models and collaborative research projects. The web application implemented using Ruby on Rails framework is freely available for web access at http://kimosys.org, along with its full documentation. PMID:25115331

SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals

PubMed Central

Damienikan, Aliaksandr U.

2016-01-01

The majority of bacterial genome annotations are currently automated and based on a ‘gene by gene’ approach. Regulatory signals and operon structures are rarely taken into account which often results in incomplete and even incorrect gene function assignments. Here we present SigmoID, a cross-platform (OS X, Linux and Windows) open-source application aiming at simplifying the identification of transcription regulatory sites (promoters, transcription factor binding sites and terminators) in bacterial genomes and providing assistance in correcting annotations in accordance with regulatory information. SigmoID combines a user-friendly graphical interface to well known command line tools with a genome browser for visualising regulatory elements in genomic context. Integrated access to online databases with regulatory information (RegPrecise and RegulonDB) and web-based search engines speeds up genome analysis and simplifies correction of genome annotation. We demonstrate some features of SigmoID by constructing a series of regulatory protein binding site profiles for two groups of bacteria: Soft Rot Enterobacteriaceae (Pectobacterium and Dickeya spp.) and Pseudomonas spp. Furthermore, we inferred over 900 transcription factor binding sites and alternative sigma factor promoters in the annotated genome of Pectobacterium atrosepticum. These regulatory signals control putative transcription units covering about 40% of the P. atrosepticum chromosome. Reviewing the annotation in cases where it didn’t fit with regulatory information allowed us to correct product and gene names for over 300 loci. PMID:27257541

CCBuilder 2.0: Powerful and accessible coiled-coil modeling.

PubMed

Wood, Christopher W; Woolfson, Derek N

2018-01-01

The increased availability of user-friendly and accessible computational tools for biomolecular modeling would expand the reach and application of biomolecular engineering and design. For protein modeling, one key challenge is to reduce the complexities of 3D protein folds to sets of parametric equations that nonetheless capture the salient features of these structures accurately. At present, this is possible for a subset of proteins, namely, repeat proteins. The α-helical coiled coil provides one such example, which represents ≈ 3-5% of all known protein-encoding regions of DNA. Coiled coils are bundles of α helices that can be described by a small set of structural parameters. Here we describe how this parametric description can be implemented in an easy-to-use web application, called CCBuilder 2.0, for modeling and optimizing both α-helical coiled coils and polyproline-based collagen triple helices. This has many applications from providing models to aid molecular replacement for X-ray crystallography, in silico model building and engineering of natural and designed protein assemblies, and through to the creation of completely de novo "dark matter" protein structures. CCBuilder 2.0 is available as a web-based application, the code for which is open-source and can be downloaded freely. http://coiledcoils.chm.bris.ac.uk/ccbuilder2. We have created CCBuilder 2.0, an easy to use web-based application that can model structures for a whole class of proteins, the α-helical coiled coil, which is estimated to account for 3-5% of all proteins in nature. CCBuilder 2.0 will be of use to a large number of protein scientists engaged in fundamental studies, such as protein structure determination, through to more-applied research including designing and engineering novel proteins that have potential applications in biotechnology. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

StreptomycesInforSys: A web-enabled information repository

PubMed Central

Jain, Chakresh Kumar; Gupta, Vidhi; Gupta, Ashvarya; Gupta, Sanjay; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Sarethy, Indira P

2012-01-01

Members of Streptomyces produce 70% of natural bioactive products. There is considerable amount of information available based on polyphasic approach for classification of Streptomyces. However, this information based on phenotypic, genotypic and bioactive component production profiles is crucial for pharmacological screening programmes. This is scattered across various journals, books and other resources, many of which are not freely accessible. The designed database incorporates polyphasic typing information using combinations of search options to aid in efficient screening of new isolates. This will help in the preliminary categorization of appropriate groups. It is a free relational database compatible with existing operating systems. A cross platform technology with XAMPP Web server has been used to develop, manage, and facilitate the user query effectively with database support. Employment of PHP, a platform-independent scripting language, embedded in HTML and the database management software MySQL will facilitate dynamic information storage and retrieval. The user-friendly, open and flexible freeware (PHP, MySQL and Apache) is foreseen to reduce running and maintenance cost. Availability www.sis.biowaves.org PMID:23275736

StreptomycesInforSys: A web-enabled information repository.

PubMed

Jain, Chakresh Kumar; Gupta, Vidhi; Gupta, Ashvarya; Gupta, Sanjay; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Sarethy, Indira P

2012-01-01

Members of Streptomyces produce 70% of natural bioactive products. There is considerable amount of information available based on polyphasic approach for classification of Streptomyces. However, this information based on phenotypic, genotypic and bioactive component production profiles is crucial for pharmacological screening programmes. This is scattered across various journals, books and other resources, many of which are not freely accessible. The designed database incorporates polyphasic typing information using combinations of search options to aid in efficient screening of new isolates. This will help in the preliminary categorization of appropriate groups. It is a free relational database compatible with existing operating systems. A cross platform technology with XAMPP Web server has been used to develop, manage, and facilitate the user query effectively with database support. Employment of PHP, a platform-independent scripting language, embedded in HTML and the database management software MySQL will facilitate dynamic information storage and retrieval. The user-friendly, open and flexible freeware (PHP, MySQL and Apache) is foreseen to reduce running and maintenance cost. www.sis.biowaves.org.

An Automated End-To Multi-Agent Qos Based Architecture for Selection of Geospatial Web Services

NASA Astrophysics Data System (ADS)

Shah, M.; Verma, Y.; Nandakumar, R.

2012-07-01

Over the past decade, Service-Oriented Architecture (SOA) and Web services have gained wide popularity and acceptance from researchers and industries all over the world. SOA makes it easy to build business applications with common services, and it provides like: reduced integration expense, better asset reuse, higher business agility, and reduction of business risk. Building of framework for acquiring useful geospatial information for potential users is a crucial problem faced by the GIS domain. Geospatial Web services solve this problem. With the help of web service technology, geospatial web services can provide useful geospatial information to potential users in a better way than traditional geographic information system (GIS). A geospatial Web service is a modular application designed to enable the discovery, access, and chaining of geospatial information and services across the web that are often both computation and data-intensive that involve diverse sources of data and complex processing functions. With the proliferation of web services published over the internet, multiple web services may provide similar functionality, but with different non-functional properties. Thus, Quality of Service (QoS) offers a metric to differentiate the services and their service providers. In a quality-driven selection of web services, it is important to consider non-functional properties of the web service so as to satisfy the constraints or requirements of the end users. The main intent of this paper is to build an automated end-to-end multi-agent based solution to provide the best-fit web service to service requester based on QoS.

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 and obtain information for locations along streams where activities occur that may affect streamflow conditions. This functionality can be accessed through a map-based interface with the user’s Web browser, or individual functions can be requested remotely through Web services (Ries and others, 2008).

MAX UnMix: Introducing a new web application for unmixing magnetic coercivity distributions

NASA Astrophysics Data System (ADS)

Feinberg, J. M.; Maxbauer, D.; Fox, D. L.

2016-12-01

Magnetic minerals are present in a wide variety of natural systems and are often indicative of the natural or anthropogenic processes that led to their deposition, formation, or transformation. Unmixing the contribution of magnetic components to bulk field-dependent magnetization curves has become increasingly common in environmental and rock magnetic studies and has enhanced our ability to fingerprint the magnetic signatures of magnetic minerals with distinct compositions, grain sizes, and origins. A variety of programs have been developed over the past two decades to allow researchers to deconvolve field-dependent magnetization curves for these purposes, however many of these programs are either outdated or have obstacles that inhibit the programs usability. MAX UnMix is a new web application (available online at http://www.irm.umn.edu/maxunmix) built using the `shiny' package for R-studio that can be used to process coercivity distributions derived from magnetization curves (acquisition, demagnetization, or backfield data) via an online user-interface. Here, we use example datasets from lake sediments and paleosols to present details of the MAX UnMix model and the programs functionality. MAX UnMix is designed to be accessible, user friendly, and should serve as a useful resource for future research.

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 care will diffuse more rapidly when technology is employed that is simple to use and has applicable components for interactivity. This would foresee the patients' need for continuous and personalized feedback, in particular for patients with a greater need for care. From this study several factors appear to influence increased use of eHealth technologies: (1) avoiding selective enrollment, (2) making use of participatory design methods, and (3) developing push factors for persistence. Further research should focus on the causal relationship between using the system's features and actual usage, as such a view would provide important evidence on how specific technology features can engage and captivate users.

Real-Time System for Water Modeling and Management

NASA Astrophysics Data System (ADS)

Lee, J.; Zhao, T.; David, C. H.; Minsker, B.

2012-12-01

Working closely with the Texas Commission on Environmental Quality (TCEQ) and the University of Texas at Austin (UT-Austin), we are developing a real-time system for water modeling and management using advanced cyberinfrastructure, data integration and geospatial visualization, and numerical modeling. The state of Texas suffered a severe drought in 2011 that cost the state $7.62 billion in agricultural losses (crops and livestock). Devastating situations such as this could potentially be avoided with better water modeling and management strategies that incorporate state of the art simulation and digital data integration. The goal of the project is to prototype a near-real-time decision support system for river modeling and management in Texas that can serve as a national and international model to promote more sustainable and resilient water systems. The system uses National Weather Service current and predicted precipitation data as input to the Noah-MP Land Surface model, which forecasts runoff, soil moisture, evapotranspiration, and water table levels given land surface features. These results are then used by a river model called RAPID, along with an error model currently under development at UT-Austin, to forecast stream flows in the rivers. Model forecasts are visualized as a Web application for TCEQ decision makers, who issue water diversion (withdrawal) permits and any needed drought restrictions; permit holders; and reservoir operation managers. Users will be able to adjust model parameters to predict the impacts of alternative curtailment scenarios or weather forecasts. A real-time optimization system under development will help TCEQ to identify optimal curtailment strategies to minimize impacts on permit holders and protect health and safety. To develop the system we have implemented RAPID as a remotely-executed modeling service using the Cyberintegrator workflow system with input data downloaded from the North American Land Data Assimilation System. The Cyberintegrator workflow system provides RESTful web services for users to provide inputs, execute workflows, and retrieve outputs. Along with REST endpoints, PAW (Publishable Active Workflows) provides the web user interface toolkit for us to develop web applications with scientific workflows. The prototype web application is built on top of workflows with PAW, so that users will have a user-friendly web environment to provide input parameters, execute the model, and visualize/retrieve the results using geospatial mapping tools. In future work the optimization model will be developed and integrated into the workflow.; Real-Time System for Water Modeling and Management

BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes

PubMed Central

Jespersen, Martin Closter; Peters, Bjoern

2017-01-01

Abstract Antibodies have become an indispensable tool for many biotechnological and clinical applications. They bind their molecular target (antigen) by recognizing a portion of its structure (epitope) in a highly specific manner. The ability to predict epitopes from antigen sequences alone is a complex task. Despite substantial effort, limited advancement has been achieved over the last decade in the accuracy of epitope prediction methods, especially for those that rely on the sequence of the antigen only. Here, we present BepiPred-2.0 (http://www.cbs.dtu.dk/services/BepiPred/), a web server for predicting B-cell epitopes from antigen sequences. BepiPred-2.0 is based on a random forest algorithm trained on epitopes annotated from antibody-antigen protein structures. This new method was found to outperform other available tools for sequence-based epitope prediction both on epitope data derived from solved 3D structures, and on a large collection of linear epitopes downloaded from the IEDB database. The method displays results in a user-friendly and informative way, both for computer-savvy and non-expert users. We believe that BepiPred-2.0 will be a valuable tool for the bioinformatics and immunology community. PMID:28472356

Tethys: A Platform for Water Resources Modeling and Decision Support Apps

NASA Astrophysics Data System (ADS)

Swain, N. R.; Christensen, S. D.; Jones, N.; Nelson, E. J.

2014-12-01

Cloud-based applications or apps are a promising medium through which water resources models and data can be conveyed in a user-friendly environment—making them more accessible to decision-makers and stakeholders. In the context of this work, a water resources web app is a web application that exposes limited modeling functionality for a scenario exploration activity in a structured workflow (e.g.: land use change runoff analysis, snowmelt runoff prediction, and flood potential analysis). The technical expertise required to develop water resources web apps can be a barrier to many potential developers of water resources apps. One challenge that developers face is in providing spatial storage, analysis, and visualization for the spatial data that is inherent to water resources models. The software projects that provide this functionality are non-standard to web development and there are a large number of free and open source software (FOSS) projects to choose from. In addition, it is often required to synthesize several software projects to provide all of the needed functionality. Another challenge for the developer will be orchestrating the use of several software components. Consequently, the initial software development investment required to deploy an effective water resources cloud-based application can be substantial. The Tethys Platform has been developed to lower the technical barrier and minimize the initial development investment that prohibits many scientists and engineers from making use of the web app medium. Tethys synthesizes several software projects including PostGIS for spatial storage, 52°North WPS for spatial analysis, GeoServer for spatial publishing, Google Earth™, Google Maps™ and OpenLayers for spatial visualization, and Highcharts for plotting tabular data. The software selection came after a literature review of software projects being used to create existing earth sciences web apps. All of the software is linked via a Python-powered software development kit (SDK). Tethys developers use the SDK to build their apps and incorporate the needed functionality from the software suite. The presentation will include several apps that have been developed using Tethys to demonstrate its capabilities. Based upon work supported by the National Science Foundation under Grant No. 1135483.

Interactive Vulnerability Analysis Enhancement Results

DTIC Science & Technology

2012-12-01

from JavaEE web based applications to other non-web based Java programs. Technology developed in this effort should be generally applicable to other...Generating a rule is a 2 click process that requires no input from the user. • Task 3: Added support for non- Java EE applications Aspect’s...investigated a variety of Java -based technologies and how IAST can support them. We were successful in adding support for Scala, a popular new language, and

Guide to the Internet. The world wide web.

PubMed Central

Pallen, M.

