Bringing Control System User Interfaces to the Web

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

Chen, Xihui; Kasemir, Kay

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

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

NASA Astrophysics Data System (ADS)

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

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

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…

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

Employing WebGL to develop interactive stereoscopic 3D content for use in biomedical visualization

NASA Astrophysics Data System (ADS)

Johnston, Semay; Renambot, Luc; Sauter, Daniel

2013-03-01

Web Graphics Library (WebGL), the forthcoming web standard for rendering native 3D graphics in a browser, represents an important addition to the biomedical visualization toolset. It is projected to become a mainstream method of delivering 3D online content due to shrinking support for third-party plug-ins. Additionally, it provides a virtual reality (VR) experience to web users accommodated by the growing availability of stereoscopic displays (3D TV, desktop, and mobile). WebGL's value in biomedical visualization has been demonstrated by applications for interactive anatomical models, chemical and molecular visualization, and web-based volume rendering. However, a lack of instructional literature specific to the field prevents many from utilizing this technology. This project defines a WebGL design methodology for a target audience of biomedical artists with a basic understanding of web languages and 3D graphics. The methodology was informed by the development of an interactive web application depicting the anatomy and various pathologies of the human eye. The application supports several modes of stereoscopic displays for a better understanding of 3D anatomical structures.

A Semiotic Analysis of Icons on the World Wide Web.

ERIC Educational Resources Information Center

Ma, Yan

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

Interactive SIGHT: textual access to simple bar charts

NASA Astrophysics Data System (ADS)

Demir, Seniz; Oliver, David; Schwartz, Edward; Elzer, Stephanie; Carberry, Sandra; Mccoy, Kathleen F.; Chester, Daniel

2010-12-01

Information graphics, such as bar charts and line graphs, are an important component of many articles from popular media. The majority of such graphics have an intention (a high-level message) to communicate to the graph viewer. Since the intended message of a graphic is often not repeated in the accompanying text, graphics together with the textual segments contribute to the overall purpose of an article and cannot be ignored. Unfortunately, these visual displays are provided in a format which is not readily accessible to everyone. For example, individuals with sight impairments who use screen readers to listen to documents have limited access to the graphics. This article presents a new accessibility tool, the Interactive SIGHT (Summarizing Information GrapHics Textually) system, that is intended to enable visually impaired users to access the knowledge that one would gain from viewing information graphics found on the web. The current system, which is implemented as a browser extension that works on simple bar charts, can be invoked by a user via a keystroke combination while navigating the web. Once launched, Interactive SIGHT first provides a brief summary that conveys the underlying intention of a bar chart along with the chart's most significant and salient features, and then produces history-aware follow-up responses to provide further information about the chart upon request from the user. We present two user studies that were conducted with sighted and visually impaired users to determine how effective the initial summary and follow-up responses are in conveying the informational content of bar charts, and to evaluate how easy it is to use the system interface. The evaluation results are promising and indicate that the system responses are well-structured and enable visually impaired users to answer key questions about bar charts in an easy-to-use manner. Post-experimental interviews revealed that visually impaired participants were very satisfied with the system offering different options to access the content of a chart to meet their specific needs and that they would use Interactive SIGHT if it was publicly available so as not to have to ignore graphics on the web. Being a language based assistive technology designed to compensate for the lack of sight, our work paves the road for a stronger acceptance of natural language interfaces to graph interpretation that we believe will be of great benefit to the visually impaired community.

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

ERIC Educational Resources Information Center

Oulanov, Alexei; Pajarillo, Edmund J. Y.

2002-01-01

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

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

NASA Astrophysics Data System (ADS)

Made Tirta, I.; Anggraeni, Dian

2018-04-01

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

Toward the Attribution of Web Behavior

DTIC Science & Technology

2012-07-01

den Poel, “Predicting website audience demo- graphics for Web advertising targeting using multi-website clickstream data,” Fundamenta Informaticae ...and M. Sydow, “Effective prediction of web user behaviour with user-level models,” Fundamenta Informaticae , vol. 89, no. 2, pp. 189–206, 2008. [24] J

The Catalog Takes to the Highway.

ERIC Educational Resources Information Center

Chesbro, Melinda

1999-01-01

Discusses new developments in online library catalogs, including Web-based catalogs; interconnectivity within the library; interconnectivity between libraries; graphical user interfaces; pricing models; and a checklist of questions to ask when purchasing a new online catalog. (LRW)

Internet-based support for the production of holographic stereograms

NASA Astrophysics Data System (ADS)

Gustafsson, Jonny

1998-03-01

Holographic hard-copy techniques suffers from a lack of availability for ordinary users of computer graphics. The production of holograms usually requires special skills as well as expensive equipment which means that the direct production cost will be high for an ordinary user with little or no knowledge in holography. Here it is shown how a system may be created in which the users of computer graphics can do all communication with a holography studio through a Java-based web browser. This system will facilitate for the user to understand the technique of holographic stereograms, make decisions about angles, views, lighting etc., previsualizing the end result, as well as automatically submit the 3D-data to the producer of the hologram. A prototype system has been built which uses internal scripting in VRML.

Web-based, GPU-accelerated, Monte Carlo simulation and visualization of indirect radiation imaging detector performance

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

Dong, Han; Sharma, Diksha; Badano, Aldo, E-mail: aldo.badano@fda.hhs.gov

2014-12-15

Purpose: Monte Carlo simulations play a vital role in the understanding of the fundamental limitations, design, and optimization of existing and emerging medical imaging systems. Efforts in this area have resulted in the development of a wide variety of open-source software packages. One such package, hybridMANTIS, uses a novel hybrid concept to model indirect scintillator detectors by balancing the computational load using dual CPU and graphics processing unit (GPU) processors, obtaining computational efficiency with reasonable accuracy. In this work, the authors describe two open-source visualization interfaces, webMANTIS and visualMANTIS to facilitate the setup of computational experiments via hybridMANTIS. Methods: Themore » visualization tools visualMANTIS and webMANTIS enable the user to control simulation properties through a user interface. In the case of webMANTIS, control via a web browser allows access through mobile devices such as smartphones or tablets. webMANTIS acts as a server back-end and communicates with an NVIDIA GPU computing cluster that can support multiuser environments where users can execute different experiments in parallel. Results: The output consists of point response and pulse-height spectrum, and optical transport statistics generated by hybridMANTIS. The users can download the output images and statistics through a zip file for future reference. In addition, webMANTIS provides a visualization window that displays a few selected optical photon path as they get transported through the detector columns and allows the user to trace the history of the optical photons. Conclusions: The visualization tools visualMANTIS and webMANTIS provide features such as on the fly generation of pulse-height spectra and response functions for microcolumnar x-ray imagers while allowing users to save simulation parameters and results from prior experiments. The graphical interfaces simplify the simulation setup and allow the user to go directly from specifying input parameters to receiving visual feedback for the model predictions.« less

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.

Interactive Learning Environment: Web-based Virtual Hydrological Simulation System using Augmented and Immersive Reality

NASA Astrophysics Data System (ADS)

Demir, I.

2014-12-01

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. The hydrological simulation system is a web-based 3D interactive learning environment for teaching hydrological processes and concepts. The simulation systems provides a visually striking platform with realistic terrain information, and water simulation. Students can create or load predefined scenarios, control environmental parameters, and evaluate environmental mitigation alternatives. The web-based simulation system provides an environment for students to learn about the hydrological processes (e.g. flooding and flood damage), and effects of development and human activity in the floodplain. The system utilizes latest web technologies and graphics processing unit (GPU) for water simulation and object collisions 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. This presentation provides an overview of the web-based flood simulation system, and demonstrates the capabilities of the system for various visualization and interaction modes.

Designing Search: Effective Search Interfaces for Academic Library Web Sites

ERIC Educational Resources Information Center

Teague-Rector, Susan; Ghaphery, Jimmy

2008-01-01

Academic libraries customize, support, and provide access to myriad information systems, each with complex graphical user interfaces. The number of possible information entry points on an academic library Web site is both daunting to the end-user and consistently challenging to library Web site designers. Faced with the challenges inherent in…

The New Web-Based Hera Data Processing System at the HEASARC

NASA Technical Reports Server (NTRS)

Pence, W.

2011-01-01

The HEASARC at NASA/GSFC has provide an on-line astronomical data processing system called Hera for several years. Hera provides a complete data processing environment, including installed software packages, local data storage, and the CPU resources needed to process the user's data. The original design of Hera, however, has 2 requirements that has limited it's usefulness for some users, namely, that 1) the user must download and install a small helper program on their own computer before using Hera, and 2) Hera requires that several computer ports/sockets be allowed to communicate through any local firewalls on the users machine. Both of these restrictions can be problematic for some users, therefore we are now migrating Hera into a purely Web based environment which only requires a standard Web browser. The first release of Web Hera is now publicly available at http://heasarc.gsfc.nasa.gov/webheara/. It currently provides a standard graphical interface for running hundreds of different data processing programs that are available in the HEASARC's ftools software package. Over the next year we to add more features to Web Hera, including an interactive command line interface, and more display and line capabilities.

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.

WebGL and web audio software lightweight components for multimedia education

NASA Astrophysics Data System (ADS)

Chang, Xin; Yuksel, Kivanc; Skarbek, Władysław

2017-08-01

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

A brief introduction to web-based genome browsers.

PubMed

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

2013-03-01

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

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

DOE PAGES

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

2016-08-31

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

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

PubMed

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

2016-08-31

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

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

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

Peng, Jiajie; Li, Hongxiang; Liu, Yongzhuang

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

Optimization Model for Web Based Multimodal Interactive Simulations.

PubMed

Halic, Tansel; Ahn, Woojin; De, Suvranu

2015-07-15

This paper presents a technique for optimizing the performance of web based multimodal interactive simulations. For such applications where visual quality and the performance of simulations directly influence user experience, overloading of hardware resources may result in unsatisfactory reduction in the quality of the simulation and user satisfaction. However, optimization of simulation performance on individual hardware platforms is not practical. Hence, we present a mixed integer programming model to optimize the performance of graphical rendering and simulation performance while satisfying application specific constraints. Our approach includes three distinct phases: identification, optimization and update . In the identification phase, the computing and rendering capabilities of the client device are evaluated using an exploratory proxy code. This data is utilized in conjunction with user specified design requirements in the optimization phase to ensure best possible computational resource allocation. The optimum solution is used for rendering (e.g. texture size, canvas resolution) and simulation parameters (e.g. simulation domain) in the update phase. Test results are presented on multiple hardware platforms with diverse computing and graphics capabilities to demonstrate the effectiveness of our approach.

Optimization Model for Web Based Multimodal Interactive Simulations

PubMed Central

Halic, Tansel; Ahn, Woojin; De, Suvranu

2015-01-01

This paper presents a technique for optimizing the performance of web based multimodal interactive simulations. For such applications where visual quality and the performance of simulations directly influence user experience, overloading of hardware resources may result in unsatisfactory reduction in the quality of the simulation and user satisfaction. However, optimization of simulation performance on individual hardware platforms is not practical. Hence, we present a mixed integer programming model to optimize the performance of graphical rendering and simulation performance while satisfying application specific constraints. Our approach includes three distinct phases: identification, optimization and update. In the identification phase, the computing and rendering capabilities of the client device are evaluated using an exploratory proxy code. This data is utilized in conjunction with user specified design requirements in the optimization phase to ensure best possible computational resource allocation. The optimum solution is used for rendering (e.g. texture size, canvas resolution) and simulation parameters (e.g. simulation domain) in the update phase. Test results are presented on multiple hardware platforms with diverse computing and graphics capabilities to demonstrate the effectiveness of our approach. PMID:26085713

AGUIA: autonomous graphical user interface assembly for clinical trials semantic data services.

PubMed

Correa, Miria C; Deus, Helena F; Vasconcelos, Ana T; Hayashi, Yuki; Ajani, Jaffer A; Patnana, Srikrishna V; Almeida, Jonas S

2010-10-26

AGUIA is a front-end web application originally developed to manage clinical, demographic and biomolecular patient data collected during clinical trials at MD Anderson Cancer Center. The diversity of methods involved in patient screening and sample processing generates a variety of data types that require a resource-oriented architecture to capture the associations between the heterogeneous data elements. AGUIA uses a semantic web formalism, resource description framework (RDF), and a bottom-up design of knowledge bases that employ the S3DB tool as the starting point for the client's interface assembly. The data web service, S3DB, meets the necessary requirements of generating the RDF and of explicitly distinguishing the description of the domain from its instantiation, while allowing for continuous editing of both. Furthermore, it uses an HTTP-REST protocol, has a SPARQL endpoint, and has open source availability in the public domain, which facilitates the development and dissemination of this application. However, S3DB alone does not address the issue of representing content in a form that makes sense for domain experts. We identified an autonomous set of descriptors, the GBox, that provides user and domain specifications for the graphical user interface. This was achieved by identifying a formalism that makes use of an RDF schema to enable the automatic assembly of graphical user interfaces in a meaningful manner while using only resources native to the client web browser (JavaScript interpreter, document object model). We defined a generalized RDF model such that changes in the graphic descriptors are automatically and immediately (locally) reflected into the configuration of the client's interface application. The design patterns identified for the GBox benefit from and reflect the specific requirements of interacting with data generated by clinical trials, and they contain clues for a general purpose solution to the challenge of having interfaces automatically assembled for multiple and volatile views of a domain. By coding AGUIA in JavaScript, for which all browsers include a native interpreter, a solution was found that assembles interfaces that are meaningful to the particular user, and which are also ubiquitous and lightweight, allowing the computational load to be carried by the client's machine.

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.

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

NASA Astrophysics Data System (ADS)

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

2001-09-01

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

Web mapping system for complex processing and visualization of environmental geospatial datasets

NASA Astrophysics Data System (ADS)

Titov, Alexander; Gordov, Evgeny; Okladnikov, Igor

2016-04-01

Environmental geospatial datasets (meteorological observations, modeling and reanalysis results, etc.) are used in numerous research applications. Due to a number of objective reasons such as inherent heterogeneity of environmental datasets, big dataset volume, complexity of data models used, syntactic and semantic differences that complicate creation and use of unified terminology, the development of environmental geodata access, processing and visualization services as well as client applications turns out to be quite a sophisticated task. According to general INSPIRE requirements to data visualization geoportal web applications have to provide such standard functionality as data overview, image navigation, scrolling, scaling and graphical overlay, displaying map legends and corresponding metadata information. It should be noted that modern web mapping systems as integrated geoportal applications are developed based on the SOA and might be considered as complexes of interconnected software tools for working with geospatial data. In the report a complex web mapping system including GIS web client and corresponding OGC services for working with geospatial (NetCDF, PostGIS) dataset archive is presented. There are three basic tiers of the GIS web client in it: 1. Tier of geospatial metadata retrieved from central MySQL repository and represented in JSON format 2. Tier of JavaScript objects implementing methods handling: --- NetCDF metadata --- Task XML object for configuring user calculations, input and output formats --- OGC WMS/WFS cartographical services 3. Graphical user interface (GUI) tier representing JavaScript objects realizing web application business logic Metadata tier consists of a number of JSON objects containing technical information describing geospatial datasets (such as spatio-temporal resolution, meteorological parameters, valid processing methods, etc). The middleware tier of JavaScript objects implementing methods for handling geospatial metadata, task XML object, and WMS/WFS cartographical services interconnects metadata and GUI tiers. The methods include such procedures as JSON metadata downloading and update, launching and tracking of the calculation task running on the remote servers as well as working with WMS/WFS cartographical services including: obtaining the list of available layers, visualizing layers on the map, exporting layers in graphical (PNG, JPG, GeoTIFF), vector (KML, GML, Shape) and digital (NetCDF) formats. Graphical user interface tier is based on the bundle of JavaScript libraries (OpenLayers, GeoExt and ExtJS) and represents a set of software components implementing web mapping application business logic (complex menus, toolbars, wizards, event handlers, etc.). GUI provides two basic capabilities for the end user: configuring the task XML object functionality and cartographical information visualizing. The web interface developed is similar to the interface of such popular desktop GIS applications, as uDIG, QuantumGIS etc. Web mapping system developed has shown its effectiveness in the process of solving real climate change research problems and disseminating investigation results in cartographical form. The work is supported by SB RAS Basic Program Projects VIII.80.2.1 and IV.38.1.7.

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

PubMed

Sallaz-Damaz, Yoann; Ferrer, Jean Luc

2017-09-01

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

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

PubMed Central

2015-01-01

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

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

PubMed

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

2014-09-22

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

A Browser-Based Multi-User Working Environment for Physicists

NASA Astrophysics Data System (ADS)

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

2014-06-01

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

Improving the interactivity and functionality of Web-based radiology teaching files with the Java programming language.

PubMed

Eng, J

1997-01-01

Java is a programming language that runs on a "virtual machine" built into World Wide Web (WWW)-browsing programs on multiple hardware platforms. Web pages were developed with Java to enable Web-browsing programs to overlay transparent graphics and text on displayed images so that the user could control the display of labels and annotations on the images, a key feature not available with standard Web pages. This feature was extended to include the presentation of normal radiologic anatomy. Java programming was also used to make Web browsers compatible with the Digital Imaging and Communications in Medicine (DICOM) file format. By enhancing the functionality of Web pages, Java technology should provide greater incentive for using a Web-based approach in the development of radiology teaching material.

Thermal Protection System Imagery Inspection Management System -TIIMS

NASA Technical Reports Server (NTRS)

Goza, Sharon; Melendrez, David L.; Henningan, Marsha; LaBasse, Daniel; Smith, Daniel J.

2011-01-01

TIIMS is used during the inspection phases of every mission to provide quick visual feedback, detailed inspection data, and determination to the mission management team. This system consists of a visual Web page interface, an SQL database, and a graphical image generator. These combine to allow a user to ascertain quickly the status of the inspection process, and current determination of any problem zones. The TIIMS system allows inspection engineers to enter their determinations into a database and to link pertinent images and video to those database entries. The database then assigns criteria to each zone and tile, and via query, sends the information to a graphical image generation program. Using the official TIPS database tile positions and sizes, the graphical image generation program creates images of the current status of the orbiter, coloring zones, and tiles based on a predefined key code. These images are then displayed on a Web page using customized JAVA scripts to display the appropriate zone of the orbiter based on the location of the user's cursor. The close-up graphic and database entry for that particular zone can then be seen by selecting the zone. This page contains links into the database to access the images used by the inspection engineer when they make the determination entered into the database. Status for the inspection zones changes as determinations are refined and shown by the appropriate color code.

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

PubMed

Riva, A; Bellazzi, R; Stefanelli, M

1997-01-01

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

Real-Time Geospatial Data Viewer (RETIGO)

EPA Science Inventory

This is a web-based method that allows the users to upload their air monitoring data and explore the data on graphical interface. The method is optimized for mobile monitoring data sets, showing the data on a map, on a time series, and referenced to a hypothesized line and/or poi...

An Online Virtual Laboratory of Electricity

ERIC Educational Resources Information Center

Gómez Tejedor, J. A.; Moltó Martínez, G.; Barros Vidaurre, C.

2008-01-01

In this article, we describe a Java-based virtual laboratory, accessible via the Internet by means of a Web browser. This remote laboratory enables the students to build both direct and alternating current circuits. The program includes a graphical user interface which resembles the connection board, and also the electrical components and tools…

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

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

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

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

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.

AGUIA: autonomous graphical user interface assembly for clinical trials semantic data services

PubMed Central

2010-01-01

Background AGUIA is a front-end web application originally developed to manage clinical, demographic and biomolecular patient data collected during clinical trials at MD Anderson Cancer Center. The diversity of methods involved in patient screening and sample processing generates a variety of data types that require a resource-oriented architecture to capture the associations between the heterogeneous data elements. AGUIA uses a semantic web formalism, resource description framework (RDF), and a bottom-up design of knowledge bases that employ the S3DB tool as the starting point for the client's interface assembly. Methods The data web service, S3DB, meets the necessary requirements of generating the RDF and of explicitly distinguishing the description of the domain from its instantiation, while allowing for continuous editing of both. Furthermore, it uses an HTTP-REST protocol, has a SPARQL endpoint, and has open source availability in the public domain, which facilitates the development and dissemination of this application. However, S3DB alone does not address the issue of representing content in a form that makes sense for domain experts. Results We identified an autonomous set of descriptors, the GBox, that provides user and domain specifications for the graphical user interface. This was achieved by identifying a formalism that makes use of an RDF schema to enable the automatic assembly of graphical user interfaces in a meaningful manner while using only resources native to the client web browser (JavaScript interpreter, document object model). We defined a generalized RDF model such that changes in the graphic descriptors are automatically and immediately (locally) reflected into the configuration of the client's interface application. Conclusions The design patterns identified for the GBox benefit from and reflect the specific requirements of interacting with data generated by clinical trials, and they contain clues for a general purpose solution to the challenge of having interfaces automatically assembled for multiple and volatile views of a domain. By coding AGUIA in JavaScript, for which all browsers include a native interpreter, a solution was found that assembles interfaces that are meaningful to the particular user, and which are also ubiquitous and lightweight, allowing the computational load to be carried by the client's machine. PMID:20977768

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

PubMed

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

2018-06-07

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

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Web-Based Environment for Maintaining Legacy Software

NASA Technical Reports Server (NTRS)

Tigges, Michael; Thompson, Nelson; Orr, Mark; Fox, Richard

2007-01-01

Advanced Tool Integration Environment (ATIE) is the name of both a software system and a Web-based environment created by the system for maintaining an archive of legacy software and expertise involved in developing the legacy software. ATIE can also be used in modifying legacy software and developing new software. The information that can be encapsulated in ATIE includes experts documentation, input and output data of tests cases, source code, and compilation scripts. All of this information is available within a common environment and retained in a database for ease of access and recovery by use of powerful search engines. ATIE also accommodates the embedment of supporting software that users require for their work, and even enables access to supporting commercial-off-the-shelf (COTS) software within the flow of the experts work. The flow of work can be captured by saving the sequence of computer programs that the expert uses. A user gains access to ATIE via a Web browser. A modern Web-based graphical user interface promotes efficiency in the retrieval, execution, and modification of legacy code. Thus, ATIE saves time and money in the support of new and pre-existing programs.

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.

Branch: an interactive, web-based tool for testing hypotheses and developing predictive models.

PubMed

Gangavarapu, Karthik; Babji, Vyshakh; Meißner, Tobias; Su, Andrew I; Good, Benjamin M

2016-07-01

Branch is a web application that provides users with the ability to interact directly with large biomedical datasets. The interaction is mediated through a collaborative graphical user interface for building and evaluating decision trees. These trees can be used to compose and test sophisticated hypotheses and to develop predictive models. Decision trees are built and evaluated based on a library of imported datasets and can be stored in a collective area for sharing and re-use. Branch is hosted at http://biobranch.org/ and the open source code is available at http://bitbucket.org/sulab/biobranch/ asu@scripps.edu or bgood@scripps.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

SequenceCEROSENE: a computational method and web server to visualize spatial residue neighborhoods at the sequence level.

PubMed

Heinke, Florian; Bittrich, Sebastian; Kaiser, Florian; Labudde, Dirk

2016-01-01

To understand the molecular function of biopolymers, studying their structural characteristics is of central importance. Graphics programs are often utilized to conceive these properties, but with the increasing number of available structures in databases or structure models produced by automated modeling frameworks this process requires assistance from tools that allow automated structure visualization. In this paper a web server and its underlying method for generating graphical sequence representations of molecular structures is presented. The method, called SequenceCEROSENE (color encoding of residues obtained by spatial neighborhood embedding), retrieves the sequence of each amino acid or nucleotide chain in a given structure and produces a color coding for each residue based on three-dimensional structure information. From this, color-highlighted sequences are obtained, where residue coloring represent three-dimensional residue locations in the structure. This color encoding thus provides a one-dimensional representation, from which spatial interactions, proximity and relations between residues or entire chains can be deduced quickly and solely from color similarity. Furthermore, additional heteroatoms and chemical compounds bound to the structure, like ligands or coenzymes, are processed and reported as well. To provide free access to SequenceCEROSENE, a web server has been implemented that allows generating color codings for structures deposited in the Protein Data Bank or structure models uploaded by the user. Besides retrieving visualizations in popular graphic formats, underlying raw data can be downloaded as well. In addition, the server provides user interactivity with generated visualizations and the three-dimensional structure in question. Color encoded sequences generated by SequenceCEROSENE can aid to quickly perceive the general characteristics of a structure of interest (or entire sets of complexes), thus supporting the researcher in the initial phase of structure-based studies. In this respect, the web server can be a valuable tool, as users are allowed to process multiple structures, quickly switch between results, and interact with generated visualizations in an intuitive manner. The SequenceCEROSENE web server is available at https://biosciences.hs-mittweida.de/seqcerosene.

Algorithm Visualization System for Teaching Spatial Data Algorithms

ERIC Educational Resources Information Center

Nikander, Jussi; Helminen, Juha; Korhonen, Ari

2010-01-01

TRAKLA2 is a web-based learning environment for data structures and algorithms. The system delivers automatically assessed algorithm simulation exercises that are solved using a graphical user interface. In this work, we introduce a novel learning environment for spatial data algorithms, SDA-TRAKLA2, which has been implemented on top of the…

VO-KOREL: A Fourier Disentangling Service of the Virtual Observatory

NASA Astrophysics Data System (ADS)

Škoda, Petr; Hadrava, Petr; Fuchs, Jan

2012-04-01

VO-KOREL is a web service exploiting the technology of the Virtual Observatory for providing astronomers with the intuitive graphical front-end and distributed computing back-end running the most recent version of the Fourier disentangling code KOREL. The system integrates the ideas of the e-shop basket, conserving the privacy of every user by transfer encryption and access authentication, with features of laboratory notebook, allowing the easy housekeeping of both input parameters and final results, as well as it explores a newly emerging technology of cloud computing. While the web-based front-end allows the user to submit data and parameter files, edit parameters, manage a job list, resubmit or cancel running jobs and mainly watching the text and graphical results of a disentangling process, the main part of the back-end is a simple job queue submission system executing in parallel multiple instances of the FORTRAN code KOREL. This may be easily extended for GRID-based deployment on massively parallel computing clusters. The short introduction into underlying technologies is given, briefly mentioning advantages as well as bottlenecks of the design used.

Using Common Graphics Paradigms Implemented in a Java Applet to Represent Complex Scheduling Requirements

NASA Technical Reports Server (NTRS)

Jaap, John; Meyer, Patrick; Davis, Elizabeth

1997-01-01

The experiments planned for the International Space Station promise to be complex, lengthy and diverse. The scarcity of the space station resources will cause significant competition for resources between experiments. The scheduling job facing the Space Station mission planning software requires a concise and comprehensive description of the experiments' requirements (to ensure a valid schedule) and a good description of the experiments' flexibility (to effectively utilize available resources). In addition, the continuous operation of the station, the wide geographic dispersion of station users, and the budgetary pressure to reduce operations manpower make a low-cost solution mandatory. A graphical representation of the scheduling requirements for station payloads implemented via an Internet-based application promises to be an elegant solution that addresses all of these issues. The graphical representation of experiment requirements permits a station user to describe his experiment by defining "activities" and "sequences of activities". Activities define the resource requirements (with alternatives) and other quantitative constraints of tasks to be performed. Activities definitions use an "outline" graphics paradigm. Sequences define the time relationships between activities. Sequences may also define time relationships with activities of other payloads or space station systems. Sequences of activities are described by a "network" graphics paradigm. The bulk of this paper will describe the graphical approach to representing requirements and provide examples that show the ease and clarity with which complex requirements can be represented. A Java applet, to run in a web browser, is being developed to support the graphical representation of payload scheduling requirements. Implementing the entry and editing of requirements via the web solves the problems introduced by the geographic dispersion of users. Reducing manpower is accomplished by developing a concise representation which eliminates the misunderstanding possible with verbose representations and which captures the complete requirements and flexibility of the experiments.

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

PubMed

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

2017-09-13

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

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

PubMed

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

2012-01-01

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

Web-based Tsunami Early Warning System with instant Tsunami Propagation Calculations in the GPU Cloud

NASA Astrophysics Data System (ADS)

Hammitzsch, M.; Spazier, J.; Reißland, S.

2014-12-01

Usually, tsunami early warning and mitigation systems (TWS or TEWS) are based on several software components deployed in a client-server based infrastructure. The vast majority of systems importantly include desktop-based clients with a graphical user interface (GUI) for the operators in early warning centers. However, in times of cloud computing and ubiquitous computing the use of concepts and paradigms, introduced by continuously evolving approaches in information and communications technology (ICT), have to be considered even for early warning systems (EWS). Based on the experiences and the knowledge gained in three research projects - 'German Indonesian Tsunami Early Warning System' (GITEWS), 'Distant Early Warning System' (DEWS), and 'Collaborative, Complex, and Critical Decision-Support in Evolving Crises' (TRIDEC) - new technologies are exploited to implement a cloud-based and web-based prototype to open up new prospects for EWS. This prototype, named 'TRIDEC Cloud', merges several complementary external and in-house cloud-based services into one platform for automated background computation with graphics processing units (GPU), for web-mapping of hazard specific geospatial data, and for serving relevant functionality to handle, share, and communicate threat specific information in a collaborative and distributed environment. The prototype in its current version addresses tsunami early warning and mitigation. The integration of GPU accelerated tsunami simulation computations have been an integral part of this prototype to foster early warning with on-demand tsunami predictions based on actual source parameters. However, the platform is meant for researchers around the world to make use of the cloud-based GPU computation to analyze other types of geohazards and natural hazards and react upon the computed situation picture with a web-based GUI in a web browser at remote sites. The current website is an early alpha version for demonstration purposes to give the concept a whirl and to shape science's future. Further functionality, improvements and possible profound changes have to implemented successively based on the users' evolving needs.

Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web.

PubMed

Miller, Chase A; Anthony, Jon; Meyer, Michelle M; Marth, Gabor

2013-02-01

High-throughput biological research requires simultaneous visualization as well as analysis of genomic data, e.g. read alignments, variant calls and genomic annotations. Traditionally, such integrative analysis required desktop applications operating on locally stored data. Many current terabyte-size datasets generated by large public consortia projects, however, are already only feasibly stored at specialist genome analysis centers. As even small laboratories can afford very large datasets, local storage and analysis are becoming increasingly limiting, and it is likely that most such datasets will soon be stored remotely, e.g. in the cloud. These developments will require web-based tools that enable users to access, analyze and view vast remotely stored data with a level of sophistication and interactivity that approximates desktop applications. As rapidly dropping cost enables researchers to collect data intended to answer questions in very specialized contexts, developers must also provide software libraries that empower users to implement customized data analyses and data views for their particular application. Such specialized, yet lightweight, applications would empower scientists to better answer specific biological questions than possible with general-purpose genome browsers currently available. Using recent advances in core web technologies (HTML5), we developed Scribl, a flexible genomic visualization library specifically targeting coordinate-based data such as genomic features, DNA sequence and genetic variants. Scribl simplifies the development of sophisticated web-based graphical tools that approach the dynamism and interactivity of desktop applications. Software is freely available online at http://chmille4.github.com/Scribl/ and is implemented in JavaScript with all modern browsers supported.

Food Web Designer: a flexible tool to visualize interaction networks.

PubMed

Sint, Daniela; Traugott, Michael

Species are embedded in complex networks of ecological interactions and assessing these networks provides a powerful approach to understand what the consequences of these interactions are for ecosystem functioning and services. This is mandatory to develop and evaluate strategies for the management and control of pests. Graphical representations of networks can help recognize patterns that might be overlooked otherwise. However, there is a lack of software which allows visualizing these complex interaction networks. Food Web Designer is a stand-alone, highly flexible and user friendly software tool to quantitatively visualize trophic and other types of bipartite and tripartite interaction networks. It is offered free of charge for use on Microsoft Windows platforms. Food Web Designer is easy to use without the need to learn a specific syntax due to its graphical user interface. Up to three (trophic) levels can be connected using links cascading from or pointing towards the taxa within each level to illustrate top-down and bottom-up connections. Link width/strength and abundance of taxa can be quantified, allowing generating fully quantitative networks. Network datasets can be imported, saved for later adjustment and the interaction webs can be exported as pictures for graphical display in different file formats. We show how Food Web Designer can be used to draw predator-prey and host-parasitoid food webs, demonstrating that this software is a simple and straightforward tool to graphically display interaction networks for assessing pest control or any other type of interaction in both managed and natural ecosystems from an ecological network perspective.

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/.

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

PubMed Central

Kuzniar, Arnold; Kanaar, Roland

2014-01-01

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

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

PubMed

Kuzniar, Arnold; Kanaar, Roland

2014-07-01

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

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

PubMed

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

2012-12-21

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

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

A Multi-User Model for Effectively Communicating Research Through Electronic Media

NASA Astrophysics Data System (ADS)

Hinds, J. J.; Fairley, J. P.

2003-12-01

Electronic media have demonstrated potential for data exchange, dissemination of results to other scientists, communication with community interest groups, and education of the general public regarding scientific advances. Few researchers, however, receive training in the skills required to capture the attention of the broad spectrum of Internet users. Because different people assimilate information in different ways, effective communication is best accomplished using an appropriate mix of photographs, graphics, tables, and text. In addition, effective web page design requires a clear, consistent organizational structure, easily-navigated layout, and attention to details such as page printability, downloading time, and minimal page scrolling. One of the strengths of electronic media is that the user can chose an appropriate level of involvement for his or her interest. In designing a web page for the multidisciplinary NSF/EPSCoR "Biocomplexity in Extreme Environments" project, we divided potential users into three categories based on our perception of the level of detail they required: 1) project participants, 2) non-participants with technical backgrounds, and 3) the general public. By understanding the needs and expectations of potential viewers, it was possible to present each group with an appropriate balance of visual and textural elements. For example, project participants are often most interested in raw data, which can be effectively presented in tabular format. Non-participants with technical backgrounds are more interested in analyzed data, while a project overview, presented through photographs and graphics with minimal text, will be most effective for communicating with the general public. The completed web page illustrates one solution for effectively communicating with a diverse audience, and provides examples for meeting many of the challenges of web page design.

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

PDM and the Internet: A Look at Product Management and Its Internet Opportunities.

ERIC Educational Resources Information Center

Mendel, Alan

1997-01-01

Discusses the impact of internet technology on product data management (PDM) vendor's and the users' purchasing decisions. Internet users anticipate graphical user interface (GUI) and two-way communication which allow users to enter and modify data as well as access it. Examines PDM and the Internet: price and performance, the World Wide Web,…

The WebACS - An Accessible Graphical Editor.

PubMed

Parker, Stefan; Nussbaum, Gerhard; Pölzer, Stephan

2017-01-01

This paper is about the solution to accessibility problems met when implementing a graphical editor, a major challenge being the comprehension of the relationships between graphical components, which needs to be guaranteed for blind and vision impaired users. In the concrete case the HTML5 canvas and Javascript were used. Accessibility was reached by implementing a list view of elements, which also enhances the usability of the editor.

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.

NGL Viewer: a web application for molecular visualization

PubMed Central

Rose, Alexander S.; Hildebrand, Peter W.

2015-01-01

The NGL Viewer (http://proteinformatics.charite.de/ngl) is a web application for the visualization of macromolecular structures. By fully adopting capabilities of modern web browsers, such as WebGL, for molecular graphics, the viewer can interactively display large molecular complexes and is also unaffected by the retirement of third-party plug-ins like Flash and Java Applets. Generally, the web application offers comprehensive molecular visualization through a graphical user interface so that life scientists can easily access and profit from available structural data. It supports common structural file-formats (e.g. PDB, mmCIF) and a variety of molecular representations (e.g. ‘cartoon, spacefill, licorice’). Moreover, the viewer can be embedded in other web sites to provide specialized visualizations of entries in structural databases or results of structure-related calculations. PMID:25925569

Hanford Borehole Geologic Information System (HBGIS) Updated User’s Guide for Web-based Data Access and Export

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

Mackley, Rob D.; Last, George V.; Allwardt, Craig H.

2008-09-24

The Hanford Borehole Geologic Information System (HBGIS) is a prototype web-based graphical user interface (GUI) for viewing and downloading borehole geologic data. The HBGIS is being developed as part of the Remediation Decision Support function of the Soil and Groundwater Remediation Project, managed by Fluor Hanford, Inc., Richland, Washington. Recent efforts have focused on improving the functionality of the HBGIS website in order to allow more efficient access and exportation of available data in HBGIS. Users will benefit from enhancements such as a dynamic browsing, user-driven forms, and multi-select options for selecting borehole geologic data for export. The need formore » translating borehole geologic data into electronic form within the HBGIS continues to increase, and efforts to populate the database continue at an increasing rate. These new web-based tools should help the end user quickly visualize what data are available in HBGIS, select from among these data, and download the borehole geologic data into a consistent and reproducible tabular form. This revised user’s guide supersedes the previous user’s guide (PNNL-15362) for viewing and downloading data from HBGIS. It contains an updated data dictionary for tables and fields containing borehole geologic data as well as instructions for viewing and downloading borehole geologic data.« less

SVG-Based Web Publishing

NASA Astrophysics Data System (ADS)

Gao, Jerry Z.; Zhu, Eugene; Shim, Simon

2003-01-01

With the increasing applications of the Web in e-commerce, advertising, and publication, new technologies are needed to improve Web graphics technology due to the current limitation of technology. The SVG (Scalable Vector Graphics) technology is a new revolutionary solution to overcome the existing problems in the current web technology. It provides precise and high-resolution web graphics using plain text format commands. It sets a new standard for web graphic format to allow us to present complicated graphics with rich test fonts and colors, high printing quality, and dynamic layout capabilities. This paper provides a tutorial overview about SVG technology and its essential features, capability, and advantages. The reports a comparison studies between SVG and other web graphics technologies.

Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web

PubMed Central

Miller, Chase A.; Anthony, Jon; Meyer, Michelle M.; Marth, Gabor

2013-01-01

Motivation: High-throughput biological research requires simultaneous visualization as well as analysis of genomic data, e.g. read alignments, variant calls and genomic annotations. Traditionally, such integrative analysis required desktop applications operating on locally stored data. Many current terabyte-size datasets generated by large public consortia projects, however, are already only feasibly stored at specialist genome analysis centers. As even small laboratories can afford very large datasets, local storage and analysis are becoming increasingly limiting, and it is likely that most such datasets will soon be stored remotely, e.g. in the cloud. These developments will require web-based tools that enable users to access, analyze and view vast remotely stored data with a level of sophistication and interactivity that approximates desktop applications. As rapidly dropping cost enables researchers to collect data intended to answer questions in very specialized contexts, developers must also provide software libraries that empower users to implement customized data analyses and data views for their particular application. Such specialized, yet lightweight, applications would empower scientists to better answer specific biological questions than possible with general-purpose genome browsers currently available. Results: Using recent advances in core web technologies (HTML5), we developed Scribl, a flexible genomic visualization library specifically targeting coordinate-based data such as genomic features, DNA sequence and genetic variants. Scribl simplifies the development of sophisticated web-based graphical tools that approach the dynamism and interactivity of desktop applications. Availability and implementation: Software is freely available online at http://chmille4.github.com/Scribl/ and is implemented in JavaScript with all modern browsers supported. Contact: gabor.marth@bc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23172864

Visualization for genomics: the Microbial Genome Viewer.

PubMed

Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

2004-07-22

A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

A Java-Enabled Interactive Graphical Gas Turbine Propulsion System Simulator

NASA Technical Reports Server (NTRS)

Reed, John A.; Afjeh, Abdollah A.

1997-01-01

This paper describes a gas turbine simulation system which utilizes the newly developed Java language environment software system. The system provides an interactive graphical environment which allows the quick and efficient construction and analysis of arbitrary gas turbine propulsion systems. The simulation system couples a graphical user interface, developed using the Java Abstract Window Toolkit, and a transient, space- averaged, aero-thermodynamic gas turbine analysis method, both entirely coded in the Java language. The combined package provides analytical, graphical and data management tools which allow the user to construct and control engine simulations by manipulating graphical objects on the computer display screen. Distributed simulations, including parallel processing and distributed database access across the Internet and World-Wide Web (WWW), are made possible through services provided by the Java environment.

The use of interactive graphical maps for browsing medical/health Internet information resources

PubMed Central

Boulos, Maged N Kamel

2003-01-01

As online information portals accumulate metadata descriptions of Web resources, it becomes necessary to develop effective ways for visualising and navigating the resultant huge metadata repositories as well as the different semantic relationships and attributes of described Web resources. Graphical maps provide a good method to visualise, understand and navigate a world that is too large and complex to be seen directly like the Web. Several examples of maps designed as a navigational aid for Web resources are presented in this review with an emphasis on maps of medical and health-related resources. The latter include HealthCyberMap maps , which can be classified as conceptual information space maps, and the very abstract and geometric Visual Net maps of PubMed (for demos). Information resources can be also organised and navigated based on their geographic attributes. Some of the maps presented in this review use a Kohonen Self-Organising Map algorithm, and only HealthCyberMap uses a Geographic Information System to classify Web resource data and render the maps. Maps based on familiar metaphors taken from users' everyday life are much easier to understand. Associative and pictorial map icons that enable instant recognition and comprehension are preferred to geometric ones and are key to successful maps for browsing medical/health Internet information resources. PMID:12556244

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

PubMed

Zhou, Guangyan; Xia, Jianguo

2018-06-07

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

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.

Web-GIS platform for monitoring and forecasting of regional climate and ecological changes

NASA Astrophysics Data System (ADS)

Gordov, E. P.; Krupchatnikov, V. N.; Lykosov, V. N.; Okladnikov, I.; Titov, A. G.; Shulgina, T. M.

2012-12-01

Growing volume of environmental data from sensors and model outputs makes development of based on modern information-telecommunication technologies software infrastructure for information support of integrated scientific researches in the field of Earth sciences urgent and important task (Gordov et al, 2012, van der Wel, 2005). It should be considered that original heterogeneity of datasets obtained from different sources and institutions not only hampers interchange of data and analysis results but also complicates their intercomparison leading to a decrease in reliability of analysis results. However, modern geophysical data processing techniques allow combining of different technological solutions for organizing such information resources. Nowadays it becomes a generally accepted opinion that information-computational infrastructure should rely on a potential of combined usage of web- and GIS-technologies for creating applied information-computational web-systems (Titov et al, 2009, Gordov et al. 2010, Gordov, Okladnikov and Titov, 2011). Using these approaches for development of internet-accessible thematic information-computational systems, and arranging of data and knowledge interchange between them is a very promising way of creation of distributed information-computation environment for supporting of multidiscipline regional and global research in the field of Earth sciences including analysis of climate changes and their impact on spatial-temporal vegetation distribution and state. Experimental software and hardware platform providing operation of a web-oriented production and research center for regional climate change investigations which combines modern web 2.0 approach, GIS-functionality and capabilities of running climate and meteorological models, large geophysical datasets processing, visualization, joint software development by distributed research groups, scientific analysis and organization of students and post-graduate students education is presented. Platform software developed (Shulgina et al, 2012, Okladnikov et al, 2012) includes dedicated modules for numerical processing of regional and global modeling results for consequent analysis and visualization. Also data preprocessing, run and visualization of modeling results of models WRF and «Planet Simulator» integrated into the platform is provided. All functions of the center are accessible by a user through a web-portal using common graphical web-browser in the form of an interactive graphical user interface which provides, particularly, capabilities of visualization of processing results, selection of geographical region of interest (pan and zoom) and data layers manipulation (order, enable/disable, features extraction). Platform developed provides users with capabilities of heterogeneous geophysical data analysis, including high-resolution data, and discovering of tendencies in climatic and ecosystem changes in the framework of different multidisciplinary researches (Shulgina et al, 2011). Using it even unskilled user without specific knowledge can perform computational processing and visualization of large meteorological, climatological and satellite monitoring datasets through unified graphical web-interface.

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

PubMed Central

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

2016-01-01

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

Risk Management Collaboration through Sharing Interactive Graphics

NASA Astrophysics Data System (ADS)

Slingsby, Aidan; Dykes, Jason; Wood, Jo; Foote, Matthew

2010-05-01

Risk management involves the cooperation of scientists, underwriters and actuaries all of whom analyse data to support decision-making. Results are often disseminated through static documents with graphics that convey the message the analyst wishes to communicate. Interactive graphics are increasingly popular means of communicating the results of data analyses because they enable other parties to explore and visually analyse some of the data themselves prior to and during discussion. Discussion around interactive graphics can occur synchronously in face-to-face meetings or with video-conferencing and screen sharing or they can occur asynchronously through web-sites such as ManyEyes, web-based fora, blogs, wikis and email. A limitation of approaches that do not involve screen sharing is the difficulty in sharing the results of insights from interacting with the graphic. Static images accompanied can be shared but these themselves cannot be interacted, producing a discussion bottleneck (Baker, 2008). We address this limitation by allowing the state and configuration of graphics to be shared (rather than static images) so that a user can reproduce someone else's graphic, interact with it and then share the results of this accompanied with some commentary. HiVE (Slingsby et al, 2009) is a compact and intuitive text-based language that has been designed for this purpose. We will describe the vizTweets project (a 9-month project funded by JISC) in which we are applying these principles to insurance risk management in the context of the Willis Research Network, the world's largest collaboration between the insurance industry and the academia). The project aims to extend HiVE to meet the needs of the sector, design, implement free-available web services and tools and to provide case studies. We will present a case study that demonstrate the potential of this approach for collaboration within the Willis Research Network. Baker, D. Towards Transparency in Visualisation Based Research. AHRC ICT Methods Network Expert Workshop. Available at http://www.viznet.ac.uk/documents Slingsby, A., Dykes, J. and Wood, J. 2009. Configuring Hierarchical Layouts to Address Research Questions. IEEE Transactions on Visualization and Computer Graphics 15 (6), Nov-Dec 2009, pp977-984.

Web GIS in practice II: interactive SVG maps of diagnoses of sexually transmitted diseases by Primary Care Trust in London, 1997 – 2003

PubMed Central

Boulos, Maged N Kamel; Russell, Chris; Smith, Michael

2005-01-01

Background The rates of Sexually transmitted diseases (STDs) in England have been rising steadily since the mid 1990s, making them a major public health concern. In 2003, 672,718 people were diagnosed with an STD in England, and around one third of those cases were diagnosed in London. Results Using GeoReveal v1.1 for Windows, we produced Web-based interactive choropleth maps of diagnoses of STDs by Primary Care Trust (PCT) in London for the years from 1997 to 2003 . These maps are in Scalable Vector Graphics (SVG) format and require a freely available Adobe SVG browser plug-in to be displayed. They are based on data obtained from the House of Commons Hansard Written Answers for 15 October 2004. They show steadily rising rates of STDs in London over the covered seven-year period. Also, one can clearly see on the maps that PCTs located in central London had the highest numbers of STD diagnoses throughout the mapped seven years. A companion bar chart allows users to instantly compare the STD figure of a given PCT for a given year against the average figure for all 25 mapped PCTs for the same year, and also compare those figures across all seven years. The maps offer users a rich set of useful features and functions, including the ability to change the classification method in use, the number of ranges in the map, and the colour theme, among others. Conclusions Wizard-driven tools like GeoReveal have made it very easy to transform complex raw data into valuable decision support information products (interactive Web maps) in very little time and without requiring much expertise. The resultant interactive maps have the potential of further supporting health planners and decision makers in their planning and management tasks by allowing them to graphically interrogate data, instantly spot trends, and make quick and effective visual comparisons of geographically differentiated phenomena between different geographical areas and over time. SVG makes an ideal format for such maps. SVG is a World Wide Web Consortium non-proprietary, XML-based vector graphics format, and is an extremely powerful alternative to Macromedia® Flash and bitmap graphics. PMID:15655078

Dynamic Interactive Educational Diabetes Simulations Using the World Wide Web: An Experience of More Than 15 Years with AIDA Online

PubMed Central

Lehmann, Eldon D.; DeWolf, Dennis K.; Novotny, Christopher A.; Reed, Karen; Gotwals, Robert R.

2014-01-01

Background. AIDA is a widely available downloadable educational simulator of glucose-insulin interaction in diabetes. Methods. A web-based version of AIDA was developed that utilises a server-based architecture with HTML FORM commands to submit numerical data from a web-browser client to a remote web server. AIDA online, located on a remote server, passes the received data through Perl scripts which interactively produce 24 hr insulin and glucose simulations. Results. AIDA online allows users to modify the insulin regimen and diet of 40 different prestored “virtual diabetic patients” on the internet or create new “patients” with user-generated regimens. Multiple simulations can be run, with graphical results viewed via a standard web-browser window. To date, over 637,500 diabetes simulations have been run at AIDA online, from all over the world. Conclusions. AIDA online's functionality is similar to the downloadable AIDA program, but the mode of implementation and usage is different. An advantage to utilising a server-based application is the flexibility that can be offered. New modules can be added quickly to the online simulator. This has facilitated the development of refinements to AIDA online, which have instantaneously become available around the world, with no further local downloads or installations being required. PMID:24511312

Dynamic Interactive Educational Diabetes Simulations Using the World Wide Web: An Experience of More Than 15 Years with AIDA Online.

PubMed

Lehmann, Eldon D; Dewolf, Dennis K; Novotny, Christopher A; Reed, Karen; Gotwals, Robert R

2014-01-01

Background. AIDA is a widely available downloadable educational simulator of glucose-insulin interaction in diabetes. Methods. A web-based version of AIDA was developed that utilises a server-based architecture with HTML FORM commands to submit numerical data from a web-browser client to a remote web server. AIDA online, located on a remote server, passes the received data through Perl scripts which interactively produce 24 hr insulin and glucose simulations. Results. AIDA online allows users to modify the insulin regimen and diet of 40 different prestored "virtual diabetic patients" on the internet or create new "patients" with user-generated regimens. Multiple simulations can be run, with graphical results viewed via a standard web-browser window. To date, over 637,500 diabetes simulations have been run at AIDA online, from all over the world. Conclusions. AIDA online's functionality is similar to the downloadable AIDA program, but the mode of implementation and usage is different. An advantage to utilising a server-based application is the flexibility that can be offered. New modules can be added quickly to the online simulator. This has facilitated the development of refinements to AIDA online, which have instantaneously become available around the world, with no further local downloads or installations being required.

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.

A Web-based graphical user interface for evidence-based decision making for health care allocations in rural areas

PubMed Central

Schuurman, Nadine; Leight, Margo; Berube, Myriam

2008-01-01

Background The creation of successful health policy and location of resources increasingly relies on evidence-based decision-making. The development of intuitive, accessible tools to analyse, display and disseminate spatial data potentially provides the basis for sound policy and resource allocation decisions. As health services are rationalized, the development of tools such graphical user interfaces (GUIs) is especially valuable at they assist decision makers in allocating resources such that the maximum number of people are served. GIS can used to develop GUIs that enable spatial decision making. Results We have created a Web-based GUI (wGUI) to assist health policy makers and administrators in the Canadian province of British Columbia make well-informed decisions about the location and allocation of time-sensitive service capacities in rural regions of the province. This tool integrates datasets for existing hospitals and services, regional populations and road networks to allow users to ascertain the percentage of population in any given service catchment who are served by a specific health service, or baskets of linked services. The wGUI allows policy makers to map trauma and obstetric services against rural populations within pre-specified travel distances, illustrating service capacity by region. Conclusion The wGUI can be used by health policy makers and administrators with little or no formal GIS training to visualize multiple health resource allocation scenarios. The GUI is poised to become a critical decision-making tool especially as evidence is increasingly required for distribution of health services. PMID:18793428

Food Chains & Webs. A Multimedia CD-ROM. [CD-ROM].

ERIC Educational Resources Information Center

2001

This CD-ROM is designed for classroom and individual use to teach and learn about food chains and food webs. Integrated animations, custom graphics, three-dimensional representations, photographs, and sound are featured for use in user-controlled activities. Interactive lessons are available to reinforce the subject material. Pre- and post-testing…

Web Based Monitoring in the CMS Experiment at CERN

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

Badgett, William; Borrello, Laura; Chakaberia, Irakli

2014-09-03

The Compact Muon Solenoid (CMS) is a large and complex general purpose experiment at the CERN Large Hadron Collider (LHC), built and maintained by many collaborators from around the world. Efficient operation of the detector requires widespread and timely access to a broad range of monitoring and status information. To this end the Web Based Monitoring (WBM) system was developed to present data to users located anywhere from many underlying heterogeneous sources, from real time messaging systems to relational databases. This system provides the power to combine and correlate data in both graphical and tabular formats of interest to themore » experimenters, including data such as beam conditions, luminosity, trigger rates, detector conditions, and many others, allowing for flexibility on the user side. This paper describes the WBM system architecture and describes how the system was used during the first major data taking run of the LHC.« less

NGL Viewer: a web application for molecular visualization.

PubMed

Rose, Alexander S; Hildebrand, Peter W

2015-07-01

The NGL Viewer (http://proteinformatics.charite.de/ngl) is a web application for the visualization of macromolecular structures. By fully adopting capabilities of modern web browsers, such as WebGL, for molecular graphics, the viewer can interactively display large molecular complexes and is also unaffected by the retirement of third-party plug-ins like Flash and Java Applets. Generally, the web application offers comprehensive molecular visualization through a graphical user interface so that life scientists can easily access and profit from available structural data. It supports common structural file-formats (e.g. PDB, mmCIF) and a variety of molecular representations (e.g. 'cartoon, spacefill, licorice'). Moreover, the viewer can be embedded in other web sites to provide specialized visualizations of entries in structural databases or results of structure-related calculations. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Viewing ISS Data in Real Time via the Internet

NASA Technical Reports Server (NTRS)

Myers, Gerry; Chamberlain, Jim

2004-01-01

EZStream is a computer program that enables authorized users at diverse terrestrial locations to view, in real time, data generated by scientific payloads aboard the International Space Station (ISS). The only computation/communication resource needed for use of EZStream is a computer equipped with standard Web-browser software and a connection to the Internet. EZStream runs in conjunction with the TReK software, described in a prior NASA Tech Briefs article, that coordinates multiple streams of data for the ground communication system of the ISS. EZStream includes server components that interact with TReK within the ISS ground communication system and client components that reside in the users' remote computers. Once an authorized client has logged in, a server component of EZStream pulls the requested data from a TReK application-program interface and sends the data to the client. Future EZStream enhancements will include (1) extensions that enable the server to receive and process arbitrary data streams on its own and (2) a Web-based graphical-user-interface-building subprogram that enables a client who lacks programming expertise to create customized display Web pages.

Easing access to R using 'shiny' to create graphical user interfaces: An example for the R package 'Luminescence'

NASA Astrophysics Data System (ADS)

Burow, Christoph; Kreutzer, Sebastian; Dietze, Michael; Fuchs, Margret C.; Schmidt, Christoph; Fischer, Manfred; Brückner, Helmut

2017-04-01

Since the release of the R package 'Luminescence' (Kreutzer et al., 2012) the functionality of the package has been greatly enhanced by implementing further functions for measurement data processing, statistical analysis and graphical output. Despite its capabilities for complex and non-standard analysis of luminescence data, working with the command-line interface (CLI) of R can be tedious at best and overwhelming at worst, especially for users without experience in programming languages. Even though much work is put into simplifying the usage of the package to continuously lower the entry threshold, at least basic knowledge of R will always be required. Thus, the potential user base of the package cannot be exhausted, at least as long as the CLI is the only means of utilising the 'Luminescence' package. But even experienced users may find it tedious to iteratively run a function until a satisfying results is produced. For example, plotting data is also at least partly subject to personal aesthetic tastes in accordance with the information it is supposed to convey and iterating through all the possible options in the R CLI can be a time-consuming task. An alternative approach to the CLI is the graphical user interface (GUI), which allows direct, interactive manipulation and interaction with the underlying software. For users with little or no experience with command-lines a GUI offers intuitive access that counteracts the perceived steep learning curve of a CLI. Even though R lacks native support for GUI functions, its capabilities of linking it to other programming languages allows to utilise external frameworks to build graphical user interfaces. A recent attempt to provide a GUI toolkit for R was the introduction of the 'shiny' package (Chang et al., 2016), which allows automatic construction of HTML, CSS and JavaScript based user interfaces straight from R. Here, we give (1) a brief introduction to the 'shiny' framework for R, before we (2) present a GUI for the R package 'Luminescence' in the form of interactive web applications. These applications can be accessed online so that a user is not even required to have a local installation of R and which provide access to most of the plotting functions of the R package 'Luminescence'. These functionalities will be demonstrated live during the PICO session. References Chang, W., Cheng, J., Allaire, JJ., Xie, Y., McPherson, J., 2016. shiny: Web Application Framework for R. R package version 0.13.2. https://CRAN.R-project.org/package=shiny Kreutzer, S., Schmidt, C., Fuchs, M.C., Dietze, M., Fischer, M., Fuchs, M., 2012. Introducing an R package for luminescence dating analysis. Ancient TL, 30: 1-8, 2012.

Web-based, GPU-accelerated, Monte Carlo simulation and visualization of indirect radiation imaging detector performance.

PubMed

Dong, Han; Sharma, Diksha; Badano, Aldo

2014-12-01

Monte Carlo simulations play a vital role in the understanding of the fundamental limitations, design, and optimization of existing and emerging medical imaging systems. Efforts in this area have resulted in the development of a wide variety of open-source software packages. One such package, hybridmantis, uses a novel hybrid concept to model indirect scintillator detectors by balancing the computational load using dual CPU and graphics processing unit (GPU) processors, obtaining computational efficiency with reasonable accuracy. In this work, the authors describe two open-source visualization interfaces, webmantis and visualmantis to facilitate the setup of computational experiments via hybridmantis. The visualization tools visualmantis and webmantis enable the user to control simulation properties through a user interface. In the case of webmantis, control via a web browser allows access through mobile devices such as smartphones or tablets. webmantis acts as a server back-end and communicates with an NVIDIA GPU computing cluster that can support multiuser environments where users can execute different experiments in parallel. The output consists of point response and pulse-height spectrum, and optical transport statistics generated by hybridmantis. The users can download the output images and statistics through a zip file for future reference. In addition, webmantis provides a visualization window that displays a few selected optical photon path as they get transported through the detector columns and allows the user to trace the history of the optical photons. The visualization tools visualmantis and webmantis provide features such as on the fly generation of pulse-height spectra and response functions for microcolumnar x-ray imagers while allowing users to save simulation parameters and results from prior experiments. The graphical interfaces simplify the simulation setup and allow the user to go directly from specifying input parameters to receiving visual feedback for the model predictions.

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

NASA Astrophysics Data System (ADS)

Huang, L. Xinglai; Sheng, Grant

2006-10-01

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

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.

Multichannel Networked Phasemeter Readout and Analysis

NASA Technical Reports Server (NTRS)

Edmonds, Karina

2008-01-01

Netmeter software reads a data stream from up to 250 networked phasemeters, synchronizes the data, saves the reduced data to disk (after applying a low-pass filter), and provides a Web server interface for remote control. Unlike older phasemeter software that requires a special, real-time operating system, this program can run on any general-purpose computer. It needs about five percent of the CPU (central processing unit) to process 20 channels because it adds built-in data logging and network-based GUIs (graphical user interfaces) that are implemented in Scalable Vector Graphics (SVG). Netmeter runs on Linux and Windows. It displays the instantaneous displacements measured by several phasemeters at a user-selectable rate, up to 1 kHz. The program monitors the measure and reference channel frequencies. For ease of use, levels of status in Netmeter are color coded: green for normal operation, yellow for network errors, and red for optical misalignment problems. Netmeter includes user-selectable filters up to 4 k samples, and user-selectable averaging windows (after filtering). Before filtering, the program saves raw data to disk using a burst-write technique.

Preparing Colorful Astronomical Images and Illustrations

NASA Astrophysics Data System (ADS)

Levay, Z. G.; Frattare, L. M.

2001-12-01

We present techniques for using mainstream graphics software, specifically Adobe Photoshop and Illustrator, for producing composite color images and illustrations from astronomical data. These techniques have been used with numerous images from the Hubble Space Telescope to produce printed and web-based news, education and public presentation products as well as illustrations for technical publication. While Photoshop is not intended for quantitative analysis of full dynamic range data (as are IRAF or IDL, for example), we have had much success applying Photoshop's numerous, versatile tools to work with scaled images, masks, text and graphics in multiple semi-transparent layers and channels. These features, along with its user-oriented, visual interface, provide convenient tools to produce high-quality, full-color images and graphics for printed and on-line publication and presentation.

Teaching Tectonics to Undergraduates with Web GIS

NASA Astrophysics Data System (ADS)

Anastasio, D. J.; Bodzin, A.; Sahagian, D. L.; Rutzmoser, S.

2013-12-01

Geospatial reasoning skills provide a means for manipulating, interpreting, and explaining structured information and are involved in higher-order cognitive processes that include problem solving and decision-making. Appropriately designed tools, technologies, and curriculum can support spatial learning. We present Web-based visualization and analysis tools developed with Javascript APIs to enhance tectonic curricula while promoting geospatial thinking and scientific inquiry. The Web GIS interface integrates graphics, multimedia, and animations that allow users to explore and discover geospatial patterns that are not easily recognized. Features include a swipe tool that enables users to see underneath layers, query tools useful in exploration of earthquake and volcano data sets, a subduction and elevation profile tool which facilitates visualization between map and cross-sectional views, drafting tools, a location function, and interactive image dragging functionality on the Web GIS. The Web GIS platform is independent and can be implemented on tablets or computers. The GIS tool set enables learners to view, manipulate, and analyze rich data sets from local to global scales, including such data as geology, population, heat flow, land cover, seismic hazards, fault zones, continental boundaries, and elevation using two- and three- dimensional visualization and analytical software. Coverages which allow users to explore plate boundaries and global heat flow processes aided learning in a Lehigh University Earth and environmental science Structural Geology and Tectonics class and are freely available on the Web.

Web 2.0 and You

ERIC Educational Resources Information Center

Baumbach, Donna J.

2009-01-01

The World Wide Web has come a long way in a very short time. A little more than a decade ago, with the invention of Mosaic, the first browser to display images inline with text instead of displaying images in a separate window, and Netscape, the first graphical user interface (browser), people began to experience a rapid expansion of information.…

A Web-based Visualization System for Three Dimensional Geological Model using Open GIS

NASA Astrophysics Data System (ADS)

Nemoto, T.; Masumoto, S.; Nonogaki, S.

2017-12-01

A three dimensional geological model is an important information in various fields such as environmental assessment, urban planning, resource development, waste management and disaster mitigation. In this study, we have developed a web-based visualization system for 3D geological model using free and open source software. The system has been successfully implemented by integrating web mapping engine MapServer and geographic information system GRASS. MapServer plays a role of mapping horizontal cross sections of 3D geological model and a topographic map. GRASS provides the core components for management, analysis and image processing of the geological model. Online access to GRASS functions has been enabled using PyWPS that is an implementation of WPS (Web Processing Service) Open Geospatial Consortium (OGC) standard. The system has two main functions. Two dimensional visualization function allows users to generate horizontal and vertical cross sections of 3D geological model. These images are delivered via WMS (Web Map Service) and WPS OGC standards. Horizontal cross sections are overlaid on the topographic map. A vertical cross section is generated by clicking a start point and an end point on the map. Three dimensional visualization function allows users to visualize geological boundary surfaces and a panel diagram. The user can visualize them from various angles by mouse operation. WebGL is utilized for 3D visualization. WebGL is a web technology that brings hardware-accelerated 3D graphics to the browser without installing additional software. The geological boundary surfaces can be downloaded to incorporate the geologic structure in a design on CAD and model for various simulations. This study was supported by JSPS KAKENHI Grant Number JP16K00158.

WebStruct and VisualStruct: Web interfaces and visualization for Structure software implemented in a cluster environment.

PubMed

Jayashree, B; Rajgopal, S; Hoisington, D; Prasanth, V P; Chandra, S

2008-09-24

Structure, is a widely used software tool to investigate population genetic structure with multi-locus genotyping data. The software uses an iterative algorithm to group individuals into "K" clusters, representing possibly K genetically distinct subpopulations. The serial implementation of this programme is processor-intensive even with small datasets. We describe an implementation of the program within a parallel framework. Speedup was achieved by running different replicates and values of K on each node of the cluster. A web-based user-oriented GUI has been implemented in PHP, through which the user can specify input parameters for the programme. The number of processors to be used can be specified in the background command. A web-based visualization tool "Visualstruct", written in PHP (HTML and Java script embedded), allows for the graphical display of population clusters output from Structure, where each individual may be visualized as a line segment with K colors defining its possible genomic composition with respect to the K genetic sub-populations. The advantage over available programs is in the increased number of individuals that can be visualized. The analyses of real datasets indicate a speedup of up to four, when comparing the speed of execution on clusters of eight processors with the speed of execution on one desktop. The software package is freely available to interested users upon request.

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.

Information-computational platform for collaborative multidisciplinary investigations of regional climatic changes and their impacts

NASA Astrophysics Data System (ADS)

Gordov, Evgeny; Lykosov, Vasily; Krupchatnikov, Vladimir; Okladnikov, Igor; Titov, Alexander; Shulgina, Tamara

2013-04-01

Analysis of growing volume of related to climate change data from sensors and model outputs requires collaborative multidisciplinary efforts of researchers. To do it timely and in reliable way one needs in modern information-computational infrastructure supporting integrated studies in the field of environmental sciences. Recently developed experimental software and hardware platform Climate (http://climate.scert.ru/) provides required environment for regional climate change related investigations. The platform combines modern web 2.0 approach, GIS-functionality and capabilities to run climate and meteorological models, process large geophysical datasets and support relevant analysis. It also supports joint software development by distributed research groups, and organization of thematic education for students and post-graduate students. In particular, platform software developed includes dedicated modules for numerical processing of regional and global modeling results for consequent analysis and visualization. Also run of integrated into the platform WRF and «Planet Simulator» models, modeling results data preprocessing and visualization is provided. All functions of the platform are accessible by a user through a web-portal using common graphical web-browser in the form of an interactive graphical user interface which provides, particularly, capabilities of selection of geographical region of interest (pan and zoom), data layers manipulation (order, enable/disable, features extraction) and visualization of results. Platform developed provides users with capabilities of heterogeneous geophysical data analysis, including high-resolution data, and discovering of tendencies in climatic and ecosystem changes in the framework of different multidisciplinary researches. Using it even unskilled user without specific knowledge can perform reliable computational processing and visualization of large meteorological, climatic and satellite monitoring datasets through unified graphical web-interface. Partial support of RF Ministry of Education and Science grant 8345, SB RAS Program VIII.80.2 and Projects 69, 131, 140 and APN CBA2012-16NSY project is acknowledged.

Graphical user interface for accessing water-quality data for the Devils Lake basin, North Dakota

USGS Publications Warehouse

Ryberg, Karen R.; Damschen, William C.; Vecchia, Aldo V.

2005-01-01

Maintaining the quality of surface waters in the Devils Lake Basin in North Dakota is important for protecting the agricultural resources, fisheries, waterfowl and wildlife habitat, and recreational value of the basin. The U.S. Geological Survey, in cooperation with local, State, and Federal agencies, has collected and analyzed water-quality samples from streams and lakes in the basin since 1957, and the North Dakota Department of Health has collected and analyzed water-quality samples from lakes in the basin since 2001. Because water-quality data for the basin are important for numerous reasons, a graphical user interface was developed to access, view, and download the historical data for the basin. The interface is a web-based application that is available to the public and includes data through water year 2003. The interface will be updated periodically to include data for subsequent years.

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

PubMed Central

2013-01-01

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

A Web-based Distributed Voluntary Computing Platform for Large Scale Hydrological Computations

NASA Astrophysics Data System (ADS)

Demir, I.; Agliamzanov, R.

2014-12-01

Distributed volunteer computing can enable researchers and scientist to form large parallel computing environments to utilize the computing power of the millions of computers on the Internet, and use them towards running large scale environmental simulations and models to serve the common good of local communities and the world. Recent developments in web technologies and standards allow client-side scripting languages to run at speeds close to native application, and utilize the power of Graphics Processing Units (GPU). Using a client-side scripting language like JavaScript, we have developed an open distributed computing framework that makes it easy for researchers to write their own hydrologic models, and run them on volunteer computers. Users will easily enable their websites for visitors to volunteer sharing their computer resources to contribute running advanced hydrological models and simulations. Using a web-based system allows users to start volunteering their computational resources within seconds without installing any software. The framework distributes the model simulation to thousands of nodes in small spatial and computational sizes. A relational database system is utilized for managing data connections and queue management for the distributed computing nodes. In this paper, we present a web-based distributed volunteer computing platform to enable large scale hydrological simulations and model runs in an open and integrated environment.

Immunogenetic Management Software: a new tool for visualization and analysis of complex immunogenetic datasets

PubMed Central

Johnson, Z. P.; Eady, R. D.; Ahmad, S. F.; Agravat, S.; Morris, T; Else, J; Lank, S. M.; Wiseman, R. W.; O’Connor, D. H.; Penedo, M. C. T.; Larsen, C. P.

2012-01-01

Here we describe the Immunogenetic Management Software (IMS) system, a novel web-based application that permitsmultiplexed analysis of complex immunogenetic traits that are necessary for the accurate planning and execution of experiments involving large animal models, including nonhuman primates. IMS is capable of housing complex pedigree relationships, microsatellite-based MHC typing data, as well as MHC pyrosequencing expression analysis of class I alleles. It includes a novel, automated MHC haplotype naming algorithm and has accomplished an innovative visualization protocol that allows users to view multiple familial and MHC haplotype relationships through a single, interactive graphical interface. Detailed DNA and RNA-based data can also be queried and analyzed in a highly accessible fashion, and flexible search capabilities allow experimental choices to be made based on multiple, individualized and expandable immunogenetic factors. This web application is implemented in Java, MySQL, Tomcat, and Apache, with supported browsers including Internet Explorer and Firefox onWindows and Safari on Mac OS. The software is freely available for distribution to noncommercial users by contacting Leslie. kean@emory.edu. A demonstration site for the software is available at http://typing.emory.edu/typing_demo, user name: imsdemo7@gmail.com and password: imsdemo. PMID:22080300

Immunogenetic Management Software: a new tool for visualization and analysis of complex immunogenetic datasets.

PubMed

Johnson, Z P; Eady, R D; Ahmad, S F; Agravat, S; Morris, T; Else, J; Lank, S M; Wiseman, R W; O'Connor, D H; Penedo, M C T; Larsen, C P; Kean, L S

2012-04-01

Here we describe the Immunogenetic Management Software (IMS) system, a novel web-based application that permits multiplexed analysis of complex immunogenetic traits that are necessary for the accurate planning and execution of experiments involving large animal models, including nonhuman primates. IMS is capable of housing complex pedigree relationships, microsatellite-based MHC typing data, as well as MHC pyrosequencing expression analysis of class I alleles. It includes a novel, automated MHC haplotype naming algorithm and has accomplished an innovative visualization protocol that allows users to view multiple familial and MHC haplotype relationships through a single, interactive graphical interface. Detailed DNA and RNA-based data can also be queried and analyzed in a highly accessible fashion, and flexible search capabilities allow experimental choices to be made based on multiple, individualized and expandable immunogenetic factors. This web application is implemented in Java, MySQL, Tomcat, and Apache, with supported browsers including Internet Explorer and Firefox on Windows and Safari on Mac OS. The software is freely available for distribution to noncommercial users by contacting Leslie.kean@emory.edu. A demonstration site for the software is available at http://typing.emory.edu/typing_demo , user name: imsdemo7@gmail.com and password: imsdemo.

GenePattern | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

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

A Cloud-Based Simulation Architecture for Pandemic Influenza Simulation

PubMed Central

Eriksson, Henrik; Raciti, Massimiliano; Basile, Maurizio; Cunsolo, Alessandro; Fröberg, Anders; Leifler, Ola; Ekberg, Joakim; Timpka, Toomas

2011-01-01

High-fidelity simulations of pandemic outbreaks are resource consuming. Cluster-based solutions have been suggested for executing such complex computations. We present a cloud-based simulation architecture that utilizes computing resources both locally available and dynamically rented online. The approach uses the Condor framework for job distribution and management of the Amazon Elastic Computing Cloud (EC2) as well as local resources. The architecture has a web-based user interface that allows users to monitor and control simulation execution. In a benchmark test, the best cost-adjusted performance was recorded for the EC2 H-CPU Medium instance, while a field trial showed that the job configuration had significant influence on the execution time and that the network capacity of the master node could become a bottleneck. We conclude that it is possible to develop a scalable simulation environment that uses cloud-based solutions, while providing an easy-to-use graphical user interface. PMID:22195089

Design Options for Multimodal Web Applications

NASA Astrophysics Data System (ADS)

Stanciulescu, Adrian; Vanderdonckt, Jean

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

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

PubMed

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

2015-01-01

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

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

PubMed Central

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

2015-01-01

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

ARCAS (ACACIA Regional Climate-data Access System) -- a Web Access System for Climate Model Data Access, Visualization and Comparison

NASA Astrophysics Data System (ADS)

Hakkarinen, C.; Brown, D.; Callahan, J.; hankin, S.; de Koningh, M.; Middleton-Link, D.; Wigley, T.

2001-05-01

A Web-based access system to climate model output data sets for intercomparison and analysis has been produced, using the NOAA-PMEL developed Live Access Server software as host server and Ferret as the data serving and visualization engine. Called ARCAS ("ACACIA Regional Climate-data Access System"), and publicly accessible at http://dataserver.ucar.edu/arcas, the site currently serves climate model outputs from runs of the NCAR Climate System Model for the 21st century, for Business as Usual and Stabilization of Greenhouse Gas Emission scenarios. Users can select, download, and graphically display single variables or comparisons of two variables from either or both of the CSM model runs, averaged for monthly, seasonal, or annual time resolutions. The time length of the averaging period, and the geographical domain for download and display, are fully selectable by the user. A variety of arithmetic operations on the data variables can be computed "on-the-fly", as defined by the user. Expansions of the user-selectable options for defining analysis options, and for accessing other DOD-compatible ("Distributed Ocean Data System-compatible") data sets, residing at locations other than the NCAR hardware server on which ARCAS operates, are planned for this year. These expansions are designed to allow users quick and easy-to-operate web-based access to the largest possible selection of climate model output data sets available throughout the world.

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

PubMed

Mohebifar, Mohamad; Sajadi, Fatemehsadat

2015-01-01

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

Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists.

PubMed

Zhu, Xun; Wolfgruber, Thomas K; Tasato, Austin; Arisdakessian, Cédric; Garmire, David G; Garmire, Lana X

2017-12-05

Single-cell RNA sequencing (scRNA-Seq) is an increasingly popular platform to study heterogeneity at the single-cell level. Computational methods to process scRNA-Seq data are not very accessible to bench scientists as they require a significant amount of bioinformatic skills. We have developed Granatum, a web-based scRNA-Seq analysis pipeline to make analysis more broadly accessible to researchers. Without a single line of programming code, users can click through the pipeline, setting parameters and visualizing results via the interactive graphical interface. Granatum conveniently walks users through various steps of scRNA-Seq analysis. It has a comprehensive list of modules, including plate merging and batch-effect removal, outlier-sample removal, gene-expression normalization, imputation, gene filtering, cell clustering, differential gene expression analysis, pathway/ontology enrichment analysis, protein network interaction visualization, and pseudo-time cell series construction. Granatum enables broad adoption of scRNA-Seq technology by empowering bench scientists with an easy-to-use graphical interface for scRNA-Seq data analysis. The package is freely available for research use at http://garmiregroup.org/granatum/app.

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.

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

PubMed

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

2018-01-01

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

Web Program for Development of GUIs for Cluster Computers

NASA Technical Reports Server (NTRS)

Czikmantory, Akos; Cwik, Thomas; Klimeck, Gerhard; Hua, Hook; Oyafuso, Fabiano; Vinyard, Edward

2003-01-01

WIGLAF (a Web Interface Generator and Legacy Application Facade) is a computer program that provides a Web-based, distributed, graphical-user-interface (GUI) framework that can be adapted to any of a broad range of application programs, written in any programming language, that are executed remotely on any cluster computer system. WIGLAF enables the rapid development of a GUI for controlling and monitoring a specific application program running on the cluster and for transferring data to and from the application program. The only prerequisite for the execution of WIGLAF is a Web-browser program on a user's personal computer connected with the cluster via the Internet. WIGLAF has a client/server architecture: The server component is executed on the cluster system, where it controls the application program and serves data to the client component. The client component is an applet that runs in the Web browser. WIGLAF utilizes the Extensible Markup Language to hold all data associated with the application software, Java to enable platform-independent execution on the cluster system and the display of a GUI generator through the browser, and the Java Remote Method Invocation software package to provide simple, effective client/server networking.