1995-01-01

The world wide web provides a uniform, user friendly interface to the Internet. Web pages can contain text and pictures and are interconnected by hypertext links. The addresses of web pages are recorded as uniform resource locators (URLs), transmitted by hypertext transfer protocol (HTTP), and written in hypertext markup language (HTML). Programs that allow you to use the web are available for most operating systems. Powerful on line search engines make it relatively easy to find information on the web. Browsing through the web--"net surfing"--is both easy and enjoyable. Contributing to the web is not difficult, and the web opens up new possibilities for electronic publishing and electronic journals. Images p1554-a Fig 5 PMID:8520402

Cloud computing geospatial application for water resources based on free and open source software and open standards - a prototype

NASA Astrophysics Data System (ADS)

Delipetrev, Blagoj

2016-04-01

Presently, most of the existing software is desktop-based, designed to work on a single computer, which represents a major limitation in many ways, starting from limited computer processing, storage power, accessibility, availability, etc. The only feasible solution lies in the web and cloud. This abstract presents research and development of a cloud computing geospatial application for water resources based on free and open source software and open standards using hybrid deployment model of public - private cloud, running on two separate virtual machines (VMs). The first one (VM1) is running on Amazon web services (AWS) and the second one (VM2) is running on a Xen cloud platform. The presented cloud application is developed using free and open source software, open standards and prototype code. The cloud application presents a framework how to develop specialized cloud geospatial application that needs only a web browser to be used. This cloud application is the ultimate collaboration geospatial platform because multiple users across the globe with internet connection and browser can jointly model geospatial objects, enter attribute data and information, execute algorithms, and visualize results. The presented cloud application is: available all the time, accessible from everywhere, it is scalable, works in a distributed computer environment, it creates a real-time multiuser collaboration platform, the programing languages code and components are interoperable, and it is flexible in including additional components. The cloud geospatial application is implemented as a specialized water resources application with three web services for 1) data infrastructure (DI), 2) support for water resources modelling (WRM), 3) user management. The web services are running on two VMs that are communicating over the internet providing services to users. The application was tested on the Zletovica river basin case study with concurrent multiple users. The application is a state-of-the-art cloud geospatial collaboration platform. The presented solution is a prototype and can be used as a foundation for developing of any specialized cloud geospatial applications. Further research will be focused on distributing the cloud application on additional VMs, testing the scalability and availability of services.

An Intelligent Tool for Activity Data Collection

PubMed Central

Jehad Sarkar, A. M.

2011-01-01

Activity recognition systems using simple and ubiquitous sensors require a large variety of real-world sensor data for not only evaluating their performance but also training the systems for better functioning. However, a tremendous amount of effort is required to setup an environment for collecting such data. For example, expertise and resources are needed to design and install the sensors, controllers, network components, and middleware just to perform basic data collections. It is therefore desirable to have a data collection method that is inexpensive, flexible, user-friendly, and capable of providing large and diverse activity datasets. In this paper, we propose an intelligent activity data collection tool which has the ability to provide such datasets inexpensively without physically deploying the testbeds. It can be used as an inexpensive and alternative technique to collect human activity data. The tool provides a set of web interfaces to create a web-based activity data collection environment. It also provides a web-based experience sampling tool to take the user’s activity input. The tool generates an activity log using its activity knowledge and the user-given inputs. The activity knowledge is mined from the web. We have performed two experiments to validate the tool’s performance in producing reliable datasets. PMID:22163832

Development of a geotechnical information database.

DOT National Transportation Integrated Search

2009-08-01

The purpose of this project was to create a user-friendly geotechnical Web site, so the LADOTD Headquarters Geotechnical Design Section and other LADOTD sections will have access to the appropriate and necessary resources to make the best design d...

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

PubMed Central

Muin, Michael; Fontelo, Paul

2006-01-01

Background The project aims to create an alternative search interface for MEDLINE/PubMed that may provide assistance to the novice user and added convenience to the advanced user. An earlier version of the project was the 'Slider Interface for MEDLINE/PubMed searches' (SLIM) which provided JavaScript slider bars to control search parameters. In this new version, recent developments in Web-based technologies were implemented. These changes may prove to be even more valuable in enhancing user interactivity through client-side manipulation and management of results. Results PubMed Interact is a Web-based MEDLINE/PubMed search application built with HTML, JavaScript and PHP. It is implemented on a Windows Server 2003 with Apache 2.0.52, PHP 4.4.1 and MySQL 4.1.18. PHP scripts provide the backend engine that connects with E-Utilities and parses XML files. JavaScript manages client-side functionalities and converts Web pages into interactive platforms using dynamic HTML (DHTML), Document Object Model (DOM) tree manipulation and Ajax methods. With PubMed Interact, users can limit searches with JavaScript slider bars, preview result counts, delete citations from the list, display and add related articles and create relevance lists. Many interactive features occur at client-side, which allow instant feedback without reloading or refreshing the page resulting in a more efficient user experience. Conclusion PubMed Interact is a highly interactive Web-based search application for MEDLINE/PubMed that explores recent trends in Web technologies like DOM tree manipulation and Ajax. It may become a valuable technical development for online medical search applications. PMID:17083729

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

PubMed Central

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

2010-01-01

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

SurvNet: a web server for identifying network-based biomarkers that most correlate with patient survival data.

PubMed

Li, Jun; Roebuck, Paul; Grünewald, Stefan; Liang, Han

2012-07-01

An important task in biomedical research is identifying biomarkers that correlate with patient clinical data, and these biomarkers then provide a critical foundation for the diagnosis and treatment of disease. Conventionally, such an analysis is based on individual genes, but the results are often noisy and difficult to interpret. Using a biological network as the searching platform, network-based biomarkers are expected to be more robust and provide deep insights into the molecular mechanisms of disease. We have developed a novel bioinformatics web server for identifying network-based biomarkers that most correlate with patient survival data, SurvNet. The web server takes three input files: one biological network file, representing a gene regulatory or protein interaction network; one molecular profiling file, containing any type of gene- or protein-centred high-throughput biological data (e.g. microarray expression data or DNA methylation data); and one patient survival data file (e.g. patients' progression-free survival data). Given user-defined parameters, SurvNet will automatically search for subnetworks that most correlate with the observed patient survival data. As the output, SurvNet will generate a list of network biomarkers and display them through a user-friendly interface. SurvNet can be accessed at http://bioinformatics.mdanderson.org/main/SurvNet.

Post Graduations in Technologies and Computing Applied to Education: From F2F Classes to Multimedia Online Open Courses

ERIC Educational Resources Information Center

Marques, Bertil P.; Carvalho, Piedade; Escudeiro, Paula; Barata, Ana; Silva, Ana; Queiros, Sandra

2017-01-01

Promoted by the significant increase of large scale internet access, many audiences have turned to the web and to its resources for learning and inspiration, with diverse sets of skills and intents. In this context, Multimedia Online Open Courses (MOOC) consist in learning models supported on user-friendly web tools that allow anyone with minimum…

Accredited hand surgery fellowship Web sites: analysis of content and accessibility.

PubMed

Trehan, Samir K; Morrell, Nathan T; Akelman, Edward

2015-04-01

To assess the accessibility and content of accredited hand surgery fellowship Web sites. A list of all accredited hand surgery fellowships was obtained from the online database of the American Society for Surgery of the Hand (ASSH). Fellowship program information on the ASSH Web site was recorded. All fellowship program Web sites were located via Google search. Fellowship program Web sites were analyzed for accessibility and content in 3 domains: program overview, application information/recruitment, and education. At the time of this study, there were 81 accredited hand surgery fellowships with 169 available positions. Thirty of 81 programs (37%) had a functional link on the ASSH online hand surgery fellowship directory; however, Google search identified 78 Web sites. Three programs did not have a Web site. Analysis of content revealed that most Web sites contained contact information, whereas information regarding the anticipated clinical, research, and educational experiences during fellowship was less often present. Furthermore, information regarding past and present fellows, salary, application process/requirements, call responsibilities, and case volume was frequently lacking. Overall, 52 of 81 programs (64%) had the minimal online information required for residents to independently complete the fellowship application process. Hand fellowship program Web sites could be accessed either via the ASSH online directory or Google search, except for 3 programs that did not have Web sites. Although most fellowship program Web sites contained contact information, other content such as application information/recruitment and education, was less frequently present. This study provides comparative data regarding the clinical and educational experiences outlined on hand fellowship program Web sites that are of relevance to residents, fellows, and academic hand surgeons. This study also draws attention to various ways in which the hand surgery fellowship application process can be made more user-friendly and efficient. Copyright © 2015 American Society for Surgery of the Hand. Published by Elsevier Inc. All rights reserved.

MyOcean Central Information System - Achievements and Perspectives

NASA Astrophysics Data System (ADS)

Claverie, Vincent; Loubrieu, Thomas; Jolibois, Tony; de Dianous, Rémi; Blower, Jon; Romero, Laia; Griffiths, Guy

2013-04-01

Since 2009, MyOcean (http://www.myocean.eu) is providing an operational service, for forecasts, analysis and expertise on ocean currents, temperature, salinity, sea level, primary ecosystems and ice coverage. The production of observation and forecasting data is done by 42 Production Units (PU). Product download and visualisation are hosted by 25 Dissemination Units (DU). All these products and associated services are gathered in a single catalogue hiding the intricate distributed organization of PUs and DUs. Besides applying INSPIRE directive and OGC recommendations, MyOcean overcomes technical choices and challenges. This presentation focuses on 3 specific issues met by MyOcean and relevant for many Spatial Data Infrastructures: user's transaction accounting, large volume download and stream line the catalogue maintenance. Transaction Accounting: Set up powerful means to get detailed knowledge of system usage in order to subsequently improve the products (ocean observations, analysis and forecast dataset) and services (view, download) offer. This subject drives the following ones: Central authentication management for the distributed web services implementations: add-on to THREDDS Data Server for WMS and NETCDF sub-setting service, specific FTP. Share user management with co-funding projects. In addition to MyOcean, alternate projects also need consolidated information about the use of the cofunded products. Provide a central facility for the user management. This central facility provides users' rights to geographically distributed services and gathers transaction accounting history from these distributed services. Propose a user-friendly web interface to download large volume of data (several GigaBytes) as robust as basic FTP but intuitive and file/directory independent. This should rely on a web service drafting the INSPIRE to-be specification and OGC recommendations for download taking into account that FTP server is not enough friendly (need to know filenames, directories) and Web-page not allowing downloading several files. Streamline the maintenance of the central catalogue. The major update for MyOcean v3 (April 2013) is the usage of Geonetwork for catalogue management. This improves the system at different levels : The editing interface is more user-friendly and the catalogue updates are managed in a workflow. This workflow allows higher flexibility for minor updates without giving up the high level qualification requirements for the catalogue content. The distributed web services (download, view) are automatically harvested from the THREDDS Data Server. Thus the manual editing on the catalogue is reduced, the associated typos are avoided and the quality of information is finally improved.

Secure Web-Site Access with Tickets and Message-Dependent Digests

USGS Publications Warehouse

Donato, David I.

2008-01-01

Although there are various methods for restricting access to documents stored on a World Wide Web (WWW) site (a Web site), none of the widely used methods is completely suitable for restricting access to Web applications hosted on an otherwise publicly accessible Web site. A new technique, however, provides a mix of features well suited for restricting Web-site or Web-application access to authorized users, including the following: secure user authentication, tamper-resistant sessions, simple access to user state variables by server-side applications, and clean session terminations. This technique, called message-dependent digests with tickets, or MDDT, maintains secure user sessions by passing single-use nonces (tickets) and message-dependent digests of user credentials back and forth between client and server. Appendix 2 provides a working implementation of MDDT with PHP server-side code and JavaScript client-side code.

VisPort: Web-Based Access to Community-Specific Visualization Functionality [Shedding New Light on Exploding Stars: Visualization for TeraScale Simulation of Neutrino-Driven Supernovae (Final Technical Report)

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

Baker, M Pauline

2007-06-30

The VisPort visualization portal is an experiment in providing Web-based access to visualization functionality from any place and at any time. VisPort adopts a service-oriented architecture to encapsulate visualization functionality and to support remote access. Users employ browser-based client applications to choose data and services, set parameters, and launch visualization jobs. Visualization products typically images or movies are viewed in the user's standard Web browser. VisPort emphasizes visualization solutions customized for specific application communities. Finally, VisPort relies heavily on XML, and introduces the notion of visualization informatics - the formalization and specialization of information related to the process and productsmore » of visualization.« less

Application of Multiprotocol Medical Imaging Communications and an Extended DICOM WADO Service in a Teleradiology Architecture

PubMed Central

Koutelakis, George V.; Anastassopoulos, George K.; Lymberopoulos, Dimitrios K.

2012-01-01

Multiprotocol medical imaging communication through the Internet is more flexible than the tight DICOM transfers. This paper introduces a modular multiprotocol teleradiology architecture that integrates DICOM and common Internet services (based on web, FTP, and E-mail) into a unique operational domain. The extended WADO service (a web extension of DICOM) and the other proposed services allow access to all levels of the DICOM information hierarchy as opposed to solely Object level. A lightweight client site is considered adequate, because the server site of the architecture provides clients with service interfaces through the web as well as invulnerable space for temporary storage, called as User Domains, so that users fulfill their applications' tasks. The proposed teleradiology architecture is pilot implemented using mainly Java-based technologies and is evaluated by engineers in collaboration with doctors. The new architecture ensures flexibility in access, user mobility, and enhanced data security. PMID:22489237

TRMM Precipitation Application Examples Using Data Services at NASA GES DISC

NASA Technical Reports Server (NTRS)

Liu, Zhong; Ostrenga, D.; Teng, W.; Kempler, S.; Greene, M.

2012-01-01

Data services to support precipitation applications are important for maximizing the NASA TRMM (Tropical Rainfall Measuring Mission) and the future GPM (Global Precipitation Mission) mission's societal benefits. TRMM Application examples using data services at the NASA GES DISC, including samples from users around the world will be presented in this poster. Precipitation applications often require near-real-time support. The GES DISC provides such support through: 1) Providing near-real-time precipitation products through TOVAS; 2) Maps of current conditions for monitoring precipitation and its anomaly around the world; 3) A user friendly tool (TOVAS) to analyze and visualize near-real-time and historical precipitation products; and 4) The GES DISC Hurricane Portal that provides near-real-time monitoring services for the Atlantic basin. Since the launch of TRMM, the GES DISC has developed data services to support precipitation applications around the world. In addition to the near-real-time services, other services include: 1) User friendly TRMM Online Visualization and Analysis System (TOVAS; URL: http://disc2.nascom.nasa.gov/Giovanni/tovas/); 2) Mirador (http://mirador.gsfc.nasa.gov/), a simplified interface for searching, browsing, and ordering Earth science data at GES DISC. Mirador is designed to be fast and easy to learn; 3) Data via OPeNDAP (http://disc.sci.gsfc.nasa.gov/services/opendap/). The OPeNDAP provides remote access to individual variables within datasets in a form usable by many tools, such as IDV, McIDAS-V, Panoply, Ferret and GrADS; and 4) The Open Geospatial Consortium (OGC) Web Map Service (WMS) (http://disc.sci.gsfc.nasa.gov/services/wxs_ogc.shtml). The WMS is an interface that allows the use of data and enables clients to build customized maps with data coming from a different network.

Trace saver: A tool for network service improvement and personalised analysis of user centric statistics

NASA Astrophysics Data System (ADS)

Bilal, Muhammad; Asfand-e-Yar, Mockford, Steve; Khan, Wasiq; Awan, Irfan

2012-11-01

Mobile technology is among the fastest growing technologies in today's world with low cost and highly effective benefits. Most important and entertaining areas in mobile technology development and usage are location based services, user friendly networked applications and gaming applications. However, concern towards network operator service provision and improvement has been very low. The portable applications available for a range of mobile operating systems which help improve the network operator services are desirable by the mobile operators. This paper proposes a state of the art mobile application Tracesaver, which provides a great achievement over the barriers in gathering device and network related information, for network operators to improve their network service provision. Tracesaver is available for a broad range of mobile devices with different mobile operating systems and computational capabilities. The availability of Tracesaver in market has proliferated over the last year since it was published. The survey and results show that Tracesaver is being used by millions of mobile users and provides novel ways of network service improvement with its highly user friendly interface.

GeoBrain Computational Cyber-laboratory for Earth Science Studies

NASA Astrophysics Data System (ADS)

Deng, M.; di, L.

2009-12-01

Computational approaches (e.g., computer-based data visualization, analysis and modeling) are critical for conducting increasingly data-intensive Earth science (ES) studies to understand functions and changes of the Earth system. However, currently Earth scientists, educators, and students have met two major barriers that prevent them from being effectively using computational approaches in their learning, research and application activities. The two barriers are: 1) difficulties in finding, obtaining, and using multi-source ES data; and 2) lack of analytic functions and computing resources (e.g., analysis software, computing models, and high performance computing systems) to analyze the data. Taking advantages of recent advances in cyberinfrastructure, Web service, and geospatial interoperability technologies, GeoBrain, a project funded by NASA, has developed a prototype computational cyber-laboratory to effectively remove the two barriers. The cyber-laboratory makes ES data and computational resources at large organizations in distributed locations available to and easily usable by the Earth science community through 1) enabling seamless discovery, access and retrieval of distributed data, 2) federating and enhancing data discovery with a catalogue federation service and a semantically-augmented catalogue service, 3) customizing data access and retrieval at user request with interoperable, personalized, and on-demand data access and services, 4) automating or semi-automating multi-source geospatial data integration, 5) developing a large number of analytic functions as value-added, interoperable, and dynamically chainable geospatial Web services and deploying them in high-performance computing facilities, 6) enabling the online geospatial process modeling and execution, and 7) building a user-friendly extensible web portal for users to access the cyber-laboratory resources. Users can interactively discover the needed data and perform on-demand data analysis and modeling through the web portal. The GeoBrain cyber-laboratory provides solutions to meet common needs of ES research and education, such as, distributed data access and analysis services, easy access to and use of ES data, and enhanced geoprocessing and geospatial modeling capability. It greatly facilitates ES research, education, and applications. The development of the cyber-laboratory provides insights, lessons-learned, and technology readiness to build more capable computing infrastructure for ES studies, which can meet wide-range needs of current and future generations of scientists, researchers, educators, and students for their formal or informal educational training, research projects, career development, and lifelong learning.

Tavaxy: integrating Taverna and Galaxy workflows with cloud computing support.

PubMed

Abouelhoda, Mohamed; Issa, Shadi Alaa; Ghanem, Moustafa

2012-05-04

Over the past decade the workflow system paradigm has evolved as an efficient and user-friendly approach for developing complex bioinformatics applications. Two popular workflow systems that have gained acceptance by the bioinformatics community are Taverna and Galaxy. Each system has a large user-base and supports an ever-growing repository of application workflows. However, workflows developed for one system cannot be imported and executed easily on the other. The lack of interoperability is due to differences in the models of computation, workflow languages, and architectures of both systems. This lack of interoperability limits sharing of workflows between the user communities and leads to duplication of development efforts. In this paper, we present Tavaxy, a stand-alone system for creating and executing workflows based on using an extensible set of re-usable workflow patterns. Tavaxy offers a set of new features that simplify and enhance the development of sequence analysis applications: It allows the integration of existing Taverna and Galaxy workflows in a single environment, and supports the use of cloud computing capabilities. The integration of existing Taverna and Galaxy workflows is supported seamlessly at both run-time and design-time levels, based on the concepts of hierarchical workflows and workflow patterns. The use of cloud computing in Tavaxy is flexible, where the users can either instantiate the whole system on the cloud, or delegate the execution of certain sub-workflows to the cloud infrastructure. Tavaxy reduces the workflow development cycle by introducing the use of workflow patterns to simplify workflow creation. It enables the re-use and integration of existing (sub-) workflows from Taverna and Galaxy, and allows the creation of hybrid workflows. Its additional features exploit recent advances in high performance cloud computing to cope with the increasing data size and complexity of analysis.The system can be accessed either through a cloud-enabled web-interface or downloaded and installed to run within the user's local environment. All resources related to Tavaxy are available at http://www.tavaxy.org.

CASAS: A tool for composing automatically and semantically astrophysical services

NASA Astrophysics Data System (ADS)

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

2017-07-01

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

Happier Together: Integrating a Wellness Application into a Social Network Site

NASA Astrophysics Data System (ADS)

Munson, Sean A.; Lauterbach, Debra; Newman, Mark W.; Resnick, Paul

What are the benefits and drawbacks of integrating health and wellness interventions into existing online social network websites? In this paper, we report on a case study of deploying the Three Good Things positive psychology exercise as a Facebook application. Our experience shows that embedding a wellness intervention in an existing social website is a viable option. In particular, we find adherence rates on par with or better than many other Internet-based wellness interventions. We also gained insights about users' privacy and audience concerns that inform the design of social network-based wellness applications. Participants did not want all of their entries to be shared with all their Facebook friends, both because they did not want others to know some things and because they did not want to clutter others' newsfeeds. Users found it compelling, however, to interact with their friends around some "Good Things" they had posted.

TRENT2D WG: a smart web infrastructure for debris-flow modelling and hazard assessment

NASA Astrophysics Data System (ADS)

Zorzi, Nadia; Rosatti, Giorgio; Zugliani, Daniel; Rizzi, Alessandro; Piffer, Stefano

2016-04-01

Mountain regions are naturally exposed to geomorphic flows, which involve large amounts of sediments and induce significant morphological modifications. The physical complexity of this class of phenomena represents a challenging issue for modelling, leading to elaborate theoretical frameworks and sophisticated numerical techniques. In general, geomorphic-flows models proved to be valid tools in hazard assessment and management. However, model complexity seems to represent one of the main obstacles to the diffusion of advanced modelling tools between practitioners and stakeholders, although the UE Flood Directive (2007/60/EC) requires risk management and assessment to be based on "best practices and best available technologies". Furthermore, several cutting-edge models are not particularly user-friendly and multiple stand-alone software are needed to pre- and post-process modelling data. For all these reasons, users often resort to quicker and rougher approaches, leading possibly to unreliable results. Therefore, some effort seems to be necessary to overcome these drawbacks, with the purpose of supporting and encouraging a widespread diffusion of the most reliable, although sophisticated, modelling tools. With this aim, this work presents TRENT2D WG, a new smart modelling solution for the state-of-the-art model TRENT2D (Armanini et al., 2009, Rosatti and Begnudelli, 2013), which simulates debris flows and hyperconcentrated flows adopting a two-phase description over a mobile bed. TRENT2D WG is a web infrastructure joining advantages offered by the software-delivering model SaaS (Software as a Service) and by WebGIS technology and hosting a complete and user-friendly working environment for modelling. In order to develop TRENT2D WG, the model TRENT2D was converted into a service and exposed on a cloud server, transferring computational burdens from the user hardware to a high-performing server and reducing computational time. Then, the system was equipped with an interface supporting Web-based GIS functionalities, making the model accessible through the World Wide Web. Furthermore, WebGIS technology allows georeferenced model input data and simulation results to be produced, managed, displayed and processed in a unique and intuitive working environment. Thanks to its large flexibility, TRENT2D WG was equipped also with a BUWAL-type procedure (Heinimann et al., 1998) to assess and map debris-flow hazard. In this way, model results can be used straightforwardly as input data of the hazard-mapping procedure, avoiding work fragmentation and taking wide advantage of the functionalities offered by WebGIS technology. TRENT2D WG is intended to become a reliable tool for researchers, practitioners and stakeholders, supporting modelling and hazard mapping effectively and encouraging connections between the research field and professional needs at a working scale.

Research on the Application of Persona in Book Recommendation System

NASA Astrophysics Data System (ADS)

Gao, Baozhong; Du, Shouyan; Li, Xinzhi; Liu, Fangai

2017-10-01

Currently, there still exists a host of problems in the book recommendation system, such as low accuracy, weak correlation and poor pertinence. Aiming to unravel these problems, this paper based on the theory of big data and data mining technology, through analyzing internet user behavior and the “5C” model of personal credit evaluation, combined with joint impact weight calculation method, which involves user grade, borrowing credit, book friend recommendation degree, book friend recommended adoption degree, borrowing frequency, borrowing number, and borrowing time interval. User activity and credit are also taken into account in the process of establishing user tagging system so as to build classified book recommendation service. This method is of universal meaning to the book recommendation service of smart campus with user as the core under big data environment.

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.

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

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

NASA Astrophysics Data System (ADS)

Demir, I.

2015-12-01

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

Ontology Design of Influential People Identification Using Centrality

NASA Astrophysics Data System (ADS)

Maulana Awangga, Rolly; Yusril, Muhammad; Setyawan, Helmi

2018-04-01

Identifying influential people as a node in a graph theory commonly calculated by social network analysis. The social network data has the user as node and edge as relation forming a friend relation graph. This research is conducting different meaning of every nodes relation in the social network. Ontology was perfect match science to describe the social network data as conceptual and domain. Ontology gives essential relationship in a social network more than a current graph. Ontology proposed as a standard for knowledge representation for the semantic web by World Wide Web Consortium. The formal data representation use Resource Description Framework (RDF) and Web Ontology Language (OWL) which is strategic for Open Knowledge-Based website data. Ontology used in the semantic description for a relationship in the social network, it is open to developing semantic based relationship ontology by adding and modifying various and different relationship to have influential people as a conclusion. This research proposes a model using OWL and RDF for influential people identification in the social network. The study use degree centrality, between ness centrality, and closeness centrality measurement for data validation. As a conclusion, influential people identification in Facebook can use proposed Ontology model in the Group, Photos, Photo Tag, Friends, Events and Works data.

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

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

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

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

Web 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.

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/.

Orthoscape: a cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles.

PubMed

Mustafin, Zakhar Sergeevich; Lashin, Sergey Alexandrovich; Matushkin, Yury Georgievich; Gunbin, Konstantin Vladimirovich; Afonnikov, Dmitry Arkadievich

2017-01-27

There are many available software tools for visualization and analysis of biological networks. Among them, Cytoscape ( http://cytoscape.org/ ) is one of the most comprehensive packages, with many plugins and applications which extends its functionality by providing analysis of protein-protein interaction, gene regulatory and gene co-expression networks, metabolic, signaling, neural as well as ecological-type networks including food webs, communities networks etc. Nevertheless, only three plugins tagged 'network evolution' found in Cytoscape official app store and in literature. We have developed a new Cytoscape 3.0 application Orthoscape aimed to facilitate evolutionary analysis of gene networks and visualize the results. Orthoscape aids in analysis of evolutionary information available for gene sets and networks by highlighting: (1) the orthology relationships between genes; (2) the evolutionary origin of gene network components; (3) the evolutionary pressure mode (diversifying or stabilizing, negative or positive selection) of orthologous groups in general and/or branch-oriented mode. The distinctive feature of Orthoscape is the ability to control all data analysis steps via user-friendly interface. Orthoscape allows its users to analyze gene networks or separated gene sets in the context of evolution. At each step of data analysis, Orthoscape also provides for convenient visualization and data manipulation.

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.

Creating and testing a deaf-friendly, stop-smoking web site intervention.

PubMed

Jones, Elaine G; Goldsmith, Melissa; Effken, Judith; Button, Kevin; Crago, Michael

2010-01-01

Deaf adults' access to smoking cessation programs is limited due to cultural, linguistic, and geographic barriers. Web-based stop-smoking interventions have demonstrated cessation rates comparable to other interventions. The Internet is widely used by Deaf adults, but difficulties with online English text remain. We found no published accounts of Internet interventions promoting smoking cessation among Deaf individuals. The purpose of our project was to create and pilot test a prototype interactive Web site that provides users with information in American Sign Language related to smoking cessation. We utilized web cams to create real-time "video chat rooms" for virtual support groups and had an "ask the experts" feature. Deaf community members participated in all phases of development and testing, and a Deaf former smoker served as the moderator for the site. Evaluations were positive, with emphasis on interactive and visual aspects of the site.

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

PubMed

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

2016-07-08

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

Panoptes: web-based exploration of large scale genome variation data.