Interaction Design and Usability of Learning Spaces in 3D Multi-user Virtual Worlds

NASA Astrophysics Data System (ADS)

Minocha, Shailey; Reeves, Ahmad John

Three-dimensional virtual worlds are multimedia, simulated environments, often managed over the Web, which users can 'inhabit' and interact via their own graphical, self-representations known as 'avatars'. 3D virtual worlds are being used in many applications: education/training, gaming, social networking, marketing and commerce. Second Life is the most widely used 3D virtual world in education. However, problems associated with usability, navigation and way finding in 3D virtual worlds may impact on student learning and engagement. Based on empirical investigations of learning spaces in Second Life, this paper presents design guidelines to improve the usability and ease of navigation in 3D spaces. Methods of data collection include semi-structured interviews with Second Life students, educators and designers. The findings have revealed that design principles from the fields of urban planning, Human- Computer Interaction, Web usability, geography and psychology can influence the design of spaces in 3D multi-user virtual environments.

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

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2014-01-01

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

a Web-Based Interactive Platform for Co-Clustering Spatio-Temporal Data

NASA Astrophysics Data System (ADS)

Wu, X.; Poorthuis, A.; Zurita-Milla, R.; Kraak, M.-J.

2017-09-01

Since current studies on clustering analysis mainly focus on exploring spatial or temporal patterns separately, a co-clustering algorithm is utilized in this study to enable the concurrent analysis of spatio-temporal patterns. To allow users to adopt and adapt the algorithm for their own analysis, it is integrated within the server side of an interactive web-based platform. The client side of the platform, running within any modern browser, is a graphical user interface (GUI) with multiple linked visualizations that facilitates the understanding, exploration and interpretation of the raw dataset and co-clustering results. Users can also upload their own datasets and adjust clustering parameters within the platform. To illustrate the use of this platform, an annual temperature dataset from 28 weather stations over 20 years in the Netherlands is used. After the dataset is loaded, it is visualized in a set of linked visualizations: a geographical map, a timeline and a heatmap. This aids the user in understanding the nature of their dataset and the appropriate selection of co-clustering parameters. Once the dataset is processed by the co-clustering algorithm, the results are visualized in the small multiples, a heatmap and a timeline to provide various views for better understanding and also further interpretation. Since the visualization and analysis are integrated in a seamless platform, the user can explore different sets of co-clustering parameters and instantly view the results in order to do iterative, exploratory data analysis. As such, this interactive web-based platform allows users to analyze spatio-temporal data using the co-clustering method and also helps the understanding of the results using multiple linked visualizations.

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.

Gene Graphics: a genomic neighborhood data visualization web application.

PubMed

Harrison, Katherine J; Crécy-Lagard, Valérie de; Zallot, Rémi

2018-04-15

The examination of gene neighborhood is an integral part of comparative genomics but no tools to produce publication quality graphics of gene clusters are available. Gene Graphics is a straightforward web application for creating such visuals. Supported inputs include National Center for Biotechnology Information gene and protein identifiers with automatic fetching of neighboring information, GenBank files and data extracted from the SEED database. Gene representations can be customized for many parameters including gene and genome names, colors and sizes. Gene attributes can be copied and pasted for rapid and user-friendly customization of homologous genes between species. In addition to Portable Network Graphics and Scalable Vector Graphics, produced representations can be exported as Tagged Image File Format or Encapsulated PostScript, formats that are standard for publication. Hands-on tutorials with real life examples inspired from publications are available for training. Gene Graphics is freely available at https://katlabs.cc/genegraphics/ and source code is hosted at https://github.com/katlabs/genegraphics. katherinejh@ufl.edu or remizallot@ufl.edu. Supplementary data are available at Bioinformatics online.

Weather information network including graphical display

NASA Technical Reports Server (NTRS)

Leger, Daniel R. (Inventor); Burdon, David (Inventor); Son, Robert S. (Inventor); Martin, Kevin D. (Inventor); Harrison, John (Inventor); Hughes, Keith R. (Inventor)

2006-01-01

An apparatus for providing weather information onboard an aircraft includes a processor unit and a graphical user interface. The processor unit processes weather information after it is received onboard the aircraft from a ground-based source, and the graphical user interface provides a graphical presentation of the weather information to a user onboard the aircraft. Preferably, the graphical user interface includes one or more user-selectable options for graphically displaying at least one of convection information, turbulence information, icing information, weather satellite information, SIGMET information, significant weather prognosis information, and winds aloft information.

A Web-Based Decision Support System for Assessing Regional Water-Quality Conditions and Management Actions

NASA Astrophysics Data System (ADS)

Booth, N. L.; Everman, E.; Kuo, I.; Sprague, L.; Murphy, L.

2011-12-01

A new web-based decision support system has been developed as part of the U.S. Geological Survey (USGS) National Water Quality Assessment Program's (NAWQA) effort to provide ready access to Spatially Referenced Regressions On Watershed attributes (SPARROW) results of stream water-quality conditions and to offer sophisticated scenario testing capabilities for research and water-quality planning via an intuitive graphical user interface with a map-based display. The SPARROW Decision Support System (DSS) is delivered through a web browser over an Internet connection, making it widely accessible to the public in a format that allows users to easily display water-quality conditions, distribution of nutrient sources, nutrient delivery to downstream waterbodies, and simulations of altered nutrient inputs including atmospheric and agricultural sources. The DSS offers other features for analysis including various background map layers, model output exports, and the ability to save and share prediction scenarios. SPARROW models currently supported by the DSS are based on the modified digital versions of the 1:500,000-scale River Reach File (RF1) and 1:100,000-scale National Hydrography Dataset (medium-resolution, NHDPlus) stream networks. The underlying modeling framework and server infrastructure illustrate innovations in the information technology and geosciences fields for delivering SPARROW model predictions over the web by performing intensive model computations and map visualizations of the predicted conditions within the stream network.

A Prototype Lisp-Based Soft Real-Time Object-Oriented Graphical User Interface for Control System Development

NASA Technical Reports Server (NTRS)

Litt, Jonathan; Wong, Edmond; Simon, Donald L.

1994-01-01

A prototype Lisp-based soft real-time object-oriented Graphical User Interface for control system development is presented. The Graphical User Interface executes alongside a test system in laboratory conditions to permit observation of the closed loop operation through animation, graphics, and text. Since it must perform interactive graphics while updating the screen in real time, techniques are discussed which allow quick, efficient data processing and animation. Examples from an implementation are included to demonstrate some typical functionalities which allow the user to follow the control system's operation.

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

Development of an integrated e-health tool for people with, or at high risk of, cardiovascular disease: The Consumer Navigation of Electronic Cardiovascular Tools (CONNECT) web application.

PubMed

Neubeck, Lis; Coorey, Genevieve; Peiris, David; Mulley, John; Heeley, Emma; Hersch, Fred; Redfern, Julie

2016-12-01

Cardiovascular disease is the leading killer globally and secondary prevention substantially reduces risk. Uptake of, and adherence to, face-to-face preventive programs is often low. Alternative models of care are exploiting the prominence of technology in daily life to facilitate lifestyle behavior change. To inform the development of a web-based application integrated with the primary care electronic health record, we undertook a collaborative user-centered design process to develop a consumer-focused e-health tool for cardiovascular disease risk reduction. A four-phase iterative process involved ten multidisciplinary clinicians and academics (primary care physician, nurses and allied health professionals), two design consultants, one graphic designer, three software developers and fourteen proposed end-users. This 18-month process involved, (1) defining the target audience and needs, (2) pilot testing and refinement, (3) software development including validation and testing the algorithm, (4) user acceptance testing and beta testing. From this process, researchers were able to better understand end-user needs and preferences, thereby improving and enriching the increasingly detailed system designs and prototypes for a mobile responsive web application. We reviewed 14 relevant applications/websites and sixteen observational and interventional studies to derive a set of core components and ideal features for the system. These included the need for interactivity, visual appeal, credible health information, virtual rewards, and emotional and physical support. The features identified as essential were: (i) both mobile and web-enabled 'apps', (ii) an emphasis on medication management, (iii) a strong psychosocial support component. Subsequent workshops (n=6; 2×1.5h) informed the development of functionality and lo-fidelity sketches of application interfaces. These ideas were next tested in consumer focus groups (n=9; 3×1.5h). Specifications for the application were refined from this feedback and a graphic designer iteratively developed the interface. Concurrently, the electronic health record was linked to the consumer portal. A written description of the final algorithms for all decisions and outputs was provided to software programmers. These algorithmic outputs to the app were first validated against those obtained from an independently programmed version in STATA 11. User acceptance testing (n=5, 2×1.0h) and beta testing revealed technical bugs and interface concerns across commonly-used web browsers and smartphones. These were resolved and re-tested until functionality was optimized. End-users of a cardiovascular disease prevention program have complex needs. A user-centered design approach aided the integration of these needs into the concept, specifications, development and refinement of a responsive web application for risk factor reduction and disease prevention. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Advanced Query and Data Mining Capabilities for MaROS

NASA Technical Reports Server (NTRS)

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

2013-01-01

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

Data display and analysis with μView

NASA Astrophysics Data System (ADS)

Tucakov, Ivan; Cosman, Jacob; Brewer, Jess H.

2006-03-01

The μView utility is a new Java applet version of the old db program, extended to include direct access to MUD data files, from which it can construct a variety of spectrum types, including complex and RRF-transformed spectra. By using graphics features built into all modern Web browsers, it provides full graphical display capabilities consistently across all platforms. It has the full command-line functionality of db as well as a more intuitive graphical user interface and extensive documentation, and can read and write db, csv and XML format files.

Web-Based Customizable Viewer for Mars Network Overflight Opportunities

NASA Technical Reports Server (NTRS)

Gladden, Roy E.; Wallick, Michael N.; Allard, Daniel A.

2012-01-01

This software displays a full summary of information regarding the overflight opportunities between any set of lander and orbiter pairs that the user has access to view. The information display can be customized, allowing the user to choose which fields to view/hide and filter. The software works from a Web browser on any modern operating system. A full summary of information pertaining to an overflight is available, including the proposed, tentative, requested, planned, and implemented. This gives the user a chance to quickly check for inconsistencies and fix any problems. Overflights from multiple lander/ orbiter pairs can be compared instantly, and information can be filtered through the query and shown/hidden, giving the user a customizable view of the data. The information can be exported to a CSV (comma separated value) or XML (extensible markup language) file. The software only grants access to users who are authorized to view the information. This application is an addition to the MaROS Web suite. Prior to this addition, information pertaining to overflight opportunities would have a limited amount of data (displayed graphically) and could only be shown in strict temporal ordering. This new display shows more information, allows direct comparisons between overflights, and allows the data to be manipulated in ways that it was unable to be done in the past. The current software solution is to use CSV files to view the overflight opportunities.

Climatological Data Option in My Weather Impacts Decision Aid (MyWIDA) Overview

DTIC Science & Technology

2017-07-18

rules. It consists of 2 databases, a data service server, a collection of web service, and web applications that show weather impacts on selected...3.1.2 ClimoDB 5 3.2 Data Service 5 3.2.1 Data Requestor 5 3.2.2 Data Decoder 6 3.2.3 Post Processor 6 3.2.4 Job Scheduler 6 3.3 Web Service 6...6.1 Additional Data Option 9 6.2 Impact Overlay Web Service 9 6.3 Graphical User Interface 9 7. References 10 List of Symbols, Abbreviations, and

Multimedia data repository for the World Wide Web

NASA Astrophysics Data System (ADS)

Chen, Ken; Lu, Dajin; Xu, Duanyi

1998-08-01

This paper introduces the design and implementation of a Multimedia Data Repository served as a multimedia information system, which provides users a Web accessible, platform independent interface to query, browse, and retrieve multimedia data such as images, graphics, audio, video from a large multimedia data repository. By integrating the multimedia DBMS, in which the textual information and samples of the multimedia data is organized and stored, and Web server together into the Microsoft ActiveX Server Framework, users can access the DBMS and query the information by simply using a Web browser at the client-side. The original multimedia data can then be located and transmitted through the Internet from the tertiary storage device, a 400 CDROM optical jukebox at the server-side, to the client-side for further use.

The strategies WDK: a graphical search interface and web development kit for functional genomics databases

PubMed Central

Fischer, Steve; Aurrecoechea, Cristina; Brunk, Brian P.; Gao, Xin; Harb, Omar S.; Kraemer, Eileen T.; Pennington, Cary; Treatman, Charles; Kissinger, Jessica C.; Roos, David S.; Stoeckert, Christian J.

2011-01-01

Web sites associated with the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) have recently introduced a graphical user interface, the Strategies WDK, intended to make advanced searching and set and interval operations easy and accessible to all users. With a design guided by usability studies, the system helps motivate researchers to perform dynamic computational experiments and explore relationships across data sets. For example, PlasmoDB users seeking novel therapeutic targets may wish to locate putative enzymes that distinguish pathogens from their hosts, and that are expressed during appropriate developmental stages. When a researcher runs one of the approximately 100 searches available on the site, the search is presented as a first step in a strategy. The strategy is extended by running additional searches, which are combined with set operators (union, intersect or minus), or genomic interval operators (overlap, contains). A graphical display uses Venn diagrams to make the strategy’s flow obvious. The interface facilitates interactive adjustment of the component searches with changes propagating forward through the strategy. Users may save their strategies, creating protocols that can be shared with colleagues. The strategy system has now been deployed on all EuPathDB databases, and successfully deployed by other projects. The Strategies WDK uses a configurable MVC architecture that is compatible with most genomics and biological warehouse databases, and is available for download at code.google.com/p/strategies-wdk. Database URL: www.eupathdb.org PMID:21705364

Experimental Internet Environment Software Development

NASA Technical Reports Server (NTRS)

Maddux, Gary A.

1998-01-01

Geographically distributed project teams need an Internet based collaborative work environment or "Intranet." The Virtual Research Center (VRC) is an experimental Intranet server that combines several services such as desktop conferencing, file archives, on-line publishing, and security. Using the World Wide Web (WWW) as a shared space paradigm, the Graphical User Interface (GUI) presents users with images of a lunar colony. Each project has a wing of the colony and each wing has a conference room, library, laboratory, and mail station. In FY95, the VRC development team proved the feasibility of this shared space concept by building a prototype using a Netscape commerce server and several public domain programs. Successful demonstrations of the prototype resulted in approval for a second phase. Phase 2, documented by this report, will produce a seamlessly integrated environment by introducing new technologies such as Java and Adobe Web Links to replace less efficient interface software.

Integration of gel-based proteome data with pProRep.

PubMed

Laukens, Kris; Matthiesen, Rune; Lemière, Filip; Esmans, Eddy; Onckelen, Harry Van; Jensen, Ole Nørregaard; Witters, Erwin

2006-11-15

pProRep is a web application integrating electrophoretic and mass spectral data from proteome analyses into a relational database. The graphical web-interface allows users to upload, analyse and share experimental proteome data. It offers researchers the possibility to query all previously analysed datasets and can visualize selected features, such as the presence of a certain set of ions in a peptide mass spectrum, on the level of the two-dimensional gel. The pProRep package and instructions for its use can be downloaded from http://www.ptools.ua.ac.be/pProRep. The application requires a web server that runs PHP 5 (http://www.php.net) and MySQL. Some (non-essential) extensions need additional freely available libraries: details are described in the installation instructions.

shinyheatmap: Ultra fast low memory heatmap web interface for big data genomics.

PubMed

Khomtchouk, Bohdan B; Hennessy, James R; Wahlestedt, Claes

2017-01-01

Transcriptomics, metabolomics, metagenomics, and other various next-generation sequencing (-omics) fields are known for their production of large datasets, especially across single-cell sequencing studies. Visualizing such big data has posed technical challenges in biology, both in terms of available computational resources as well as programming acumen. Since heatmaps are used to depict high-dimensional numerical data as a colored grid of cells, efficiency and speed have often proven to be critical considerations in the process of successfully converting data into graphics. For example, rendering interactive heatmaps from large input datasets (e.g., 100k+ rows) has been computationally infeasible on both desktop computers and web browsers. In addition to memory requirements, programming skills and knowledge have frequently been barriers-to-entry for creating highly customizable heatmaps. We propose shinyheatmap: an advanced user-friendly heatmap software suite capable of efficiently creating highly customizable static and interactive biological heatmaps in a web browser. shinyheatmap is a low memory footprint program, making it particularly well-suited for the interactive visualization of extremely large datasets that cannot typically be computed in-memory due to size restrictions. Also, shinyheatmap features a built-in high performance web plug-in, fastheatmap, for rapidly plotting interactive heatmaps of datasets as large as 105-107 rows within seconds, effectively shattering previous performance benchmarks of heatmap rendering speed. shinyheatmap is hosted online as a freely available web server with an intuitive graphical user interface: http://shinyheatmap.com. The methods are implemented in R, and are available as part of the shinyheatmap project at: https://github.com/Bohdan-Khomtchouk/shinyheatmap. Users can access fastheatmap directly from within the shinyheatmap web interface, and all source code has been made publicly available on Github: https://github.com/Bohdan-Khomtchouk/fastheatmap.

3D Graphics Through the Internet: A "Shoot-Out"

NASA Technical Reports Server (NTRS)

Watson, Val; Lasinski, T. A. (Technical Monitor)

1995-01-01

3D graphics through the Internet needs to move beyond the current lowest common denominator of pre-computed movies, which consume bandwidth and are non-interactive. Panelists will demonstrate and compare 3D graphical tools for accessing, analyzing, and collaborating on information through the Internet and World-wide web. The "shoot-out" will illustrate which tools are likely to be the best for the various types of information, including dynamic scientific data, 3-D objects, and virtual environments. The goal of the panel is to encourage more effective use of the Internet by encouraging suppliers and users of information to adopt the next generation of graphical tools.

A Web simulation of medical image reconstruction and processing as an educational tool.

PubMed

Papamichail, Dimitrios; Pantelis, Evaggelos; Papagiannis, Panagiotis; Karaiskos, Pantelis; Georgiou, Evangelos

2015-02-01

Web educational resources integrating interactive simulation tools provide students with an in-depth understanding of the medical imaging process. The aim of this work was the development of a purely Web-based, open access, interactive application, as an ancillary learning tool in graduate and postgraduate medical imaging education, including a systematic evaluation of learning effectiveness. The pedagogic content of the educational Web portal was designed to cover the basic concepts of medical imaging reconstruction and processing, through the use of active learning and motivation, including learning simulations that closely resemble actual tomographic imaging systems. The user can implement image reconstruction and processing algorithms under a single user interface and manipulate various factors to understand the impact on image appearance. A questionnaire for pre- and post-training self-assessment was developed and integrated in the online application. The developed Web-based educational application introduces the trainee in the basic concepts of imaging through textual and graphical information and proceeds with a learning-by-doing approach. Trainees are encouraged to participate in a pre- and post-training questionnaire to assess their knowledge gain. An initial feedback from a group of graduate medical students showed that the developed course was considered as effective and well structured. An e-learning application on medical imaging integrating interactive simulation tools was developed and assessed in our institution.

Situational Lightning Climatologies for Central Florida, Phase 2, Part 3

NASA Technical Reports Server (NTRS)

Bauman, William H., III

2007-01-01

The threat of lightning is a daily concern during the warm season in Florida. The forecasters at the Spaceflight Meteorology Group (SMG) at Johnson Spaceflight Center in Houston, TX consider lightning in their landing forecasts for space shuttles at the Kennedy Space Center (KSC), FL Shuttle Landing Facility (SLF). The forecasters at the National Weather Service in Melbourne, FL (NWS MLB) do the same in their routine Terminal Aerodrome Forecasts (TAFs) for seven airports in the NWS MLB County Warning Area (CWA). The Applied Meteorology Unit created flow regime climatologies of lightning probability in the 5-, 10-, 20-, and 30-n mi circles surrounding the Shuttle Landing Facility (SLF) and all airports in the NWS MLB county warning area in 1-, 3-, and 6-hour increments. The results were presented in tabular and graphical format and incorporated into a web-based graphical user interface so forecasters could easily navigate through the data and to make the GUI usable in any web browser on computers with different operating systems.

Software for Allocating Resources in the Deep Space Network

NASA Technical Reports Server (NTRS)

Wang, Yeou-Fang; Borden, Chester; Zendejas, Silvino; Baldwin, John

2003-01-01

TIGRAS 2.0 is a computer program designed to satisfy a need for improved means for analyzing the tracking demands of interplanetary space-flight missions upon the set of ground antenna resources of the Deep Space Network (DSN) and for allocating those resources. Written in Microsoft Visual C++, TIGRAS 2.0 provides a single rich graphical analysis environment for use by diverse DSN personnel, by connecting to various data sources (relational databases or files) based on the stages of the analyses being performed. Notable among the algorithms implemented by TIGRAS 2.0 are a DSN antenna-load-forecasting algorithm and a conflict-aware DSN schedule-generating algorithm. Computers running TIGRAS 2.0 can also be connected using SOAP/XML to a Web services server that provides analysis services via the World Wide Web. TIGRAS 2.0 supports multiple windows and multiple panes in each window for users to view and use information, all in the same environment, to eliminate repeated switching among various application programs and Web pages. TIGRAS 2.0 enables the use of multiple windows for various requirements, trajectory-based time intervals during which spacecraft are viewable, ground resources, forecasts, and schedules. Each window includes a time navigation pane, a selection pane, a graphical display pane, a list pane, and a statistics pane.

Advances in the TRIDEC Cloud

NASA Astrophysics Data System (ADS)

Hammitzsch, Martin; Spazier, Johannes; Reißland, Sven

2016-04-01

The TRIDEC Cloud is a platform that merges several complementary cloud-based services for instant tsunami propagation calculations and automated background computation with graphics processing units (GPU), for web-mapping of hazard specific geospatial data, and for serving relevant functionality to handle, share, and communicate threat specific information in a collaborative and distributed environment. The platform offers a modern web-based graphical user interface so that operators in warning centres and stakeholders of other involved parties (e.g. CPAs, ministries) just need a standard web browser to access a full-fledged early warning and information system with unique interactive features such as Cloud Messages and Shared Maps. Furthermore, the TRIDEC Cloud can be accessed in different modes, e.g. the monitoring mode, which provides important functionality required to act in a real event, and the exercise-and-training mode, which enables training and exercises with virtual scenarios re-played by a scenario player. The software system architecture and open interfaces facilitate global coverage so that the system is applicable for any region in the world and allow the integration of different sensor systems as well as the integration of other hazard types and use cases different to tsunami early warning. Current advances of the TRIDEC Cloud platform will be summarized in this presentation.

Graphical User Interfaces and Library Systems: End-User Reactions.

ERIC Educational Resources Information Center

Zorn, Margaret; Marshall, Lucy

1995-01-01

Describes a study by Parke-Davis Pharmaceutical Research Library to determine user satisfaction with the graphical user interface-based (GUI) Dynix Marquis compared with the text-based Dynix Classic Online Public Access Catalog (OPAC). Results show that the GUI-based OPAC was preferred by endusers over the text-based OPAC. (eight references) (DGM)

The Evolvable Advanced Multi-Mission Operations System (AMMOS): Making Systems Interoperable

NASA Technical Reports Server (NTRS)

Ko, Adans Y.; Maldague, Pierre F.; Bui, Tung; Lam, Doris T.; McKinney, John C.

2010-01-01

The Advanced Multi-Mission Operations System (AMMOS) provides a common Mission Operation System (MOS) infrastructure to NASA deep space missions. The evolution of AMMOS has been driven by two factors: increasingly challenging requirements from space missions, and the emergence of new IT technology. The work described in this paper focuses on three key tasks related to IT technology requirements: first, to eliminate duplicate functionality; second, to promote the use of loosely coupled application programming interfaces, text based file interfaces, web-based frameworks and integrated Graphical User Interfaces (GUI) to connect users, data, and core functionality; and third, to build, develop, and deploy AMMOS services that are reusable, agile, adaptive to project MOS configurations, and responsive to industrially endorsed information technology standards.

Arkheia: Data Management and Communication for Open Computational Neuroscience

PubMed Central

Antolík, Ján; Davison, Andrew P.

2018-01-01

Two trends have been unfolding in computational neuroscience during the last decade. First, a shift of focus to increasingly complex and heterogeneous neural network models, with a concomitant increase in the level of collaboration within the field (whether direct or in the form of building on top of existing tools and results). Second, a general trend in science toward more open communication, both internally, with other potential scientific collaborators, and externally, with the wider public. This multi-faceted development toward more integrative approaches and more intense communication within and outside of the field poses major new challenges for modelers, as currently there is a severe lack of tools to help with automatic communication and sharing of all aspects of a simulation workflow to the rest of the community. To address this important gap in the current computational modeling software infrastructure, here we introduce Arkheia. Arkheia is a web-based open science platform for computational models in systems neuroscience. It provides an automatic, interactive, graphical presentation of simulation results, experimental protocols, and interactive exploration of parameter searches, in a web browser-based application. Arkheia is focused on automatic presentation of these resources with minimal manual input from users. Arkheia is written in a modular fashion with a focus on future development of the platform. The platform is designed in an open manner, with a clearly defined and separated API for database access, so that any project can write its own backend translating its data into the Arkheia database format. Arkheia is not a centralized platform, but allows any user (or group of users) to set up their own repository, either for public access by the general population, or locally for internal use. Overall, Arkheia provides users with an automatic means to communicate information about not only their models but also individual simulation results and the entire experimental context in an approachable graphical manner, thus facilitating the user's ability to collaborate in the field and outreach to a wider audience. PMID:29556187

Arkheia: Data Management and Communication for Open Computational Neuroscience.

PubMed

Antolík, Ján; Davison, Andrew P

2018-01-01

Two trends have been unfolding in computational neuroscience during the last decade. First, a shift of focus to increasingly complex and heterogeneous neural network models, with a concomitant increase in the level of collaboration within the field (whether direct or in the form of building on top of existing tools and results). Second, a general trend in science toward more open communication, both internally, with other potential scientific collaborators, and externally, with the wider public. This multi-faceted development toward more integrative approaches and more intense communication within and outside of the field poses major new challenges for modelers, as currently there is a severe lack of tools to help with automatic communication and sharing of all aspects of a simulation workflow to the rest of the community. To address this important gap in the current computational modeling software infrastructure, here we introduce Arkheia. Arkheia is a web-based open science platform for computational models in systems neuroscience. It provides an automatic, interactive, graphical presentation of simulation results, experimental protocols, and interactive exploration of parameter searches, in a web browser-based application. Arkheia is focused on automatic presentation of these resources with minimal manual input from users. Arkheia is written in a modular fashion with a focus on future development of the platform. The platform is designed in an open manner, with a clearly defined and separated API for database access, so that any project can write its own backend translating its data into the Arkheia database format. Arkheia is not a centralized platform, but allows any user (or group of users) to set up their own repository, either for public access by the general population, or locally for internal use. Overall, Arkheia provides users with an automatic means to communicate information about not only their models but also individual simulation results and the entire experimental context in an approachable graphical manner, thus facilitating the user's ability to collaborate in the field and outreach to a wider audience.

Designing a data portal for synthesis modeling

NASA Astrophysics Data System (ADS)

Holmes, M. A.

2006-12-01

Processing of field and model data in multi-disciplinary integrated science studies is a vital part of synthesis modeling. Collection and storage techniques for field data vary greatly between the participating scientific disciplines due to the nature of the data being collected, whether it be in situ, remotely sensed, or recorded by automated data logging equipment. Spreadsheets, personal databases, text files and binary files are used in the initial storage and processing of the raw data. In order to be useful to scientists, engineers and modelers the data need to be stored in a format that is easily identifiable, accessible and transparent to a variety of computing environments. The Model Operations and Synthesis (MOAS) database and associated web portal were created to provide such capabilities. The industry standard relational database is comprised of spatial and temporal data tables, shape files and supporting metadata accessible over the network, through a menu driven web-based portal or spatially accessible through ArcSDE connections from the user's local GIS desktop software. A separate server provides public access to spatial data and model output in the form of attributed shape files through an ArcIMS web-based graphical user interface.

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

Cancer.gov

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

UI Review Results and NARAC Response

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

Fisher, J.; Eme, B.; Kim, S.

2017-03-08

This report describes the results of an inter-program design review completed February 16th, 2017, during the second year of a FY16-FY18 NA-84 Technology Integration (TI) project to modernize the core software system used in DOE/NNSA's National Atmospheric Release Advisory Center (NARAC, narac.llnl.gov). This review focused on the graphical user interfaces (GUI) frameworks. Reviewers (described in Appendix 2) were selected from multiple areas of the LLNL Computation directorate, based on their expertise in GUI and Web technologies.

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

Training Joint, Interagency, Intergovernmental, and Multinational (JIIM) Participants for Stability Operations

DTIC Science & Technology

2012-09-01

boxes) using a third-party commercial software component. When creating version 1, it was necessary to enter raw Hypertext Markup Language (HTML) tags...Markup Language (HTML) web page. Figure 12. Authors create procedures using the Procedure Editor. Users run procedures using the...step presents instructions to the user using formatted text and graphics specified using the Hypertext Markup Language (HTML). Instructions can

SSBRP User Operations Facility (UOF) Overview and Development Strategy

NASA Technical Reports Server (NTRS)

Picinich, Lou; Stone, Thom; Sun, Charles; Windrem, May; Givens, John J. (Technical Monitor)

1995-01-01

This paper will present the Space Station Biological Research Project (SSBRP) User Operations Facility (UOF) architecture and development strategy. A major element of the UOF at NASA Ames Research Center, the Communication and Data System (CDS) will be the primary focus of the discussions. CDS operational, telescience, security, and development objectives will be discussed along with CDS implementation strategy. The implementation strategy discussions will include: Object Oriented Analysis & Design, System & Software Prototyping, and Technology Utilization. A CDS design overview that includes: CDS Context Diagram, CDS Architecture, Object Models, Use Cases, and User Interfaces will also be presented. CDS development brings together "cutting edge" technologies and techniques such as: object oriented development, network security, multimedia networking, web-based data distribution, JAVA, and graphical user interfaces. Use of these "cutting edge" technologies and techniques translates directly to lower development and operations costs.

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

A web implementation: the good and the not-so-good.

PubMed

Bergsneider, C; Piraino, D; Fuerst, M

2001-06-01

E-commerce, e-mail, e-greeting, e-this, and e-that everywhere you turn there is a new "e" word for an internet or Web application. We, at the Cleveland Clinic Foundation, have been "e-nlightened" and will discuss in this report the implementation of a web-based radiology information system (RIS) in our radiology division or "e-radiology" division. The application, IDXRad Version 10.0 from IDX Corp, Burlington, VT, is in use at the Cleveland Clinic Foundation and has both intranet (for use in Radiology) and internet (referring physician viewing) modules. We will concentrate on the features of using a web browser for the application's front-end, including easy prototyping for screen review, easier mock-ups of demonstrations by vendors and developers, and easier training as more people become web-addicted. Project communication can be facilitated with an internal project web page, and use of the web browser can accommodate quicker turnaround of software upgrades as the software code is centrally located. Compared with other technologies, including client/server, there is a smaller roll out cost when using a standard web browser. However, the new technology requires a change and changes are never implemented without challenges. A seasoned technologist using a legacy system can enter data quicker using function keys than using a graphical user interface and pointing and clicking through a series of pop-up windows. Also, effective use of a web browser depends on intuitive design for it to be easily implemented and accepted by the user. Some software packages will not work on both of the popular web browsers and then are tailored to specific release levels. As computer-based patient records become a standard, patient confidentiality must be enforced. The technical design and application security features that support the web-based software package will be discussed. Also web technologies have their own implementation issues.

Maser: one-stop platform for NGS big data from analysis to visualization

PubMed Central

Kinjo, Sonoko; Monma, Norikazu; Misu, Sadahiko; Kitamura, Norikazu; Imoto, Junichi; Yoshitake, Kazutoshi; Gojobori, Takashi; Ikeo, Kazuho

2018-01-01

Abstract A major challenge in analyzing the data from high-throughput next-generation sequencing (NGS) is how to handle the huge amounts of data and variety of NGS tools and visualize the resultant outputs. To address these issues, we developed a cloud-based data analysis platform, Maser (Management and Analysis System for Enormous Reads), and an original genome browser, Genome Explorer (GE). Maser enables users to manage up to 2 terabytes of data to conduct analyses with easy graphical user interface operations and offers analysis pipelines in which several individual tools are combined as a single pipeline for very common and standard analyses. GE automatically visualizes genome assembly and mapping results output from Maser pipelines, without requiring additional data upload. With this function, the Maser pipelines can graphically display the results output from all the embedded tools and mapping results in a web browser. Therefore Maser realized a more user-friendly analysis platform especially for beginners by improving graphical display and providing the selected standard pipelines that work with built-in genome browser. In addition, all the analyses executed on Maser are recorded in the analysis history, helping users to trace and repeat the analyses. The entire process of analysis and its histories can be shared with collaborators or opened to the public. In conclusion, our system is useful for managing, analyzing, and visualizing NGS data and achieves traceability, reproducibility, and transparency of NGS analysis. Database URL: http://cell-innovation.nig.ac.jp/maser/ PMID:29688385

Program for Generating Graphs and Charts

NASA Technical Reports Server (NTRS)

Ackerson, C. T.

1986-01-01

Office Automation Pilot (OAP) Graphics Database system offers IBM personal computer user assistance in producing wide variety of graphs and charts and convenient data-base system, called chart base, for creating and maintaining data associated with graphs and charts. Thirteen different graphics packages available. Access graphics capabilities obtained in similar manner. User chooses creation, revision, or chartbase-maintenance options from initial menu; Enters or modifies data displayed on graphic chart. OAP graphics data-base system written in Microsoft PASCAL.

Database and Analytical Tool Development for the Management of Data Derived from US DOE (NETL) Funded Fine Particulate (PM2.5) Research

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

Robinson Khosah

2007-07-31

Advanced Technology Systems, Inc. (ATS) was contracted by the U. S. Department of Energy's National Energy Technology Laboratory (DOE-NETL) to develop a state-of-the-art, scalable and robust web-accessible database application to manage the extensive data sets resulting from the DOE-NETL-sponsored ambient air monitoring programs in the upper Ohio River valley region. The data management system was designed to include a web-based user interface that will allow easy access to the data by the scientific community, policy- and decision-makers, and other interested stakeholders, while providing detailed information on sampling, analytical and quality control parameters. In addition, the system will provide graphical analyticalmore » tools for displaying, analyzing and interpreting the air quality data. The system will also provide multiple report generation capabilities and easy-to-understand visualization formats that can be utilized by the media and public outreach/educational institutions. The project was conducted in two phases. Phase One included the following tasks: (1) data inventory/benchmarking, including the establishment of an external stakeholder group; (2) development of a data management system; (3) population of the database; (4) development of a web-based data retrieval system, and (5) establishment of an internal quality assurance/quality control system on data management. Phase Two involved the development of a platform for on-line data analysis. Phase Two included the following tasks: (1) development of a sponsor and stakeholder/user website with extensive online analytical tools; (2) development of a public website; (3) incorporation of an extensive online help system into each website; and (4) incorporation of a graphical representation (mapping) system into each website. The project is now technically completed.« less

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

PubMed

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

2012-10-01

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

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

PubMed

Burger, Melanie C

2015-01-01

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

An Android based location service using GSMCellID and GPS to obtain a graphical guide to the nearest cash machine

NASA Astrophysics Data System (ADS)

Jacobsen, Jurma; Edlich, Stefan

2009-02-01

There is a broad range of potential useful mobile location-based applications. One crucial point seems to be to make them available to the public at large. This case illuminates the abilities of Android - the operating system for mobile devices - to fulfill this demand in the mashup way by use of some special geocoding web services and one integrated web service for getting the nearest cash machines data. It shows an exemplary approach for building mobile location-based mashups for everyone: 1. As a basis for reaching as many people as possible the open source Android OS is assumed to spread widely. 2. Everyone also means that the handset has not to be an expensive GPS device. This is realized by re-utilization of the existing GSM infrastructure with the Cell of Origin (COO) method which makes a lookup of the CellID in one of the growing web available CellID databases. Some of these databases are still undocumented and not yet published. Furthermore the Google Maps API for Mobile (GMM) and the open source counterpart OpenCellID are used. The user's current position localization via lookup of the closest cell to which the handset is currently connected to (COO) is not as precise as GPS, but appears to be sufficient for lots of applications. For this reason the GPS user is the most pleased one - for this user the system is fully automated. In contrary there could be some users who doesn't own a GPS cellular. This user should refine his/her location by one click on the map inside of the determined circular region. The users are then shown and guided by a path to the nearest cash machine by integrating Google Maps API with an overlay. Additionally, the GPS user can keep track of him- or herself by getting a frequently updated view via constantly requested precise GPS data for his or her position.

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

PubMed

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

2005-01-01

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

The Graphical User Interface: Crisis, Danger, and Opportunity.

ERIC Educational Resources Information Center

Boyd, L. H.; And Others

1990-01-01

This article describes differences between the graphical user interface and traditional character-based interface systems, identifies potential problems posed by graphic computing environments for blind computer users, and describes some programs and strategies that are being developed to provide access to those environments. (Author/JDD)

Advancing the Implementation of Hydrologic Models as Web-based Applications

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

What words and where? Applying usability testing techniques to name a new live reference service.

PubMed

Duncan, Vicky; Fichter, Darlene M

2004-04-01

A user-focused design approach was taken to develop a new "live reference" service at the Health Sciences Library, University of Saskatchewan. The name of the service, the placement of the links, and the design of a graphical button were seen as key elements in creating service awareness and its subsequent use. To ensure library users recognized and understood the label for the new service, selected library users were given an opportunity to choose a phrase that would best describe the service. The top two preferred phrases were then placed on the library Web pages as text and graphic images for further testing. Some pages had links in multiple locations to determine which placement worked best. Task-based usability testing was carried out with participants who were unaware of the new service. Participants were observed as they completed seven Website tasks arranged in increasing levels of difficulty to see whether they would notice the live reference service and seek assistance. The high level of recognition and use of the service indicate that the label name and link placement were effective with library Website users. Using user-centered design methodology helped ensure that the new live reference service was visible and used and demonstrated the effectiveness of the user-centered design approach for adding new services to an existing Website.