PubMed

Vauterin, Paul; Jeffery, Ben; Miles, Alistair; Amato, Roberto; Hart, Lee; Wright, Ian; Kwiatkowski, Dominic

2017-10-15

The size and complexity of modern large-scale genome variation studies demand novel approaches for exploring and sharing the data. In order to unlock the potential of these data for a broad audience of scientists with various areas of expertise, a unified exploration framework is required that is accessible, coherent and user-friendly. Panoptes is an open-source software framework for collaborative visual exploration of large-scale genome variation data and associated metadata in a web browser. It relies on technology choices that allow it to operate in near real-time on very large datasets. It can be used to browse rich, hybrid content in a coherent way, and offers interactive visual analytics approaches to assist the exploration. We illustrate its application using genome variation data of Anopheles gambiae, Plasmodium falciparum and Plasmodium vivax. Freely available at https://github.com/cggh/panoptes, under the GNU Affero General Public License. paul.vauterin@gmail.com. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Biomathematical Description of Synthetic Peptide Libraries

PubMed Central

Trepel, Martin

2015-01-01

Libraries of randomised peptides displayed on phages or viral particles are essential tools in a wide spectrum of applications. However, there is only limited understanding of a library's fundamental dynamics and the influences of encoding schemes and sizes on their quality. Numeric properties of libraries, such as the expected number of different peptides and the library's coverage, have long been in use as measures of a library's quality. Here, we present a graphical framework of these measures together with a library's relative efficiency to help to describe libraries in enough detail for researchers to plan new experiments in a more informed manner. In particular, these values allow us to answer-in a probabilistic fashion-the question of whether a specific library does indeed contain one of the "best" possible peptides. The framework is implemented in a web-interface based on two packages, discreteRV and peptider, to the statistical software environment R. We further provide a user-friendly web-interface called PeLiCa (Peptide Library Calculator, http://www.pelica.org), allowing scientists to plan and analyse their peptide libraries. PMID:26042419

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.

A web based relational database management system for filariasis control

PubMed Central

Murty, Upadhyayula Suryanarayana; Kumar, Duvvuri Venkata Rama Satya; Sriram, Kumaraswamy; Rao, Kadiri Madhusudhan; Bhattacharyulu, Chakravarthula Hayageeva Narasimha Venakata; Praveen, Bhoopathi; Krishna, Amirapu Radha

2005-01-01

The present study describes a RDBMS (relational database management system) for the effective management of Filariasis, a vector borne disease. Filariasis infects 120 million people from 83 countries. The possible re-emergence of the disease and the complexity of existing control programs warrant the development of new strategies. A database containing comprehensive data associated with filariasis finds utility in disease control. We have developed a database containing information on the socio-economic status of patients, mosquito collection procedures, mosquito dissection data, filariasis survey report and mass blood data. The database can be searched using a user friendly web interface. Availability http://www.webfil.org (login and password can be obtained from the authors) PMID:17597846

User-Friendly Interface Developed for a Web-Based Service for SpaceCAL Emulations

NASA Technical Reports Server (NTRS)

Liszka, Kathy J.; Holtz, Allen P.

2004-01-01

A team at the NASA Glenn Research Center is developing a Space Communications Architecture Laboratory (SpaceCAL) for protocol development activities for coordinated satellite missions. SpaceCAL will provide a multiuser, distributed system to emulate space-based Internet architectures, backbone networks, formation clusters, and constellations. As part of a new effort in 2003, building blocks are being defined for an open distributed system to make the satellite emulation test bed accessible through an Internet connection. The first step in creating a Web-based service to control the emulation remotely is providing a user-friendly interface for encoding the data into a well-formed and complete Extensible Markup Language (XML) document. XML provides coding that allows data to be transferred between dissimilar systems. Scenario specifications include control parameters, network routes, interface bandwidths, delay, and bit error rate. Specifications for all satellite, instruments, and ground stations in a given scenario are also included in the XML document. For the SpaceCAL emulation, the XML document can be created using XForms, a Webbased forms language for data collection. Contrary to older forms technology, the interactive user interface makes the science prevalent, not the data representation. Required versus optional input fields, default values, automatic calculations, data validation, and reuse will help researchers quickly and accurately define missions. XForms can apply any XML schema defined for the test mission to validate data before forwarding it to the emulation facility. New instrument definitions, facilities, and mission types can be added to the existing schema. The first prototype user interface incorporates components for interactive input and form processing. Internet address, data rate, and the location of the facility are implemented with basic form controls with default values provided for convenience and efficiency using basic XForms operations. Because different emulation scenarios will vary widely in their component structure, more complex operations are used to add and delete facilities.

Relatives and friends queries on a psychologists "question and answer" forum online - authorship and contents.

PubMed

Stjernswärd, Sigrid

2015-03-01

Families living with mental illness can experience added burden and eventually own ill health. National and international guidelines support the development of web based solutions to cost-effectively address health care needs. Mapping patterns of internet use may help tailor interventions to effectively address users' needs. The study's aim was to explore the contents of relatives' and friends' queries on a psychologists' website with professional feedback. All visible questions [n = 59] classified under the website's "helping a relative/friend" category between 20 090 615-20 130 927 were printed out and analyzed using content analysis. The analysis resulted in four categories and subcategories illuminating families'/friends' areas of concern: support to help; concerns with health care; young children's welfare; and repercussions on own health. "Question & Answer" [Q&A] forums can shed light onto health seekers' online behavior and may be a way of addressing families' needs of support and information. Further studies are needed to assess the replies' therapeutic value for their recipients.

Efficacy of Web-Based Instruction to Provide Training on Federal Motor Carrier Safety Regulations

DOT National Transportation Integrated Search

2011-05-01

This report presents an evaluation of the current state-of-the-art Web-based instruction (WBI), reviews the current computer platforms of potential users of WBI, reviews the current status of WBI applications for Federal Motor Carrier Safety Administ...

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

The system is developed to collect, process, store and present the information provided by the radio frequency identification (RFID) devices. The system contains three parts, the application software, the database and the web page. The application software manages multiple RFID devices, such as readers and portals, simultaneously. It communicates with the devices through application programming interface (API) provided by the device vendor. The application software converts data collected by the RFID readers and portals to readable information. It is capable of encrypting data using 256 bits advanced encryption standard (AES). The application software has a graphical user interface (GUI). Themore » GUI mimics the configurations of the nucler material storage sites or transport vehicles. The GUI gives the user and system administrator an intuitive way to read the information and/or configure the devices. The application software is capable of sending the information to a remote, dedicated and secured web and database server. Two captured screen samples, one for storage and transport, are attached. The database is constructed to handle a large number of RFID tag readers and portals. A SQL server is employed for this purpose. An XML script is used to update the database once the information is sent from the application software. The design of the web page imitates the design of the application software. The web page retrieves data from the database and presents it in different panels. The user needs a user name combined with a password to access the web page. The web page is capable of sending e-mail and text messages based on preset criteria, such as when alarm thresholds are excceeded. A captured screen sample is attached. The application software is designed to be installed on a local computer. The local computer is directly connected to the RFID devices and can be controlled locally or remotely. There are multiple local computers managing different sites or transport vehicles. The control from remote sites and information transmitted to a central database server is through secured internet. The information stored in the central databaser server is shown on the web page. The users can view the web page on the internet. A dedicated and secured web and database server (https) is used to provide information security.« less

A web-oriented software for the optimization of pooled experiments in NGS for detection of rare mutations.

PubMed

Evangelista, Daniela; Zuccaro, Antonio; Lančinskas, Algirdas; Žilinskas, Julius; Guarracino, Mario R

2016-02-17

The cost per patient of next generation sequencing for detection of rare mutations may be significantly reduced using pooled experiments. Recently, some techniques have been proposed for the planning of pooled experiments and for the optimal allocation of patients into pools. However, the lack of a user friendly resource for planning the design of pooled experiments forces the scientists to do frequent, complex and long computations. OPENDoRM is a powerful collection of novel mathematical algorithms usable via an intuitive graphical user interface. It enables researchers to speed up the planning of their routine experiments, as well as, to support scientists without specific bioinformatics expertises. Users can automatically carry out analysis in terms of costs associated with the optimal allocation of patients in pools. They are also able to choose between three distinct pooling mathematical methods, each of which also suggests the optimal configuration for the submitted experiment. Importantly, in order to keep track of the performed experiments, users can save and export the results of their experiments in standard tabular and charts contents. OPENDoRM is a freely available web-oriented application for the planning of pooled NGS experiments, available at: http://www-labgtp.na.icar.cnr.it/OPENDoRM. Its easy and intuitive graphical user interface enables researchers to plan theirs experiments using novel algorithms, and to interactively visualize the results.

CONSUME: users guide.

Treesearch

R.D. Ottmar; M.F. Burns; J.N. Hall; A.D. Hanson

1993-01-01

CONSUME is a user-friendly computer program designed for resource managers with some working knowledge of IBM-PC applications. The software predicts the amount of fuel consumption on logged units based on weather data, the amount and fuel moisture of fuels, and a number of other factors. Using these predictions, the resource manager can accurately determine when and...

Development of a functional, internet-accessible department of surgery outcomes database.

PubMed

Newcomb, William L; Lincourt, Amy E; Gersin, Keith; Kercher, Kent; Iannitti, David; Kuwada, Tim; Lyons, Cynthia; Sing, Ronald F; Hadzikadic, Mirsad; Heniford, B Todd; Rucho, Susan

2008-06-01

The need for surgical outcomes data is increasing due to pressure from insurance companies, patients, and the need for surgeons to keep their own "report card". Current data management systems are limited by inability to stratify outcomes based on patients, surgeons, and differences in surgical technique. Surgeons along with research and informatics personnel from an academic, hospital-based Department of Surgery and a state university's Department of Information Technology formed a partnership to develop a dynamic, internet-based, clinical data warehouse. A five-component model was used: data dictionary development, web application creation, participating center education and management, statistics applications, and data interpretation. A data dictionary was developed from a list of data elements to address needs of research, quality assurance, industry, and centers of excellence. A user-friendly web interface was developed with menu-driven check boxes, multiple electronic data entry points, direct downloads from hospital billing information, and web-based patient portals. Data were collected on a Health Insurance Portability and Accountability Act-compliant server with a secure firewall. Protected health information was de-identified. Data management strategies included automated auditing, on-site training, a trouble-shooting hotline, and Institutional Review Board oversight. Real-time, daily, monthly, and quarterly data reports were generated. Fifty-eight publications and 109 abstracts have been generated from the database during its development and implementation. Seven national academic departments now use the database to track patient outcomes. The development of a robust surgical outcomes database requires a combination of clinical, informatics, and research expertise. Benefits of surgeon involvement in outcomes research include: tracking individual performance, patient safety, surgical research, legal defense, and the ability to provide accurate information to patient and payers.

Current uses of Web 2.0 applications in transportation : case studies of select state departments of transportation

DOT National Transportation Integrated Search

2010-03-01

Web 2.0 is an umbrella term for websites or online applications that are user-driven and emphasize collaboration and user interactivity. The trend away from static web pages to a more user-driven Internet model has also occurred in the public s...

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 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

Usability evaluation of the SMART application for youth with mTBI.

PubMed

Dexheimer, Judith W; Kurowski, Brad G; Anders, Shilo H; McClanahan, Nicole; Wade, Shari L; Babcock, Lynn

2017-01-01

There is a dearth of evidence-based treatments available to address the significant morbidity associated with mild traumatic brain injury (mTBI). To address this gap, we designed a novel user-friendly, web-based application. We describe the preliminary evaluation of feasibility and usability of the application to promote recovery following mTBI in youth, the Self-Monitoring Activity-Restriction and Relaxation Treatment (SMART). SMART incorporates real-time recommendations for individualized symptom management and activity restriction along with training in cognitive-behavioral coping strategies. We conducted a usability evaluation to assess and modify the SMART system prior to further study and deployment. Children ages 11-18 years presenting to the emergency department were recruited after symptoms resolved. Usability was assessed using a 60-min think-aloud protocol of teens and parents describing their interaction with the application. Upon completion of the tasks, each participant also completed the system usability scale (SUS). We performed tests with 4 parent/child dyads. The average age of the children was 13 years (standard deviation=1.8). The parents were an average of 41.5 years old (standard deviation=6.2). Research revealed that the participants were enthusiastic about the interactive portions of the tool particularly the video based sessions. Parents were concerned about the speed at which their child might move through the program and the children thought that the system required large amounts of reading. Based on user feedback, researchers modified SMART to include an audio file in every module and improved the system's aesthetic properties. The mean SUS score was 85, with high SUS scores (>68) indicating satisfactory usability. High initial usability and favorable user feedback provide a foundation for further iterative development and testing of the SMART application as a tool for managing recovery from concussion. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Data Access System for Hydrology

NASA Astrophysics Data System (ADS)

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

2007-12-01

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

Launch of Village Blue Web Application Shares Water Monitoring Data with Baltimore Community

EPA Pesticide Factsheets

EPA and the U.S. Geological Survey (USGS) have launched their mobile-friendly web application for Village Blue, a project that provides real-time water quality monitoring data to the Baltimore, Maryland community.

Automatic public access to documents and maps stored on and internal secure system.

NASA Astrophysics Data System (ADS)

Trench, James; Carter, Mary

2013-04-01

The Geological Survey of Ireland operates a Document Management System for providing documents and maps stored internally in high resolution and in a high level secure environment, to an external service where the documents are automatically presented in a lower resolution to members of the public. Security is devised through roles and Individual Users where role level and folder level can be set. The application is an electronic document/data management (EDM) system which has a Geographical Information System (GIS) component integrated to allow users to query an interactive map of Ireland for data that relates to a particular area of interest. The data stored in the database consists of Bedrock Field Sheets, Bedrock Notebooks, Bedrock Maps, Geophysical Surveys, Geotechnical Maps & Reports, Groundwater, GSI Publications, Marine, Mine Records, Mineral Localities, Open File, Quaternary and Unpublished Reports. The Konfig application Tool is both an internal and public facing application. It acts as a tool for high resolution data entry which are stored in a high resolution vault. The public facing application is a mirror of the internal application and differs only in that the application furnishes high resolution data into low resolution format which is stored in a low resolution vault thus, making the data web friendly to the end user for download.

Surfing for Data: A Gathering Trend in Data Storage Is the Use of Web-Based Applications that Make It Easy for Authorized Users to Access Hosted Server Content with Just a Computing Device and Browser

ERIC Educational Resources Information Center

Technology & Learning, 2005

2005-01-01

In recent years, the widespread availability of networks and the flexibility of Web browsers have shifted the industry from a client-server model to a Web-based one. In the client-server model of computing, clients run applications locally, with the servers managing storage, printing functions, and network traffic. Because every client is…

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.

Application of WebGIS for traffic risk assessment

NASA Astrophysics Data System (ADS)

Voumard, Jérémie; Aye, Zar Chi; Derron, Marc-Henri; Jaboyedoff, Michel

2015-04-01

Roads and railways are threatened throughout the year by several natural hazards around the world, leading to the closing of transportation corridors, loss of access, deviation travels and potentially infrastructures damages and loss of human lives and also financial, social and economic consequences. Protection measures used to reduce the exposure to natural hazards are usually expensive and cannot be deployed on an entire transportation network. It is thus necessary to choose priority areas where protection measures need to be built. The aim of this study is to propose a friendly tool to evaluate and to understand issues and consequences of section closing and affected parts of a transportation network at small region scale. The proposed tool, currently in its design and building phase, will provide ways to simulate different closure scenarios and to analyze their consequences on transportation network; like deviating traffic on others roads and railways sections, additional time and distance travel or accessibility for emergency services like police, firefighters and ambulances. The tool is based on OpenGeo architecture, which is composed of open-source components. It integrates PostGIS for database, GeoServer and GeoWebCache for application servers and finally GeoExt and OpenLayers for user interface. Users will be able to attribute quantitative (like roads and railway type and closure consequences) and qualitative (like section unavailability duration, season, etc.) data to the different roads and railways sections based on their user rights. They will also be able to evaluate different track closures consequences in terms of different scenarios. Once finalized, the goal of this project including natural hazards, traffic and geomatic thematic is to propose a decision support tool for public authorities firstly and for specialists secondly so that they can evaluate easily and accurately as much as possible to highlight the weakpoints of the transportation network in the case track closures due to natural hazards.

Relationship-Relevant and Family-Friendly eHealth: Innovations in Interactive Health Communication Systems

PubMed Central

ROBERTS, LINDA J.; JAPUNTICH, SANDRA

2012-01-01

As the reach of the Internet grows, eHealth is fast becoming a major adjunct to traditional delivery of health information and support worldwide. Existing Interactive health communication systems, however, typically target individual users, focus on individual rather than on relational health, and neglect the relational and familial context of individual health issues. Reviewing developments primarily in the United States, this article applies a “marriage and family lens” to examine web-based technologies for health and well-being and suggests innovations to make eHealth both relationship relevant and family friendly. Although recent innovations offer great promise for supporting the relational “fabric” of family life, specific cautions and the need for research on effectiveness are underscored. PMID:23144519

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

PubMed

Thriskos, P; Zintzaras, E; Germenis, A

2007-03-01

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

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

ERIC Educational Resources Information Center

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

1998-01-01

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

Clinicians’ Expectations of Web 2.0 as a Mechanism for Knowledge Transfer of Stroke Best Practices

PubMed Central

David, Isabelle; Rochette, Annie

2012-01-01

Background Health professionals are increasingly encouraged to adopt an evidence-based practice to ensure greater efficiency of their services. To promote this practice, several strategies exist: distribution of educational materials, local consensus processes, educational outreach visits, local opinion leaders, and reminders. Despite these strategies, gaps continue to be observed between practice and scientific evidence. Therefore, it is important to implement innovative knowledge transfer strategies that will change health professionals’ practices. Through its interactive capacities, Web 2.0 applications are worth exploring. As an example, virtual communities of practice have already begun to influence professional practice. Objective This study was initially developed to help design a Web 2.0 platform for health professionals working with stroke patients. The aim was to gain a better understanding of professionals’ perceptions of Web 2.0 before the development of the platform. Methods A qualitative study following a phenomenological approach was chosen. We conducted individual semi-structured interviews with clinicians and managers. Interview transcripts were subjected to a content analysis. Results Twenty-four female clinicians and managers in Quebec, Canada, aged 28-66 participated. Most participants identified knowledge transfer as the most useful outcome of a Web 2.0 platform. Respondents also expressed their need for a user-friendly platform. Accessibility to a computer and the Internet, features of the Web 2.0 platform, user support, technology skills, and previous technological experience were found to influence perceived ease of use and usefulness. Our results show that the perceived lack of time of health professionals has an influence on perceived behavioral intention to use it despite favorable perception of the usefulness of the Web 2.0 platform. Conclusions In conclusion, female health professionals in Quebec believe that Web 2.0 may be a useful mechanism for knowledge transfer. However, lack of time and lack of technological skills may limit their use of a future Web 2.0 platform. Further studies are required with other populations and in other regions to confirm these findings. PMID:23195753

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 correct API interface from within C++ and/or C/Fortran). This poster presentation will provide descriptions of the following selected web services and their origin as scientific application codes: 3D community velocity models for Southern California, geocoordinate conversions (latitude/longitude to UTM), execution of GMT graphical scripts, data format conversions (Gocad to Matlab format), and implementation of Seismic Hazard Analysis application programs that calculate hazard curve and hazard map data sets.

Crowdsourcing quality control for Dark Energy Survey images

DOE PAGES

Melchior, P.

2016-07-01

We have developed a crowdsourcing web application for image quality control employed by the Dark Energy Survey. Dubbed the "DES exposure checker", it renders science-grade images directly to a web browser and allows users to mark problematic features from a set of predefined classes. Users can also generate custom labels and thus help identify previously unknown problem classes. User reports are fed back to hardware and software experts to help mitigate and eliminate recognized issues. We report on the implementation of the application and our experience with its over 100 users, the majority of which are professional or prospective astronomersmore » but not data management experts. We discuss aspects of user training and engagement, and demonstrate how problem reports have been pivotal to rapidly correct artifacts which would likely have been too subtle or infrequent to be recognized otherwise. We conclude with a number of important lessons learned, suggest possible improvements, and recommend this collective exploratory approach for future astronomical surveys or other extensive data sets with a sufficiently large user base. We also release open-source code of the web application and host an online demo versionat http://des-exp-checker.pmelchior.net« less

Crowdsourcing quality control for Dark Energy Survey images

NASA Astrophysics Data System (ADS)

Melchior, P.; Sheldon, E.; Drlica-Wagner, A.; Rykoff, E. S.; Abbott, T. M. C.; Abdalla, F. B.; Allam, S.; Benoit-Lévy, A.; Brooks, D.; Buckley-Geer, E.; Carnero Rosell, A.; Carrasco Kind, M.; Carretero, J.; Crocce, M.; D'Andrea, C. B.; da Costa, L. N.; Desai, S.; Doel, P.; Evrard, A. E.; Finley, D. A.; Flaugher, B.; Frieman, J.; Gaztanaga, E.; Gerdes, D. W.; Gruen, D.; Gruendl, R. A.; Honscheid, K.; James, D. J.; Jarvis, M.; Kuehn, K.; Li, T. S.; Maia, M. A. G.; March, M.; Marshall, J. L.; Nord, B.; Ogando, R.; Plazas, A. A.; Romer, A. K.; Sanchez, E.; Scarpine, V.; Sevilla-Noarbe, I.; Smith, R. C.; Soares-Santos, M.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Vikram, V.; Walker, A. R.; Wester, W.; Zhang, Y.

2016-07-01

We have developed a crowdsourcing web application for image quality control employed by the Dark Energy Survey. Dubbed the "DES exposure checker", it renders science-grade images directly to a web browser and allows users to mark problematic features from a set of predefined classes. Users can also generate custom labels and thus help identify previously unknown problem classes. User reports are fed back to hardware and software experts to help mitigate and eliminate recognized issues. We report on the implementation of the application and our experience with its over 100 users, the majority of which are professional or prospective astronomers but not data management experts. We discuss aspects of user training and engagement, and demonstrate how problem reports have been pivotal to rapidly correct artifacts which would likely have been too subtle or infrequent to be recognized otherwise. We conclude with a number of important lessons learned, suggest possible improvements, and recommend this collective exploratory approach for future astronomical surveys or other extensive data sets with a sufficiently large user base. We also release open-source code of the web application and host an online demo version at http://des-exp-checker.pmelchior.net.

Crowdsourcing quality control for Dark Energy Survey images

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

Melchior, P.

We have developed a crowdsourcing web application for image quality control employed by the Dark Energy Survey. Dubbed the "DES exposure checker", it renders science-grade images directly to a web browser and allows users to mark problematic features from a set of predefined classes. Users can also generate custom labels and thus help identify previously unknown problem classes. User reports are fed back to hardware and software experts to help mitigate and eliminate recognized issues. We report on the implementation of the application and our experience with its over 100 users, the majority of which are professional or prospective astronomersmore » but not data management experts. We discuss aspects of user training and engagement, and demonstrate how problem reports have been pivotal to rapidly correct artifacts which would likely have been too subtle or infrequent to be recognized otherwise. We conclude with a number of important lessons learned, suggest possible improvements, and recommend this collective exploratory approach for future astronomical surveys or other extensive data sets with a sufficiently large user base. We also release open-source code of the web application and host an online demo versionat http://des-exp-checker.pmelchior.net« less

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

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

King, Zachary A.; Drager, Andreas; Ebrahim, Ali

Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way. Second, users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzymes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g. RNA-Seq, proteomics, ChIP)—in conjunction with metabolite- and reaction-oriented data types (e.g. metabolomics, fluxomics).more » Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools.« less

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

PubMed Central

King, Zachary A.; Dräger, Andreas; Ebrahim, Ali; Sonnenschein, Nikolaus; Lewis, Nathan E.; Palsson, Bernhard O.

2015-01-01

Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way. Second, users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzymes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g. RNA-Seq, proteomics, ChIP)—in conjunction with metabolite- and reaction-oriented data types (e.g. metabolomics, fluxomics). Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools. PMID:26313928

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

DOE PAGES

King, Zachary A.; Drager, Andreas; Ebrahim, Ali; ...

2015-08-27

Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way. Second, users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzymes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g. RNA-Seq, proteomics, ChIP)—in conjunction with metabolite- and reaction-oriented data types (e.g. metabolomics, fluxomics).more » Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools.« less

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 diabetes duration (P = .03). Conclusion Innovations in health care will diffuse more rapidly when technology is employed that is simple to use and has applicable components for interactivity. This would foresee the patients’ need for continuous and personalized feedback, in particular for patients with a greater need for care. From this study several factors appear to influence increased use of eHealth technologies: (1) avoiding selective enrollment, (2) making use of participatory design methods, and (3) developing push factors for persistence. Further research should focus on the causal relationship between using the system’s features and actual usage, as such a view would provide important evidence on how specific technology features can engage and captivate users. PMID:21959968

Use of the World Wide Web for multisite data collection.

PubMed

Subramanian, A K; McAfee, A T; Getzinger, J P

1997-08-01

As access to the Internet becomes increasingly available, research applications in medicine will increase. This paper describes the use of the Internet, and, more specifically, the World Wide Web (WWW), as a channel of communication between EDs throughout the world and investigators who are interested in facilitating the collection of data from multiple sites. Data entered into user-friendly electronic surveys can be transmitted over the Internet to a database located at the site of the study, rendering geographic separation less of a barrier to the conduction of multisite studies. The electronic format of the data can enable real-time statistical processing while data are stored using existing database technologies. In theory, automated processing of variables within such a database enables early identification of data trends. Methods of ensuring validity, security, and compliance are discussed.

The Climate-G Portal: a Grid Enabled Scientifc Gateway for Climate Change

NASA Astrophysics Data System (ADS)

Fiore, Sandro; Negro, Alessandro; Aloisio, Giovanni

2010-05-01

Grid portals are web gateways aiming at concealing the underlying infrastructure through a pervasive, transparent, user-friendly, ubiquitous and seamless access to heterogeneous and geographical spread resources (i.e. storage, computational facilities, services, sensors, network, databases). Definitively they provide an enhanced problem-solving environment able to deal with modern, large scale scientific and engineering problems. Scientific gateways are able to introduce a revolution in the way scientists and researchers organize and carry out their activities. Access to distributed resources, complex workflow capabilities, and community-oriented functionalities are just some of the features that can be provided by such a web-based environment. In the context of the EGEE NA4 Earth Science Cluster, Climate-G is a distributed testbed focusing on climate change research topics. The Euro-Mediterranean Center for Climate Change (CMCC) is actively participating in the testbed providing the scientific gateway (Climate-G Portal) to access to the entire infrastructure. The Climate-G Portal has to face important and critical challenges as well as has to satisfy and address key requirements. In the following, the most relevant ones are presented and discussed. Transparency: the portal has to provide a transparent access to the underlying infrastructure preventing users from dealing with low level details and the complexity of a distributed grid environment. Security: users must be authenticated and authorized on the portal to access and exploit portal functionalities. A wide set of roles is needed to clearly assign the proper one to each user. The access to the computational grid must be completely secured, since the target infrastructure to run jobs is a production grid environment. A security infrastructure (based on X509v3 digital certificates) is strongly needed. Pervasivity and ubiquity: the access to the system must be pervasive and ubiquitous. This is easily true due to the nature of the needed web approach. Usability and simplicity: the portal has to provide simple, high level and user friendly interfaces to ease the access and exploitation of the entire system. Coexistence of general purpose and domain oriented services: along with general purpose services (file transfer, job submission, etc.), the portal has to provide domain based services and functionalities. Subsetting of data, visualization of 2D maps around a virtual globe, delivery of maps through OGC compliant interfaces (i.e. Web Map Service - WMS) are just some examples. Since april 2009, about 70 users (85% coming from the climate change community) got access to the portal. A key challenge of this work is the idea to provide users with an integrated working environment, that is a place where scientists can find huge amount of data, complete metadata support, a wide set of data access services, data visualization and analysis tools, easy access to the underlying grid infrastructure and advanced monitoring interfaces.