Making large amounts of meteorological plots easily accessible to users

NASA Astrophysics Data System (ADS)

Lamy-Thepaut, Sylvie; Siemen, Stephan; Sahin, Cihan; Raoult, Baudouin

2015-04-01

The European Centre for Medium-Range Weather Forecasts (ECMWF) is an international organisation providing its member organisations with forecasts in the medium time range of 3 to 15 days, and some longer-range forecasts for up to a year ahead, with varying degrees of detail. As part of its mission, ECMWF generates an increasing number of forecast data products for its users. To support the work of forecasters and researchers and to let them make best use of ECMWF forecasts, the Centre also provides tools and interfaces to visualise their products. This allows users to make use of and explore forecasts without having to transfer large amounts of raw data. This is especially true for products based on ECMWF's 50 member ensemble forecast, where some specific processing and visualisation are applied to extract information. Every day, thousands of raw data are being pushed to the ECMWF's interactive web charts application called ecCharts, and thousands of products are processed and pushed to ECMWF's institutional web site ecCharts provides a highly interactive application to display and manipulate recent numerical forecasts to forecasters in national weather services and ECMWF's commercial customers. With ecCharts forecasters are able to explore ECMWF's medium-range forecasts in far greater detail than has previously been possible on the web, and this as soon as the forecast becomes available. All ecCharts's products are also available through a machine-to-machine web map service based on the OGC Web Map Service (WMS) standard. ECMWF institutional web site provides access to a large number of graphical products. It was entirely redesigned last year. It now shares the same infrastructure as ECMWF's ecCharts, and can benefit of some ecCharts functionalities, for example the dashboard. The dashboard initially developed for ecCharts allows users to organise their own collection of products depending on their work flow, and is being further developed. In its first implementation, It presents the user's products in a single interface with fast access to the original product, and possibilities of synchronous animations between them. But its functionalities are being extended to give users the freedom to collect not only ecCharts's 2D maps and graphs, but also other ECMWF Web products such as monthly and seasonal products, scores, and observation monitoring. The dashboard will play a key role to help the user to interpret the large amount of information that ECMWF is providing. This talk will present examples of how the new user interface can organise complex meteorological maps and graphs and show the new possibilities users have gained by using the web as a medium.

Draper Station Analysis Tool

NASA Technical Reports Server (NTRS)

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

2011-01-01

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

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.

eWaterCycle visualisation. combining the strength of NetCDF and Web Map Service: ncWMS

NASA Astrophysics Data System (ADS)

Hut, R.; van Meersbergen, M.; Drost, N.; Van De Giesen, N.

2016-12-01

As a result of the eWatercycle global hydrological forecast we have created Cesium-ncWMS, a web application based on ncWMS and Cesium. ncWMS is a server side application capable of reading any NetCDF file written using the Climate and Forecasting (CF) conventions, and making the data available as a Web Map Service(WMS). ncWMS automatically determines available variables in a file, and creates maps colored according to map data and a user selected color scale. Cesium is a Javascript 3D virtual Globe library. It uses WebGL for rendering, which makes it very fast, and it is capable of displaying a wide variety of data types such as vectors, 3D models, and 2D maps. The forecast results are automatically uploaded to our web server running ncWMS. In turn, the web application can be used to change the settings for color maps and displayed data. The server uses the settings provided by the web application, together with the data in NetCDF to provide WMS image tiles, time series data and legend graphics to the Cesium-NcWMS web application. The user can simultaneously zoom in to the very high resolution forecast results anywhere on the world, and get time series data for any point on the globe. The Cesium-ncWMS visualisation combines a global overview with local relevant information in any browser. See the visualisation live at forecast.ewatercycle.org

Evaluating virtual hosted desktops for graphics-intensive astronomy

NASA Astrophysics Data System (ADS)

Meade, B. F.; Fluke, C. J.

2018-04-01

Visualisation of data is critical to understanding astronomical phenomena. Today, many instruments produce datasets that are too big to be downloaded to a local computer, yet many of the visualisation tools used by astronomers are deployed only on desktop computers. Cloud computing is increasingly used to provide a computation and simulation platform in astronomy, but it also offers great potential as a visualisation platform. Virtual hosted desktops, with graphics processing unit (GPU) acceleration, allow interactive, graphics-intensive desktop applications to operate co-located with astronomy datasets stored in remote data centres. By combining benchmarking and user experience testing, with a cohort of 20 astronomers, we investigate the viability of replacing physical desktop computers with virtual hosted desktops. In our work, we compare two Apple MacBook computers (one old and one new, representing hardware and opposite ends of the useful lifetime) with two virtual hosted desktops: one commercial (Amazon Web Services) and one in a private research cloud (the Australian NeCTAR Research Cloud). For two-dimensional image-based tasks and graphics-intensive three-dimensional operations - typical of astronomy visualisation workflows - we found that benchmarks do not necessarily provide the best indication of performance. When compared to typical laptop computers, virtual hosted desktops can provide a better user experience, even with lower performing graphics cards. We also found that virtual hosted desktops are equally simple to use, provide greater flexibility in choice of configuration, and may actually be a more cost-effective option for typical usage profiles.

Online plasma calculator

NASA Astrophysics Data System (ADS)

Wisniewski, H.; Gourdain, P.-A.

2017-10-01

APOLLO is an online, Linux based plasma calculator. Users can input variables that correspond to their specific plasma, such as ion and electron densities, temperatures, and external magnetic fields. The system is based on a webserver where a FastCGI protocol computes key plasma parameters including frequencies, lengths, velocities, and dimensionless numbers. FastCGI was chosen to overcome security problems caused by JAVA-based plugins. The FastCGI also speeds up calculations over PHP based systems. APOLLO is built upon the WT library, which turns any web browser into a versatile, fast graphic user interface. All values with units are expressed in SI units except temperature, which is in electron-volts. SI units were chosen over cgs units because of the gradual shift to using SI units within the plasma community. APOLLO is intended to be a fast calculator that also provides the user with the proper equations used to calculate the plasma parameters. This system is intended to be used by undergraduates taking plasma courses as well as graduate students and researchers who need a quick reference calculation.

e-Ana and e-Mia: A Content Analysis of Pro–Eating Disorder Web Sites

PubMed Central

Schenk, Summer; Wilson, Jenny L.; Peebles, Rebecka

2010-01-01

Objectives. The Internet offers Web sites that describe, endorse, and support eating disorders. We examined the features of pro–eating disorder Web sites and the messages to which users may be exposed. Methods. We conducted a systematic content analysis of 180 active Web sites, noting site logistics, site accessories, “thinspiration” material (images and prose intended to inspire weight loss), tips and tricks, recovery, themes, and perceived harm. Results. Practically all (91%) of the Web sites were open to the public, and most (79%) had interactive features. A large majority (84%) offered pro-anorexia content, and 64% provided pro-bulimia content. Few sites focused on eating disorders as a lifestyle choice. Thinspiration material appeared on 85% of the sites, and 83% provided overt suggestions on how to engage in eating-disordered behaviors. Thirty-eight percent of the sites included recovery-oriented information or links. Common themes were success, control, perfection, and solidarity. Conclusions. Pro–eating disorder Web sites present graphic material to encourage, support, and motivate site users to continue their efforts with anorexia and bulimia. Continued monitoring will offer a valuable foundation to build a better understanding of the effects of these sites on their users. PMID:20558807

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.

ADF/ADC Web Tools for Browsing and Visualizing Astronomical Catalogs and NASA Astrophysics Mission Metadata

NASA Astrophysics Data System (ADS)

Shaya, E.; Kargatis, V.; Blackwell, J.; Borne, K.; White, R. A.; Cheung, C.

1998-05-01

Several new web based services have been introduced this year by the Astrophysics Data Facility (ADF) at the NASA Goddard Space Flight Center. IMPReSS is a graphical interface to astrophysics databases that presents the user with the footprints of observations of space-based missions. It also aids astronomers in retrieving these data by sending requests to distributed data archives. The VIEWER is a reader of ADC astronomical catalogs and journal tables that allows subsetting of catalogs by column choices and range selection and provides database-like search capability within each table. With it, the user can easily find the table data most appropriate for their purposes and then download either the subset table or the original table. CATSEYE is a tool that plots output tables from the VIEWER (and soon AMASE), making exploring the datasets fast and easy. Having completed the basic functionality of these systems, we are enhancing the site to provide advanced functionality. These will include: market basket storage of tables and records of VIEWER output for IMPReSS and AstroBrowse queries, non-HTML table responses to AstroBrowse type queries, general column arithmetic, modularity to allow entrance into the sequence of web pages at any point, histogram plots, navigable maps, and overplotting of catalog objects on mission footprint maps. When completed, the ADF/ADC web facilities will provide astronomical tabled data and mission retrieval information in several hyperlinked environments geared for users at any level, from the school student to the typical astronomer to the expert datamining tools at state-of-the-art data centers.

Genomecmp: computer software to detect genomic rearrangements using markers

NASA Astrophysics Data System (ADS)

Kulawik, Maciej; Nowak, Robert M.

2017-08-01

Detection of genomics rearrangements is a tough task, because of the size of data to be processed. As genome sequences may consist of hundreds of millions symbols, it is not only practically impossible to compare them by hand, but it is also complex problem for computer software. The way to significantly accelerate the process is to use rearrangement detection algorithm based on unique short sequences called markers. The algorithm described in this paper develops markers using base genome and find the markers positions on other genome. The algorithm has been extended by support for ambiguity symbols. Web application with graphical user interface has been created using three-layer architecture, where users could run the task simultaneously. The accuracy and efficiency of proposed solution has been studied using generated and real data.

Using USNO's API to Obtain Data

NASA Astrophysics Data System (ADS)

Lesniak, Michael V.; Pozniak, Daniel; Punnoose, Tarun

2015-01-01

The U.S. Naval Observatory (USNO) is in the process of modernizing its publicly available web services into APIs (Application Programming Interfaces). Services configured as APIs offer greater flexibility to the user and allow greater usage. Depending on the particular service, users who implement our APIs will receive either a PNG (Portable Network Graphics) image or data in JSON (JavaScript Object Notation) format. This raw data can then be embedded in third-party web sites or in apps.Part of the USNO's mission is to provide astronomical and timing data to government agencies and the general public. To this end, the USNO provides accurate computations of astronomical phenomena such as dates of lunar phases, rise and set times of the Moon and Sun, and lunar and solar eclipse times. Users who navigate to our web site and select one of our 18 services are prompted to complete a web form, specifying parameters such as date, time, location, and object. Many of our services work for years between 1700 and 2100, meaning that past, present, and future events can be computed. Upon form submission, our web server processes the request, computes the data, and outputs it to the user.Over recent years, the use of the web by the general public has vastly changed. In response to this, the USNO is modernizing its web-based data services. This includes making our computed data easier to embed within third-party web sites as well as more easily querying from apps running on tablets and smart phones. To facilitate this, the USNO has begun converting its services into APIs. In addition to the existing web forms for the various services, users are able to make direct URL requests that return either an image or numerical data.To date, four of our web services have been configured to run with APIs. Two are image-producing services: "Apparent Disk of a Solar System Object" and "Day and Night Across the Earth." Two API data services are "Complete Sun and Moon Data for One Day" and "Dates of Primary Phases of the Moon." Instructions for how to use our API services as well as examples of their use can be found on one of our explanatory web pages and will be discussed here.

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy.

PubMed

Letunic, Ivica; Bork, Peer

2011-07-01

Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. In addition to classical tree viewer functions, iTOL offers many novel ways of annotating trees with various additional data. Current version introduces numerous new features and greatly expands the number of supported data set types. Trees can be interactively manipulated and edited. A free personal account system is available, providing management and sharing of trees in user defined workspaces and projects. Export to various bitmap and vector graphics formats is supported. Batch access interface is available for programmatic access or inclusion of interactive trees into other web services.

Web-based reactive transport modeling using PFLOTRAN

NASA Astrophysics Data System (ADS)

Zhou, H.; Karra, S.; Lichtner, P. C.; Versteeg, R.; Zhang, Y.

2017-12-01

Actionable understanding of system behavior in the subsurface is required for a wide spectrum of societal and engineering needs by both commercial firms and government entities and academia. These needs include, for example, water resource management, precision agriculture, contaminant remediation, unconventional energy production, CO2 sequestration monitoring, and climate studies. Such understanding requires the ability to numerically model various coupled processes that occur across different temporal and spatial scales as well as multiple physical domains (reservoirs - overburden, surface-subsurface, groundwater-surface water, saturated-unsaturated zone). Currently, this ability is typically met through an in-house approach where computational resources, model expertise, and data for model parameterization are brought together to meet modeling needs. However, such an approach has multiple drawbacks which limit the application of high-end reactive transport codes such as the Department of Energy funded[?] PFLOTRAN code. In addition, while many end users have a need for the capabilities provided by high-end reactive transport codes, they do not have the expertise - nor the time required to obtain the expertise - to effectively use these codes. We have developed and are actively enhancing a cloud-based software platform through which diverse users are able to easily configure, execute, visualize, share, and interpret PFLOTRAN models. This platform consists of a web application and available on-demand HPC computational infrastructure. The web application consists of (1) a browser-based graphical user interface which allows users to configure models and visualize results interactively, and (2) a central server with back-end relational databases which hold configuration, data, modeling results, and Python scripts for model configuration, and (3) a HPC environment for on-demand model execution. We will discuss lessons learned in the development of this platform, the rationale for different interfaces, implementation choices, as well as the planned path forward.

Valorisation of Como Historical Cadastral Maps Through Modern Web Geoservices

NASA Astrophysics Data System (ADS)

Brovelli, M. A.; Minghini, M.; Zamboni, G.

2012-07-01

Cartographic cultural heritage preserved in worldwide archives is often stored in the original paper version only, thus restricting both the chances of utilization and the range of possible users. The Web C.A.R.T.E. system addressed this issue with regard to the precious cadastral maps preserved at the State Archive of Como. Aim of the project was to improve the visibility and accessibility of this heritage using the latest free and open source tools for processing, cataloguing and web publishing the maps. The resulting architecture should therefore assist the State Archive of Como in managing its cartographic contents. After a pre-processing consisting of digitization and georeferencing steps, maps were provided with metadata, compiled according to the current Italian standards and managed through an ad hoc version of the GeoNetwork Opensource geocatalog software. A dedicated MapFish-based webGIS client, with an optimized version also for mobile platforms, was built for maps publication and 2D navigation. A module for 3D visualization of cadastral maps was finally developed using the NASA World Wind Virtual Globe. Thanks to a temporal slidebar, time was also included in the system producing a 4D Graphical User Interface. The overall architecture was totally built with free and open source software and allows a direct and intuitive consultation of historical maps. Besides the notable advantage of keeping original paper maps intact, the system greatly simplifies the work of the State Archive of Como common users and together widens the same range of users thanks to the modernization of map consultation tools.

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

NASA Astrophysics Data System (ADS)

Gordov, Evgeny; Okladnikov, Igor; Titov, Alexander

2017-04-01

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

MrEnt: an editor for publication-quality phylogenetic tree illustrations.

PubMed

Zuccon, Alessandro; Zuccon, Dario

2014-09-01

We developed MrEnt, a Windows-based, user-friendly software that allows the production of complex, high-resolution, publication-quality phylogenetic trees in few steps, directly from the analysis output. The program recognizes the standard Nexus tree format and the annotated tree files produced by BEAST and MrBayes. MrEnt combines in a single software a large suite of tree manipulation functions (e.g. handling of multiple trees, tree rotation, character mapping, node collapsing, compression of large clades, handling of time scale and error bars for chronograms) with drawing tools typical of standard graphic editors, including handling of graphic elements and images. The tree illustration can be printed or exported in several standard formats suitable for journal publication, PowerPoint presentation or Web publication. © 2014 John Wiley & Sons Ltd.

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels.

PubMed

Berka, Karel; Hanák, Ondrej; Sehnal, David; Banás, Pavel; Navrátilová, Veronika; Jaiswal, Deepti; Ionescu, Crina-Maria; Svobodová Vareková, Radka; Koca, Jaroslav; Otyepka, Michal

2012-07-01

Biomolecular channels play important roles in many biological systems, e.g. enzymes, ribosomes and ion channels. This article introduces a web-based interactive MOLEonline 2.0 application for the analysis of access/egress paths to interior molecular voids. MOLEonline 2.0 enables platform-independent, easy-to-use and interactive analyses of (bio)macromolecular channels, tunnels and pores. Results are presented in a clear manner, making their interpretation easy. For each channel, MOLEonline displays a 3D graphical representation of the channel, its profile accompanied by a list of lining residues and also its basic physicochemical properties. The users can tune advanced parameters when performing a channel search to direct the search according to their needs. The MOLEonline 2.0 application is freely available via the Internet at http://ncbr.muni.cz/mole or http://mole.upol.cz.

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

PubMed

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

2018-06-28

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

CADB: Conformation Angles DataBase of proteins

PubMed Central

Sheik, S. S.; Ananthalakshmi, P.; Bhargavi, G. Ramya; Sekar, K.

2003-01-01

Conformation Angles DataBase (CADB) provides an online resource to access data on conformation angles (both main-chain and side-chain) of protein structures in two data sets corresponding to 25% and 90% sequence identity between any two proteins, available in the Protein Data Bank. In addition, the database contains the necessary crystallographic parameters. The package has several flexible options and display facilities to visualize the main-chain and side-chain conformation angles for a particular amino acid residue. The package can also be used to study the interrelationship between the main-chain and side-chain conformation angles. A web based JAVA graphics interface has been deployed to display the user interested information on the client machine. The database is being updated at regular intervals and can be accessed over the World Wide Web interface at the following URL: http://144.16.71.148/cadb/. PMID:12520049

MetaboAnalyst 3.0--making metabolomics more meaningful.

PubMed

Xia, Jianguo; Sinelnikov, Igor V; Han, Beomsoo; Wishart, David S

2015-07-01

MetaboAnalyst (www.metaboanalyst.ca) is a web server designed to permit comprehensive metabolomic data analysis, visualization and interpretation. It supports a wide range of complex statistical calculations and high quality graphical rendering functions that require significant computational resources. First introduced in 2009, MetaboAnalyst has experienced more than a 50X growth in user traffic (>50 000 jobs processed each month). In order to keep up with the rapidly increasing computational demands and a growing number of requests to support translational and systems biology applications, we performed a substantial rewrite and major feature upgrade of the server. The result is MetaboAnalyst 3.0. By completely re-implementing the MetaboAnalyst suite using the latest web framework technologies, we have been able substantially improve its performance, capacity and user interactivity. Three new modules have also been added including: (i) a module for biomarker analysis based on the calculation of receiver operating characteristic curves; (ii) a module for sample size estimation and power analysis for improved planning of metabolomics studies and (iii) a module to support integrative pathway analysis for both genes and metabolites. In addition, popular features found in existing modules have been significantly enhanced by upgrading the graphical output, expanding the compound libraries and by adding support for more diverse organisms. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-01-01

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

THGS: a web-based database of Transmembrane Helices in Genome Sequences

PubMed Central

Fernando, S. A.; Selvarani, P.; Das, Soma; Kumar, Ch. Kiran; Mondal, Sukanta; Ramakumar, S.; Sekar, K.

2004-01-01

Transmembrane Helices in Genome Sequences (THGS) is an interactive web-based database, developed to search the transmembrane helices in the user-interested gene sequences available in the Genome Database (GDB). The proposed database has provision to search sequence motifs in transmembrane and globular proteins. In addition, the motif can be searched in the other sequence databases (Swiss-Prot and PIR) or in the macromolecular structure database, Protein Data Bank (PDB). Further, the 3D structure of the corresponding queried motif, if it is available in the solved protein structures deposited in the Protein Data Bank, can also be visualized using the widely used graphics package RASMOL. All the sequence databases used in the present work are updated frequently and hence the results produced are up to date. The database THGS is freely available via the world wide web and can be accessed at http://pranag.physics.iisc.ernet.in/thgs/ or http://144.16.71.10/thgs/. PMID:14681375

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

PubMed

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

2005-05-01

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

FNV: light-weight flash-based network and pathway viewer.

PubMed

Dannenfelser, Ruth; Lachmann, Alexander; Szenk, Mariola; Ma'ayan, Avi

2011-04-15

Network diagrams are commonly used to visualize biochemical pathways by displaying the relationships between genes, proteins, mRNAs, microRNAs, metabolites, regulatory DNA elements, diseases, viruses and drugs. While there are several currently available web-based pathway viewers, there is still room for improvement. To this end, we have developed a flash-based network viewer (FNV) for the visualization of small to moderately sized biological networks and pathways. Written in Adobe ActionScript 3.0, the viewer accepts simple Extensible Markup Language (XML) formatted input files to display pathways in vector graphics on any web-page providing flexible layout options, interactivity with the user through tool tips, hyperlinks and the ability to rearrange nodes on the screen. FNV was utilized as a component in several web-based systems, namely Genes2Networks, Lists2Networks, KEA, ChEA and PathwayGenerator. In addition, FVN can be used to embed pathways inside pdf files for the communication of pathways in soft publication materials. FNV is available for use and download along with the supporting documentation and sample networks at http://www.maayanlab.net/FNV. avi.maayan@mssm.edu.

ShinyGPAS: interactive genomic prediction accuracy simulator based on deterministic formulas.

PubMed

Morota, Gota

2017-12-20

Deterministic formulas for the accuracy of genomic predictions highlight the relationships among prediction accuracy and potential factors influencing prediction accuracy prior to performing computationally intensive cross-validation. Visualizing such deterministic formulas in an interactive manner may lead to a better understanding of how genetic factors control prediction accuracy. The software to simulate deterministic formulas for genomic prediction accuracy was implemented in R and encapsulated as a web-based Shiny application. Shiny genomic prediction accuracy simulator (ShinyGPAS) simulates various deterministic formulas and delivers dynamic scatter plots of prediction accuracy versus genetic factors impacting prediction accuracy, while requiring only mouse navigation in a web browser. ShinyGPAS is available at: https://chikudaisei.shinyapps.io/shinygpas/ . ShinyGPAS is a shiny-based interactive genomic prediction accuracy simulator using deterministic formulas. It can be used for interactively exploring potential factors that influence prediction accuracy in genome-enabled prediction, simulating achievable prediction accuracy prior to genotyping individuals, or supporting in-class teaching. ShinyGPAS is open source software and it is hosted online as a freely available web-based resource with an intuitive graphical user interface.

Plugin free remote visualization in the browser

NASA Astrophysics Data System (ADS)

Tamm, Georg; Slusallek, Philipp

2015-01-01

Today, users access information and rich media from anywhere using the web browser on their desktop computers, tablets or smartphones. But the web evolves beyond media delivery. Interactive graphics applications like visualization or gaming become feasible as browsers advance in the functionality they provide. However, to deliver large-scale visualization to thin clients like mobile devices, a dedicated server component is necessary. Ideally, the client runs directly within the browser the user is accustomed to, requiring no installation of a plugin or native application. In this paper, we present the state-of-the-art of technologies which enable plugin free remote rendering in the browser. Further, we describe a remote visualization system unifying these technologies. The system transfers rendering results to the client as images or as a video stream. We utilize the upcoming World Wide Web Consortium (W3C) conform Web Real-Time Communication (WebRTC) standard, and the Native Client (NaCl) technology built into Chrome, to deliver video with low latency.

Earth Science Mining Web Services

NASA Astrophysics Data System (ADS)

Pham, L. B.; Lynnes, C. S.; Hegde, M.; Graves, S.; Ramachandran, R.; Maskey, M.; Keiser, K.

2008-12-01

To allow scientists further capabilities in the area of data mining and web services, the Goddard Earth Sciences Data and Information Services Center (GES DISC) and researchers at the University of Alabama in Huntsville (UAH) have developed a system to mine data at the source without the need of network transfers. The system has been constructed by linking together several pre-existing technologies: the Simple Scalable Script-based Science Processor for Measurements (S4PM), a processing engine at the GES DISC; the Algorithm Development and Mining (ADaM) system, a data mining toolkit from UAH that can be configured in a variety of ways to create customized mining processes; ActiveBPEL, a workflow execution engine based on BPEL (Business Process Execution Language); XBaya, a graphical workflow composer; and the EOS Clearinghouse (ECHO). XBaya is used to construct an analysis workflow at UAH using ADaM components, which are also installed remotely at the GES DISC, wrapped as Web Services. The S4PM processing engine searches ECHO for data using space-time criteria, staging them to cache, allowing the ActiveBPEL engine to remotely orchestrates the processing workflow within S4PM. As mining is completed, the output is placed in an FTP holding area for the end user. The goals are to give users control over the data they want to process, while mining data at the data source using the server's resources rather than transferring the full volume over the internet. These diverse technologies have been infused into a functioning, distributed system with only minor changes to the underlying technologies. The key to this infusion is the loosely coupled, Web- Services based architecture: All of the participating components are accessible (one way or another) through (Simple Object Access Protocol) SOAP-based Web Services.

Earth Science Mining Web Services

NASA Technical Reports Server (NTRS)

Pham, Long; Lynnes, Christopher; Hegde, Mahabaleshwa; Graves, Sara; Ramachandran, Rahul; Maskey, Manil; Keiser, Ken

2008-01-01

To allow scientists further capabilities in the area of data mining and web services, the Goddard Earth Sciences Data and Information Services Center (GES DISC) and researchers at the University of Alabama in Huntsville (UAH) have developed a system to mine data at the source without the need of network transfers. The system has been constructed by linking together several pre-existing technologies: the Simple Scalable Script-based Science Processor for Measurements (S4PM), a processing engine at he GES DISC; the Algorithm Development and Mining (ADaM) system, a data mining toolkit from UAH that can be configured in a variety of ways to create customized mining processes; ActiveBPEL, a workflow execution engine based on BPEL (Business Process Execution Language); XBaya, a graphical workflow composer; and the EOS Clearinghouse (ECHO). XBaya is used to construct an analysis workflow at UAH using ADam components, which are also installed remotely at the GES DISC, wrapped as Web Services. The S4PM processing engine searches ECHO for data using space-time criteria, staging them to cache, allowing the ActiveBPEL engine to remotely orchestras the processing workflow within S4PM. As mining is completed, the output is placed in an FTP holding area for the end user. The goals are to give users control over the data they want to process, while mining data at the data source using the server's resources rather than transferring the full volume over the internet. These diverse technologies have been infused into a functioning, distributed system with only minor changes to the underlying technologies. The key to the infusion is the loosely coupled, Web-Services based architecture: All of the participating components are accessible (one way or another) through (Simple Object Access Protocol) SOAP-based Web Services.

Reasoning about Users' Actions in a Graphical User Interface.

ERIC Educational Resources Information Center

Virvou, Maria; Kabassi, Katerina

2002-01-01

Describes a graphical user interface called IFM (Intelligent File Manipulator) that provides intelligent help to users. Explains two underlying reasoning mechanisms, one an adaptation of human plausible reasoning and one that performs goal recognition based on the effects of users' commands; and presents results of an empirical study that…

The missing graphical user interface for genomics.

PubMed

Schatz, Michael C

2010-01-01

The Galaxy package empowers regular users to perform rich DNA sequence analysis through a much-needed and user-friendly graphical web interface. See research article http://genomebiology.com/2010/11/8/R86 RESEARCH HIGHLIGHT: With the advent of affordable and high-throughput DNA sequencing, sequencing is becoming an essential component in nearly every genetics lab. These data are being generated to probe sequence variations, to understand transcribed, regulated or methylated DNA elements, and to explore a host of other biological features across the tree of life and across a range of environments and conditions. Given this deluge of data, novices and experts alike are facing the daunting challenge of trying to analyze the raw sequence data computationally. With so many tools available and so many assays to analyze, how can one be expected to stay current with the state of the art? How can one be expected to learn to use each tool and construct robust end-to-end analysis pipelines, all while ensuring that input formats, command-line options, sequence databases and program libraries are set correctly? Finally, once the analysis is complete, how does one ensure the results are reproducible and transparent for others to scrutinize and study?In an article published in Genome Biology, Jeremy Goecks, Anton Nekrutenko, James Taylor and the rest of the Galaxy Team (Goecks et al. 1) make a great advance towards resolving these critical questions with the latest update to their Galaxy Project. The ambitious goal of Galaxy is to empower regular users to carry out their own computational analysis without having to be an expert in computational biology or computer science. Galaxy adds a desperately needed graphical user interface to genomics research, making data analysis universally accessible in a web browser, and freeing users from the minutiae of archaic command-line parameters, data formats and scripting languages. Data inputs and computational steps are selected from dynamic graphical menus, and the results are displayed in intuitive plots and summaries that encourage interactive workflows and the exploration of hypotheses. The underlying data analysis tools can be almost any piece of software, written in any language, but all their complexity is neatly hidden inside of Galaxy, allowing users to focus on scientific rather than technical questions.

Multimodal browsing using VoiceXML

NASA Astrophysics Data System (ADS)

Caccia, Giuseppe; Lancini, Rosa C.; Peschiera, Giuseppe

2003-06-01

With the increasing development of devices such as personal computers, WAP and personal digital assistants connected to the World Wide Web, end users feel the need to browse the Internet through multiple modalities. We intend to investigate on how to create a user interface and a service distribution platform granting the user access to the Internet through standard I/O modalities and voice simultaneously. Different architectures are evaluated suggesting the more suitable for each client terminal (PC o WAP). In particular the design of the multimodal usermachine interface considers the synchronization issue between graphical and voice contents.

Eodataservice.org: Big Data Platform to Enable Multi-disciplinary Information Extraction from Geospatial Data

NASA Astrophysics Data System (ADS)

Natali, S.; Mantovani, S.; Barboni, D.; Hogan, P.

2017-12-01

In 1999, US Vice-President Al Gore outlined the concept of `Digital Earth' as a multi-resolution, three-dimensional representation of the planet to find, visualise and make sense of vast amounts of geo- referenced information on physical and social environments, allowing to navigate through space and time, accessing historical and forecast data to support scientists, policy-makers, and any other user. The eodataservice platform (http://eodataservice.org/) implements the Digital Earth Concept: eodatasevice is a cross-domain platform that makes available a large set of multi-year global environmental collections allowing data discovery, visualization, combination, processing and download. It implements a "virtual datacube" approach where data stored on distributed data centers are made available via standardized OGC-compliant interfaces. Dedicated web-based Graphic User Interfaces (based on the ESA-NASA WebWorldWind technology) as well as web-based notebooks (e.g. Jupyter notebook), deskop GIS tools and command line interfaces can be used to access and manipulate the data. The platform can be fully customized on users' needs. So far eodataservice has been used for the following thematic applications: High resolution satellite data distribution Land surface monitoring using SAR surface deformation data Atmosphere, ocean and climate applications Climate-health applications Urban Environment monitoring Safeguard of cultural heritage sites Support to farmers and (re)-insurances in the agriculturés field In the current work, the EO Data Service concept is presented as key enabling technology; furthermore various examples are provided to demonstrate the high level of interdisciplinarity of the platform.

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.

Approaches to communication in response to geo-hydrological risk: POLARIS an Italian web initiative.

NASA Astrophysics Data System (ADS)

Salvati, Paola; Pernice, Umberto; Bianchi, Cinzia; Fiorucci, Federica; Marchesini, Ivan; Guzzetti, Fausto

2015-04-01

In the contemporary information and knowledge-based society, communication can foster effective responses to geo-hydrological risks, by increasing awareness on the causes and consequences of specific hazards, e.g., landslides, debris flows, and floods, and by fostering the capacity of individuals, groups, and organizations to prepare, manage and recover from geo-hydrological events. In this context, communication plays a vital role in all phases of the disaster cycle. Although in the last few years the scientific community has begun to disseminate information on geo-hydrological hazards and the associated risks through thematic websites, these remain mainly addressed to experts for specific technical purposes with contents and web interfaces hardly appreciated by a wider audience and rarely synchronised with social networks. To address the problem posed by the lack of communication on geo-hydrological hazards with potential human consequence in Italy, we designed the POLARIS Web site. The initiative we are conducting has the main object of contributing, in different ways and at different geographical scales, to raise awareness about landslides and floods, and their impact on the Italian society. The website is structured into six main sections (i.e. Reports, Are you ready, Events, Alert Zones, Focus and Blog) that provide different and complementary information including, respectively: periodical reports on landslide and flood risk to the population of Italy, suitable behaviors to adopt during damaging events, data and analyses on specific events, visual and detailed info on damaging events of the Italian Alert Zones defined by the Civil Protection Authority and blog-posts on landslide and flood events encouraging citizens' participation to crowd-sourcing information. Consultants experienced in project management, web-communication strategies on natural hazards, info-graphics, and user experience design were involved in the initiative to arrange and publish the information, considering usability and accessibility of the website, and key graphic aspects of web 2.0 information, making the web site communication more effective to users pertaining to diversified audiences. Specific icons are designed to describe the geo-hydrological events and maps to visualize their impact on the territory. The scientific and technical contents are edited using appropriate communication strategies which adopt a less technical and more widely comprehensible language, using intuitive and engaging web interfaces and linking messages to social media that encourage citizens' interactions. Monitoring the access of users to the website during more than a year after its publication, we noticed how the majority of the access corresponds to the occurrence of the worst geo-hydrological events and, in particular, when journalists or scientists promoted the website through television. Such a positive effect on the growth of users access suggested us to enhance our collaboration with scientific journalists by linking traditional (i.e. TV) and social media to further enlarge the awareness of website and to better explain users how to use the website information for increasing their resilience to geo-hydrological hazards.

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/.

A Web-Based Decision Support System for Assessing Regional Water-Quality Conditions and Management Actions

USGS Publications Warehouse

Booth, N.L.; Everman, E.J.; Kuo, I.-L.; Sprague, L.; Murphy, L.

2011-01-01

The U.S. Geological Survey National Water Quality Assessment Program has completed a number of water-quality prediction models for nitrogen and phosphorus for the conterminous United States as well as for regional areas of the nation. In addition to estimating water-quality conditions at unmonitored streams, the calibrated SPAtially Referenced Regressions On Watershed attributes (SPARROW) models can be used to produce estimates of yield, flow-weighted concentration, or load of constituents in water under various land-use condition, change, or resource management scenarios. A web-based decision support infrastructure has been developed to provide access to SPARROW simulation results on stream water-quality conditions and to offer sophisticated scenario testing capabilities for research and water-quality planning via a graphical user interface with familiar controls. The SPARROW decision support system (DSS) is delivered through a web browser over an Internet connection, making it widely accessible to the public in a format that allows users to easily display water-quality conditions and to describe, test, and share modeled scenarios of future conditions. SPARROW models currently supported by the DSS are based on the modified digital versions of the 1:500,000-scale River Reach File (RF1) and 1:100,000-scale National Hydrography Dataset (medium-resolution, NHDPlus) stream networks. ?? 2011 American Water Resources Association. This article is a U.S. Government work and is in the public domain in the USA.

Browsing the World Wide Web from behind a firewall

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

Simons, R.W.

1995-02-01

The World Wide Web provides a unified method of access to various information services on the Internet via a variety of protocols. Mosaic and other browsers give users a graphical interface to the Web that is easier to use and more visually pleasing than any other common Internet information service today. The availability of information via the Web and the number of users accessing it have both grown rapidly in the last year. The interest and investment of commercial firms in this technology suggest that in the near future, access to the Web may become as necessary to doing businessmore » as a telephone. This is problematical for organizations that use firewalls to protect their internal networks from the Internet. Allowing all the protocols and types of information found in the Web to pass their firewall will certainly increase the risk of attack by hackers on the Internet. But not allowing access to the Web could be even more dangerous, as frustrated users of the internal network are either unable to do their jobs, or find creative new ways to get around the firewall. The solution to this dilemma adopted at Sandia National Laboratories is described. Discussion also covers risks of accessing the Web, design alternatives considered, and trade-offs used to find the proper balance between access and protection.« less

Neurotree: a collaborative, graphical database of the academic genealogy of neuroscience.

PubMed

David, Stephen V; Hayden, Benjamin Y

2012-01-01

Neurotree is an online database that documents the lineage of academic mentorship in neuroscience. Modeled on the tree format typically used to describe biological genealogies, the Neurotree web site provides a concise summary of the intellectual history of neuroscience and relationships between individuals in the current neuroscience community. The contents of the database are entirely crowd-sourced: any internet user can add information about researchers and the connections between them. As of July 2012, Neurotree has collected information from 10,000 users about 35,000 researchers and 50,000 mentor relationships, and continues to grow. The present report serves to highlight the utility of Neurotree as a resource for academic research and to summarize some basic analysis of its data. The tree structure of the database permits a variety of graphical analyses. We find that the connectivity and graphical distance between researchers entered into Neurotree early has stabilized and thus appears to be mostly complete. The connectivity of more recent entries continues to mature. A ranking of researcher fecundity based on their mentorship reveals a sustained period of influential researchers from 1850-1950, with the most influential individuals active at the later end of that period. Finally, a clustering analysis reveals that some subfields of neuroscience are reflected in tightly interconnected mentor-trainee groups.

Neurotree: A Collaborative, Graphical Database of the Academic Genealogy of Neuroscience

PubMed Central

David, Stephen V.; Hayden, Benjamin Y.

2012-01-01

Neurotree is an online database that documents the lineage of academic mentorship in neuroscience. Modeled on the tree format typically used to describe biological genealogies, the Neurotree web site provides a concise summary of the intellectual history of neuroscience and relationships between individuals in the current neuroscience community. The contents of the database are entirely crowd-sourced: any internet user can add information about researchers and the connections between them. As of July 2012, Neurotree has collected information from 10,000 users about 35,000 researchers and 50,000 mentor relationships, and continues to grow. The present report serves to highlight the utility of Neurotree as a resource for academic research and to summarize some basic analysis of its data. The tree structure of the database permits a variety of graphical analyses. We find that the connectivity and graphical distance between researchers entered into Neurotree early has stabilized and thus appears to be mostly complete. The connectivity of more recent entries continues to mature. A ranking of researcher fecundity based on their mentorship reveals a sustained period of influential researchers from 1850–1950, with the most influential individuals active at the later end of that period. Finally, a clustering analysis reveals that some subfields of neuroscience are reflected in tightly interconnected mentor-trainee groups. PMID:23071595

BIRCH: a user-oriented, locally-customizable, bioinformatics system.