Helpers Program: A Pilot Test of Brief Tobacco Intervention Training in Three Corporations

PubMed Central

Muramoto, Myra L.; Wassum, Ken; Connolly, Tim; Matthews, Eva; Floden, Lysbeth

2014-01-01

Background Quitlines and worksite-sponsored cessation programs are effective and highly accessible, but limited by low utilization. Efforts to encourage use of cessation aids have focused almost exclusively on the smoker, overlooking the potential for friends, family, coworkers and others in a tobacco user’s social network to influence quitting and use of effective treatment. Methods Longitudinal, observational pilot feasibility study with six-week follow-up survey. Setting/Participants Employees of three national corporations, with a combined target audience of 102,100 employees. Intervention The Helpers Program offers Web-based brief intervention (BI) training to activate social networks of tobacco users to encourage quitting and use of effective treatment. Helpers was offered from 1/10/08 to 3/31/08, as a treatment engagement strategy, together with Free and Clear’s (F&C) telephone/Web-based cessation services. Main outcome measures web-site utilization, training completion, post-training changes in knowledge and self-efficacy with delivery of BIs, referrals to F&C, and use of BI training. Results There were 19,109 unique visitors to the Helpers Web-site. Of these, 4727 created user accounts; 1427 registered for Helpers Training; 766 completed training. There were 445 visits to the referral page and 201 e-mail or letter referrals generated. There were 67 requests for technical support. Of follow-up survey respondents (n=289), 78.9% reported offering a BI. Conclusions Offering the Helpers Program Web-site to a large, diverse audience as part of an employer-sponsored worksite health promotion program is both feasible and well accepted by employees. Website users will participate in training, encourage quitting, and refer smokers to quitline services. PMID:20176303

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.

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

PubMed

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

2016-12-22

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

Microarray R-based analysis of complex lysate experiments with MIRACLE

PubMed Central

List, Markus; Block, Ines; Pedersen, Marlene Lemvig; Christiansen, Helle; Schmidt, Steffen; Thomassen, Mads; Tan, Qihua; Baumbach, Jan; Mollenhauer, Jan

2014-01-01

Motivation: Reverse-phase protein arrays (RPPAs) allow sensitive quantification of relative protein abundance in thousands of samples in parallel. Typical challenges involved in this technology are antibody selection, sample preparation and optimization of staining conditions. The issue of combining effective sample management and data analysis, however, has been widely neglected. Results: This motivated us to develop MIRACLE, a comprehensive and user-friendly web application bridging the gap between spotting and array analysis by conveniently keeping track of sample information. Data processing includes correction of staining bias, estimation of protein concentration from response curves, normalization for total protein amount per sample and statistical evaluation. Established analysis methods have been integrated with MIRACLE, offering experimental scientists an end-to-end solution for sample management and for carrying out data analysis. In addition, experienced users have the possibility to export data to R for more complex analyses. MIRACLE thus has the potential to further spread utilization of RPPAs as an emerging technology for high-throughput protein analysis. Availability: Project URL: http://www.nanocan.org/miracle/ Contact: mlist@health.sdu.dk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25161257

Microarray R-based analysis of complex lysate experiments with MIRACLE.

PubMed

List, Markus; Block, Ines; Pedersen, Marlene Lemvig; Christiansen, Helle; Schmidt, Steffen; Thomassen, Mads; Tan, Qihua; Baumbach, Jan; Mollenhauer, Jan

2014-09-01

Reverse-phase protein arrays (RPPAs) allow sensitive quantification of relative protein abundance in thousands of samples in parallel. Typical challenges involved in this technology are antibody selection, sample preparation and optimization of staining conditions. The issue of combining effective sample management and data analysis, however, has been widely neglected. This motivated us to develop MIRACLE, a comprehensive and user-friendly web application bridging the gap between spotting and array analysis by conveniently keeping track of sample information. Data processing includes correction of staining bias, estimation of protein concentration from response curves, normalization for total protein amount per sample and statistical evaluation. Established analysis methods have been integrated with MIRACLE, offering experimental scientists an end-to-end solution for sample management and for carrying out data analysis. In addition, experienced users have the possibility to export data to R for more complex analyses. MIRACLE thus has the potential to further spread utilization of RPPAs as an emerging technology for high-throughput protein analysis. Project URL: http://www.nanocan.org/miracle/. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Hyper-Fit: Fitting Linear Models to Multidimensional Data with Multivariate Gaussian Uncertainties

NASA Astrophysics Data System (ADS)

Robotham, A. S. G.; Obreschkow, D.

2015-09-01

Astronomical data is often uncertain with errors that are heteroscedastic (different for each data point) and covariant between different dimensions. Assuming that a set of D-dimensional data points can be described by a (D - 1)-dimensional plane with intrinsic scatter, we derive the general likelihood function to be maximised to recover the best fitting model. Alongside the mathematical description, we also release the hyper-fit package for the R statistical language (http://github.com/asgr/hyper.fit) and a user-friendly web interface for online fitting (http://hyperfit.icrar.org). The hyper-fit package offers access to a large number of fitting routines, includes visualisation tools, and is fully documented in an extensive user manual. Most of the hyper-fit functionality is accessible via the web interface. In this paper, we include applications to toy examples and to real astronomical data from the literature: the mass-size, Tully-Fisher, Fundamental Plane, and mass-spin-morphology relations. In most cases, the hyper-fit solutions are in good agreement with published values, but uncover more information regarding the fitted model.

Advanced Software Development Workstation Project, phase 3

NASA Technical Reports Server (NTRS)

1991-01-01

ACCESS provides a generic capability to develop software information system applications which are explicitly intended to facilitate software reuse. In addition, it provides the capability to retrofit existing large applications with a user friendly front end for preparation of input streams in a way that will reduce required training time, improve the productivity even of experienced users, and increase accuracy. Current and past work shows that ACCESS will be scalable to much larger object bases.

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

PubMed Central

2014-01-01

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

Web3DMol: interactive protein structure visualization based on WebGL.

PubMed

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

2017-07-03

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

Web-based 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.

Implementing an SIG based platform of application and service for city spatial information in Shanghai

NASA Astrophysics Data System (ADS)

Yu, Bailang; Wu, Jianping

2006-10-01

Spatial Information Grid (SIG) is an infrastructure that has the ability to provide the services for spatial information according to users' needs by means of collecting, sharing, organizing and processing the massive distributed spatial information resources. This paper presents the architecture, technologies and implementation of the Shanghai City Spatial Information Application and Service System, a SIG based platform, which is an integrated platform that serves for administration, planning, construction and development of the city. In the System, there are ten categories of spatial information resources, including city planning, land-use, real estate, river system, transportation, municipal facility construction, environment protection, sanitation, urban afforestation and basic geographic information data. In addition, spatial information processing services are offered as a means of GIS Web Services. The resources and services are all distributed in different web-based nodes. A single database is created to store the metadata of all the spatial information. A portal site is published as the main user interface of the System. There are three main functions in the portal site. First, users can search the metadata and consequently acquire the distributed data by using the searching results. Second, some spatial processing web applications that developed with GIS Web Services, such as file format conversion, spatial coordinate transfer, cartographic generalization and spatial analysis etc, are offered to use. Third, GIS Web Services currently available in the System can be searched and new ones can be registered. The System has been working efficiently in Shanghai Government Network since 2005.

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.

Overview of long-term field experiments in Germany - metadata visualization

NASA Astrophysics Data System (ADS)

Muqit Zoarder, Md Abdul; Heinrich, Uwe; Svoboda, Nikolai; Grosse, Meike; Hierold, Wilfried

2017-04-01

BonaRes ("soil as a sustainable resource for the bioeconomy") is conducting to collect data and metadata of agricultural long-term field experiments (LTFE) of Germany. It is funded by the German Federal Ministry of Education and Research (BMBF) under the umbrella of the National Research Strategy BioEconomy 2030. BonaRes consists of ten interdisciplinary research project consortia and the 'BonaRes - Centre for Soil Research'. BonaRes Data Centre is responsible for collecting all LTFE data and regarding metadata into an enterprise database upon higher level of security and visualization of the data and metadata through data portal. In the frame of the BonaRes project, we are compiling an overview of long-term field experiments in Germany that is based on a literature review, the results of the online survey and direct contacts with LTFE operators. Information about research topic, contact person, website, experiment setup and analyzed parameters are collected. Based on the collected LTFE data, an enterprise geodatabase is developed and a GIS-based web-information system about LTFE in Germany is also settled. Various aspects of the LTFE, like experiment type, land-use type, agricultural category and duration of experiment, are presented in thematic maps. This information system is dynamically linked to the database, which means changes in the data directly affect the presentation. An easy data searching option using LTFE name, -location or -operators and the dynamic layer selection ensure a user-friendly web application. Dispersion and visualization of the overlapping LTFE points on the overview map are also challenging and we make it automatized at very zoom level which is also a consistent part of this application. The application provides both, spatial location and meta-information of LTFEs, which is backed-up by an enterprise geodatabase, GIS server for hosting map services and Java script API for web application development.

Impact of the social networking applications for health information management for patients and physicians.

PubMed

Sahama, Tony; Liang, Jian; Iannella, Renato

2012-01-01

Most social network users hold more than one social network account and utilize them in different ways depending on the digital context. For example, friendly chat on Facebook, professional discussion on LinkedIn, and health information exchange on PatientsLikeMe. Thus many web users need to manage many disparate profiles across many distributed online sources. Maintaining these profiles is cumbersome, time consuming, inefficient, and leads to lost opportunity. In this paper we propose a framework for multiple profile management of online social networks and showcase a demonstrator utilising an open source platform. The result of the research enables a user to create and manage an integrated profile and share/synchronise their profiles with their social networks. A number of use cases were created to capture the functional requirements and describe the interactions between users and the online services. An innovative application of this project is in public health informatics. We utilize the prototype to examine how the framework can benefit patients and physicians. The framework can greatly enhance health information management for patients and more importantly offer a more comprehensive personal health overview of patients to physicians.

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.

A Web-Based Psychoeducational Intervention for Adolescent Depression: Design and Development of MoodHwb.

PubMed

Bevan Jones, Rhys; Thapar, Anita; Rice, Frances; Beeching, Harriet; Cichosz, Rachel; Mars, Becky; Smith, Daniel J; Merry, Sally; Stallard, Paul; Jones, Ian; Thapar, Ajay K; Simpson, Sharon A

2018-02-15

Depression is common in adolescence and leads to distress and impairment in individuals, families and carers. Treatment and prevention guidelines highlight the key role of information and evidence-based psychosocial interventions not only for individuals but also for their families and carers. Engaging young people in prevention and early intervention programs is a challenge, and early treatment and prevention of adolescent depression is a major public health concern. There has been growing interest in psychoeducational interventions to provide accurate information about health issues and to enhance and develop self-management skills. However, for adolescents with, or at high risk of depression, there is a lack of engaging Web-based psychoeducation programs that have been developed with user input and in line with research guidelines and targeted at both the individual and their family or carer. There are also few studies published on the process of development of Web-based psychoeducational interventions. The aim of this study was to describe the process underlying the design and development of MoodHwb (HwbHwyliau in Welsh): a Web-based psychoeducation multimedia program for young people with, or at high risk of, depression and their families, carers, friends, and professionals. The initial prototype was informed by (1) a systematic review of psychoeducational interventions for adolescent depression; (2) findings from semistructured interviews and focus groups conducted with adolescents (with depressive symptoms or at high risk), parents or carers, and professionals working with young people; and (3) workshops and discussions with a multimedia company and experts (in clinical, research, and multimedia work). Twelve interviews were completed (four each with young people, parents or carers, and professionals) and six focus groups (three with young people, one with parents and carers, one with professionals, and one with academics). Key themes from the interviews and focus groups were: aims of the program, design and content issues, and integration and context of the program. The prototype was designed to be person-centered, multiplatform, engaging, interactive, and bilingual. It included mood-monitoring and goal-setting components and was available as a Web-based program and an app for mobile technologies. MoodHwb is a Web-based psychoeducational intervention developed for young people with, or at high risk of, depression and their families and carers. It was developed with user input using qualitative methods as well as user-centered design and educational and psychological theory. Further research is needed to evaluate the effectiveness of the program in a randomized controlled trial. If found to be effective, it could be implemented in health, education, youth and social services, and charities, to not only help young people but also families, carers, friends, and professionals involved in their care. ©Rhys Bevan Jones, Anita Thapar, Frances Rice, Harriet Beeching, Rachel Cichosz, Becky Mars, Daniel J Smith, Sally Merry, Paul Stallard, Ian Jones, Ajay K Thapar, Sharon A Simpson. Originally published in JMIR Mental Health (http://mental.jmir.org), 15.02.2018.

The EPA CompTox Chemistry Dashboard - an online resource ...

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data. Recent work has focused on the development of a new architecture that assembles the resources into a single platform. With a focus on delivering access to Open Data streams, web service integration accessibility and a user-friendly web application the CompTox Dashboard provides access to data associated with ~720,000 chemical substances. These data include research data in the form of bioassay screening data associated with the ToxCast program, experimental and predicted physicochemical properties, product and functional use information and related data of value to environmental scientists. This presentation will provide an overview of the CompTox Dashboard and its va

The informatics superhighway: prototyping on the World Wide Web.

PubMed

Cimino, J J; Socratous, S A; Grewal, R

1995-01-01

We have experimented with developing a prototype Surgeon's Workstation which makes use of the World Wide Web client-server architecture. Although originally intended merely as a means for obtaining user feedback for use in designing a "real" system, the application has been adopted for use by our Department of Surgery. As they begin to use the application, they have suggested changes and we have responded. This paper illustrates some of the advantages we have found for prototyping with Web-based applications, including security aspects.

Collaborative Information Agents on the World Wide Web

NASA Technical Reports Server (NTRS)

Chen, James R.; Mathe, Nathalie; Wolfe, Shawn; Koga, Dennis J. (Technical Monitor)

1998-01-01

In this paper, we present DIAMS, a system of distributed, collaborative information agents which help users access, collect, organize, and exchange information on the World Wide Web. Personal agents provide their owners dynamic displays of well organized information collections, as well as friendly information management utilities. Personal agents exchange information with one another. They also work with other types of information agents such as matchmakers and knowledge experts to facilitate collaboration and communication.

Multimedia Data Capture with Multicast Dissemination for Online Distance Learning

DTIC Science & Technology

2001-12-01

Juan Gril and Dr. Don Brutzman to wrap the multiple videos in a user- friendly environment. The web pages also contain the original PowerPoint...this CD, Juan Gril , a volunteer for the Siggraph 2001 Online Committee, created web pages that match the style and functionality desired by the...leader. The Committee for 2001 consisted of Don Brutzman, Stephen. Matsuba, Mike Collins, Allen Dutton, Juan Gril , Mike Hunsberger, Jerry Isdale

WebEQ: a web-GIS System to collect, display and query data for the management of the earthquake emergency in Central Italy

NASA Astrophysics Data System (ADS)

Carbone, Gianluca; Cosentino, Giuseppe; Pennica, Francesco; Moscatelli, Massimiliano; Stigliano, Francesco

2017-04-01

After the strong earthquakes that hit central Italy in recent months, the Center for Seismic Microzonation and its applications (CentroMS) was commissioned by the Italian Department of Civil Protection to conduct the study of seismic microzonation of the territories affected by the earthquake of August 24, 2016. As part of the activities of microzonation, IGAG CNR has created WebEQ, a management tool of the data that have been acquired by all participants (i.e., more than twenty research institutes and university departments). The data collection was organized and divided into sub-areas, assigned to working groups with multidisciplinary expertise in geology, geophysics and engineering. WebEQ is a web-GIS System that helps all the subjects involved in the data collection activities, through tools aimed at data uploading and validation, and with a simple GIS interface to display, query and download geographic data. WebEQ is contributing to the creation of a large database containing geographical data, both vector and raster, from various sources and types: - Regional Technical Map em Geological and geomorphological maps em Data location maps em Maps of microzones homogeneous in seismic perspective and seismic microzonation maps em National strong motion network location. Data loading is done through simple input masks that ensure consistency with the database structure, avoiding possible errors and helping users to interact with the map through user-friendly tools. All the data are thematized through standardized symbologies and colors (Gruppo di lavoro MS 2008), in order to allow the easy interpretation by all users. The data download tools allow data exchange between working groups and the scientific community to benefit from the activities. The seismic microzonation activities are still ongoing. WebEQ is enabling easy management of large amounts of data and will form a basis for the development of tools for the management of the upcoming seismic emergencies.

DataFed: A Federated Data System for Visualization and Analysis of Spatio-Temporal Air Quality Data

NASA Astrophysics Data System (ADS)

Husar, R. B.; Hoijarvi, K.

2017-12-01

DataFed is a distributed web-services-based computing environment for accessing, processing, and visualizing atmospheric data in support of air quality science and management. The flexible, adaptive environment facilitates the access and flow of atmospheric data from provider to users by enabling the creation of user-driven data processing/visualization applications. DataFed `wrapper' components, non-intrusively wrap heterogeneous, distributed datasets for access by standards-based GIS web services. The mediator components (also web services) map the heterogeneous data into a spatio-temporal data model. Chained web services provide homogeneous data views (e.g., geospatial, time views) using a global multi-dimensional data model. In addition to data access and rendering, the data processing component services can be programmed for filtering, aggregation, and fusion of multidimensional data. A complete application software is written in a custom made data flow language. Currently, the federated data pool consists of over 50 datasets originating from globally distributed data providers delivering surface-based air quality measurements, satellite observations, emissions data as well as regional and global-scale air quality models. The web browser-based user interface allows point and click navigation and browsing the XYZT multi-dimensional data space. The key applications of DataFed are for exploring spatial pattern of pollutants, seasonal, weekly, diurnal cycles and frequency distributions for exploratory air quality research. Since 2008, DataFed has been used to support EPA in the implementation of the Exceptional Event Rule. The data system is also used at universities in the US, Europe and Asia.

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

PubMed

McMurdie, Paul J; Holmes, Susan

2015-01-15

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

Challenges in Personalizing and Decentralizing the Web: An Overview of GOSSPLE

NASA Astrophysics Data System (ADS)

Kermarrec, Anne-Marie

Social networks and collaborative tagging systems have taken off at an unexpected scale and speed (Facebook, YouTube, Flickr, Last.fm, Delicious, etc). Web content is now generated by you, me, our friends and millions of others. This represents a revolution in usage and a great opportunity to leverage collaborative knowledge to enhance the user's Internet experience. The GOSSPLE project aims at precisely achieving this: automatically capturing affinities between users that are potentially unknown yet share similar interests, or exhibiting similar behaviors on the Web. This fully personalizes the search process, increasing the ability of a user to find relevant content. This personalization calls for decentralization. (1) Centralized servers might dissuade users from generating new content for they expose their privacy and represent a single point of attack. (2) The amount of information to store grows exponentially with the size of the system and centralized systems cannot sustain storing a growing amount of data at a user granularity. We believe that the salvation can only come from a fully decentralized user centric approach where every participant is entrusted to harvest the Web with information relevant to her own activity. This poses a number of scientific challenges: How to discover similar users, how to define the relevant metrics for such personalization, how to preserve privacy when needed, how to deal with free-riders and misheavior and how to manage efficiently a growing amount of data.

Towards a Ubiquitous User Model for Profile Sharing and Reuse

PubMed Central

de Lourdes Martinez-Villaseñor, Maria; Gonzalez-Mendoza, Miguel; Hernandez-Gress, Neil

2012-01-01

People interact with systems and applications through several devices and are willing to share information about preferences, interests and characteristics. Social networking profiles, data from advanced sensors attached to personal gadgets, and semantic web technologies such as FOAF and microformats are valuable sources of personal information that could provide a fair understanding of the user, but profile information is scattered over different user models. Some researchers in the ubiquitous user modeling community envision the need to share user model's information from heterogeneous sources. In this paper, we address the syntactic and semantic heterogeneity of user models in order to enable user modeling interoperability. We present a dynamic user profile structure based in Simple Knowledge Organization for the Web (SKOS) to provide knowledge representation for ubiquitous user model. We propose a two-tier matching strategy for concept schemas alignment to enable user modeling interoperability. Our proposal is proved in the application scenario of sharing and reusing data in order to deal with overweight and obesity. PMID:23201995

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.

WALK 2.0 - using Web 2.0 applications to promote health-related physical activity: a randomised controlled trial protocol.

PubMed

Kolt, Gregory S; Rosenkranz, Richard R; Savage, Trevor N; Maeder, Anthony J; Vandelanotte, Corneel; Duncan, Mitch J; Caperchione, Cristina M; Tague, Rhys; Hooker, Cindy; Mummery, W Kerry

2013-05-03

Physical inactivity is one of the leading modifiable causes of death and disease in Australia. National surveys indicate less than half of the Australian adult population are sufficiently active to obtain health benefits. The Internet is a potentially important medium for successfully communicating health messages to the general population and enabling individual behaviour change. Internet-based interventions have proven efficacy; however, intervention studies describing website usage objectively have reported a strong decline in usage, and high attrition rate, over the course of the interventions. Web 2.0 applications give users control over web content generated and present innovative possibilities to improve user engagement. There is, however, a need to assess the effectiveness of these applications in the general population. The Walk 2.0 project is a 3-arm randomised controlled trial investigating the effects of "next generation" web-based applications on engagement, retention, and subsequent physical activity behaviour change. 504 individuals will be recruited from two sites in Australia, randomly allocated to one of two web-based interventions (Web 1.0 or Web 2.0) or a control group, and provided with a pedometer to monitor physical activity. The Web 1.0 intervention will provide participants with access to an existing physical activity website with limited interactivity. The Web 2.0 intervention will provide access to a website featuring Web 2.0 content, including social networking, blogs, and virtual walking groups. Control participants will receive a logbook to record their steps. All groups will receive similar educational material on setting goals and increasing physical activity. The primary outcomes are objectively measured physical activity and website engagement and retention. Other outcomes measured include quality of life, psychosocial correlates, and anthropometric measurements. Outcomes will be measured at baseline, 3, 12 and 18 months. The findings of this study will provide increased understanding of the benefit of new web-based technologies and applications in engaging and retaining participants on web-based intervention sites, with the aim of improved health behaviour change outcomes. Australian New Zealand Clinical Trials Registry, ACTRN12611000157976.

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.

Caching strategies for improving performance of web-based Geographic applications

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

Nessi: An EEG-Controlled Web Browser for Severely Paralyzed Patients

PubMed Central

Bensch, Michael; Karim, Ahmed A.; Mellinger, Jürgen; Hinterberger, Thilo; Tangermann, Michael; Bogdan, Martin; Rosenstiel, Wolfgang; Birbaumer, Niels

2007-01-01

We have previously demonstrated that an EEG-controlled web browser based on self-regulation of slow cortical potentials (SCPs) enables severely paralyzed patients to browse the internet independently of any voluntary muscle control. However, this system had several shortcomings, among them that patients could only browse within a limited number of web pages and had to select links from an alphabetical list, causing problems if the link names were identical or if they were unknown to the user (as in graphical links). Here we describe a new EEG-controlled web browser, called Nessi, which overcomes these shortcomings. In Nessi, the open source browser, Mozilla, was extended by graphical in-place markers, whereby different brain responses correspond to different frame colors placed around selectable items, enabling the user to select any link on a web page. Besides links, other interactive elements are accessible to the user, such as e-mail and virtual keyboards, opening up a wide range of hypertext-based applications. PMID:18350132

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.

iDrug: a web-accessible and interactive drug discovery and design platform

PubMed Central

2014-01-01

Background The progress in computer-aided drug design (CADD) approaches over the past decades accelerated the early-stage pharmaceutical research. Many powerful standalone tools for CADD have been developed in academia. As programs are developed by various research groups, a consistent user-friendly online graphical working environment, combining computational techniques such as pharmacophore mapping, similarity calculation, scoring, and target identification is needed. Results We presented a versatile, user-friendly, and efficient online tool for computer-aided drug design based on pharmacophore and 3D molecular similarity searching. The web interface enables binding sites detection, virtual screening hits identification, and drug targets prediction in an interactive manner through a seamless interface to all adapted packages (e.g., Cavity, PocketV.2, PharmMapper, SHAFTS). Several commercially available compound databases for hit identification and a well-annotated pharmacophore database for drug targets prediction were integrated in iDrug as well. The web interface provides tools for real-time molecular building/editing, converting, displaying, and analyzing. All the customized configurations of the functional modules can be accessed through featured session files provided, which can be saved to the local disk and uploaded to resume or update the history work. Conclusions iDrug is easy to use, and provides a novel, fast and reliable tool for conducting drug design experiments. By using iDrug, various molecular design processing tasks can be submitted and visualized simply in one browser without installing locally any standalone modeling softwares. iDrug is accessible free of charge at http://lilab.ecust.edu.cn/idrug. PMID:24955134

dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface.

PubMed

Rot, Gregor; Parikh, Anup; Curk, Tomaz; Kuspa, Adam; Shaulsky, Gad; Zupan, Blaz

2009-08-25

Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive web technologies require us to rethink the standard submit-and-wait paradigm, and craft bioinformatics web applications that share analytical and interactive power with their desktop relatives, while retaining simplicity and availability. We have developed dictyExpress, a web application that features a graphical, highly interactive explorative interface to our database that consists of more than 1000 Dictyostelium discoideum gene expression experiments. In dictyExpress, the user can select experiments and genes, perform gene clustering, view gene expression profiles across time, view gene co-expression networks, perform analyses of Gene Ontology term enrichment, and simultaneously display expression profiles for a selected gene in various experiments. Most importantly, these tasks are achieved through web applications whose components are seamlessly interlinked and immediately respond to events triggered by the user, thus providing a powerful explorative data analysis environment. dictyExpress is a precursor for a new generation of web-based bioinformatics applications with simple but powerful interactive interfaces that resemble that of the modern desktop. While dictyExpress serves mainly the Dictyostelium research community, it is relatively easy to adapt it to other datasets. We propose that the design ideas behind dictyExpress will influence the development of similar applications for other model organisms.

dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface

PubMed Central

Rot, Gregor; Parikh, Anup; Curk, Tomaz; Kuspa, Adam; Shaulsky, Gad; Zupan, Blaz

2009-01-01

Background Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive web technologies require us to rethink the standard submit-and-wait paradigm, and craft bioinformatics web applications that share analytical and interactive power with their desktop relatives, while retaining simplicity and availability. Results We have developed dictyExpress, a web application that features a graphical, highly interactive explorative interface to our database that consists of more than 1000 Dictyostelium discoideum gene expression experiments. In dictyExpress, the user can select experiments and genes, perform gene clustering, view gene expression profiles across time, view gene co-expression networks, perform analyses of Gene Ontology term enrichment, and simultaneously display expression profiles for a selected gene in various experiments. Most importantly, these tasks are achieved through web applications whose components are seamlessly interlinked and immediately respond to events triggered by the user, thus providing a powerful explorative data analysis environment. Conclusion dictyExpress is a precursor for a new generation of web-based bioinformatics applications with simple but powerful interactive interfaces that resemble that of the modern desktop. While dictyExpress serves mainly the Dictyostelium research community, it is relatively easy to adapt it to other datasets. We propose that the design ideas behind dictyExpress will influence the development of similar applications for other model organisms. PMID:19706156

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

NASA Astrophysics Data System (ADS)

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

2000-04-01

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

Construction and validation of a web-based epidemiological database for inflammatory bowel diseases in Europe An EpiCom study.

PubMed

Burisch, Johan; Cukovic-Cavka, Silvija; Kaimakliotis, Ioannis; Shonová, Olga; Andersen, Vibeke; Dahlerup, Jens F; Elkjaer, Margarita; Langholz, Ebbe; Pedersen, Natalia; Salupere, Riina; Kolho, Kaija-Leena; Manninen, Pia; Lakatos, Peter Laszlo; Shuhaibar, Mary; Odes, Selwyn; Martinato, Matteo; Mihu, Ion; Magro, Fernando; Belousova, Elena; Fernandez, Alberto; Almer, Sven; Halfvarson, Jonas; Hart, Ailsa; Munkholm, Pia

2011-08-01

The EpiCom-study investigates a possible East-West-gradient in Europe in the incidence of IBD and the association with environmental factors. A secured web-based database is used to facilitate and centralize data registration. To construct and validate a web-based inception cohort database available in both English and Russian language. The EpiCom database has been constructed in collaboration with all 34 participating centers. The database was translated into Russian using forward translation, patient questionnaires were translated by simplified forward-backward translation. Data insertion implies fulfillment of international diagnostic criteria, disease activity, medical therapy, quality of life, work productivity and activity impairment, outcome of pregnancy, surgery, cancer and death. Data is secured by the WinLog3 System, developed in cooperation with the Danish Data Protection Agency. Validation of the database has been performed in two consecutive rounds, each followed by corrections in accordance with comments. The EpiCom database fulfills the requirements of the participating countries' local data security agencies by being stored at a single location. The database was found overall to be "good" or "very good" by 81% of the participants after the second validation round and the general applicability of the database was evaluated as "good" or "very good" by 77%. In the inclusion period January 1st -December 31st 2010 1336 IBD patients have been included in the database. A user-friendly, tailor-made and secure web-based inception cohort database has been successfully constructed, facilitating remote data input. The incidence of IBD in 23 European countries can be found at www.epicom-ecco.eu. Copyright © 2011 European Crohn's and Colitis Organisation. All rights reserved.