PubMed

Fristensky, Brian

2007-02-09

Molecular biologists need sophisticated analytical tools which often demand extensive computational resources. While finding, installing, and using these tools can be challenging, pipelining data from one program to the next is particularly awkward, especially when using web-based programs. At the same time, system administrators tasked with maintaining these tools do not always appreciate the needs of research biologists. BIRCH (Biological Research Computing Hierarchy) is an organizational framework for delivering bioinformatics resources to a user group, scaling from a single lab to a large institution. The BIRCH core distribution includes many popular bioinformatics programs, unified within the GDE (Genetic Data Environment) graphic interface. Of equal importance, BIRCH provides the system administrator with tools that simplify the job of managing a multiuser bioinformatics system across different platforms and operating systems. These include tools for integrating locally-installed programs and databases into BIRCH, and for customizing the local BIRCH system to meet the needs of the user base. BIRCH can also act as a front end to provide a unified view of already-existing collections of bioinformatics software. Documentation for the BIRCH and locally-added programs is merged in a hierarchical set of web pages. In addition to manual pages for individual programs, BIRCH tutorials employ step by step examples, with screen shots and sample files, to illustrate both the important theoretical and practical considerations behind complex analytical tasks. BIRCH provides a versatile organizational framework for managing software and databases, and making these accessible to a user base. Because of its network-centric design, BIRCH makes it possible for any user to do any task from anywhere.

BIRCH: A user-oriented, locally-customizable, bioinformatics system

PubMed Central

Fristensky, Brian

2007-01-01

Background Molecular biologists need sophisticated analytical tools which often demand extensive computational resources. While finding, installing, and using these tools can be challenging, pipelining data from one program to the next is particularly awkward, especially when using web-based programs. At the same time, system administrators tasked with maintaining these tools do not always appreciate the needs of research biologists. Results BIRCH (Biological Research Computing Hierarchy) is an organizational framework for delivering bioinformatics resources to a user group, scaling from a single lab to a large institution. The BIRCH core distribution includes many popular bioinformatics programs, unified within the GDE (Genetic Data Environment) graphic interface. Of equal importance, BIRCH provides the system administrator with tools that simplify the job of managing a multiuser bioinformatics system across different platforms and operating systems. These include tools for integrating locally-installed programs and databases into BIRCH, and for customizing the local BIRCH system to meet the needs of the user base. BIRCH can also act as a front end to provide a unified view of already-existing collections of bioinformatics software. Documentation for the BIRCH and locally-added programs is merged in a hierarchical set of web pages. In addition to manual pages for individual programs, BIRCH tutorials employ step by step examples, with screen shots and sample files, to illustrate both the important theoretical and practical considerations behind complex analytical tasks. Conclusion BIRCH provides a versatile organizational framework for managing software and databases, and making these accessible to a user base. Because of its network-centric design, BIRCH makes it possible for any user to do any task from anywhere. PMID:17291351

Studying the co-evolution of protein families with the Mirrortree web server.

PubMed

Ochoa, David; Pazos, Florencio

2010-05-15

The Mirrortree server allows to graphically and interactively study the co-evolution of two protein families, and investigate their possible interactions and functional relationships in a taxonomic context. The server includes the possibility of starting from single sequences and hence it can be used by non-expert users. The web server is freely available at http://csbg.cnb.csic.es/mtserver. It was tested in the main web browsers. Adobe Flash Player is required at the client side to perform the interactive assessment of co-evolution. pazos@cnb.csic.es Supplementary data are available at Bioinformatics online.

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

World Wide Web Page Design: A Structured Approach.

ERIC Educational Resources Information Center

Gregory, Gwen; Brown, M. Marlo

1997-01-01

Describes how to develop a World Wide Web site based on structured programming concepts. Highlights include flowcharting, first page design, evaluation, page titles, documenting source code, text, graphics, and browsers. Includes a template for HTML writers, tips for using graphics, a sample homepage, guidelines for authoring structured HTML, and…

What Tomorrow May Bring: Trends in Technology and Education.

ERIC Educational Resources Information Center

Molebash, Philip E.

This paper analyzes trends in technology and how they relate to education and then extrapolates these trends in order to predict the future of technology and education. The paper examines how the trends of Moore's Law, the graphical user interface, telecommunications/networks and Metcalfe's Law, the Internet and the World Wide Web, technology…

Bandwidth Constraints to Using Video and Other Rich Media in Behavior Change Websites

PubMed Central

Jazdzewski, Stephen A; McKay, H Garth; Hudson, Clinton R

2005-01-01

Background Web-based behavior change interventions often include rich media (eg, video, audio, and large graphics). The rationale for using rich media includes the need to reach users who are not inclined or able to use text-based website content, encouragement of program engagement, and following the precedent set by news and sports websites. Objectives We describe the development of a bandwidth usage index, which seeks to provide a practical method to gauge the extent to which websites can successfully be used within different Internet access scenarios (eg, dial-up and broadband). Methods We conducted three studies to measure bandwidth consumption. In Study 1, we measured the bandwidth usage index for three video-rich websites (for smoking cessation, for caregivers, and for improving eldercare by family members). We then estimated the number of concurrent users that could be accommodated by each website under various Internet access scenarios. In Study 2, we sought to validate our estimated threshold number of concurrent users by testing the video-rich smoking cessation website with different numbers of concurrent users. In Study 3, we calculated the bandwidth usage index and threshold number of concurrent users for three versions of the smoking cessation website: the video-rich version (tested in Study 1), an audio-rich version, and a Web-enabled CD-ROM version in which all media-rich content was placed on a CD-ROM on the client computer. Results In Study 1, we found that the bandwidth usage index of the video-rich websites ranged from 144 Kbps to 93 Kbps. These results indicated that dial-up modem users would not achieve a “good user experience” with any of the three rich media websites. Results for Study 2 confirmed that usability was compromised when the estimated threshold number of concurrent users was exceeded. Results for Study 3 indicated that changing a website from video- to audio-rich content reduced the bandwidth requirement by almost 50%, but it remained too large to allow satisfactory use in dial-up modem scenarios. The Web-enabled CD-ROM reduced bandwidth requirements such that even a dial-up modem user could have a good user experience with the rich media content. Conclusions We conclude that the bandwidth usage index represents a practical tool that can help developers and researchers to measure the bandwidth requirements of their websites as well as to evaluate the feasibility of certain website designs in terms of specific use cases. These findings are discussed in terms of reaching different groups of users as well accommodating the intended number of concurrent users. We also discuss the promising option of using Web-enabled CD-ROMs to deliver rich media content to users with dial-up Internet access. We introduce a number of researchable themes for improving our ability to develop Web-based behavior change interventions that can better deliver what they promise. PMID:16236701

Bandwidth constraints to using video and other rich media in behavior change websites.

PubMed

Danaher, Brian G; Jazdzewski, Stephen A; McKay, H Garth; Hudson, Clinton R

2005-09-16

Web-based behavior change interventions often include rich media (eg, video, audio, and large graphics). The rationale for using rich media includes the need to reach users who are not inclined or able to use text-based website content, encouragement of program engagement, and following the precedent set by news and sports websites. We describe the development of a bandwidth usage index, which seeks to provide a practical method to gauge the extent to which websites can successfully be used within different Internet access scenarios (eg, dial-up and broadband). We conducted three studies to measure bandwidth consumption. In Study 1, we measured the bandwidth usage index for three video-rich websites (for smoking cessation, for caregivers, and for improving eldercare by family members). We then estimated the number of concurrent users that could be accommodated by each website under various Internet access scenarios. In Study 2, we sought to validate our estimated threshold number of concurrent users by testing the video-rich smoking cessation website with different numbers of concurrent users. In Study 3, we calculated the bandwidth usage index and threshold number of concurrent users for three versions of the smoking cessation website: the video-rich version (tested in Study 1), an audio-rich version, and a Web-enabled CD-ROM version in which all media-rich content was placed on a CD-ROM on the client computer. In Study 1, we found that the bandwidth usage index of the video-rich websites ranged from 144 Kbps to 93 Kbps. These results indicated that dial-up modem users would not achieve a "good user experience" with any of the three rich media websites. Results for Study 2 confirmed that usability was compromised when the estimated threshold number of concurrent users was exceeded. Results for Study 3 indicated that changing a website from video- to audio-rich content reduced the bandwidth requirement by almost 50%, but it remained too large to allow satisfactory use in dial-up modem scenarios. The Web-enabled CD-ROM reduced bandwidth requirements such that even a dial-up modem user could have a good user experience with the rich media content. We conclude that the bandwidth usage index represents a practical tool that can help developers and researchers to measure the bandwidth requirements of their websites as well as to evaluate the feasibility of certain website designs in terms of specific use cases. These findings are discussed in terms of reaching different groups of users as well accommodating the intended number of concurrent users. We also discuss the promising option of using Web-enabled CD-ROMs to deliver rich media content to users with dial-up Internet access. We introduce a number of researchable themes for improving our ability to develop Web-based behavior change interventions that can better deliver what they promise.

Mars Data analysis and visualization with Marsoweb

NASA Astrophysics Data System (ADS)

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

2003-04-01

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

Common Graphics Library (CGL). Volume 1: LEZ user's guide

NASA Technical Reports Server (NTRS)

Taylor, Nancy L.; Hammond, Dana P.; Hofler, Alicia S.; Miner, David L.

1988-01-01

Users are introduced to and instructed in the use of the Langley Easy (LEZ) routines of the Common Graphics Library (CGL). The LEZ routines form an application independent graphics package which enables the user community to view data quickly and easily, while providing a means of generating scientific charts conforming to the publication and/or viewgraph process. A distinct advantage for using the LEZ routines is that the underlying graphics package may be replaced or modified without requiring the users to change their application programs. The library is written in ANSI FORTRAN 77, and currently uses a CORE-based underlying graphics package, and is therefore machine independent, providing support for centralized and/or distributed computer systems.

Downsizer - A Graphical User Interface-Based Application for Browsing, Acquiring, and Formatting Time-Series Data for Hydrologic Modeling

USGS Publications Warehouse

Ward-Garrison, Christian; Markstrom, Steven L.; Hay, Lauren E.

2009-01-01

The U.S. Geological Survey Downsizer is a computer application that selects, downloads, verifies, and formats station-based time-series data for environmental-resource models, particularly the Precipitation-Runoff Modeling System. Downsizer implements the client-server software architecture. The client presents a map-based, graphical user interface that is intuitive to modelers; the server provides streamflow and climate time-series data from over 40,000 measurement stations across the United States. This report is the Downsizer user's manual and provides (1) an overview of the software design, (2) installation instructions, (3) a description of the graphical user interface, (4) a description of selected output files, and (5) troubleshooting information.

User-driven Cloud Implementation of environmental models and data for all

NASA Astrophysics Data System (ADS)

Gurney, R. J.; Percy, B. J.; Elkhatib, Y.; Blair, G. S.

2014-12-01

Environmental data and models come from disparate sources over a variety of geographical and temporal scales with different resolutions and data standards, often including terabytes of data and model simulations. Unfortunately, these data and models tend to remain solely within the custody of the private and public organisations which create the data, and the scientists who build models and generate results. Although many models and datasets are theoretically available to others, the lack of ease of access tends to keep them out of reach of many. We have developed an intuitive web-based tool that utilises environmental models and datasets located in a cloud to produce results that are appropriate to the user. Storyboards showing the interfaces and visualisations have been created for each of several exemplars. A library of virtual machine images has been prepared to serve these exemplars. Each virtual machine image has been tailored to run computer models appropriate to the end user. Two approaches have been used; first as RESTful web services conforming to the Open Geospatial Consortium (OGC) Web Processing Service (WPS) interface standard using the Python-based PyWPS; second, a MySQL database interrogated using PHP code. In all cases, the web client sends the server an HTTP GET request to execute the process with a number of parameter values and, once execution terminates, an XML or JSON response is sent back and parsed at the client side to extract the results. All web services are stateless, i.e. application state is not maintained by the server, reducing its operational overheads and simplifying infrastructure management tasks such as load balancing and failure recovery. A hybrid cloud solution has been used with models and data sited on both private and public clouds. The storyboards have been transformed into intuitive web interfaces at the client side using HTML, CSS and JavaScript, utilising plug-ins such as jQuery and Flot (for graphics), and Google Maps APIs. We have demonstrated that a cloud infrastructure can be used to assemble a virtual research environment that, coupled with a user-driven development approach, is able to cater to the needs of a wide range of user groups, from domain experts to concerned members of the general public.

The Web Based Monitoring Project at the CMS Experiment

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

Lopez-Perez, Juan Antonio; Badgett, William; Behrens, Ulf

The Compact Muon Solenoid is a large a complex general purpose experiment at the CERN Large Hadron Collider (LHC), built and maintained by many collaborators from around the world. Efficient operation of the detector requires widespread and timely access to a broad range of monitoring and status information. To the end the Web Based Monitoring (WBM) system was developed to present data to users located anywhere from many underlying heterogeneous sources, from real time messaging systems to relational databases. This system provides the power to combine and correlate data in both graphical and tabular formats of interest to the experimenters,more » including data such as beam conditions, luminosity, trigger rates, detector conditions, and many others, allowing for flexibility on the user’s side. This paper describes the WBM system architecture and describes how the system has been used from the beginning of data taking until now (Run1 and Run 2).« less

The web based monitoring project at the CMS experiment

NASA Astrophysics Data System (ADS)

Lopez-Perez, Juan Antonio; Badgett, William; Behrens, Ulf; Chakaberia, Irakli; Jo, Youngkwon; Maeshima, Kaori; Maruyama, Sho; Patrick, James; Rapsevicius, Valdas; Soha, Aron; Stankevicius, Mantas; Sulmanas, Balys; Toda, Sachiko; Wan, Zongru

2017-10-01

The Compact Muon Solenoid is a large a complex general purpose experiment at the CERN Large Hadron Collider (LHC), built and maintained by many collaborators from around the world. Efficient operation of the detector requires widespread and timely access to a broad range of monitoring and status information. To that end the Web Based Monitoring (WBM) system was developed to present data to users located anywhere from many underlying heterogeneous sources, from real time messaging systems to relational databases. This system provides the power to combine and correlate data in both graphical and tabular formats of interest to the experimenters, including data such as beam conditions, luminosity, trigger rates, detector conditions, and many others, allowing for flexibility on the user’s side. This paper describes the WBM system architecture and describes how the system has been used from the beginning of data taking until now (Run1 and Run 2).

An Object-Oriented Graphical User Interface for a Reusable Rocket Engine Intelligent Control System

NASA Technical Reports Server (NTRS)

Litt, Jonathan S.; Musgrave, Jeffrey L.; Guo, Ten-Huei; Paxson, Daniel E.; Wong, Edmond; Saus, Joseph R.; Merrill, Walter C.

1994-01-01

An intelligent control system for reusable rocket engines under development at NASA Lewis Research Center requires a graphical user interface to allow observation of the closed-loop system in operation. The simulation testbed consists of a real-time engine simulation computer, a controls computer, and several auxiliary computers for diagnostics and coordination. The system is set up so that the simulation computer could be replaced by the real engine and the change would be transparent to the control system. Because of the hard real-time requirement of the control computer, putting a graphical user interface on it was not an option. Thus, a separate computer used strictly for the graphical user interface was warranted. An object-oriented LISP-based graphical user interface has been developed on a Texas Instruments Explorer 2+ to indicate the condition of the engine to the observer through plots, animation, interactive graphics, and text.

Web-Beagle: a web server for the alignment of RNA secondary structures.

PubMed

Mattei, Eugenio; Pietrosanto, Marco; Ferrè, Fabrizio; Helmer-Citterich, Manuela

2015-07-01

Web-Beagle (http://beagle.bio.uniroma2.it) is a web server for the pairwise global or local alignment of RNA secondary structures. The server exploits a new encoding for RNA secondary structure and a substitution matrix of RNA structural elements to perform RNA structural alignments. The web server allows the user to compute up to 10 000 alignments in a single run, taking as input sets of RNA sequences and structures or primary sequences alone. In the latter case, the server computes the secondary structure prediction for the RNAs on-the-fly using RNAfold (free energy minimization). The user can also compare a set of input RNAs to one of five pre-compiled RNA datasets including lncRNAs and 3' UTRs. All types of comparison produce in output the pairwise alignments along with structural similarity and statistical significance measures for each resulting alignment. A graphical color-coded representation of the alignments allows the user to easily identify structural similarities between RNAs. Web-Beagle can be used for finding structurally related regions in two or more RNAs, for the identification of homologous regions or for functional annotation. Benchmark tests show that Web-Beagle has lower computational complexity, running time and better performances than other available methods. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Tele-rehabilitation using in-house wearable ankle rehabilitation robot.

PubMed

Jamwal, Prashant K; Hussain, Shahid; Mir-Nasiri, Nazim; Ghayesh, Mergen H; Xie, Sheng Q

2018-01-01

This article explores wide-ranging potential of the wearable ankle robot for in-house rehabilitation. The presented robot has been conceptualized following a brief analysis of the existing technologies, systems, and solutions for in-house physical ankle rehabilitation. Configuration design analysis and component selection for ankle robot have been discussed as part of the conceptual design. The complexities of human robot interaction are closely encountered while maneuvering a rehabilitation robot. We present a fuzzy logic-based controller to perform the required robot-assisted ankle rehabilitation treatment. Designs of visual haptic interfaces have also been discussed, which will make the treatment interesting, and the subject will be motivated to exert more and regain lost functions rapidly. The complex nature of web-based communication between user and remotely sitting physiotherapy staff has also been discussed. A high-level software architecture appended with robot ensures user-friendly operations. This software is made up of three important components: patient-related database, graphical user interface (GUI), and a library of exercises creating virtual reality-specifically developed for ankle rehabilitation.

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

NASA Astrophysics Data System (ADS)

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

2013-04-01

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

The Graphical User Interface Crisis: Danger and Opportunity.

ERIC Educational Resources Information Center

Boyd, Lawrence H.; And Others

This paper examines graphic computing environments, identifies potential problems in providing access to blind people, and describes programs and strategies being developed to provide this access. The paper begins with an explanation of how graphic user interfaces differ from character-based systems in their use of pixels, visual metaphors such as…

Advancements in RNASeqGUI towards a Reproducible Analysis of RNA-Seq Experiments

PubMed Central

Russo, Francesco; Righelli, Dario

2016-01-01

We present the advancements and novelties recently introduced in RNASeqGUI, a graphical user interface that helps biologists to handle and analyse large data collected in RNA-Seq experiments. This work focuses on the concept of reproducible research and shows how it has been incorporated in RNASeqGUI to provide reproducible (computational) results. The novel version of RNASeqGUI combines graphical interfaces with tools for reproducible research, such as literate statistical programming, human readable report, parallel executions, caching, and interactive and web-explorable tables of results. These features allow the user to analyse big datasets in a fast, efficient, and reproducible way. Moreover, this paper represents a proof of concept, showing a simple way to develop computational tools for Life Science in the spirit of reproducible research. PMID:26977414

Automatic page layout using genetic algorithms for electronic albuming

NASA Astrophysics Data System (ADS)

Geigel, Joe; Loui, Alexander C. P.

2000-12-01

In this paper, we describe a flexible system for automatic page layout that makes use of genetic algorithms for albuming applications. The system is divided into two modules, a page creator module which is responsible for distributing images amongst various album pages, and an image placement module which positions images on individual pages. Final page layouts are specified in a textual form using XML for printing or viewing over the Internet. The system makes use of genetic algorithms, a class of search and optimization algorithms that are based on the concepts of biological evolution, for generating solutions with fitness based on graphic design preferences supplied by the user. The genetic page layout algorithm has been incorporated into a web-based prototype system for interactive page layout over the Internet. The prototype system is built using client-server architecture and is implemented in java. The system described in this paper has demonstrated the feasibility of using genetic algorithms for automated page layout in albuming and web-based imaging applications. We believe that the system adequately proves the validity of the concept, providing creative layouts in a reasonable number of iterations. By optimizing the layout parameters of the fitness function, we hope to further improve the quality of the final layout in terms of user preference and computation speed.

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

Database and Analytical Tool Development for the Management of Data Derived from US DOE (NETL) Funded Fine Particulate (PM2.5) Research

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

Robinson P. Khosah; Frank T. Alex

2007-02-11

Advanced Technology Systems, Inc. (ATS) was contracted by the U. S. Department of Energy's National Energy Technology Laboratory (DOE-NETL) to develop a state-of-the-art, scalable and robust web-accessible database application to manage the extensive data sets resulting from the DOE-NETL-sponsored ambient air monitoring programs in the upper Ohio River valley region. The data management system was designed to include a web-based user interface that will allow easy access to the data by the scientific community, policy- and decision-makers, and other interested stakeholders, while providing detailed information on sampling, analytical and quality control parameters. In addition, the system will provide graphical analyticalmore » tools for displaying, analyzing and interpreting the air quality data. The system will also provide multiple report generation capabilities and easy-to-understand visualization formats that can be utilized by the media and public outreach/educational institutions. The project is being conducted in two phases. Phase One includes the following tasks: (1) data inventory/benchmarking, including the establishment of an external stakeholder group; (2) development of a data management system; (3) population of the database; (4) development of a web-based data retrieval system, and (5) establishment of an internal quality assurance/quality control system on data management. Phase Two, which is currently underway, involves the development of a platform for on-line data analysis. Phase Two includes the following tasks: (1) development of a sponsor and stakeholder/user website with extensive online analytical tools; (2) development of a public website; (3) incorporation of an extensive online help system into each website; and (4) incorporation of a graphical representation (mapping) system into each website. The project is now into its forty-eighth month of development activities.« less

DATABASE AND ANALYTICAL TOOL DEVELOPMENT FOR THE MANAGEMENT OF DATA DERIVED FROM US DOE (NETL) FUNDED FINE PARTICULATE (PM 2.5) RESEARCH

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

Robinson P. Khosah; Charles G. Crawford

2006-02-11

Advanced Technology Systems, Inc. (ATS) was contracted by the U. S. Department of Energy's National Energy Technology Laboratory (DOE-NETL) to develop a state-of-the-art, scalable and robust web-accessible database application to manage the extensive data sets resulting from the DOE-NETL-sponsored ambient air monitoring programs in the upper Ohio River valley region. The data management system was designed to include a web-based user interface that will allow easy access to the data by the scientific community, policy- and decision-makers, and other interested stakeholders, while providing detailed information on sampling, analytical and quality control parameters. In addition, the system will provide graphical analyticalmore » tools for displaying, analyzing and interpreting the air quality data. The system will also provide multiple report generation capabilities and easy-to-understand visualization formats that can be utilized by the media and public outreach/educational institutions. The project is being conducted in two phases. Phase One includes the following tasks: (1) data inventory/benchmarking, including the establishment of an external stakeholder group; (2) development of a data management system; (3) population of the database; (4) development of a web-based data retrieval system, and (5) establishment of an internal quality assurance/quality control system on data management. Phase Two, which is currently underway, involves the development of a platform for on-line data analysis. Phase Two includes the following tasks: (1) development of a sponsor and stakeholder/user website with extensive online analytical tools; (2) development of a public website; (3) incorporation of an extensive online help system into each website; and (4) incorporation of a graphical representation (mapping) system into each website. The project is now into its forty-second month of development activities.« less

DATABASE AND ANALYTICAL TOOL DEVELOPMENT FOR THE MANAGEMENT OF DATA DERIVED FROM US DOE (NETL) FUNDED FINE PARTICULATE (PM2.5) RESEARCH

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

Robinson P. Khosah; Charles G. Crawford

Advanced Technology Systems, Inc. (ATS) was contracted by the U. S. Department of Energy's National Energy Technology Laboratory (DOE-NETL) to develop a state-of-the-art, scalable and robust web-accessible database application to manage the extensive data sets resulting from the DOE-NETL-sponsored ambient air monitoring programs in the upper Ohio River valley region. The data management system was designed to include a web-based user interface that will allow easy access to the data by the scientific community, policy- and decision-makers, and other interested stakeholders, while providing detailed information on sampling, analytical and quality control parameters. In addition, the system will provide graphical analyticalmore » tools for displaying, analyzing and interpreting the air quality data. The system will also provide multiple report generation capabilities and easy-to-understand visualization formats that can be utilized by the media and public outreach/educational institutions. The project is being conducted in two phases. Phase 1, which is currently in progress and will take twelve months to complete, will include the following tasks: (1) data inventory/benchmarking, including the establishment of an external stakeholder group; (2) development of a data management system; (3) population of the database; (4) development of a web-based data retrieval system, and (5) establishment of an internal quality assurance/quality control system on data management. In Phase 2, which will be completed in the second year of the project, a platform for on-line data analysis will be developed. Phase 2 will include the following tasks: (1) development of a sponsor and stakeholder/user website with extensive online analytical tools; (2) development of a public website; (3) incorporation of an extensive online help system into each website; and (4) incorporation of a graphical representation (mapping) system into each website. The project is now into its eleventh month of Phase 1 development activities.« less

Common Graphics Library (CGL). Volume 2: Low-level user's guide

NASA Technical Reports Server (NTRS)

Taylor, Nancy L.; Hammond, Dana P.; Theophilos, Pauline M.

1989-01-01

The intent is to instruct the users of the Low-Level routines of the Common Graphics Library (CGL). The Low-Level routines form an application-independent graphics package enabling the user community to construct and design scientific charts conforming to the publication and/or viewgraph process. The Low-Level routines allow the user to design unique or unusual report-quality charts from a set of graphics utilities. The features of these routines can be used stand-alone or in conjunction with other packages to enhance or augment their capabilities. This library is written in ANSI FORTRAN 77, and currently uses a CORE-based underlying graphics package, and is therefore machine-independent, providing support for centralized and/or distributed computer systems.

Semantic integration of information about orthologs and diseases: the OGO system.

PubMed

Miñarro-Gimenez, Jose Antonio; Egaña Aranguren, Mikel; Martínez Béjar, Rodrigo; Fernández-Breis, Jesualdo Tomás; Madrid, Marisa

2011-12-01

Semantic Web technologies like RDF and OWL are currently applied in life sciences to improve knowledge management by integrating disparate information. Many of the systems that perform such task, however, only offer a SPARQL query interface, which is difficult to use for life scientists. We present the OGO system, which consists of a knowledge base that integrates information of orthologous sequences and genetic diseases, providing an easy to use ontology-constrain driven query interface. Such interface allows the users to define SPARQL queries through a graphical process, therefore not requiring SPARQL expertise. Copyright © 2011 Elsevier Inc. All rights reserved.

Storyboard method of end-user programming with natural language configuration

DOEpatents

Bouchard, Ann M; Osbourn, Gordon C

2013-11-19

A technique for end-user programming includes populating a template with graphically illustrated actions and then invoking a command to generate a screen element based on the template. The screen element is rendered within a computing environment and provides a mechanism for triggering execution of a sequence of user actions. The sequence of user actions is based at least in part on the graphically illustrated actions populated into the template.

HERA: A dynamic web application for visualizing community exposure to flood hazards based on storm and sea level rise scenarios

NASA Astrophysics Data System (ADS)

Jones, Jeanne M.; Henry, Kevin; Wood, Nathan; Ng, Peter; Jamieson, Matthew

2017-12-01

The Hazard Exposure Reporting and Analytics (HERA) dynamic web application was created to provide a platform that makes research on community exposure to coastal-flooding hazards influenced by sea level rise accessible to planners, decision makers, and the public in a manner that is both easy to use and easily accessible. HERA allows users to (a) choose flood-hazard scenarios based on sea level rise and storm assumptions, (b) appreciate the modeling uncertainty behind a chosen hazard zone, (c) select one or several communities to examine exposure, (d) select the category of population or societal asset, and (e) choose how to look at results. The application is designed to highlight comparisons between (a) varying levels of sea level rise and coastal storms, (b) communities, (c) societal asset categories, and (d) spatial scales. Through a combination of spatial and graphical visualizations, HERA aims to help individuals and organizations to craft more informed mitigation and adaptation strategies for climate-driven coastal hazards. This paper summarizes the technologies used to maximize the user experience, in terms of interface design, visualization approaches, and data processing.

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

PubMed

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

2018-05-25

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

HERA: A dynamic web application for visualizing community exposure to flood hazards based on storm and sea level rise scenarios

USGS Publications Warehouse

Jones, Jeanne M.; Henry, Kevin; Wood, Nathan J.; Ng, Peter; Jamieson, Matthew

2017-01-01

The Hazard Exposure Reporting and Analytics (HERA) dynamic web application was created to provide a platform that makes research on community exposure to coastal-flooding hazards influenced by sea level rise accessible to planners, decision makers, and the public in a manner that is both easy to use and easily accessible. HERA allows users to (a) choose flood-hazard scenarios based on sea level rise and storm assumptions, (b) appreciate the modeling uncertainty behind a chosen hazard zone, (c) select one or several communities to examine exposure, (d) select the category of population or societal asset, and (e) choose how to look at results. The application is designed to highlight comparisons between (a) varying levels of sea level rise and coastal storms, (b) communities, (c) societal asset categories, and (d) spatial scales. Through a combination of spatial and graphical visualizations, HERA aims to help individuals and organizations to craft more informed mitigation and adaptation strategies for climate-driven coastal hazards. This paper summarizes the technologies used to maximize the user experience, in terms of interface design, visualization approaches, and data processing.

Data mining in newt-omics, the repository for omics data from the newt.

PubMed

Looso, Mario; Braun, Thomas

2015-01-01

Salamanders are an excellent model organism to study regenerative processes due to their unique ability to regenerate lost appendages or organs. Straightforward bioinformatics tools to analyze and take advantage of the growing number of "omics" studies performed in salamanders were lacking so far. To overcome this limitation, we have generated a comprehensive data repository for the red-spotted newt Notophthalmus viridescens, named newt-omics, merging omics style datasets on the transcriptome and proteome level including expression values and annotations. The resource is freely available via a user-friendly Web-based graphical user interface ( http://newt-omics.mpi-bn.mpg.de) that allows access and queries to the database without prior bioinformatical expertise. The repository is updated regularly, incorporating new published datasets from omics technologies.

CARL Corporation to Market Knight Ridder DIALOG Databases to the Academic and Public Library Market.

ERIC Educational Resources Information Center

Machovec, George S.

1996-01-01

With the advent of CD-ROMs, libraries began to limit online searching via DIALOG. To increase DIALOG's market share, Colorado Alliance of Research Libraries (CARL) Corporation is developing graphical user interfaces using World Wide Web and Windows technology and has reached agreements with Knight Ridder Information and with most of their database…

A Web-Based Development Environment for Collaborative Data Analysis

NASA Astrophysics Data System (ADS)

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

2014-06-01

Visual Physics Analysis (VISPA) is a web-based development environment addressing high energy and astroparticle physics. It covers the entire analysis spectrum from the design and validation phase to the execution of analyses and the visualization of results. VISPA provides a graphical steering of the analysis flow, which consists of self-written, re-usable Python and C++ modules for more demanding tasks. All common operating systems are supported since a standard internet browser is the only software requirement for users. Even access via mobile and touch-compatible devices is possible. In this contribution, we present the most recent developments of our web application concerning technical, state-of-the-art approaches as well as practical experiences. One of the key features is the use of workspaces, i.e. user-configurable connections to remote machines supplying resources and local file access. Thereby, workspaces enable the management of data, computing resources (e.g. remote clusters or computing grids), and additional software either centralized or individually. We further report on the results of an application with more than 100 third-year students using VISPA for their regular particle physics exercises during the winter term 2012/13. Besides the ambition to support and simplify the development cycle of physics analyses, new use cases such as fast, location-independent status queries, the validation of results, and the ability to share analyses within worldwide collaborations with a single click become conceivable.

AEGIS: a wildfire prevention and management information system

NASA Astrophysics Data System (ADS)

Kalabokidis, K.; Ager, A.; Finney, M.; Athanasis, N.; Palaiologou, P.; Vasilakos, C.

2015-10-01

A Web-GIS wildfire prevention and management platform (AEGIS) was developed as an integrated and easy-to-use decision support tool (http://aegis.aegean.gr). The AEGIS platform assists with early fire warning, fire planning, fire control and coordination of firefighting forces by providing access to information that is essential for wildfire management. Databases were created with spatial and non-spatial data to support key system functionalities. Updated land use/land cover maps were produced by combining field inventory data with high resolution multispectral satellite images (RapidEye) to be used as inputs in fire propagation modeling with the Minimum Travel Time algorithm. End users provide a minimum number of inputs such as fire duration, ignition point and weather information to conduct a fire simulation. AEGIS offers three types of simulations; i.e. single-fire propagations, conditional burn probabilities and at the landscape-level, similar to the FlamMap fire behavior modeling software. Artificial neural networks (ANN) were utilized for wildfire ignition risk assessment based on various parameters, training methods, activation functions, pre-processing methods and network structures. The combination of ANNs and expected burned area maps produced an integrated output map for fire danger prediction. The system also incorporates weather measurements from remote automatic weather stations and weather forecast maps. The structure of the algorithms relies on parallel processing techniques (i.e. High Performance Computing and Cloud Computing) that ensure computational power and speed. All AEGIS functionalities are accessible to authorized end users through a web-based graphical user interface. An innovative mobile application, AEGIS App, acts as a complementary tool to the web-based version of the system.

Sally Ride EarthKAM - Automated Image Geo-Referencing Using Google Earth Web Plug-In

NASA Technical Reports Server (NTRS)

Andres, Paul M.; Lazar, Dennis K.; Thames, Robert Q.

2013-01-01

Sally Ride EarthKAM is an educational program funded by NASA that aims to provide the public the ability to picture Earth from the perspective of the International Space Station (ISS). A computer-controlled camera is mounted on the ISS in a nadir-pointing window; however, timing limitations in the system cause inaccurate positional metadata. Manually correcting images within an orbit allows the positional metadata to be improved using mathematical regressions. The manual correction process is time-consuming and thus, unfeasible for a large number of images. The standard Google Earth program allows for the importing of KML (keyhole markup language) files that previously were created. These KML file-based overlays could then be manually manipulated as image overlays, saved, and then uploaded to the project server where they are parsed and the metadata in the database is updated. The new interface eliminates the need to save, download, open, re-save, and upload the KML files. Everything is processed on the Web, and all manipulations go directly into the database. Administrators also have the control to discard any single correction that was made and validate a correction. This program streamlines a process that previously required several critical steps and was probably too complex for the average user to complete successfully. The new process is theoretically simple enough for members of the public to make use of and contribute to the success of the Sally Ride EarthKAM project. Using the Google Earth Web plug-in, EarthKAM images, and associated metadata, this software allows users to interactively manipulate an EarthKAM image overlay, and update and improve the associated metadata. The Web interface uses the Google Earth JavaScript API along with PHP-PostgreSQL to present the user the same interface capabilities without leaving the Web. The simpler graphical user interface will allow the public to participate directly and meaningfully with EarthKAM. The use of similar techniques is being investigated to place ground-based observations in a Google Mars environment, allowing the MSL (Mars Science Laboratory) Science Team a means to visualize the rover and its environment.

[Preliminary construction of three-dimensional visual educational system for clinical dentistry based on world wide web webpage].

PubMed

Hu, Jian; Xu, Xiang-yang; Song, En-min; Tan, Hong-bao; Wang, Yi-ning

2009-09-01

To establish a new visual educational system of virtual reality for clinical dentistry based on world wide web (WWW) webpage in order to provide more three-dimensional multimedia resources to dental students and an online three-dimensional consulting system for patients. Based on computer graphics and three-dimensional webpage technologies, the software of 3Dsmax and Webmax were adopted in the system development. In the Windows environment, the architecture of whole system was established step by step, including three-dimensional model construction, three-dimensional scene setup, transplanting three-dimensional scene into webpage, reediting the virtual scene, realization of interactions within the webpage, initial test, and necessary adjustment. Five cases of three-dimensional interactive webpage for clinical dentistry were completed. The three-dimensional interactive webpage could be accessible through web browser on personal computer, and users could interact with the webpage through rotating, panning and zooming the virtual scene. It is technically feasible to implement the visual educational system of virtual reality for clinical dentistry based on WWW webpage. Information related to clinical dentistry can be transmitted properly, visually and interactively through three-dimensional webpage.

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 3D character animation engine for multimodal interaction on mobile devices

NASA Astrophysics Data System (ADS)

Sandali, Enrico; Lavagetto, Fabio; Pisano, Paolo

2005-03-01

Talking virtual characters are graphical simulations of real or imaginary persons that enable natural and pleasant multimodal interaction with the user, by means of voice, eye gaze, facial expression and gestures. This paper presents an implementation of a 3D virtual character animation and rendering engine, compliant with the MPEG-4 standard, running on Symbian-based SmartPhones. Real-time animation of virtual characters on mobile devices represents a challenging task, since many limitations must be taken into account with respect to processing power, graphics capabilities, disk space and execution memory size. The proposed optimization techniques allow to overcome these issues, guaranteeing a smooth and synchronous animation of facial expressions and lip movements on mobile phones such as Sony-Ericsson's P800 and Nokia's 6600. The animation engine is specifically targeted to the development of new "Over The Air" services, based on embodied conversational agents, with applications in entertainment (interactive story tellers), navigation aid (virtual guides to web sites and mobile services), news casting (virtual newscasters) and education (interactive virtual teachers).

A web-based system for home monitoring of patients with Parkinson's disease using wearable sensors.

PubMed

Chen, Bor-Rong; Patel, Shyamal; Buckley, Thomas; Rednic, Ramona; McClure, Douglas J; Shih, Ludy; Tarsy, Daniel; Welsh, Matt; Bonato, Paolo

2011-03-01

This letter introduces MercuryLive, a platform to enable home monitoring of patients with Parkinson's disease (PD) using wearable sensors. MercuryLive contains three tiers: a resource-aware data collection engine that relies upon wearable sensors, web services for live streaming and storage of sensor data, and a web-based graphical user interface client with video conferencing capability. Besides, the platform has the capability of analyzing sensor (i.e., accelerometer) data to reliably estimate clinical scores capturing the severity of tremor, bradykinesia, and dyskinesia. Testing results showed an average data latency of less than 400 ms and video latency of about 200 ms with video frame rate of about 13 frames/s when 800 kb/s of bandwidth were available and we used a 40% video compression, and data feature upload requiring 1 min of extra time following a 10 min interactive session. These results indicate that the proposed platform is suitable to monitor patients with PD to facilitate the titration of medications in the late stages of the disease.