Web-based multimedia courseware for emergency cardiac patient management simulations.

PubMed

Ambrosiadou, V; Compton, T; Panchal, T; Polovina, S

2000-01-01

This is a multidisciplinary inter-departmental/faculty project between the departments of computer science, electronic, communications and electrical engineering and nursing and paramedic sciences. The objective is to develop a web based multimedia front end to existing simulations of cardiac emergency scenaria. It will be used firstly in the teaching of nurses. The University of Hertfordshire is the only University in Britain using simulations of cardiac emergency scenaria for nurse and paramedic science education and therefore this project will add the multimedia dimension in distributed courses over the web and will assess the improvement in the educational process. The use of network and multimedia technologies, provide interactive learning, immediate feedback to students' responses, individually tailored instructions, objective testing and entertaining delivery. The end product of this project will serve as interactive material to enhance experiential learning for nursing students using the simulations of cardiac emergency scenaria. The emergency treatment simulations have been developed using VisSim and may be compiled as C code. The objective of the project is to provide a web based user friendly multimedia interface in order to demonstrate the way in which patients may be managed in critical situations by applying advanced technological equipment and drug administration. Then the user will be able to better appreciate the concepts involved by running the VisSim simulations. The evaluation group for the proposed software will be the Department of Nursing and Paramedic Sciences About 200 nurses use simulations every year for training purposes as part of their course requirements.

The online Tabloid Proteome: an annotated database of protein associations

PubMed Central

Turan, Demet; Tavernier, Jan

2018-01-01

Abstract A complete knowledge of the proteome can only be attained by determining the associations between proteins, along with the nature of these associations (e.g. physical contact in protein–protein interactions, participation in complex formation or different roles in the same pathway). Despite extensive efforts in elucidating direct protein interactions, our knowledge on the complete spectrum of protein associations remains limited. We therefore developed a new approach that detects protein associations from identifications obtained after re-processing of large-scale, public mass spectrometry-based proteomics data. Our approach infers protein association based on the co-occurrence of proteins across many different proteomics experiments, and provides information that is almost completely complementary to traditional direct protein interaction studies. We here present a web interface to query and explore the associations derived from this method, called the online Tabloid Proteome. The online Tabloid Proteome also integrates biological knowledge from several existing resources to annotate our derived protein associations. The online Tabloid Proteome is freely available through a user-friendly web interface, which provides intuitive navigation and data exploration options for the user at http://iomics.ugent.be/tabloidproteome. PMID:29040688

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

PubMed

Jeliazkova, Nina; Jeliazkov, Vedrin

2011-05-16

The AMBIT web services package is one of the several existing independent implementations of the OpenTox Application Programming Interface and is built according to the principles of the Representational State Transfer (REST) architecture. The Open Source Predictive Toxicology Framework, developed by the partners in the EC FP7 OpenTox project, aims at providing a unified access to toxicity data and predictive models, as well as validation procedures. This is achieved by i) an information model, based on a common OWL-DL ontology ii) links to related ontologies; iii) data and algorithms, available through a standardized REST web services interface, where every compound, data set or predictive method has a unique web address, used to retrieve its Resource Description Framework (RDF) representation, or initiate the associated calculations.The AMBIT web services package has been developed as an extension of AMBIT modules, adding the ability to create (Quantitative) Structure-Activity Relationship (QSAR) models and providing an OpenTox API compliant interface. The representation of data and processing resources in W3C Resource Description Framework facilitates integrating the resources as Linked Data. By uploading datasets with chemical structures and arbitrary set of properties, they become automatically available online in several formats. The services provide unified interfaces to several descriptor calculation, machine learning and similarity searching algorithms, as well as to applicability domain and toxicity prediction models. All Toxtree modules for predicting the toxicological hazard of chemical compounds are also integrated within this package. The complexity and diversity of the processing is reduced to the simple paradigm "read data from a web address, perform processing, write to a web address". The online service allows to easily run predictions, without installing any software, as well to share online datasets and models. The downloadable web application 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

The AMBIT web services package is one of the several existing independent implementations of the OpenTox Application Programming Interface and is built according to the principles of the Representational State Transfer (REST) architecture. The Open Source Predictive Toxicology Framework, developed by the partners in the EC FP7 OpenTox project, aims at providing a unified access to toxicity data and predictive models, as well as validation procedures. This is achieved by i) an information model, based on a common OWL-DL ontology ii) links to related ontologies; iii) data and algorithms, available through a standardized REST web services interface, where every compound, data set or predictive method has a unique web address, used to retrieve its Resource Description Framework (RDF) representation, or initiate the associated calculations. The AMBIT web services package has been developed as an extension of AMBIT modules, adding the ability to create (Quantitative) Structure-Activity Relationship (QSAR) models and providing an OpenTox API compliant interface. The representation of data and processing resources in W3C Resource Description Framework facilitates integrating the resources as Linked Data. By uploading datasets with chemical structures and arbitrary set of properties, they become automatically available online in several formats. The services provide unified interfaces to several descriptor calculation, machine learning and similarity searching algorithms, as well as to applicability domain and toxicity prediction models. All Toxtree modules for predicting the toxicological hazard of chemical compounds are also integrated within this package. The complexity and diversity of the processing is reduced to the simple paradigm "read data from a web address, perform processing, write to a web address". The online service allows to easily run predictions, without installing any software, as well to share online datasets and models. The downloadable web application 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

Role-Based And Adaptive User Interface Designs In A Teledermatology Consult System: A Way To Secure And A Way To Enhance

PubMed Central

Lin, Yi-Jung; Speedie, Stuart

2003-01-01

User interface design is one of the most important parts of developing applications. Nowadays, a quality user interface must not only accommodate interaction between machines and users, but also needs to recognize the differences and provide functionalities for users from role-to-role or even individual-to-individual. With the web-based application of our Teledermatology consult system, the development environment provides us highly useful opportunities to create dynamic user interfaces, which lets us to gain greater access control and has the potential to increase efficiency of the system. We will describe the two models of user interfaces in our system: Role-based and Adaptive. PMID:14728419

Effectiveness of Smartphone Application for the Development of Youth Anthusiasm to Malay Culture

NASA Astrophysics Data System (ADS)

Asril, Elvira; Fajrizal; Wiza, Fana

2017-12-01

This study will measure the effectiveness of Malay cultural applications, by socializing Melayu.com web, then distributing questionnaires to them (young people / high school students), and will be able to find out what features are of interest to them. With this smartphone introduction application of Malay culture, it is expected to increase young enthusiasm towards Malay culture which is really beautiful if it is known and understood. After the socialization of 30 high school students, the results obtained that they are less interested in the application. Because it is not user friendly, not interactive and rigid. Eventhough they have interest in this Malay culture, they have not found an app or media that can attract attention. Thus, they ask if the application of Malay culture can add game content later, eg War games using background and other elements related to Malay culture.

Performance Analysis of Web-Based Ppp Services with DİFFERENT Visibility Conditions

NASA Astrophysics Data System (ADS)

Albayrak, M.; Erkaya, H.; Ozludemir, M. T.; Ocalan, T.

2016-12-01

GNSS is being used effectively to precise position for many measuring and geodetic purposes at the present time. There is an increasing variety of these systems including the post-processing calculations in terms of number, quality and features and many different techniques are developed to determine position. Precise positioning intend to derive requires user experience and scientific or commercial software with costly license fees. However, in recent years important alternatives to this software that are user friendly and offer free web-based online precise point positioning service have become widely used in geodetic applications. The aim of this study is to test the performance of PPP techniques on ground control points with different visibility conditions. Within this framework, static observations were carried out for three hours a day repeatedly for six days, in YTU Davutpasa Campus on three different ground control points. The locations of these stations were selected by taking into account the impact of natural (trees, etc.) and artificial (buildings, etc.) obstacles. In order to compare the obtained GPS observations with PPP performances, first of all the accurate coordinates of the control points were computed with relative positioning technique in connection with the IGS stations using Bernese v5.0 software. Afterwards, three different web-based positioning services (CSRS-PPP, magicGNSS, GAPS) were used to analyze the GPS observations via PPP technique. To compare all of the obtained results, ITRF2008 datum measurement epoch coordinates were preferred by taking the service result criteria into consideration. In coordinate comparison, for the first station located nearby a building and possibly subjected to multipath effect horizontal discrepancies vary between 2-14.5 cm while vertical differences are between 3.5-16 cm. For the second point located partly in a forestry area, the discrepancies have been obtained as 1.5-8 cm and 2-10 cm for horizontal and vertical components, respectively. For the third point located in an area with no obstacles, 1.5-7 cm horizontal and 1-7 cm vertical differences have been obtained. The results show that the PPP technique could be used effectively in several positioning applications.

A Multifunctional Brain-Computer Interface Intended for Home Use: An Evaluation with Healthy Participants and Potential End Users with Dry and Gel-Based Electrodes

PubMed Central

Käthner, Ivo; Halder, Sebastian; Hintermüller, Christoph; Espinosa, Arnau; Guger, Christoph; Miralles, Felip; Vargiu, Eloisa; Dauwalder, Stefan; Rafael-Palou, Xavier; Solà, Marc; Daly, Jean M.; Armstrong, Elaine; Martin, Suzanne; Kübler, Andrea

2017-01-01

Current brain-computer interface (BCIs) software is often tailored to the needs of scientists and technicians and therefore complex to allow for versatile use. To facilitate home use of BCIs a multifunctional P300 BCI with a graphical user interface intended for non-expert set-up and control was designed and implemented. The system includes applications for spelling, web access, entertainment, artistic expression and environmental control. In addition to new software, it also includes new hardware for the recording of electroencephalogram (EEG) signals. The EEG system consists of a small and wireless amplifier attached to a cap that can be equipped with gel-based or dry contact electrodes. The system was systematically evaluated with a healthy sample, and targeted end users of BCI technology, i.e., people with a varying degree of motor impairment tested the BCI in a series of individual case studies. Usability was assessed in terms of effectiveness, efficiency and satisfaction. Feedback of users was gathered with structured questionnaires. Two groups of healthy participants completed an experimental protocol with the gel-based and the dry contact electrodes (N = 10 each). The results demonstrated that all healthy participants gained control over the system and achieved satisfactory to high accuracies with both gel-based and dry electrodes (average error rates of 6 and 13%). Average satisfaction ratings were high, but certain aspects of the system such as the wearing comfort of the dry electrodes and design of the cap, and speed (in both groups) were criticized by some participants. Six potential end users tested the system during supervised sessions. The achieved accuracies varied greatly from no control to high control with accuracies comparable to that of healthy volunteers. Satisfaction ratings of the two end-users that gained control of the system were lower as compared to healthy participants. The advantages and disadvantages of the BCI and its applications are discussed and suggestions are presented for improvements to pave the way for user friendly BCIs intended to be used as assistive technology by persons with severe paralysis. PMID:28588442

A Multifunctional Brain-Computer Interface Intended for Home Use: An Evaluation with Healthy Participants and Potential End Users with Dry and Gel-Based Electrodes.

PubMed

Käthner, Ivo; Halder, Sebastian; Hintermüller, Christoph; Espinosa, Arnau; Guger, Christoph; Miralles, Felip; Vargiu, Eloisa; Dauwalder, Stefan; Rafael-Palou, Xavier; Solà, Marc; Daly, Jean M; Armstrong, Elaine; Martin, Suzanne; Kübler, Andrea

2017-01-01

Current brain-computer interface (BCIs) software is often tailored to the needs of scientists and technicians and therefore complex to allow for versatile use. To facilitate home use of BCIs a multifunctional P300 BCI with a graphical user interface intended for non-expert set-up and control was designed and implemented. The system includes applications for spelling, web access, entertainment, artistic expression and environmental control. In addition to new software, it also includes new hardware for the recording of electroencephalogram (EEG) signals. The EEG system consists of a small and wireless amplifier attached to a cap that can be equipped with gel-based or dry contact electrodes. The system was systematically evaluated with a healthy sample, and targeted end users of BCI technology, i.e., people with a varying degree of motor impairment tested the BCI in a series of individual case studies. Usability was assessed in terms of effectiveness, efficiency and satisfaction. Feedback of users was gathered with structured questionnaires. Two groups of healthy participants completed an experimental protocol with the gel-based and the dry contact electrodes ( N = 10 each). The results demonstrated that all healthy participants gained control over the system and achieved satisfactory to high accuracies with both gel-based and dry electrodes (average error rates of 6 and 13%). Average satisfaction ratings were high, but certain aspects of the system such as the wearing comfort of the dry electrodes and design of the cap, and speed (in both groups) were criticized by some participants. Six potential end users tested the system during supervised sessions. The achieved accuracies varied greatly from no control to high control with accuracies comparable to that of healthy volunteers. Satisfaction ratings of the two end-users that gained control of the system were lower as compared to healthy participants. The advantages and disadvantages of the BCI and its applications are discussed and suggestions are presented for improvements to pave the way for user friendly BCIs intended to be used as assistive technology by persons with severe paralysis.

Semantic Annotation of Video Fragments as Learning Objects: A Case Study with "YouTube" Videos and the Gene Ontology

ERIC Educational Resources Information Center

Garcia-Barriocanal, Elena; Sicilia, Miguel-Angel; Sanchez-Alonso, Salvador; Lytras, Miltiadis

2011-01-01

Web 2.0 technologies can be considered a loosely defined set of Web application styles that foster a kind of media consumer more engaged, and usually active in creating and maintaining Internet contents. Thus, Web 2.0 applications have resulted in increased user participation and massive user-generated (or user-published) open multimedia content,…

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.

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

NASA Astrophysics Data System (ADS)

Ruegg, C. S.

2011-12-01

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