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

PubMed

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

2003-10-01

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

A tool for NDVI time series extraction from wide-swath remotely sensed images

NASA Astrophysics Data System (ADS)

Li, Zhishan; Shi, Runhe; Zhou, Cong

2015-09-01

Normalized Difference Vegetation Index (NDVI) is one of the most widely used indicators for monitoring the vegetation coverage in land surface. The time series features of NDVI are capable of reflecting dynamic changes of various ecosystems. Calculating NDVI via Moderate Resolution Imaging Spectrometer (MODIS) and other wide-swath remotely sensed images provides an important way to monitor the spatial and temporal characteristics of large-scale NDVI. However, difficulties are still existed for ecologists to extract such information correctly and efficiently because of the problems in several professional processes on the original remote sensing images including radiometric calibration, geometric correction, multiple data composition and curve smoothing. In this study, we developed an efficient and convenient online toolbox for non-remote sensing professionals who want to extract NDVI time series with a friendly graphic user interface. It is based on Java Web and Web GIS technically. Moreover, Struts, Spring and Hibernate frameworks (SSH) are integrated in the system for the purpose of easy maintenance and expansion. Latitude, longitude and time period are the key inputs that users need to provide, and the NDVI time series are calculated automatically.

User centered and ontology based information retrieval system for life sciences.

PubMed

Sy, Mohameth-François; Ranwez, Sylvie; Montmain, Jacky; Regnault, Armelle; Crampes, Michel; Ranwez, Vincent

2012-01-25

Because of the increasing number of electronic resources, designing efficient tools to retrieve and exploit them is a major challenge. Some improvements have been offered by semantic Web technologies and applications based on domain ontologies. In life science, for instance, the Gene Ontology is widely exploited in genomic applications and the Medical Subject Headings is the basis of biomedical publications indexation and information retrieval process proposed by PubMed. However current search engines suffer from two main drawbacks: there is limited user interaction with the list of retrieved resources and no explanation for their adequacy to the query is provided. Users may thus be confused by the selection and have no idea on how to adapt their queries so that the results match their expectations. This paper describes an information retrieval system that relies on domain ontology to widen the set of relevant documents that is retrieved and that uses a graphical rendering of query results to favor user interactions. Semantic proximities between ontology concepts and aggregating models are used to assess documents adequacy with respect to a query. The selection of documents is displayed in a semantic map to provide graphical indications that make explicit to what extent they match the user's query; this man/machine interface favors a more interactive and iterative exploration of data corpus, by facilitating query concepts weighting and visual explanation. We illustrate the benefit of using this information retrieval system on two case studies one of which aiming at collecting human genes related to transcription factors involved in hemopoiesis pathway. The ontology based information retrieval system described in this paper (OBIRS) is freely available at: http://www.ontotoolkit.mines-ales.fr/ObirsClient/. This environment is a first step towards a user centred application in which the system enlightens relevant information to provide decision help.

User centered and ontology based information retrieval system for life sciences

PubMed Central

2012-01-01

Background Because of the increasing number of electronic resources, designing efficient tools to retrieve and exploit them is a major challenge. Some improvements have been offered by semantic Web technologies and applications based on domain ontologies. In life science, for instance, the Gene Ontology is widely exploited in genomic applications and the Medical Subject Headings is the basis of biomedical publications indexation and information retrieval process proposed by PubMed. However current search engines suffer from two main drawbacks: there is limited user interaction with the list of retrieved resources and no explanation for their adequacy to the query is provided. Users may thus be confused by the selection and have no idea on how to adapt their queries so that the results match their expectations. Results This paper describes an information retrieval system that relies on domain ontology to widen the set of relevant documents that is retrieved and that uses a graphical rendering of query results to favor user interactions. Semantic proximities between ontology concepts and aggregating models are used to assess documents adequacy with respect to a query. The selection of documents is displayed in a semantic map to provide graphical indications that make explicit to what extent they match the user's query; this man/machine interface favors a more interactive and iterative exploration of data corpus, by facilitating query concepts weighting and visual explanation. We illustrate the benefit of using this information retrieval system on two case studies one of which aiming at collecting human genes related to transcription factors involved in hemopoiesis pathway. Conclusions The ontology based information retrieval system described in this paper (OBIRS) is freely available at: http://www.ontotoolkit.mines-ales.fr/ObirsClient/. This environment is a first step towards a user centred application in which the system enlightens relevant information to provide decision help. PMID:22373375

Visualization of Vgi Data Through the New NASA Web World Wind Virtual Globe

NASA Astrophysics Data System (ADS)

Brovelli, M. A.; Kilsedar, C. E.; Zamboni, G.

2016-06-01

GeoWeb 2.0, laying the foundations of Volunteered Geographic Information (VGI) systems, has led to platforms where users can contribute to the geographic knowledge that is open to access. Moreover, as a result of the advancements in 3D visualization, virtual globes able to visualize geographic data even on browsers emerged. However the integration of VGI systems and virtual globes has not been fully realized. The study presented aims to visualize volunteered data in 3D, considering also the ease of use aspects for general public, using Free and Open Source Software (FOSS). The new Application Programming Interface (API) of NASA, Web World Wind, written in JavaScript and based on Web Graphics Library (WebGL) is cross-platform and cross-browser, so that the virtual globe created using this API can be accessible through any WebGL supported browser on different operating systems and devices, as a result not requiring any installation or configuration on the client-side, making the collected data more usable to users, which is not the case with the World Wind for Java as installation and configuration of the Java Virtual Machine (JVM) is required. Furthermore, the data collected through various VGI platforms might be in different formats, stored in a traditional relational database or in a NoSQL database. The project developed aims to visualize and query data collected through Open Data Kit (ODK) platform and a cross-platform application, where data is stored in a relational PostgreSQL and NoSQL CouchDB databases respectively.

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

PubMed

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

2016-06-13

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

A tool for multi-scale modelling of the renal nephron

PubMed Central

Nickerson, David P.; Terkildsen, Jonna R.; Hamilton, Kirk L.; Hunter, Peter J.

2011-01-01

We present the development of a tool, which provides users with the ability to visualize and interact with a comprehensive description of a multi-scale model of the renal nephron. A one-dimensional anatomical model of the nephron has been created and is used for visualization and modelling of tubule transport in various nephron anatomical segments. Mathematical models of nephron segments are embedded in the one-dimensional model. At the cellular level, these segment models use models encoded in CellML to describe cellular and subcellular transport kinetics. A web-based presentation environment has been developed that allows the user to visualize and navigate through the multi-scale nephron model, including simulation results, at the different spatial scales encompassed by the model description. The Zinc extension to Firefox is used to provide an interactive three-dimensional view of the tubule model and the native Firefox rendering of scalable vector graphics is used to present schematic diagrams for cellular and subcellular scale models. The model viewer is embedded in a web page that dynamically presents content based on user input. For example, when viewing the whole nephron model, the user might be presented with information on the various embedded segment models as they select them in the three-dimensional model view. Alternatively, the user chooses to focus the model viewer on a cellular model located in a particular nephron segment in order to view the various membrane transport proteins. Selecting a specific protein may then present the user with a description of the mathematical model governing the behaviour of that protein—including the mathematical model itself and various simulation experiments used to validate the model against the literature. PMID:22670210

Real-Time Payload Control and Monitoring on the World Wide Web

NASA Technical Reports Server (NTRS)

Sun, Charles; Windrem, May; Givens, John J. (Technical Monitor)

1998-01-01

World Wide Web (W3) technologies such as the Hypertext Transfer Protocol (HTTP) and the Java object-oriented programming environment offer a powerful, yet relatively inexpensive, framework for distributed application software development. This paper describes the design of a real-time payload control and monitoring system that was developed with W3 technologies at NASA Ames Research Center. Based on Java Development Toolkit (JDK) 1.1, the system uses an event-driven "publish and subscribe" approach to inter-process communication and graphical user-interface construction. A C Language Integrated Production System (CLIPS) compatible inference engine provides the back-end intelligent data processing capability, while Oracle Relational Database Management System (RDBMS) provides the data management function. Preliminary evaluation shows acceptable performance for some classes of payloads, with Java's portability and multimedia support identified as the most significant benefit.

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

NASA Astrophysics Data System (ADS)

Jiang, Wenping; Zou, Ziming

With the development of research on space environment and space science, how to develop network online computing environment of space weather, space environment and space physics models for Chinese scientific community is becoming more and more important in recent years. Currently, There are two software modes on space physics multi-model application integrated system (SPMAIS) such as C/S and B/S. the C/S mode which is traditional and stand-alone, demands a team or workshop from many disciplines and specialties to build their own multi-model application integrated system, that requires the client must be deployed in different physical regions when user visits the integrated system. Thus, this requirement brings two shortcomings: reducing the efficiency of researchers who use the models to compute; inconvenience of accessing the data. Therefore, it is necessary to create a shared network resource access environment which could help users to visit the computing resources of space physics models through the terminal quickly for conducting space science research and forecasting spatial environment. The SPMAIS develops high-performance, first-principles in B/S mode based on computational models of the space environment and uses these models to predict "Space Weather", to understand space mission data and to further our understanding of the solar system. the main goal of space physics multi-model application integration system (SPMAIS) is to provide an easily and convenient user-driven online models operating environment. up to now, the SPMAIS have contained dozens of space environment models , including international AP8/AE8 IGRF T96 models and solar proton prediction model geomagnetic transmission model etc. which are developed by Chinese scientists. another function of SPMAIS is to integrate space observation data sets which offers input data for models online high-speed computing. In this paper, service-oriented architecture (SOA) concept that divides system into independent modules according to different business needs is applied to solve the problem of the independence of the physical space between multiple models. The classic MVC(Model View Controller) software design pattern is concerned to build the architecture of space physics multi-model application integrated system. The JSP+servlet+javabean technology is used to integrate the web application programs of space physics multi-model. It solves the problem of multi-user requesting the same job of model computing and effectively balances each server computing tasks. In addition, we also complete follow tasks: establishing standard graphical user interface based on Java Applet application program; Designing the interface between model computing and model computing results visualization; Realizing three-dimensional network visualization without plug-ins; Using Java3D technology to achieve a three-dimensional network scene interaction; Improved ability to interact with web pages and dynamic execution capabilities, including rendering three-dimensional graphics, fonts and color control. Through the design and implementation of the SPMAIS based on Web, we provide an online computing and application runtime environment of space physics multi-model. The practical application improves that researchers could be benefit from our system in space physics research and engineering applications.

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

PubMed

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

2018-06-05

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

Long-range wireless mesh network for weather monitoring in unfriendly geographic conditions.

PubMed

Toledano-Ayala, Manuel; Herrera-Ruiz, Gilberto; Soto-Zarazúa, Genaro M; Rivas-Araiza, Edgar A; Bazán Trujillo, Rey D; Porrás-Trejo, Rafael E

2011-01-01

In this paper a long-range wireless mesh network system is presented. It consists of three main parts: Remote Terminal Units (RTUs), Base Terminal Units (BTUs) and a Central Server (CS). The RTUs share a wireless network transmitting in the industrial, scientific and medical applications ISM band, which reaches up to 64 Km in a single point-to-point communication. A BTU controls the traffic within the network and has as its main task interconnecting it to a Ku-band satellite link using an embedded microcontroller-based gateway. Collected data is stored in a CS and presented to the final user in a numerical and a graphical form in a web portal.

DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation sequencing data.

PubMed

Nagasaki, Hideki; Mochizuki, Takako; Kodama, Yuichi; Saruhashi, Satoshi; Morizaki, Shota; Sugawara, Hideaki; Ohyanagi, Hajime; Kurata, Nori; Okubo, Kousaku; Takagi, Toshihisa; Kaminuma, Eli; Nakamura, Yasukazu

2013-08-01

High-performance next-generation sequencing (NGS) technologies are advancing genomics and molecular biological research. However, the immense amount of sequence data requires computational skills and suitable hardware resources that are a challenge to molecular biologists. The DNA Data Bank of Japan (DDBJ) of the National Institute of Genetics (NIG) has initiated a cloud computing-based analytical pipeline, the DDBJ Read Annotation Pipeline (DDBJ Pipeline), for a high-throughput annotation of NGS reads. The DDBJ Pipeline offers a user-friendly graphical web interface and processes massive NGS datasets using decentralized processing by NIG supercomputers currently free of charge. The proposed pipeline consists of two analysis components: basic analysis for reference genome mapping and de novo assembly and subsequent high-level analysis of structural and functional annotations. Users may smoothly switch between the two components in the pipeline, facilitating web-based operations on a supercomputer for high-throughput data analysis. Moreover, public NGS reads of the DDBJ Sequence Read Archive located on the same supercomputer can be imported into the pipeline through the input of only an accession number. This proposed pipeline will facilitate research by utilizing unified analytical workflows applied to the NGS data. The DDBJ Pipeline is accessible at http://p.ddbj.nig.ac.jp/.

DDBJ Read Annotation Pipeline: A Cloud Computing-Based Pipeline for High-Throughput Analysis of Next-Generation Sequencing Data

PubMed Central

Nagasaki, Hideki; Mochizuki, Takako; Kodama, Yuichi; Saruhashi, Satoshi; Morizaki, Shota; Sugawara, Hideaki; Ohyanagi, Hajime; Kurata, Nori; Okubo, Kousaku; Takagi, Toshihisa; Kaminuma, Eli; Nakamura, Yasukazu

2013-01-01

High-performance next-generation sequencing (NGS) technologies are advancing genomics and molecular biological research. However, the immense amount of sequence data requires computational skills and suitable hardware resources that are a challenge to molecular biologists. The DNA Data Bank of Japan (DDBJ) of the National Institute of Genetics (NIG) has initiated a cloud computing-based analytical pipeline, the DDBJ Read Annotation Pipeline (DDBJ Pipeline), for a high-throughput annotation of NGS reads. The DDBJ Pipeline offers a user-friendly graphical web interface and processes massive NGS datasets using decentralized processing by NIG supercomputers currently free of charge. The proposed pipeline consists of two analysis components: basic analysis for reference genome mapping and de novo assembly and subsequent high-level analysis of structural and functional annotations. Users may smoothly switch between the two components in the pipeline, facilitating web-based operations on a supercomputer for high-throughput data analysis. Moreover, public NGS reads of the DDBJ Sequence Read Archive located on the same supercomputer can be imported into the pipeline through the input of only an accession number. This proposed pipeline will facilitate research by utilizing unified analytical workflows applied to the NGS data. The DDBJ Pipeline is accessible at http://p.ddbj.nig.ac.jp/. PMID:23657089

xiSPEC: web-based visualization, analysis and sharing of proteomics data.

PubMed

Kolbowski, Lars; Combe, Colin; Rappsilber, Juri

2018-05-08

We present xiSPEC, a standard compliant, next-generation web-based spectrum viewer for visualizing, analyzing and sharing mass spectrometry data. Peptide-spectrum matches from standard proteomics and cross-linking experiments are supported. xiSPEC is to date the only browser-based tool supporting the standardized file formats mzML and mzIdentML defined by the proteomics standards initiative. Users can either upload data directly or select files from the PRIDE data repository as input. xiSPEC allows users to save and share their datasets publicly or password protected for providing access to collaborators or readers and reviewers of manuscripts. The identification table features advanced interaction controls and spectra are presented in three interconnected views: (i) annotated mass spectrum, (ii) peptide sequence fragmentation key and (iii) quality control error plots of matched fragments. Highlighting or selecting data points in any view is represented in all other views. Views are interactive scalable vector graphic elements, which can be exported, e.g. for use in publication. xiSPEC allows for re-annotation of spectra for easy hypothesis testing by modifying input data. xiSPEC is freely accessible at http://spectrumviewer.org and the source code is openly available on https://github.com/Rappsilber-Laboratory/xiSPEC.

AEGIS: a wildfire prevention and management information system

NASA Astrophysics Data System (ADS)

Kalabokidis, Kostas; Ager, Alan; Finney, Mark; Athanasis, Nikos; Palaiologou, Palaiologos; Vasilakos, Christos

2016-03-01

We describe a Web-GIS wildfire prevention and management platform (AEGIS) developed as an integrated and easy-to-use decision support tool to manage wildland fire hazards in Greece (http://aegis.aegean.gr). The AEGIS platform assists with early fire warning, fire planning, fire control and coordination of firefighting forces by providing online access to information that is essential for wildfire management. The system uses a number of spatial and non-spatial data sources to support key system functionalities. Land use/land cover maps were produced by combining field inventory data with high-resolution multispectral satellite images (RapidEye). These data support wildfire simulation tools that allow the users to examine potential fire behavior and hazard with the Minimum Travel Time fire spread algorithm. End-users provide a minimum number of inputs such as fire duration, ignition point and weather information to conduct a fire simulation. AEGIS offers three types of simulations, i.e., single-fire propagation, point-scale calculation of potential fire behavior, and burn probability analysis, similar to the FlamMap fire behavior modeling software. Artificial neural networks (ANNs) were utilized for wildfire ignition risk assessment based on various parameters, training methods, activation functions, pre-processing methods and network structures. The combination of ANNs and expected burned area maps are used to generate integrated output map of fire hazard prediction. The system also incorporates weather information obtained from remote automatic weather stations and weather forecast maps. The system and associated computation algorithms leverage parallel processing techniques (i.e., High Performance Computing and Cloud Computing) that ensure computational power required for real-time application. All AEGIS functionalities are accessible to authorized end-users through a web-based graphical user interface. An innovative smartphone application, AEGIS App, also provides mobile access to the web-based version of the system.

Development of the Virtual Visitor Center at SLAC

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

McDunn, Ruth

1999-11-17

The Virtual Visitor Center (VVC) web site (www2.slac.stanford.edu/vvc) is a ''virtual'' version of the Visitor Center, a mini science museum that opened at SLAC in 1996. The VVC was made public in December 1998. Both centers contribute to SLAC mission regarding education of the next generation and increasing scientific awareness of the public. The site is designed to mimic the real visitor center and allow a larger audience to the information. The intent was to reach the 8th-12th grade audience. Considerable effort was made to organize the content, including color-coding graphical elements for each main topic area. Tables of contents,more » a search tool, several photo tours, as well as graphical and non-graphical menu bars allow users many methods of navigating the site. The site was developed over almost two years using an estimated .95 FTE, split between a program manager, graphic designer, content provider (theoretical physicist), and a summer intern (high school teacher). As of November 1999, the site consists of 1,147 files, 935 images, 3,080 internal hyperlinks, and 190 external hyperlinks. The site has had over 1 million hits between January and mid-October 1999 and averages about 600 page views each day. Future plans include bringing the web site into compliance with the W3Cs Web Content Accessibility guidelines, thoroughly integrating the glossary terms, continued incorporation of current research at SLAC, and adding more interactivity.« less

Upgrades to the TPSX Material Properties Database

NASA Technical Reports Server (NTRS)

Squire, T. H.; Milos, F. S.; Partridge, Harry (Technical Monitor)

2001-01-01

The TPSX Material Properties Database is a web-based tool that serves as a database for properties of advanced thermal protection materials. TPSX provides an easy user interface for retrieving material property information in a variety of forms, both graphical and text. The primary purpose and advantage of TPSX is to maintain a high quality source of often used thermal protection material properties in a convenient, easily accessible form, for distribution to government and aerospace industry communities. Last year a major upgrade to the TPSX web site was completed. This year, through the efforts of researchers at several NASA centers, the Office of the Chief Engineer awarded funds to update and expand the databases in TPSX. The FY01 effort focuses on updating correcting the Ames and Johnson thermal protection materials databases. In this session we will summarize the improvements made to the web site last year, report on the status of the on-going database updates, describe the planned upgrades for FY02 and FY03, and provide a demonstration of TPSX.

VISIBIOweb: visualization and layout services for BioPAX pathway models

PubMed Central

Dilek, Alptug; Belviranli, Mehmet E.; Dogrusoz, Ugur

2010-01-01

With recent advancements in techniques for cellular data acquisition, information on cellular processes has been increasing at a dramatic rate. Visualization is critical to analyzing and interpreting complex information; representing cellular processes or pathways is no exception. VISIBIOweb is a free, open-source, web-based pathway visualization and layout service for pathway models in BioPAX format. With VISIBIOweb, one can obtain well-laid-out views of pathway models using the standard notation of the Systems Biology Graphical Notation (SBGN), and can embed such views within one's web pages as desired. Pathway views may be navigated using zoom and scroll tools; pathway object properties, including any external database references available in the data, may be inspected interactively. The automatic layout component of VISIBIOweb may also be accessed programmatically from other tools using Hypertext Transfer Protocol (HTTP). The web site is free and open to all users and there is no login requirement. It is available at: http://visibioweb.patika.org. PMID:20460470

Graphical user interfaces for symbol-oriented database visualization and interaction

NASA Astrophysics Data System (ADS)

Brinkschulte, Uwe; Siormanolakis, Marios; Vogelsang, Holger

1997-04-01

In this approach, two basic services designed for the engineering of computer based systems are combined: a symbol-oriented man-machine-service and a high speed database-service. The man-machine service is used to build graphical user interfaces (GUIs) for the database service; these interfaces are stored using the database service. The idea is to create a GUI-builder and a GUI-manager for the database service based upon the man-machine service using the concept of symbols. With user-definable and predefined symbols, database contents can be visualized and manipulated in a very flexible and intuitive way. Using the GUI-builder and GUI-manager, a user can build and operate its own graphical user interface for a given database according to its needs without writing a single line of code.

A browser-based event display for the CMS Experiment at the LHC using WebGL

NASA Astrophysics Data System (ADS)

McCauley, T.

2017-10-01

Modern web browsers are powerful and sophisticated applications that support an ever-wider range of uses. One such use is rendering high-quality, GPU-accelerated, interactive 2D and 3D graphics in an HTML canvas. This can be done via WebGL, a JavaScript API based on OpenGL ES. Applications delivered via the browser have several distinct benefits for the developer and user. For example, they can be implemented using well-known and well-developed technologies, while distribution and use via a browser allows for rapid prototyping and deployment and ease of installation. In addition, delivery of applications via the browser allows for easy use on mobile, touch-enabled devices such as phones and tablets. iSpy WebGL is an application for visualization of events detected and reconstructed by the CMS Experiment at the Large Hadron Collider at CERN. The first event display developed for an LHC experiment to use WebGL, iSpy WebGL is a client-side application written in JavaScript, HTML, and CSS and uses the WebGL API three.js. iSpy WebGL is used for monitoring of CMS detector performance, for production of images and animations of CMS collisions events for the public, as a virtual reality application using Google Cardboard, and asa tool available for public education and outreach such as in the CERN Open Data Portal and the CMS masterclasses. We describe here its design, development, and usage as well as future plans.

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.

medplot: a web application for dynamic summary and analysis of longitudinal medical data based on R.

PubMed

Ahlin, Črt; Stupica, Daša; Strle, Franc; Lusa, Lara

2015-01-01

In biomedical studies the patients are often evaluated numerous times and a large number of variables are recorded at each time-point. Data entry and manipulation of longitudinal data can be performed using spreadsheet programs, which usually include some data plotting and analysis capabilities and are straightforward to use, but are not designed for the analyses of complex longitudinal data. Specialized statistical software offers more flexibility and capabilities, but first time users with biomedical background often find its use difficult. We developed medplot, an interactive web application that simplifies the exploration and analysis of longitudinal data. The application can be used to summarize, visualize and analyze data by researchers that are not familiar with statistical programs and whose knowledge of statistics is limited. The summary tools produce publication-ready tables and graphs. The analysis tools include features that are seldom available in spreadsheet software, such as correction for multiple testing, repeated measurement analyses and flexible non-linear modeling of the association of the numerical variables with the outcome. medplot is freely available and open source, it has an intuitive graphical user interface (GUI), it is accessible via the Internet and can be used within a web browser, without the need for installing and maintaining programs locally on the user's computer. This paper describes the application and gives detailed examples describing how to use the application on real data from a clinical study including patients with early Lyme borreliosis.

Web-GIS-based SARS epidemic situation visualization

NASA Astrophysics Data System (ADS)

Lu, Xiaolin

2004-03-01

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

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

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

SWATMOD-PREP: Graphical user interface for preparing coupled SWAT-modflow simulations

USDA-ARS?s Scientific Manuscript database

This paper presents SWATMOD-Prep, a graphical user interface that couples a SWAT watershed model with a MODFLOW groundwater flow model. The interface is based on a recently published SWAT-MODFLOW code that couples the models via mapping schemes. The spatial layout of SWATMOD-Prep guides the user t...

ESO Reflex: a graphical workflow engine for data reduction

NASA Astrophysics Data System (ADS)

Hook, Richard; Ullgrén, Marko; Romaniello, Martino; Maisala, Sami; Oittinen, Tero; Solin, Otto; Savolainen, Ville; Järveläinen, Pekka; Tyynelä, Jani; Péron, Michèle; Ballester, Pascal; Gabasch, Armin; Izzo, Carlo

ESO Reflex is a prototype software tool that provides a novel approach to astronomical data reduction by integrating a modern graphical workflow system (Taverna) with existing legacy data reduction algorithms. Most of the raw data produced by instruments at the ESO Very Large Telescope (VLT) in Chile are reduced using recipes. These are compiled C applications following an ESO standard and utilising routines provided by the Common Pipeline Library (CPL). Currently these are run in batch mode as part of the data flow system to generate the input to the ESO/VLT quality control process and are also exported for use offline. ESO Reflex can invoke CPL-based recipes in a flexible way through a general purpose graphical interface. ESO Reflex is based on the Taverna system that was originally developed within the UK life-sciences community. Workflows have been created so far for three VLT/VLTI instruments, and the GUI allows the user to make changes to these or create workflows of their own. Python scripts or IDL procedures can be easily brought into workflows and a variety of visualisation and display options, including custom product inspection and validation steps, are available. Taverna is intended for use with web services and experiments using ESO Reflex to access Virtual Observatory web services have been successfully performed. ESO Reflex is the main product developed by Sampo, a project led by ESO and conducted by a software development team from Finland as an in-kind contribution to joining ESO. The goal was to look into the needs of the ESO community in the area of data reduction environments and to create pilot software products that illustrate critical steps along the road to a new system. Sampo concluded early in 2008. This contribution will describe ESO Reflex and show several examples of its use both locally and using Virtual Observatory remote web services. ESO Reflex is expected to be released to the community in early 2009.

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

PubMed Central

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

2016-01-01

Background An increasing number of patients from diverse demographic groups share and search for health-related information on Web-based social media. However, little is known about the content of the posted information with respect to the users’ demographics. Objective The aims of this study were to analyze the content of Web-based health-related social media based on users’ demographics to identify which health topics are discussed in which social media by which demographic groups and to help guide educational and research activities. Methods We analyze 3 different types of health-related social media: (1) general Web-based social networks Twitter and Google+; (2) drug review websites; and (3) health Web forums, with a total of about 6 million users and 20 million posts. We analyzed the content of these posts based on the demographic group of their authors, in terms of sentiment and emotion, top distinctive terms, and top medical concepts. Results The results of this study are: (1) Pregnancy is the dominant topic for female users in drug review websites and health Web forums, whereas for male users, it is cardiac problems, HIV, and back pain, but this is not the case for Twitter; (2) younger users (0-17 years) mainly talk about attention-deficit hyperactivity disorder (ADHD) and depression-related drugs, users aged 35-44 years discuss about multiple sclerosis (MS) drugs, and middle-aged users (45-64 years) talk about alcohol and smoking; (3) users from the Northeast United States talk about physical disorders, whereas users from the West United States talk about mental disorders and addictive behaviors; (4) Users with higher writing level express less anger in their posts. Conclusion We studied the popular topics and the sentiment based on users' demographics in Web-based health-related social media. Our results provide valuable information, which can help create targeted and effective educational campaigns and guide experts to reach the right users on Web-based social chatter. PMID:27296242

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

PubMed

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

2014-11-01

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

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.

A 3D Model Based Imdoor Navigation System for Hubei Provincial Museum

NASA Astrophysics Data System (ADS)

Xu, W.; Kruminaite, M.; Onrust, B.; Liu, H.; Xiong, Q.; Zlatanova, S.

2013-11-01

3D models are more powerful than 2D maps for indoor navigation in a complicate space like Hubei Provincial Museum because they can provide accurate descriptions of locations of indoor objects (e.g., doors, windows, tables) and context information of these objects. In addition, the 3D model is the preferred navigation environment by the user according to the survey. Therefore a 3D model based indoor navigation system is developed for Hubei Provincial Museum to guide the visitors of museum. The system consists of three layers: application, web service and navigation, which is built to support localization, navigation and visualization functions of the system. There are three main strengths of this system: it stores all data needed in one database and processes most calculations on the webserver which make the mobile client very lightweight, the network used for navigation is extracted semi-automatically and renewable, the graphic user interface (GUI), which is based on a game engine, has high performance of visualizing 3D model on a mobile display.

phiGENOME: an integrative navigation throughout bacteriophage genomes.

PubMed

Stano, Matej; Klucar, Lubos

2011-11-01

phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and designed for graphical representation of gene regulations. Bringing 542 complete genome sequences accompanied with their rich annotations and references, makes phiGENOME a unique information resource in the field of phage genomics. Copyright © 2011 Elsevier Inc. All rights reserved.

Journal searching in non-MEDLINE resources on Internet Web sites.

PubMed

Lingle, V A

1997-01-01

Internet access to the medical journal literature is absorbing the attention of all relevant parties, i.e., publishers, journal vendors, librarians, commercial providers, government agencies, and end users. Journal content on the Web sites spans the range from advertising and ordering information for the print version, to table of contents and abstracts, to downloadable full text and graphics of articles. The searching parameters for systems other than MEDLINE also differ extensively with a wide variety of features and resulting retrieval. This discussion reviews a selection of providers of medical information (particularly the journal literature) on the Internet, making a comparison of what is available on Web sites and how it can be searched.

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…

Mfold web server for nucleic acid folding and hybridization prediction.

PubMed

Zuker, Michael

2003-07-01

The abbreviated name, 'mfold web server', describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software. Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and 'energy dot plots', are available for the folding of single sequences. A variety of 'bulk' servers give less information, but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as 'MFOLDROOT'.

Simulation environment and graphical visualization environment: a COPD use-case

PubMed Central

2014-01-01

Background Today, many different tools are developed to execute and visualize physiological models that represent the human physiology. Most of these tools run models written in very specific programming languages which in turn simplify the communication among models. Nevertheless, not all of these tools are able to run models written in different programming languages. In addition, interoperability between such models remains an unresolved issue. Results In this paper we present a simulation environment that allows, first, the execution of models developed in different programming languages and second the communication of parameters to interconnect these models. This simulation environment, developed within the Synergy-COPD project, aims at helping and supporting bio-researchers and medical students understand the internal mechanisms of the human body through the use of physiological models. This tool is composed of a graphical visualization environment, which is a web interface through which the user can interact with the models, and a simulation workflow management system composed of a control module and a data warehouse manager. The control module monitors the correct functioning of the whole system. The data warehouse manager is responsible for managing the stored information and supporting its flow among the different modules. This simulation environment has been validated with the integration of three models: two deterministic, i.e. based on linear and differential equations, and one probabilistic, i.e., based on probability theory. These models have been selected based on the disease under study in this project, i.e., chronic obstructive pulmonary disease. Conclusion It has been proved that the simulation environment presented here allows the user to research and study the internal mechanisms of the human physiology by the use of models via a graphical visualization environment. A new tool for bio-researchers is ready for deployment in various use cases scenarios. PMID:25471327

KAGLVis - On-line 3D Visualisation of Earth-observing-satellite Data

NASA Astrophysics Data System (ADS)

Szuba, Marek; Ameri, Parinaz; Grabowski, Udo; Maatouki, Ahmad; Meyer, Jörg

2015-04-01

One of the goals of the Large-Scale Data Management and Analysis project is to provide a high-performance framework facilitating management of data acquired by Earth-observing satellites such as Envisat. On the client-facing facet of this framework, we strive to provide visualisation and basic analysis tool which could be used by scientists with minimal to no knowledge of the underlying infrastructure. Our tool, KAGLVis, is a JavaScript client-server Web application which leverages modern Web technologies to provide three-dimensional visualisation of satellite observables on a wide range of client systems. It takes advantage of the WebGL API to employ locally available GPU power for 3D rendering; this approach has been demonstrated to perform well even on relatively weak hardware such as integrated graphics chipsets found in modern laptop computers and with some user-interface tuning could even be usable on embedded devices such as smartphones or tablets. Data is fetched from the database back-end using a ReST API and cached locally, both in memory and using HTML5 Web Storage, to minimise network use. Computations, calculation of cloud altitude from cloud-index measurements for instance, can depending on configuration be performed on either the client or the server side. Keywords: satellite data, Envisat, visualisation, 3D graphics, Web application, WebGL, MEAN stack.

OWLing Clinical Data Repositories With the Ontology Web Language

PubMed Central

Pastor, Xavier; Lozano, Esther

2014-01-01

Background The health sciences are based upon information. Clinical information is usually stored and managed by physicians with precarious tools, such as spreadsheets. The biomedical domain is more complex than other domains that have adopted information and communication technologies as pervasive business tools. Moreover, medicine continuously changes its corpus of knowledge because of new discoveries and the rearrangements in the relationships among concepts. This scenario makes it especially difficult to offer good tools to answer the professional needs of researchers and constitutes a barrier that needs innovation to discover useful solutions. Objective The objective was to design and implement a framework for the development of clinical data repositories, capable of facing the continuous change in the biomedicine domain and minimizing the technical knowledge required from final users. Methods We combined knowledge management tools and methodologies with relational technology. We present an ontology-based approach that is flexible and efficient for dealing with complexity and change, integrated with a solid relational storage and a Web graphical user interface. Results Onto Clinical Research Forms (OntoCRF) is a framework for the definition, modeling, and instantiation of data repositories. It does not need any database design or programming. All required information to define a new project is explicitly stated in ontologies. Moreover, the user interface is built automatically on the fly as Web pages, whereas data are stored in a generic repository. This allows for immediate deployment and population of the database as well as instant online availability of any modification. Conclusions OntoCRF is a complete framework to build data repositories with a solid relational storage. Driven by ontologies, OntoCRF is more flexible and efficient to deal with complexity and change than traditional systems and does not require very skilled technical people facilitating the engineering of clinical software systems. PMID:25599697

OWLing Clinical Data Repositories With the Ontology Web Language.

PubMed

Lozano-Rubí, Raimundo; Pastor, Xavier; Lozano, Esther

2014-08-01

The health sciences are based upon information. Clinical information is usually stored and managed by physicians with precarious tools, such as spreadsheets. The biomedical domain is more complex than other domains that have adopted information and communication technologies as pervasive business tools. Moreover, medicine continuously changes its corpus of knowledge because of new discoveries and the rearrangements in the relationships among concepts. This scenario makes it especially difficult to offer good tools to answer the professional needs of researchers and constitutes a barrier that needs innovation to discover useful solutions. The objective was to design and implement a framework for the development of clinical data repositories, capable of facing the continuous change in the biomedicine domain and minimizing the technical knowledge required from final users. We combined knowledge management tools and methodologies with relational technology. We present an ontology-based approach that is flexible and efficient for dealing with complexity and change, integrated with a solid relational storage and a Web graphical user interface. Onto Clinical Research Forms (OntoCRF) is a framework for the definition, modeling, and instantiation of data repositories. It does not need any database design or programming. All required information to define a new project is explicitly stated in ontologies. Moreover, the user interface is built automatically on the fly as Web pages, whereas data are stored in a generic repository. This allows for immediate deployment and population of the database as well as instant online availability of any modification. OntoCRF is a complete framework to build data repositories with a solid relational storage. Driven by ontologies, OntoCRF is more flexible and efficient to deal with complexity and change than traditional systems and does not require very skilled technical people facilitating the engineering of clinical software systems.

WebMeV | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

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

Computer-Based Tools for Evaluating Graphical User Interfaces

NASA Technical Reports Server (NTRS)

Moore, Loretta A.

1997-01-01

The user interface is the component of a software system that connects two very complex system: humans and computers. Each of these two systems impose certain requirements on the final product. The user is the judge of the usability and utility of the system; the computer software and hardware are the tools with which the interface is constructed. Mistakes are sometimes made in designing and developing user interfaces because the designers and developers have limited knowledge about human performance (e.g., problem solving, decision making, planning, and reasoning). Even those trained in user interface design make mistakes because they are unable to address all of the known requirements and constraints on design. Evaluation of the user inter-face is therefore a critical phase of the user interface development process. Evaluation should not be considered the final phase of design; but it should be part of an iterative design cycle with the output of evaluation being feed back into design. The goal of this research was to develop a set of computer-based tools for objectively evaluating graphical user interfaces. The research was organized into three phases. The first phase resulted in the development of an embedded evaluation tool which evaluates the usability of a graphical user interface based on a user's performance. An expert system to assist in the design and evaluation of user interfaces based upon rules and guidelines was developed during the second phase. During the final phase of the research an automatic layout tool to be used in the initial design of graphical inter- faces was developed. The research was coordinated with NASA Marshall Space Flight Center's Mission Operations Laboratory's efforts in developing onboard payload display specifications for the Space Station.

SpecPad: device-independent NMR data visualization and processing based on the novel DART programming language and Html5 Web technology.

PubMed

Guigas, Bruno

2017-09-01

SpecPad is a new device-independent software program for the visualization and processing of one-dimensional and two-dimensional nuclear magnetic resonance (NMR) time domain (FID) and frequency domain (spectrum) data. It is the result of a project to investigate whether the novel programming language DART, in combination with Html5 Web technology, forms a suitable base to write an NMR data evaluation software which runs on modern computing devices such as Android, iOS, and Windows tablets as well as on Windows, Linux, and Mac OS X desktop PCs and notebooks. Another topic of interest is whether this technique also effectively supports the required sophisticated graphical and computational algorithms. SpecPad is device-independent because DART's compiled executable code is JavaScript and can, therefore, be run by the browsers of PCs and tablets. Because of Html5 browser cache technology, SpecPad may be operated off-line. Network access is only required during data import or export, e.g. via a Cloud service, or for software updates. A professional and easy to use graphical user interface consistent across all hardware platforms supports touch screen features on mobile devices for zooming and panning and for NMR-related interactive operations such as phasing, integration, peak picking, or atom assignment. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

A simple and reliable health monitoring system for shoulder health: proposal.

PubMed

Liu, Shuo-Fang; Lee, Yann-Long

2014-02-26

The current health care system is complex and inefficient. A simple and reliable health monitoring system that can help patients perform medical self-diagnosis is seldom readily available. Because the medical system is vast and complex, it has hampered or delayed patients in seeking medical advice or treatment in a timely manner, which may potentially affect the patient's chances of recovery, especially those with severe sicknesses such as cancer, and heart disease. The purpose of this paper is to propose a methodology in designing a simple, low cost, Internet-based health-screening platform. This health-screening platform will enable patients to perform medical self-diagnosis over the Internet. Historical data has shown the importance of early detection to ensure patients receive proper treatment and speedy recovery. The platform is designed with special emphasis on the user interface. Standard Web-based user-interface design is adopted so the user feels ease to operate in a familiar Web environment. In addition, graphics such as charts and graphs are used generously to help users visualize and understand the result of the diagnostic. The system is developed using hypertext preprocessor (PHP) programming language. One important feature of this system platform is that it is built to be a stand-alone platform, which tends to have better user privacy security. The prototype system platform was developed by the National Cheng Kung University Ergonomic and Design Laboratory. The completed prototype of this system platform was submitted to the Taiwan Medical Institute for evaluation. The evaluation of 120 participants showed that this platform system is a highly effective tool in health-screening applications, and has great potential for improving the medical care quality for the general public.

ARDesigner: a web-based system for allosteric RNA design.

PubMed

Shu, Wenjie; Liu, Ming; Chen, Hebing; Bo, Xiaochen; Wang, Shengqi

2010-12-01

RNA molecules play vital informational, structural, and functional roles in molecular biology, making them ideal targets for synthetic biology. However, several challenges remain for engineering novel allosteric RNA molecules, and the development of efficient computational design techniques is vitally needed. Here we describe the development of Allosteric RNA Designer (ARDesigner), a user-friendly and freely available web-based system for allosteric RNA design that incorporates mutational robustness in the design process. The system output includes detailed design information in a graphical HTML format. We used ARDesigner to engineer a temperature-sensitive AR, and found that the resulting design satisfied the prescribed properties/input. ARDesigner provides a simple means for researchers to design allosteric RNAs with specific properties. With its versatile framework and possibilities for further enhancement, ARDesigner may serve as a useful tool for synthetic biologists and therapeutic design. ARDesigner and its executable version are freely available at http://biotech.bmi.ac.cn/ARDesigner. Crown Copyright © 2010. Published by Elsevier B.V. All rights reserved.

The Lake Tahoe Basin Land Use Simulation Model

USGS Publications Warehouse

Forney, William M.; Oldham, I. Benson

2011-01-01

This U.S. Geological Survey Open-File Report describes the final modeling product for the Tahoe Decision Support System project for the Lake Tahoe Basin funded by the Southern Nevada Public Land Management Act and the U.S. Geological Survey's Geographic Analysis and Monitoring Program. This research was conducted by the U.S. Geological Survey Western Geographic Science Center. The purpose of this report is to describe the basic elements of the novel Lake Tahoe Basin Land Use Simulation Model, publish samples of the data inputs, basic outputs of the model, and the details of the Python code. The results of this report include a basic description of the Land Use Simulation Model, descriptions and summary statistics of model inputs, two figures showing the graphical user interface from the web-based tool, samples of the two input files, seven tables of basic output results from the web-based tool and descriptions of their parameters, and the fully functional Python code.

User's manual for the two-dimensional transputer graphics toolkit

NASA Technical Reports Server (NTRS)

Ellis, Graham K.

1988-01-01

The user manual for the 2-D graphics toolkit for a transputer based parallel processor is presented. The toolkit consists of a package of 2-D display routines that can be used for the simulation visualizations. It supports multiple windows, double buffered screens for animations, and simple graphics transformations such as translation, rotation, and scaling. The display routines are written in occam to take advantage of the multiprocessing features available on transputers. The package is designed to run on a transputer separate from the graphics board.

The DICOM-based radiation therapy information system

NASA Astrophysics Data System (ADS)

Law, Maria Y. Y.; Chan, Lawrence W. C.; Zhang, Xiaoyan; Zhang, Jianguo

2004-04-01

Similar to DICOM for PACS (Picture Archiving and Communication System), standards for radiotherapy (RT) information have been ratified with seven DICOM-RT objects and their IODs (Information Object Definitions), which are more than just images. This presentation describes how a DICOM-based RT Information System Server can be built based on the PACS technology and its data model for a web-based distribution. Methods: The RT information System consists of a Modality Simulator, a data format translator, a RT Gateway, the DICOM RT Server, and the Web-based Application Server. The DICOM RT Server was designed based on a PACS data model and was connected to a Web application Server for distribution of the RT information including therapeutic plans, structures, dose distribution, images and records. Various DICOM RT objects of the patient transmitted to the RT Server were routed to the Web Application Server where the contents of the DICOM RT objects were decoded and mapped to the corresponding location of the RT data model for display in the specially-designed Graphic User Interface. The non-DICOM objects were first rendered to DICOM RT Objects in the translator before they were sent to the RT Server. Results: Ten clinical cases have been collected from different hopsitals for evaluation of the DICOM-based RT Information System. They were successfully routed through the data flow and displayed in the client workstation of the RT information System. Conclusion: Using the DICOM-RT standards, integration of RT data from different vendors is possible.

Data deluxe

NASA Astrophysics Data System (ADS)

Carlowicz, Michael

Several new web pages from the National Oceanic and Atmospheric Administration (NOAA) will allow scientists and nonscientists alike to view graphic displays of weather and space weather data from around the world. Users can select a region of the Earth and a time period to see plots and data sets of everything from severe storms to aurorae.The National Climate Data Center has made available weather data from 8000 stations around the world, 160 satellite images of hurricanes from the GOES satellites, and technical reports about weather events such as the East Coast blizzard of 1996. The web address is http://www.ncdc.noaa.gov.

CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research

PubMed Central

Sherif, Tarek; Rioux, Pierre; Rousseau, Marc-Etienne; Kassis, Nicolas; Beck, Natacha; Adalat, Reza; Das, Samir; Glatard, Tristan; Evans, Alan C.

2014-01-01

The Canadian Brain Imaging Research Platform (CBRAIN) is a web-based collaborative research platform developed in response to the challenges raised by data-heavy, compute-intensive neuroimaging research. CBRAIN offers transparent access to remote data sources, distributed computing sites, and an array of processing and visualization tools within a controlled, secure environment. Its web interface is accessible through any modern browser and uses graphical interface idioms to reduce the technical expertise required to perform large-scale computational analyses. CBRAIN's flexible meta-scheduling has allowed the incorporation of a wide range of heterogeneous computing sites, currently including nine national research High Performance Computing (HPC) centers in Canada, one in Korea, one in Germany, and several local research servers. CBRAIN leverages remote computing cycles and facilitates resource-interoperability in a transparent manner for the end-user. Compared with typical grid solutions available, our architecture was designed to be easily extendable and deployed on existing remote computing sites with no tool modification, administrative intervention, or special software/hardware configuration. As October 2013, CBRAIN serves over 200 users spread across 53 cities in 17 countries. The platform is built as a generic framework that can accept data and analysis tools from any discipline. However, its current focus is primarily on neuroimaging research and studies of neurological diseases such as Autism, Parkinson's and Alzheimer's diseases, Multiple Sclerosis as well as on normal brain structure and development. This technical report presents the CBRAIN Platform, its current deployment and usage and future direction. PMID:24904400

CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research.

PubMed

Sherif, Tarek; Rioux, Pierre; Rousseau, Marc-Etienne; Kassis, Nicolas; Beck, Natacha; Adalat, Reza; Das, Samir; Glatard, Tristan; Evans, Alan C

2014-01-01

The Canadian Brain Imaging Research Platform (CBRAIN) is a web-based collaborative research platform developed in response to the challenges raised by data-heavy, compute-intensive neuroimaging research. CBRAIN offers transparent access to remote data sources, distributed computing sites, and an array of processing and visualization tools within a controlled, secure environment. Its web interface is accessible through any modern browser and uses graphical interface idioms to reduce the technical expertise required to perform large-scale computational analyses. CBRAIN's flexible meta-scheduling has allowed the incorporation of a wide range of heterogeneous computing sites, currently including nine national research High Performance Computing (HPC) centers in Canada, one in Korea, one in Germany, and several local research servers. CBRAIN leverages remote computing cycles and facilitates resource-interoperability in a transparent manner for the end-user. Compared with typical grid solutions available, our architecture was designed to be easily extendable and deployed on existing remote computing sites with no tool modification, administrative intervention, or special software/hardware configuration. As October 2013, CBRAIN serves over 200 users spread across 53 cities in 17 countries. The platform is built as a generic framework that can accept data and analysis tools from any discipline. However, its current focus is primarily on neuroimaging research and studies of neurological diseases such as Autism, Parkinson's and Alzheimer's diseases, Multiple Sclerosis as well as on normal brain structure and development. This technical report presents the CBRAIN Platform, its current deployment and usage and future direction.

A web-based Tamsui River flood early-warning system with correction of real-time water stage using monitoring data

NASA Astrophysics Data System (ADS)

Liao, H. Y.; Lin, Y. J.; Chang, H. K.; Shang, R. K.; Kuo, H. C.; Lai, J. S.; Tan, Y. C.

2017-12-01

Taiwan encounters heavy rainfalls frequently. There are three to four typhoons striking Taiwan every year. To provide lead time for reducing flood damage, this study attempt to build a flood early-warning system (FEWS) in Tanshui River using time series correction techniques. The predicted rainfall is used as the input for the rainfall-runoff model. Then, the discharges calculated by the rainfall-runoff model is converted to the 1-D river routing model. The 1-D river routing model will output the simulating water stages in 487 cross sections for the future 48-hr. The downstream water stage at the estuary in 1-D river routing model is provided by storm surge simulation. Next, the water stages of 487 cross sections are corrected by time series model such as autoregressive (AR) model using real-time water stage measurements to improve the predicted accuracy. The results of simulated water stages are displayed on a web-based platform. In addition, the models can be performed remotely by any users with web browsers through a user interface. The on-line video surveillance images, real-time monitoring water stages, and rainfalls can also be shown on this platform. If the simulated water stage exceeds the embankments of Tanshui River, the alerting lights of FEWS will be flashing on the screen. This platform runs periodically and automatically to generate the simulation graphic data of flood water stages for flood disaster prevention and decision making.

IsoCleft Finder – a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities

PubMed Central

Najmanovich, Rafael

2013-01-01

IsoCleft Finder is a web-based tool for the detection of local geometric and chemical similarities between potential small-molecule binding cavities and a non-redundant dataset of ligand-bound known small-molecule binding-sites. The non-redundant dataset developed as part of this study is composed of 7339 entries representing unique Pfam/PDB-ligand (hetero group code) combinations with known levels of cognate ligand similarity. The query cavity can be uploaded by the user or detected automatically by the system using existing PDB entries as well as user-provided structures in PDB format. In all cases, the user can refine the definition of the cavity interactively via a browser-based Jmol 3D molecular visualization interface. Furthermore, users can restrict the search to a subset of the dataset using a cognate-similarity threshold. Local structural similarities are detected using the IsoCleft software and ranked according to two criteria (number of atoms in common and Tanimoto score of local structural similarity) and the associated Z-score and p-value measures of statistical significance. The results, including predicted ligands, target proteins, similarity scores, number of atoms in common, etc., are shown in a powerful interactive graphical interface. This interface permits the visualization of target ligands superimposed on the query cavity and additionally provides a table of pairwise ligand topological similarities. Similarities between top scoring ligands serve as an additional tool to judge the quality of the results obtained. We present several examples where IsoCleft Finder provides useful functional information. IsoCleft Finder results are complementary to existing approaches for the prediction of protein function from structure, rational drug design and x-ray crystallography. IsoCleft Finder can be found at: http://bcb.med.usherbrooke.ca/isocleftfinder. PMID:24555058

Design features of on-line anatomy information resources: a comparison with the Digital Anatomist.

PubMed

Kim, S; Brinkley, J F; Rosse, C

1999-01-01

In order to update the design of the next generation of the Digital Anatomist, we have surveyed teaching assistants who have used the Digital Anatomist for learning and teaching anatomy as medical students, and have also examined available anatomy web sites with sufficient content to support learning. The majority of web sites function in an atlas mode and provide for the identification of structures. These atlases incorporate a variety of features for interactivity with 2D images, some of which are not available in the Digital Anatomist. The surveys suggest that the greatest need is for on-line access to comprehensive and detailed anatomical information and for the development of knowledge-based methods that allow the direct manipulation of segmented 3D graphical models by the user. The requirement for such interactivity is a comprehensive symbolic model of the physical organization of the body that can support inference.

PhamDB: a web-based application for building Phamerator databases.

PubMed

Lamine, James G; DeJong, Randall J; Nelesen, Serita M

2016-07-01

PhamDB is a web application which creates databases of bacteriophage genes, grouped by gene similarity. It is backwards compatible with the existing Phamerator desktop software while providing an improved database creation workflow. Key features include a graphical user interface, validation of uploaded GenBank files, and abilities to import phages from existing databases, modify existing databases and queue multiple jobs. Source code and installation instructions for Linux, Windows and Mac OSX are freely available at https://github.com/jglamine/phage PhamDB is also distributed as a docker image which can be managed via Kitematic. This docker image contains the application and all third party software dependencies as a pre-configured system, and is freely available via the installation instructions provided. snelesen@calvin.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

NASA Astrophysics Data System (ADS)

Robal, Tarmo; Kalja, Ahto

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

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.

Earth Science Data Education through Cooking Up Recipes

NASA Astrophysics Data System (ADS)

Weigel, A. M.; Maskey, M.; Smith, T.; Conover, H.

2016-12-01

One of the major challenges in Earth science research and applications is understanding and applying the proper methods, tools, and software for using scientific data. These techniques are often difficult and time consuming to identify, requiring novel users to conduct extensive research, take classes, and reach out for assistance, thus hindering scientific discovery and real-world applications. To address these challenges, the Global Hydrology Resource Center (GHRC) DAAC has developed a series of data recipes that novel users such as students, decision makers, and general Earth scientists can leverage to learn how to use Earth science datasets. Once the data recipe content had been finalized, GHRC computer and Earth scientists collaborated with a web and graphic designer to ensure the content is both attractively presented to data users, and clearly communicated to promote the education and use of Earth science data. The completed data recipes include, but are not limited to, tutorials, iPython Notebooks, resources, and tools necessary for addressing key difficulties in data use across a broad user base. These recipes enable non-traditional users to learn how to use data, but also curates and communicates common methods and approaches that may be difficult and time consuming for these users to identify.

Processing biological literature with customizable Web services supporting interoperable formats.

PubMed

Rak, Rafal; Batista-Navarro, Riza Theresa; Carter, Jacob; Rowley, Andrew; Ananiadou, Sophia

2014-01-01

Web services have become a popular means of interconnecting solutions for processing a body of scientific literature. This has fuelled research on high-level data exchange formats suitable for a given domain and ensuring the interoperability of Web services. In this article, we focus on the biological domain and consider four interoperability formats, BioC, BioNLP, XMI and RDF, that represent domain-specific and generic representations and include well-established as well as emerging specifications. We use the formats in the context of customizable Web services created in our Web-based, text-mining workbench Argo that features an ever-growing library of elementary analytics and capabilities to build and deploy Web services straight from a convenient graphical user interface. We demonstrate a 2-fold customization of Web services: by building task-specific processing pipelines from a repository of available analytics, and by configuring services to accept and produce a combination of input and output data interchange formats. We provide qualitative evaluation of the formats as well as quantitative evaluation of automatic analytics. The latter was carried out as part of our participation in the fourth edition of the BioCreative challenge. Our analytics built into Web services for recognizing biochemical concepts in BioC collections achieved the highest combined scores out of 10 participating teams. Database URL: http://argo.nactem.ac.uk. © The Author(s) 2014. Published by Oxford University Press.

Processing biological literature with customizable Web services supporting interoperable formats

PubMed Central

Rak, Rafal; Batista-Navarro, Riza Theresa; Carter, Jacob; Rowley, Andrew; Ananiadou, Sophia

2014-01-01

Web services have become a popular means of interconnecting solutions for processing a body of scientific literature. This has fuelled research on high-level data exchange formats suitable for a given domain and ensuring the interoperability of Web services. In this article, we focus on the biological domain and consider four interoperability formats, BioC, BioNLP, XMI and RDF, that represent domain-specific and generic representations and include well-established as well as emerging specifications. We use the formats in the context of customizable Web services created in our Web-based, text-mining workbench Argo that features an ever-growing library of elementary analytics and capabilities to build and deploy Web services straight from a convenient graphical user interface. We demonstrate a 2-fold customization of Web services: by building task-specific processing pipelines from a repository of available analytics, and by configuring services to accept and produce a combination of input and output data interchange formats. We provide qualitative evaluation of the formats as well as quantitative evaluation of automatic analytics. The latter was carried out as part of our participation in the fourth edition of the BioCreative challenge. Our analytics built into Web services for recognizing biochemical concepts in BioC collections achieved the highest combined scores out of 10 participating teams. Database URL: http://argo.nactem.ac.uk. PMID:25006225

Distributed health care imaging information systems

NASA Astrophysics Data System (ADS)

Thompson, Mary R.; Johnston, William E.; Guojun, Jin; Lee, Jason; Tierney, Brian; Terdiman, Joseph F.

1997-05-01

We have developed an ATM network-based system to collect and catalogue cardio-angiogram videos from the source at a Kaiser central facility and make them available for viewing by doctors at primary care Kaiser facilities. This an example of the general problem of diagnostic data being generated at tertiary facilities, while the images, or other large data objects they produce, need to be used from a variety of other locations such as doctor's offices or local hospitals. We describe the use of a highly distributed computing and storage architecture to provide all aspects of collecting, storing, analyzing, and accessing such large data-objects in a metropolitan area ATM network. Our large data-object management system provides network interface between the object sources, the data management system and the user of the data. As the data is being stored, a cataloguing system automatically creates and stores condensed versions of the data, textural metadata and pointers to the original data. The catalogue system provides a Web-based graphical interface to the data. The user is able the view the low-resolution data with a standard Internet connection and Web browser. If high-resolution is required, a high-speed connection and special application programs can be used to view the high-resolution original data.

-A curated transcriptomic dataset collection relevant to embryonic development associated with in vitro fertilization in healthy individuals and patients with polycystic ovary syndrome.

PubMed

Mackeh, Rafah; Boughorbel, Sabri; Chaussabel, Damien; Kino, Tomoshige

2017-01-01

The collection of large-scale datasets available in public repositories is rapidly growing and providing opportunities to identify and fill gaps in different fields of biomedical research. However, users of these datasets should be able to selectively browse datasets related to their field of interest. Here we made available a collection of transcriptome datasets related to human follicular cells from normal individuals or patients with polycystic ovary syndrome, in the process of their development, during in vitro fertilization. After RNA-seq dataset exclusion and careful selection based on study description and sample information, 12 datasets, encompassing a total of 85 unique transcriptome profiles, were identified in NCBI Gene Expression Omnibus and uploaded to the Gene Expression Browser (GXB), a web application specifically designed for interactive query and visualization of integrated large-scale data. Once annotated in GXB, multiple sample grouping has been made in order to create rank lists to allow easy data interpretation and comparison. The GXB tool also allows the users to browse a single gene across multiple projects to evaluate its expression profiles in multiple biological systems/conditions in a web-based customized graphical views. The curated dataset is accessible at the following link: http://ivf.gxbsidra.org/dm3/landing.gsp.

A Web-Based Tool for Automatic Data Collection, Curation, and Visualization of Complex Healthcare Survey Studies including Social Network Analysis.

PubMed

Benítez, José Alberto; Labra, José Emilio; Quiroga, Enedina; Martín, Vicente; García, Isaías; Marqués-Sánchez, Pilar; Benavides, Carmen

2017-01-01

There is a great concern nowadays regarding alcohol consumption and drug abuse, especially in young people. Analyzing the social environment where these adolescents are immersed, as well as a series of measures determining the alcohol abuse risk or personal situation and perception using a number of questionnaires like AUDIT, FAS, KIDSCREEN, and others, it is possible to gain insight into the current situation of a given individual regarding his/her consumption behavior. But this analysis, in order to be achieved, requires the use of tools that can ease the process of questionnaire creation, data gathering, curation and representation, and later analysis and visualization to the user. This research presents the design and construction of a web-based platform able to facilitate each of the mentioned processes by integrating the different phases into an intuitive system with a graphical user interface that hides the complexity underlying each of the questionnaires and techniques used and presenting the results in a flexible and visual way, avoiding any manual handling of data during the process. Advantages of this approach are shown and compared to the previous situation where some of the tasks were accomplished by time consuming and error prone manipulations of data.

­A curated transcriptomic dataset collection relevant to embryonic development associated with in vitro fertilization in healthy individuals and patients with polycystic ovary syndrome

PubMed Central

Mackeh, Rafah; Boughorbel, Sabri; Chaussabel, Damien; Kino, Tomoshige

2017-01-01

The collection of large-scale datasets available in public repositories is rapidly growing and providing opportunities to identify and fill gaps in different fields of biomedical research. However, users of these datasets should be able to selectively browse datasets related to their field of interest. Here we made available a collection of transcriptome datasets related to human follicular cells from normal individuals or patients with polycystic ovary syndrome, in the process of their development, during in vitro fertilization. After RNA-seq dataset exclusion and careful selection based on study description and sample information, 12 datasets, encompassing a total of 85 unique transcriptome profiles, were identified in NCBI Gene Expression Omnibus and uploaded to the Gene Expression Browser (GXB), a web application specifically designed for interactive query and visualization of integrated large-scale data. Once annotated in GXB, multiple sample grouping has been made in order to create rank lists to allow easy data interpretation and comparison. The GXB tool also allows the users to browse a single gene across multiple projects to evaluate its expression profiles in multiple biological systems/conditions in a web-based customized graphical views. The curated dataset is accessible at the following link: http://ivf.gxbsidra.org/dm3/landing.gsp. PMID:28413616

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.

Designing Websites for Displaying Large Data Sets and Images on Multiple Platforms

NASA Astrophysics Data System (ADS)

Anderson, A.; Wolf, V. G.; Garron, J.; Kirschner, M.

2012-12-01

The desire to build websites to analyze and display ever increasing amounts of scientific data and images pushes for web site designs which utilize large displays, and to use the display area as efficiently as possible. Yet, scientists and users of their data are increasingly wishing to access these websites in the field and on mobile devices. This results in the need to develop websites that can support a wide range of devices and screen sizes, and to optimally use whatever display area is available. Historically, designers have addressed this issue by building two websites; one for mobile devices, and one for desktop environments, resulting in increased cost, duplicity of work, and longer development times. Recent advancements in web design technology and techniques have evolved which allow for the development of a single website that dynamically adjusts to the type of device being used to browse the website (smartphone, tablet, desktop). In addition they provide the opportunity to truly optimize whatever display area is available. HTML5 and CSS3 give web designers media query statements which allow design style sheets to be aware of the size of the display being used, and to format web content differently based upon the queried response. Web elements can be rendered in a different size, position, or even removed from the display entirely, based upon the size of the display area. Using HTML5/CSS3 media queries in this manner is referred to as "Responsive Web Design" (RWD). RWD in combination with technologies such as LESS and Twitter Bootstrap allow the web designer to build web sites which not only dynamically respond to the browser display size being used, but to do so in very controlled and intelligent ways, ensuring that good layout and graphic design principles are followed while doing so. At the University of Alaska Fairbanks, the Alaska Satellite Facility SAR Data Center (ASF) recently redesigned their popular Vertex application and converted it from a traditional, fixed-layout website into a RWD site built on HTML5, LESS and Twitter Bootstrap. Vertex is a data portal for remotely sensed imagery of the earth, offering Synthetic Aperture Radar (SAR) data products from the global ASF archive. By using Responsive Web Design, ASF is able to provide access to a massive collection of SAR imagery and allow the user to use mobile devices and desktops to maximum advantage. ASF's Vertex web site demonstrates that with increased interface flexibility, scientists, managers and users can increase their personal effectiveness by accessing data portals from their preferred device as their science dictates.

Can Interactive Web-Based CAD Tools Improve the Learning of Engineering Drawing? A Case Study

ERIC Educational Resources Information Center

Pando Cerra, Pablo; Suárez González, Jesús M.; Busto Parra, Bernardo; Rodríguez Ortiz, Diana; Álvarez Peñín, Pedro I.

2014-01-01

Many current Web-based learning environments facilitate the theoretical teaching of a subject but this may not be sufficient for those disciplines that require a significant use of graphic mechanisms to resolve problems. This research study looks at the use of an environment that can help students learn engineering drawing with Web-based CAD…

BioCarian: search engine for exploratory searches in heterogeneous biological databases.

PubMed

Zaki, Nazar; Tennakoon, Chandana

2017-10-02

There are a large number of biological databases publicly available for scientists in the web. Also, there are many private databases generated in the course of research projects. These databases are in a wide variety of formats. Web standards have evolved in the recent times and semantic web technologies are now available to interconnect diverse and heterogeneous sources of data. Therefore, integration and querying of biological databases can be facilitated by techniques used in semantic web. Heterogeneous databases can be converted into Resource Description Format (RDF) and queried using SPARQL language. Searching for exact queries in these databases is trivial. However, exploratory searches need customized solutions, especially when multiple databases are involved. This process is cumbersome and time consuming for those without a sufficient background in computer science. In this context, a search engine facilitating exploratory searches of databases would be of great help to the scientific community. We present BioCarian, an efficient and user-friendly search engine for performing exploratory searches on biological databases. The search engine is an interface for SPARQL queries over RDF databases. We note that many of the databases can be converted to tabular form. We first convert the tabular databases to RDF. The search engine provides a graphical interface based on facets to explore the converted databases. The facet interface is more advanced than conventional facets. It allows complex queries to be constructed, and have additional features like ranking of facet values based on several criteria, visually indicating the relevance of a facet value and presenting the most important facet values when a large number of choices are available. For the advanced users, SPARQL queries can be run directly on the databases. Using this feature, users will be able to incorporate federated searches of SPARQL endpoints. We used the search engine to do an exploratory search on previously published viral integration data and were able to deduce the main conclusions of the original publication. BioCarian is accessible via http://www.biocarian.com . We have developed a search engine to explore RDF databases that can be used by both novice and advanced users.

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research

PubMed Central

Yeung, Ka Yee

2016-01-01

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface. PMID:27045593

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research.

PubMed

Hung, Ling-Hong; Kristiyanto, Daniel; Lee, Sung Bong; Yeung, Ka Yee

2016-01-01

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface.

Using ESO Reflex with Web Services

NASA Astrophysics Data System (ADS)

Järveläinen, P.; Savolainen, V.; Oittinen, T.; Maisala, S.; Ullgrén, M. Hook, R.

2008-08-01

ESO Reflex is a prototype graphical workflow system, based on Taverna, and primarily intended to be a flexible way of running ESO data reduction recipes along with other legacy applications and user-written tools. ESO Reflex can also readily use the Taverna Web Services features that are based on the Apache Axis SOAP implementation. Taverna is a general purpose Web Service client, and requires no programming to use such services. However, Taverna also has some restrictions: for example, no numerical types such integers. In addition the preferred binding style is document/literal wrapped, but most astronomical services publish the Axis default WSDL using RPC/encoded style. Despite these minor limitations we have created simple but very promising test VO workflow using the Sesame name resolver service at CDS Strasbourg, the Hubble SIAP server at the Multi-Mission Archive at Space Telescope (MAST) and the WESIX image cataloging and catalogue cross-referencing service at the University of Pittsburgh. ESO Reflex can also pass files and URIs via the PLASTIC protocol to visualisation tools and has its own viewer for VOTables. We picked these three Web Services to try to set up a realistic and useful ESO Reflex workflow. They also demonstrate ESO Reflex abilities to use many kind of Web Services because each of them requires a different interface. We describe each of these services in turn and comment on how it was used

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.

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.

Application of web-GIS approach for climate change study

NASA Astrophysics Data System (ADS)

Okladnikov, Igor; Gordov, Evgeny; Titov, Alexander; Bogomolov, Vasily; Martynova, Yuliya; Shulgina, Tamara

2013-04-01

Georeferenced datasets are currently actively used in numerous applications including modeling, interpretation and forecast of climatic and ecosystem changes for various spatial and temporal scales. Due to inherent heterogeneity of environmental datasets as well as their huge size which might constitute up to tens terabytes for a single dataset at present studies in the area of climate and environmental change require a special software support. A dedicated web-GIS information-computational system for analysis of georeferenced climatological and meteorological data has been created. It is based on OGC standards and involves many modern solutions such as object-oriented programming model, modular composition, and JavaScript libraries based on GeoExt library, ExtJS Framework and OpenLayers software. The main advantage of the system lies in a possibility to perform mathematical and statistical data analysis, graphical visualization of results with GIS-functionality, and to prepare binary output files with just only a modern graphical web-browser installed on a common desktop computer connected to Internet. Several geophysical datasets represented by two editions of NCEP/NCAR Reanalysis, JMA/CRIEPI JRA-25 Reanalysis, ECMWF ERA-40 Reanalysis, ECMWF ERA Interim Reanalysis, MRI/JMA APHRODITE's Water Resources Project Reanalysis, DWD Global Precipitation Climatology Centre's data, GMAO Modern Era-Retrospective analysis for Research and Applications, meteorological observational data for the territory of the former USSR for the 20th century, results of modeling by global and regional climatological models, and others are available for processing by the system. And this list is extending. Also a functionality to run WRF and "Planet simulator" models was implemented in the system. Due to many preset parameters and limited time and spatial ranges set in the system these models have low computational power requirements and could be used in educational workflow for better understanding of basic climatological and meteorological processes. The Web-GIS information-computational system for geophysical data analysis provides specialists involved into multidisciplinary research projects with reliable and practical instruments for complex analysis of climate and ecosystems changes on global and regional scales. Using it even unskilled user without specific knowledge can perform computational processing and visualization of large meteorological, climatological and satellite monitoring datasets through unified web-interface in a common graphical web-browser. This work is partially supported by the Ministry of education and science of the Russian Federation (contract #8345), SB RAS project VIII.80.2.1, RFBR grant #11-05-01190a, and integrated project SB RAS #131.

Personalization of Rule-based Web Services.

PubMed

Choi, Okkyung; Han, Sang Yong

2008-04-04

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

PLACNETw: a web-based tool for plasmid reconstruction from bacterial genomes.

PubMed

Vielva, Luis; de Toro, María; Lanza, Val F; de la Cruz, Fernando

2017-12-01

PLACNET is a graph-based tool for reconstruction of plasmids from next generation sequence pair-end datasets. PLACNET graphs contain two types of nodes (assembled contigs and reference genomes) and two types of edges (scaffold links and homology to references). Manual pruning of the graphs is a necessary requirement in PLACNET, but this is difficult for users without solid bioinformatic background. PLACNETw, a webtool based on PLACNET, provides an interactive graphic interface, automates BLAST searches, and extracts the relevant information for decision making. It allows a user with domain expertise to visualize the scaffold graphs and related information of contigs as well as reference sequences, so that the pruning operations can be done interactively from a personal computer without the need for additional tools. After successful pruning, each plasmid becomes a separate connected component subgraph. The resulting data are automatically downloaded by the user. PLACNETw is freely available at https://castillo.dicom.unican.es/upload/. delacruz@unican.es. A tutorial video and several solved examples are available at https://castillo.dicom.unican.es/placnetw_video/ and https://castillo.dicom.unican.es/examples/. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

An adaptive structure data acquisition system using a graphical-based programming language

NASA Technical Reports Server (NTRS)

Baroth, Edmund C.; Clark, Douglas J.; Losey, Robert W.

1992-01-01

An example of the implementation of data fusion using a PC and a graphical programming language is discussed. A schematic of the data acquisition system and user interface panel for an adaptive structure test are presented. The computer programs (a series of icons 'wired' together) are also discussed. The way in which using graphical-based programming software to control a data acquisition system can simplify analysis of data, promote multidisciplinary interaction, and provide users a more visual key to understanding their data are shown.

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

PubMed

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

2018-06-01

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

Computer systems and methods for the query and visualization of multidimensional databases

DOEpatents

Stolte, Chris; Tang, Diane L; Hanrahan, Patrick

2014-04-29

In response to a user request, a computer generates a graphical user interface on a computer display. A schema information region of the graphical user interface includes multiple operand names, each operand name associated with one or more fields of a multi-dimensional database. A data visualization region of the graphical user interface includes multiple shelves. Upon detecting a user selection of the operand names and a user request to associate each user-selected operand name with a respective shelf in the data visualization region, the computer generates a visual table in the data visualization region in accordance with the associations between the operand names and the corresponding shelves. The visual table includes a plurality of panes, each pane having at least one axis defined based on data for the fields associated with a respective operand name.

Computer systems and methods for the query and visualization of multidimensional databases

DOEpatents

Stolte, Chris [Palo Alto, CA; Tang, Diane L [Palo Alto, CA; Hanrahan, Patrick [Portola Valley, CA

2011-02-01

In response to a user request, a computer generates a graphical user interface on a computer display. A schema information region of the graphical user interface includes multiple operand names, each operand name associated with one or more fields of a multi-dimensional database. A data visualization region of the graphical user interface includes multiple shelves. Upon detecting a user selection of the operand names and a user request to associate each user-selected operand name with a respective shelf in the data visualization region, the computer generates a visual table in the data visualization region in accordance with the associations between the operand names and the corresponding shelves. The visual table includes a plurality of panes, each pane having at least one axis defined based on data for the fields associated with a respective operand name.

Computer systems and methods for the query and visualization of multidimensional databases

DOEpatents

Stolte, Chris [Palo Alto, CA; Tang, Diane L [Palo Alto, CA; Hanrahan, Patrick [Portola Valley, CA

2012-03-20

In response to a user request, a computer generates a graphical user interface on a computer display. A schema information region of the graphical user interface includes multiple operand names, each operand name associated with one or more fields of a multi-dimensional database. A data visualization region of the graphical user interface includes multiple shelves. Upon detecting a user selection of the operand names and a user request to associate each user-selected operand name with a respective shelf in the data visualization region, the computer generates a visual table in the data visualization region in accordance with the associations between the operand names and the corresponding shelves. The visual table includes a plurality of panes, each pane having at least one axis defined based on data for the fields associated with a respective operand name.

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

PubMed Central

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

2014-01-01

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

CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies.

PubMed

Wood, Christopher W; Bruning, Marc; Ibarra, Amaurys Á; Bartlett, Gail J; Thomson, Andrew R; Sessions, Richard B; Brady, R Leo; Woolfson, Derek N

2014-11-01

The ability to accurately model protein structures at the atomistic level underpins efforts to understand protein folding, to engineer natural proteins predictably and to design proteins de novo. Homology-based methods are well established and produce impressive results. However, these are limited to structures presented by and resolved for natural proteins. Addressing this problem more widely and deriving truly ab initio models requires mathematical descriptions for protein folds; the means to decorate these with natural, engineered or de novo sequences; and methods to score the resulting models. We present CCBuilder, a web-based application that tackles the problem for a defined but large class of protein structure, the α-helical coiled coils. CCBuilder generates coiled-coil backbones, builds side chains onto these frameworks and provides a range of metrics to measure the quality of the models. Its straightforward graphical user interface provides broad functionality that allows users to build and assess models, in which helix geometry, coiled-coil architecture and topology and protein sequence can be varied rapidly. We demonstrate the utility of CCBuilder by assembling models for 653 coiled-coil structures from the PDB, which cover >96% of the known coiled-coil types, and by generating models for rarer and de novo coiled-coil structures. CCBuilder is freely available, without registration, at http://coiledcoils.chm.bris.ac.uk/app/cc_builder/. © The Author 2014. Published by Oxford University Press.

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.

Lesion registration for longitudinal disease tracking in an imaging informatics-based multiple sclerosis eFolder

NASA Astrophysics Data System (ADS)

Ma, Kevin; Liu, Joseph; Zhang, Xuejun; Lerner, Alex; Shiroishi, Mark; Amezcua, Lilyana; Liu, Brent

2016-03-01

We have designed and developed a multiple sclerosis eFolder system for patient data storage, image viewing, and automatic lesion quantification results stored in DICOM-SR format. The web-based system aims to be integrated in DICOM-compliant clinical and research environments to aid clinicians in patient treatments and data analysis. The system needs to quantify lesion volumes, identify and register lesion locations to track shifts in volume and quantity of lesions in a longitudinal study. In order to perform lesion registration, we have developed a brain warping and normalizing methodology using Statistical Parametric Mapping (SPM) MATLAB toolkit for brain MRI. Patients' brain MR images are processed via SPM's normalization processes, and the brain images are analyzed and warped according to the tissue probability map. Lesion identification and contouring are completed by neuroradiologists, and lesion volume quantification is completed by the eFolder's CAD program. Lesion comparison results in longitudinal studies show key growth and active regions. The results display successful lesion registration and tracking over a longitudinal study. Lesion change results are graphically represented in the web-based user interface, and users are able to correlate patient progress and changes in the MRI images. The completed lesion and disease tracking tool would enable the eFolder to provide complete patient profiles, improve the efficiency of patient care, and perform comprehensive data analysis through an integrated imaging informatics system.

DeviceEditor visual biological CAD canvas

PubMed Central

2012-01-01

Background Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of combinatorial library design, design rule specification, and scar-less multi-part DNA assembly. Results We report the development and deployment of web-based bioCAD software, DeviceEditor, which provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. We demonstrate how biological designs are rendered on the DeviceEditor canvas, and we present effective visualizations of genetic component ordering and combinatorial variations within complex designs. Conclusions DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs. PMID:22373390

Clinician accessible tools for GUI computational models of transcranial electrical stimulation: BONSAI and SPHERES.

PubMed

Truong, Dennis Q; Hüber, Mathias; Xie, Xihe; Datta, Abhishek; Rahman, Asif; Parra, Lucas C; Dmochowski, Jacek P; Bikson, Marom

2014-01-01

Computational models of brain current flow during transcranial electrical stimulation (tES), including transcranial direct current stimulation (tDCS) and transcranial alternating current stimulation (tACS), are increasingly used to understand and optimize clinical trials. We propose that broad dissemination requires a simple graphical user interface (GUI) software that allows users to explore and design montages in real-time, based on their own clinical/experimental experience and objectives. We introduce two complimentary open-source platforms for this purpose: BONSAI and SPHERES. BONSAI is a web (cloud) based application (available at neuralengr.com/bonsai) that can be accessed through any flash-supported browser interface. SPHERES (available at neuralengr.com/spheres) is a stand-alone GUI application that allow consideration of arbitrary montages on a concentric sphere model by leveraging an analytical solution. These open-source tES modeling platforms are designed go be upgraded and enhanced. Trade-offs between open-access approaches that balance ease of access, speed, and flexibility are discussed. Copyright © 2014 Elsevier Inc. All rights reserved.

NASA Access Mechanism: Lessons learned document

NASA Technical Reports Server (NTRS)

Burdick, Lisa; Dunbar, Rick; Duncan, Denise; Generous, Curtis; Hunter, Judy; Lycas, John; Taber-Dudas, Ardeth

1994-01-01

The six-month beta test of the NASA Access Mechanism (NAM) prototype was completed on June 30, 1993. This report documents the lessons learned from the use of this Graphical User Interface to NASA databases such as the NASA STI Database, outside databases, Internet resources, and peers in the NASA R&D community. Design decisions, such as the use of XWindows software, a client-server distributed architecture, and use of the NASA Science Internet, are explained. Users' reactions to the interface and suggestions for design changes are reported, as are the changes made by the software developers based on new technology for information discovery and retrieval. The lessons learned section also reports reactions from the public, both at demonstrations and in response to articles in the trade press and journals. Recommendations are included for future versions, such as a World Wide Web (WWW) and Mosaic based interface to heterogeneous databases, and NAM-Lite, a version which allows customization to include utilities provided locally at NASA Centers.

QR Codes: Outlook for Food Science and Nutrition.

PubMed

Sanz-Valero, Javier; Álvarez Sabucedo, Luis M; Wanden-Berghe, Carmina; Santos Gago, Juan M

2016-01-01

QR codes opens up the possibility to develop simple-to-use, cost-effective-cost, and functional systems based on the optical recognition of inexpensive tags attached to physical objects. These systems, combined with Web platforms, can provide us with advanced services that are already currently broadly used on many contexts of the common life. Due to its philosophy, based on the automatic recognition of messages embedded on simple graphics by means of common devices such as mobile phones, QR codes are very convenient for the average user. Regretfully, its potential has not yet been fully exploited in the domains of food science and nutrition. This paper points out some applications to make the most of this technology for these domains in a straightforward manner. For its characteristics, we are addressing systems with low barriers to entry and high scalability for its deployment. Therefore, its launching among professional and final users is quite simple. The paper also provides high-level indications for the evaluation of the technological frame required to implement the identified possibilities of use.

Copyright Ownership in a Networked Multimedia Environment

NASA Technical Reports Server (NTRS)

Williams, Vernon E.

1994-01-01

The explosion of computer communications in the United States has spurred the development of many new technologies. One of these new technologies is Mosaic and the World-Wide Web. Mosaic is a user interface that uses the internet as a backbone for communications. The Mosaic interface enables a user to manipulate text, images and graphics produced by different authors. The flexibility that Mosaic offers raises significant copyright issues. This paper attempts to analyze these issues using current copyright law as a framework. The author then goes on to offer a different analysis that may result from future developments in copyright law.

Arkansas Groundwater-Quality Network

USGS Publications Warehouse

Pugh, Aaron L.; Jackson, Barry T.; Miller, Roger

2014-01-01

Arkansas is the fourth largest user of groundwater in the United States, where groundwater accounts for two-thirds of the total water use. Groundwater use in the State increased by 510 percent between 1965 and 2005 (Holland, 2007). The Arkansas Groundwater-Quality Network is a Web map interface (http://ar.water.usgs.gov/wqx) that provides rapid access to the U.S. Geological Survey’s (USGS) National Water Information System (NWIS) and the U.S. Environmental Protection Agency’s (USEPA) STOrage and RETrieval (STORET) databases of ambient water information. The interface enables users to perform simple graphical analysis and download selected water-quality data.

International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data.

PubMed

Zhang, Junjun; Baran, Joachim; Cros, A; Guberman, Jonathan M; Haider, Syed; Hsu, Jack; Liang, Yong; Rivkin, Elena; Wang, Jianxin; Whitty, Brett; Wong-Erasmus, Marie; Yao, Long; Kasprzyk, Arek

2011-01-01

The International Cancer Genome Consortium (ICGC) is a collaborative effort to characterize genomic abnormalities in 50 different cancer types. To make this data available, the ICGC has created the ICGC Data Portal. Powered by the BioMart software, the Data Portal allows each ICGC member institution to manage and maintain its own databases locally, while seamlessly presenting all the data in a single access point for users. The Data Portal currently contains data from 24 cancer projects, including ICGC, The Cancer Genome Atlas (TCGA), Johns Hopkins University, and the Tumor Sequencing Project. It consists of 3478 genomes and 13 cancer types and subtypes. Available open access data types include simple somatic mutations, copy number alterations, structural rearrangements, gene expression, microRNAs, DNA methylation and exon junctions. Additionally, simple germline variations are available as controlled access data. The Data Portal uses a web-based graphical user interface (GUI) to offer researchers multiple ways to quickly and easily search and analyze the available data. The web interface can assist in constructing complicated queries across multiple data sets. Several application programming interfaces are also available for programmatic access. Here we describe the organization, functionality, and capabilities of the ICGC Data Portal.

ExpTreeDB: web-based query and visualization of manually annotated gene expression profiling experiments of human and mouse from GEO.

PubMed

Ni, Ming; Ye, Fuqiang; Zhu, Juanjuan; Li, Zongwei; Yang, Shuai; Yang, Bite; Han, Lu; Wu, Yongge; Chen, Ying; Li, Fei; Wang, Shengqi; Bo, Xiaochen

2014-12-01

Numerous public microarray datasets are valuable resources for the scientific communities. Several online tools have made great steps to use these data by querying related datasets with users' own gene signatures or expression profiles. However, dataset annotation and result exhibition still need to be improved. ExpTreeDB is a database that allows for queries on human and mouse microarray experiments from Gene Expression Omnibus with gene signatures or profiles. Compared with similar applications, ExpTreeDB pays more attention to dataset annotations and result visualization. We introduced a multiple-level annotation system to depict and organize original experiments. For example, a tamoxifen-treated cell line experiment is hierarchically annotated as 'agent→drug→estrogen receptor antagonist→tamoxifen'. Consequently, retrieved results are exhibited by an interactive tree-structured graphics, which provide an overview for related experiments and might enlighten users on key items of interest. The database is freely available at http://biotech.bmi.ac.cn/ExpTreeDB. Web site is implemented in Perl, PHP, R, MySQL and Apache. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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.

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.

Flight Telerobotic Servicer prototype simulator

NASA Astrophysics Data System (ADS)

Schein, Rob; Krauze, Linda; Hartley, Craig; Dickenson, Alan; Lavecchia, Tom; Working, Bob

A prototype simulator for the Flight Telerobotic Servicer (FTS) system is described for use in the design development of the FTS, emphasizing the hand controller and user interface. The simulator utilizes a graphics workstation based on rapid prototyping tools for systems analyses of the use of the user interface and the hand controller. Kinematic modeling, manipulator-control algorithms, and communications programs are contained in the software for the simulator. The hardwired FTS panels and operator interface for use on the STS Orbiter are represented graphically, and the simulated controls function as the final FTS system configuration does. The robotic arm moves based on the user hand-controller interface, and the joint angles and other data are given on the prototype of the user interface. This graphics simulation tool provides the means for familiarizing crewmembers with the FTS system operation, displays, and controls.

A Configurable Internet Telemetry Server / Remote Client System

NASA Astrophysics Data System (ADS)

Boyd, W. T.; Hopkins, A.; Abbott, M. J.; Girouard, F. R.

2000-05-01

We have created a general, object-oriented software framework in Java for remote viewing of telemetry over the Internet. The general system consists of a data server and a remote client that can be extended by any project that uses telemetry to implement a remote telemetry viewer. We have implemented a system that serves live telemetry from NASA's Extreme Ultraviolet Explorer satellite and a client that can display the telemetry at a remote location. An authenticated user may run a standalone graphical or text-based client, or an applet on a web page, to view EUVE telemetry. In the case of the GUI client, a user can build displays to his/her own specifications using a GUI view-building tool. This work was supported by grants NCC2-947 and NCC2-966 from NASA Ames Research Center and grant JPL-960684 from NASA Jet Propulsion Laboratory.

STINGRAY: system for integrated genomic resources and analysis.

PubMed

Wagner, Glauber; Jardim, Rodrigo; Tschoeke, Diogo A; Loureiro, Daniel R; Ocaña, Kary A C S; Ribeiro, Antonio C B; Emmel, Vanessa E; Probst, Christian M; Pitaluga, André N; Grisard, Edmundo C; Cavalcanti, Maria C; Campos, Maria L M; Mattoso, Marta; Dávila, Alberto M R

2014-03-07

The STINGRAY system has been conceived to ease the tasks of integrating, analyzing, annotating and presenting genomic and expression data from Sanger and Next Generation Sequencing (NGS) platforms. STINGRAY includes: (a) a complete and integrated workflow (more than 20 bioinformatics tools) ranging from functional annotation to phylogeny; (b) a MySQL database schema, suitable for data integration and user access control; and (c) a user-friendly graphical web-based interface that makes the system intuitive, facilitating the tasks of data analysis and annotation. STINGRAY showed to be an easy to use and complete system for analyzing sequencing data. While both Sanger and NGS platforms are supported, the system could be faster using Sanger data, since the large NGS datasets could potentially slow down the MySQL database usage. STINGRAY is available at http://stingray.biowebdb.org and the open source code at http://sourceforge.net/projects/stingray-biowebdb/.

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

BIND: the Biomolecular Interaction Network Database

PubMed Central

Bader, Gary D.; Betel, Doron; Hogue, Christopher W. V.

2003-01-01

The Biomolecular Interaction Network Database (BIND: http://bind.ca) archives biomolecular interaction, complex and pathway information. A web-based system is available to query, view and submit records. BIND continues to grow with the addition of individual submissions as well as interaction data from the PDB and a number of large-scale interaction and complex mapping experiments using yeast two hybrid, mass spectrometry, genetic interactions and phage display. We have developed a new graphical analysis tool that provides users with a view of the domain composition of proteins in interaction and complex records to help relate functional domains to protein interactions. An interaction network clustering tool has also been developed to help focus on regions of interest. Continued input from users has helped further mature the BIND data specification, which now includes the ability to store detailed information about genetic interactions. The BIND data specification is available as ASN.1 and XML DTD. PMID:12519993

STINGRAY: system for integrated genomic resources and analysis

PubMed Central

2014-01-01

Background The STINGRAY system has been conceived to ease the tasks of integrating, analyzing, annotating and presenting genomic and expression data from Sanger and Next Generation Sequencing (NGS) platforms. Findings STINGRAY includes: (a) a complete and integrated workflow (more than 20 bioinformatics tools) ranging from functional annotation to phylogeny; (b) a MySQL database schema, suitable for data integration and user access control; and (c) a user-friendly graphical web-based interface that makes the system intuitive, facilitating the tasks of data analysis and annotation. Conclusion STINGRAY showed to be an easy to use and complete system for analyzing sequencing data. While both Sanger and NGS platforms are supported, the system could be faster using Sanger data, since the large NGS datasets could potentially slow down the MySQL database usage. STINGRAY is available at http://stingray.biowebdb.org and the open source code at http://sourceforge.net/projects/stingray-biowebdb/. PMID:24606808

Advanced Weather Awareness and Reporting Enhancements

NASA Technical Reports Server (NTRS)

Busquets, Anthony M. (Technical Monitor); Ruokangas, Corinne Clinton; Kelly, Wallace E., III

2005-01-01

AWARE (Aviation Weather Awareness and Reporting Enhancements) was a NASA Cooperative Research and Development program conducted jointly by Rockwell Scientific, Rockwell Collins, and NASA. The effort culminated in an enhanced weather briefing and reporting tool prototype designed to integrate graphical and text-based aviation weather data to provide clear situational awareness in the context of a specific pilot, flight and equipment profile. The initial implementation of AWARE was as a web-based preflight planning tool, specifically for general aviation pilots, who do not have access to support such as the dispatchers available for commercial airlines. Initial usability tests showed that for VFR (Visual Flight Rules) pilots, AWARE provided faster and more effective weather evaluation. In a subsequent formal usability test for IFR (Instrument Flight Rules) pilots, all users finished the AWARE tests faster than the parallel DUAT tests, and all subjects graded AWARE higher for effectiveness, efficiency, and usability. The decision analysis basis of AWARE differentiates it from other aviation safety programs, providing analysis of context-sensitive data in a personalized graphical format to aid pilots/dispatchers in their complex flight requirements.

The Universe Adventure - Credits

Science.gov Websites

Basel), and George Smoot (LBNL) Content, Graphic/Web Design Artie Konrad (student, UC Berkeley) 2004 Berkeley) Laurie Kerrigan (teacher, Mercy High School) Graphic/Web Design Melissa McClure (student ) Graphic/Web Design Paul Higgins (student, Contra Costa College) Other Gordon Aubrecht (Ohio State

Graphical explanation in an expert system for Space Station Freedom rack integration

NASA Technical Reports Server (NTRS)

Craig, F. G.; Cutts, D. E.; Fennel, T. R.; Purves, B.

1990-01-01

The rationale and methodology used to incorporate graphics into explanations provided by an expert system for Space Station Freedom rack integration is examined. The rack integration task is typical of a class of constraint satisfaction problems for large programs where expertise from several areas is required. Graphically oriented approaches are used to explain the conclusions made by the system, the knowledge base content, and even at more abstract levels the control strategies employed by the system. The implemented architecture combines hypermedia and inference engine capabilities. The advantages of this architecture include: closer integration of user interface, explanation system, and knowledge base; the ability to embed links to deeper knowledge underlying the compiled knowledge used in the knowledge base; and allowing for more direct control of explanation depth and duration by the user. The graphical techniques employed range from simple statis presentation of schematics to dynamic creation of a series of pictures presented motion picture style. User models control the type, amount, and order of information presented.

PanWeb: A web interface for pan-genomic analysis.

PubMed

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

2017-01-01

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

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

ERIC Educational Resources Information Center

Adebiaye, Richmond

2010-01-01

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

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

ERIC Educational Resources Information Center

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

2012-01-01

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

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

ERIC Educational Resources Information Center

Gupta, Naman K.; Penstein Rosé, Carolyn

2010-01-01

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

Lamprey: tracking users on the World Wide Web.

PubMed

Felciano, R M; Altman, R B

1996-01-01

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

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

PubMed

Galpern, N F; Albert, K M

1997-01-01

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

A general graphical user interface for automatic reliability modeling

NASA Technical Reports Server (NTRS)

Liceaga, Carlos A.; Siewiorek, Daniel P.

1991-01-01

Reported here is a general Graphical User Interface (GUI) for automatic reliability modeling of Processor Memory Switch (PMS) structures using a Markov model. This GUI is based on a hierarchy of windows. One window has graphical editing capabilities for specifying the system's communication structure, hierarchy, reconfiguration capabilities, and requirements. Other windows have field texts, popup menus, and buttons for specifying parameters and selecting actions. An example application of the GUI is given.

Exploring Physics with Computer Animation and PhysGL

NASA Astrophysics Data System (ADS)

Bensky, T. J.

2016-10-01

This book shows how the web-based PhysGL programming environment (http://physgl.org) can be used to teach and learn elementary mechanics (physics) using simple coding exercises. The book's theme is that the lessons encountered in such a course can be used to generate physics-based animations, providing students with compelling and self-made visuals to aid their learning. Topics presented are parallel to those found in a traditional physics text, making for straightforward integration into a typical lecture-based physics course. Users will appreciate the ease at which compelling OpenGL-based graphics and animations can be produced using PhysGL, as well as its clean, simple language constructs. The author argues that coding should be a standard part of lower-division STEM courses, and provides many anecdotal experiences and observations, that include observed benefits of the coding work.

Computerised patient record with distributed objects.

PubMed

Gornik, T; Orel, A; Roblek, D; Verhovsek, R

1999-01-01

The vast spectrum of information and functionality requirements imposed on a Computerised Patient Record (CPR), fueled by an ever changing and expanding business model demands information system interoperability. The management of information, created across the continuum of care, and associated information system functionality, can not be provided by data interchange to and from monolithic applications. WebDoctor is a Computerised Patient Record (CPR) which is fully used at the Institute of Oncology in Ljubljana, Slovenia--a hospital with 500 beds and more than 200 users, all of them medical professionals. The data are stored in an underlying Oracle hospital data base. For logging the username and password security is used. WebDoctor uses Internationalization APIs. Currently GUI is currently written in Slovenian language, but can be easily adapted to any other language. It is available in either Metal or Windows look. Search for patients is based on CPR No. or partial data from demographics. All the available patients data can be found on a single screen divided into several tab sections. The tab sections cover general and speciality data. The general data include demographics, admissions and diagnoses, meanwhile the speciality data are divided into Labs where data are represented numerically by date or by type and graphically with the ability of detailed view in separate window, Radiology where results are represented in textual form as well as pictures together with a special viewer to provide detailed analyses and Radioisotopes where results are also being represented in textual form together with a graphical representation. WebDoctor is running on virtually any platform. It achieved the 100% Java Certification which places the application among the firsts if not the first of this kind in the healthcare industry. It excels with a small and light client which doesn't exceed the 150K.

Comparing Text-based and Graphic User Interfaces for Novice and Expert Users

PubMed Central

Chen, Jung-Wei; Zhang, Jiajie

2007-01-01

Graphic User Interface (GUI) is commonly considered to be superior to Text-based User Interface (TUI). This study compares GUI and TUI in an electronic dental record system. Several usability analysis techniques compared the relative effectiveness of a GUI and a TUI. Expert users and novice users were evaluated in time required and steps needed to complete the task. A within-subject design was used to evaluate if the experience with either interface will affect task performance. The results show that the GUI interface was not better than the TUI for expert users. GUI interface was better for novice users. For novice users there was a learning transfer effect from TUI to GUI. This means a user interface is user-friendly or not depending on the mapping between the user interface and tasks. GUI by itself may or may not be better than TUI. PMID:18693811

Comparing Text-based and Graphic User Interfaces for novice and expert users.

PubMed

Chen, Jung-Wei; Zhang, Jiajie

2007-10-11

Graphic User Interface (GUI) is commonly considered to be superior to Text-based User Interface (TUI). This study compares GUI and TUI in an electronic dental record system. Several usability analysis techniques compared the relative effectiveness of a GUI and a TUI. Expert users and novice users were evaluated in time required and steps needed to complete the task. A within-subject design was used to evaluate if the experience with either interface will affect task performance. The results show that the GUI interface was not better than the TUI for expert users. GUI interface was better for novice users. For novice users there was a learning transfer effect from TUI to GUI. This means a user interface is user-friendly or not depending on the mapping between the user interface and tasks. GUI by itself may or may not be better than TUI.

ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser

PubMed Central

Almeida, Jonas S.; Iriabho, Egiebade E.; Gorrepati, Vijaya L.; Wilkinson, Sean R.; Grüneberg, Alexander; Robbins, David E.; Hackney, James R.

2012-01-01

Background: Image bioinformatics infrastructure typically relies on a combination of server-side high-performance computing and client desktop applications tailored for graphic rendering. On the server side, matrix manipulation environments are often used as the back-end where deployment of specialized analytical workflows takes place. However, neither the server-side nor the client-side desktop solution, by themselves or combined, is conducive to the emergence of open, collaborative, computational ecosystems for image analysis that are both self-sustained and user driven. Materials and Methods: ImageJS was developed as a browser-based webApp, untethered from a server-side backend, by making use of recent advances in the modern web browser such as a very efficient compiler, high-end graphical rendering capabilities, and I/O tailored for code migration. Results: Multiple versioned code hosting services were used to develop distinct ImageJS modules to illustrate its amenability to collaborative deployment without compromise of reproducibility or provenance. The illustrative examples include modules for image segmentation, feature extraction, and filtering. The deployment of image analysis by code migration is in sharp contrast with the more conventional, heavier, and less safe reliance on data transfer. Accordingly, code and data are loaded into the browser by exactly the same script tag loading mechanism, which offers a number of interesting applications that would be hard to attain with more conventional platforms, such as NIH's popular ImageJ application. Conclusions: The modern web browser was found to be advantageous for image bioinformatics in both the research and clinical environments. This conclusion reflects advantages in deployment scalability and analysis reproducibility, as well as the critical ability to deliver advanced computational statistical procedures machines where access to sensitive data is controlled, that is, without local “download and installation”. PMID:22934238

ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser.

PubMed

Almeida, Jonas S; Iriabho, Egiebade E; Gorrepati, Vijaya L; Wilkinson, Sean R; Grüneberg, Alexander; Robbins, David E; Hackney, James R

2012-01-01

Image bioinformatics infrastructure typically relies on a combination of server-side high-performance computing and client desktop applications tailored for graphic rendering. On the server side, matrix manipulation environments are often used as the back-end where deployment of specialized analytical workflows takes place. However, neither the server-side nor the client-side desktop solution, by themselves or combined, is conducive to the emergence of open, collaborative, computational ecosystems for image analysis that are both self-sustained and user driven. ImageJS was developed as a browser-based webApp, untethered from a server-side backend, by making use of recent advances in the modern web browser such as a very efficient compiler, high-end graphical rendering capabilities, and I/O tailored for code migration. Multiple versioned code hosting services were used to develop distinct ImageJS modules to illustrate its amenability to collaborative deployment without compromise of reproducibility or provenance. The illustrative examples include modules for image segmentation, feature extraction, and filtering. The deployment of image analysis by code migration is in sharp contrast with the more conventional, heavier, and less safe reliance on data transfer. Accordingly, code and data are loaded into the browser by exactly the same script tag loading mechanism, which offers a number of interesting applications that would be hard to attain with more conventional platforms, such as NIH's popular ImageJ application. The modern web browser was found to be advantageous for image bioinformatics in both the research and clinical environments. This conclusion reflects advantages in deployment scalability and analysis reproducibility, as well as the critical ability to deliver advanced computational statistical procedures machines where access to sensitive data is controlled, that is, without local "download and installation".

Distributed usability evaluation of the Pennsylvania Cancer Atlas

PubMed Central

Bhowmick, Tanuka; Robinson, Anthony C; Gruver, Adrienne; MacEachren, Alan M; Lengerich, Eugene J

2008-01-01

Background The Pennsylvania Cancer Atlas (PA-CA) is an interactive online atlas to help policy-makers, program managers, and epidemiologists with tasks related to cancer prevention and control. The PA-CA includes maps, graphs, tables, that are dynamically linked to support data exploration and decision-making with spatio-temporal cancer data. Our Atlas development process follows a user-centered design approach. To assess the usability of the initial versions of the PA-CA, we developed and applied a novel strategy for soliciting user feedback through multiple distributed focus groups and surveys. Our process of acquiring user feedback leverages an online web application (e-Delphi). In this paper we describe the PA-CA, detail how we have adapted e-Delphi web application to support usability and utility evaluation of the PA-CA, and present the results of our evaluation. Results We report results from four sets of users. Each group provided structured individual and group assessments of the PA-CA as well as input on the kinds of users and applications for which it is best suited. Overall reactions to the PA-CA are quite positive. Participants did, however, provide a range of useful suggestions. Key suggestions focused on improving interaction functions, enhancing methods of temporal analysis, addressing data issues, and providing additional data displays and help functions. These suggestions were incorporated in each design and implementation iteration for the PA-CA and used to inform a set of web-atlas design principles. Conclusion For the Atlas, we find that a design that utilizes linked map, graph, and table views is understandable to and perceived to be useful by the target audience of cancer prevention and control professionals. However, it is clear that considerable variation in experience using maps and graphics exists and for those with less experience, integrated tutorials and help features are needed. In relation to our usability assessment strategy, we find that our distributed, web-based method for soliciting user input is generally effective. Advantages include the ability to gather information from users distributed in time and space and the relative anonymity of the participants while disadvantages include less control over when and how often participants provide input and challenges for obtaining rich input. PMID:18620565

GeneXplorer: an interactive web application for microarray data visualization and analysis.

PubMed

Rees, Christian A; Demeter, Janos; Matese, John C; Botstein, David; Sherlock, Gavin

2004-10-01

When publishing large-scale microarray datasets, it is of great value to create supplemental websites where either the full data, or selected subsets corresponding to figures within the paper, can be browsed. We set out to create a CGI application containing many of the features of some of the existing standalone software for the visualization of clustered microarray data. We present GeneXplorer, a web application for interactive microarray data visualization and analysis in a web environment. GeneXplorer allows users to browse a microarray dataset in an intuitive fashion. It provides simple access to microarray data over the Internet and uses only HTML and JavaScript to display graphic and annotation information. It provides radar and zoom views of the data, allows display of the nearest neighbors to a gene expression vector based on their Pearson correlations and provides the ability to search gene annotation fields. The software is released under the permissive MIT Open Source license, and the complete documentation and the entire source code are freely available for download from CPAN http://search.cpan.org/dist/Microarray-GeneXplorer/.

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

PubMed

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

2013-12-15

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

gemcWeb: A Cloud Based Nuclear Physics Simulation Software

NASA Astrophysics Data System (ADS)

Markelon, Sam

2017-09-01

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

Web party effect: a cocktail party effect in the web environment

PubMed Central

Gerbino, Walter

2015-01-01

In goal-directed web navigation, labels compete for selection: this process often involves knowledge integration and requires selective attention to manage the dizziness of web layouts. Here we ask whether the competition for selection depends on all web navigation options or only on those options that are more likely to be useful for information seeking, and provide evidence in favor of the latter alternative. Participants in our experiment navigated a representative set of real websites of variable complexity, in order to reach an information goal located two clicks away from the starting home page. The time needed to reach the goal was accounted for by a novel measure of home page complexity based on a part of (not all) web options: the number of links embedded within web navigation elements weighted by the number and type of embedding elements. Our measure fully mediated the effect of several standard complexity metrics (the overall number of links, words, images, graphical regions, the JPEG file size of home page screenshots) on information seeking time and usability ratings. Furthermore, it predicted the cognitive demand of web navigation, as revealed by the duration judgment ratio (i.e., the ratio of subjective to objective duration of information search). Results demonstrate that focusing on relevant links while ignoring other web objects optimizes the deployment of attentional resources necessary to navigation. This is in line with a web party effect (i.e., a cocktail party effect in the web environment): users tune into web elements that are relevant for the achievement of their navigation goals and tune out all others. PMID:25802803

Web party effect: a cocktail party effect in the web environment.

PubMed

Rigutti, Sara; Fantoni, Carlo; Gerbino, Walter

2015-01-01

In goal-directed web navigation, labels compete for selection: this process often involves knowledge integration and requires selective attention to manage the dizziness of web layouts. Here we ask whether the competition for selection depends on all web navigation options or only on those options that are more likely to be useful for information seeking, and provide evidence in favor of the latter alternative. Participants in our experiment navigated a representative set of real websites of variable complexity, in order to reach an information goal located two clicks away from the starting home page. The time needed to reach the goal was accounted for by a novel measure of home page complexity based on a part of (not all) web options: the number of links embedded within web navigation elements weighted by the number and type of embedding elements. Our measure fully mediated the effect of several standard complexity metrics (the overall number of links, words, images, graphical regions, the JPEG file size of home page screenshots) on information seeking time and usability ratings. Furthermore, it predicted the cognitive demand of web navigation, as revealed by the duration judgment ratio (i.e., the ratio of subjective to objective duration of information search). Results demonstrate that focusing on relevant links while ignoring other web objects optimizes the deployment of attentional resources necessary to navigation. This is in line with a web party effect (i.e., a cocktail party effect in the web environment): users tune into web elements that are relevant for the achievement of their navigation goals and tune out all others.

Enabling Discoveries in Earth Sciences Through the Geosciences Network (GEON)

NASA Astrophysics Data System (ADS)

Seber, D.; Baru, C.; Memon, A.; Lin, K.; Youn, C.

2005-12-01

Taking advantage of the state-of-the-art information technology resources GEON researchers are building a cyberinfrastructure designed to enable data sharing, semantic data integration, high-end computations and 4D visualization in easy-to-use web-based environments. The GEON Network currently allows users to search and register Earth science resources such as data sets (GIS layers, GMT files, geoTIFF images, ASCII files, relational databases etc), software applications or ontologies. Portal based access mechanisms enable developers to built dynamic user interfaces to conduct advanced processing and modeling efforts across distributed computers and supercomputers. Researchers and educators can access the networked resources through the GEON portal and its portlets that were developed to conduct better and more comprehensive science and educational studies. For example, the SYNSEIS portlet in GEON enables users to access in near-real time seismic waveforms from the IRIS Data Management Center, easily build a 3D geologic model within the area of the seismic station(s) and the epicenter and perform a 3D synthetic seismogram analysis to understand the lithospheric structure and earthquake source parameters for any given earthquake in the US. Similarly, GEON's workbench area enables users to create their own work environment and copy, visualize and analyze any data sets within the network, and create subsets of the data sets for their own purposes. Since all these resources are built as part of a Service-oriented Architecture (SOA), they are also used in other development platforms. One such platform is Kepler Workflow system which can access web service based resources and provides users with graphical programming interfaces to build a model to conduct computations and/or visualization efforts using the networked resources. Developments in the area of semantic integration of the networked datasets continue to advance and prototype studies can be accessed via the GEON portal at www.geongrid.org

A coastal information system to propel emerging science and ...

EPA Pesticide Factsheets

The Estuary Data Mapper (EDM) is a free, interactive virtual gateway to coastal data aimed to promote research and aid in environmental management. The graphical user interface allows users to custom select and subset data based on their spatial and temporal interests giving them easy access to visualize, retrieve, and save data for further analysis. Data are accessible across estuarine systems of the Atlantic, Gulf of Mexico and Pacific regions of the United States and includes: (1) time series data including tidal, hydrologic, and weather, (2) water and sediment quality, (3) atmospheric deposition, (4) habitat, (5) coastal exposure indices, (6) historic and projected land-use and population, (7) historic and projected nitrogen and phosphorous sources and load summaries. EDM issues Web Coverage Service Interface Standard queries (WCS; simple, standard one-line text strings) to a public web service to quickly obtain data subsets by variable, for a date-time range and area selected by user. EDM is continuously being enhanced with updated data and new options. Recent additions include a comprehensive suite of nitrogen source and loading data, and inputs for supporting a modeling approach of seagrass habitat. Additions planned for the near future include 1) support for Integrated Water Resources Management cost-benefit analysis, specifically the Watershed Management Optimization Support Tool and 2) visualization of the combined effects of climate change, land-use a

Estuary Data Mapper: A coastal information system to propel ...

EPA Pesticide Factsheets

The Estuary Data Mapper (EDM) is a free, interactive virtual gateway to coastal data aimed to promote research and aid in environmental management. The graphical user interface allows users to custom select and subset data based on their spatial and temporal interests giving them easy access to visualize, retrieve, and save data for further analysis. Data are accessible across estuarine systems of the Atlantic, Gulf of Mexico and Pacific regions of the United States and includes: (1) time series data including tidal, hydrologic, and weather, (2) water and sediment quality, (3) atmospheric deposition, (4) habitat, (5) coastal exposure indices, (6) historic and projected land-use and population, (7) historic and projected nitrogen and phosphorous sources and load summaries. EDM issues Web Coverage Service Interface Standard queries (WCS; simple, standard one-line text strings) to a public web service to quickly obtain data subsets by variable, for a date-time range and area selected by user. EDM is continuously being enhanced with updated data and new options. Recent additions include a comprehensive suite of nitrogen source and loading data, and inputs for supporting a modeling approach of seagrass habitat. Additions planned for the near future include 1) support for Integrated Water Resources Management cost-benefit analysis, specifically the Watershed Management Optimization Support Tool and 2) visualization of the combined effects of climate change, land-use a

Empirical analysis of web-based user-object bipartite networks

NASA Astrophysics Data System (ADS)

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

2010-05-01

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

Advanced Visualization and Interactive Display Rapid Innovation and Discovery Evaluation Research Program task 8: Survey of WEBGL Graphics Engines

DTIC Science & Technology

2015-01-01

1 3.0 Methods, Assumptions, and Procedures ...18 4.6.3. LineUp Web... Procedures A search of the internet looking at web sites specializing in graphics, graphics engines, web browser applications, and games was conducted to

A Digital Badging Dataset Focused on Performance, Engagement and Behavior-Related Variables from Observations in Web-Based University Courses

ERIC Educational Resources Information Center

McDaniel, Rudy; Fanfarelli, Joseph R.

2015-01-01

This dataset contains participant data related to the use of badging (achievement) feedback in pedagogical design. Two sections each of web-based graphic design and web design undergraduate courses were offered at the University of Central Florida. A badging system for achievements was included in one section of each. Performance, engagement and…

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

PubMed

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

2015-01-02

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

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…

ddpcr: an R package and web application for analysis of droplet digital PCR data.

PubMed

Attali, Dean; Bidshahri, Roza; Haynes, Charles; Bryan, Jennifer

2016-01-01

Droplet digital polymerase chain reaction (ddPCR) is a novel platform for exact quantification of DNA which holds great promise in clinical diagnostics. It is increasingly popular due to its digital nature, which provides more accurate quantification and higher sensitivity than traditional real-time PCR. However, clinical adoption has been slowed in part by the lack of software tools available for analyzing ddPCR data. Here, we present ddpcr - a new R package for ddPCR visualization and analysis. In addition, ddpcr includes a web application (powered by the Shiny R package) that allows users to analyze ddPCR data using an interactive graphical interface.

An Open Source Graphical User Interface Surrogate C2 System for Battle Management Language Experimentation

DTIC Science & Technology

2011-06-01

file –  Open source at http://c4i.gmu.edu/BML 10 BMLC2GUI ICCRTS’11-175 BML C2 GUI Scripted BML Web Service v2 09F- SIW -015 11 ! BML C2...BMLC2GUI ICCRTS’11-175 17 Publish/Subscribe Architecture BMLC2GUI ICCRTS’11-175 SBML in NATO MSG-048 •  Paper 10S- SIW -049 describes a significant...from C2LG GUI: –  Open resource –  Quick response to changes –  Ease of use –  Low development cost Scripted BML Web Service v2 09F- SIW -015

Unified Desktop for Monitoring & Control Applications - The Open Navigator Framework Applied for Control Centre and EGSE Applications

NASA Astrophysics Data System (ADS)

Brauer, U.

2007-08-01

The Open Navigator Framework (ONF) was developed to provide a unified and scalable platform for user interface integration. The main objective for the framework was to raise usability of monitoring and control consoles and to provide a reuse of software components in different application areas. ONF is currently applied for the Columbus onboard crew interface, the commanding application for the Columbus Control Centre, the Columbus user facilities specialized user interfaces, the Mission Execution Crew Assistant (MECA) study and EADS Astrium internal R&D projects. ONF provides a well documented and proven middleware for GUI components (Java plugin interface, simplified concept similar to Eclipse). The overall application configuration is performed within a graphical user interface for layout and component selection. The end-user does not have to work in the underlying XML configuration files. ONF was optimized to provide harmonized user interfaces for monitoring and command consoles. It provides many convenience functions designed together with flight controllers and onboard crew: user defined workspaces, incl. support for multi screens efficient communication mechanism between the components integrated web browsing and documentation search &viewing consistent and integrated menus and shortcuts common logging and application configuration (properties) supervision interface for remote plugin GUI access (web based) A large number of operationally proven ONF components have been developed: Command Stack & History: Release of commands and follow up the command acknowledges System Message Panel: Browse, filter and search system messages/events Unified Synoptic System: Generic synoptic display system Situational Awareness : Show overall subsystem status based on monitoring of key parameters System Model Browser: Browse mission database defintions (measurements, commands, events) Flight Procedure Executor: Execute checklist and logical flow interactive procedures Web Browser : Integrated browser reference documentation and operations data Timeline Viewer: View master timeline as Gantt chart Search: Local search of operations products (e.g. documentation, procedures, displays) All GUI components access the underlying spacecraft data (commanding, reporting data, events, command history) via a common library providing adaptors for the current deployments (Columbus MCS, Columbus onboard Data Management System, Columbus Trainer raw packet protocol). New Adaptors are easy to develop. Currently an adaptor to SCOS 2000 is developed as part of a study for the ESTEC standardization section ("USS for ESTEC Reference Facility").

WMT: The CSDMS Web Modeling Tool

NASA Astrophysics Data System (ADS)

Piper, M.; Hutton, E. W. H.; Overeem, I.; Syvitski, J. P.

2015-12-01

The Community Surface Dynamics Modeling System (CSDMS) has a mission to enable model use and development for research in earth surface processes. CSDMS strives to expand the use of quantitative modeling techniques, promotes best practices in coding, and advocates for the use of open-source software. To streamline and standardize access to models, CSDMS has developed the Web Modeling Tool (WMT), a RESTful web application with a client-side graphical interface and a server-side database and API that allows users to build coupled surface dynamics models in a web browser on a personal computer or a mobile device, and run them in a high-performance computing (HPC) environment. With WMT, users can: Design a model from a set of components Edit component parameters Save models to a web-accessible server Share saved models with the community Submit runs to an HPC system Download simulation results The WMT client is an Ajax application written in Java with GWT, which allows developers to employ object-oriented design principles and development tools such as Ant, Eclipse and JUnit. For deployment on the web, the GWT compiler translates Java code to optimized and obfuscated JavaScript. The WMT client is supported on Firefox, Chrome, Safari, and Internet Explorer. The WMT server, written in Python and SQLite, is a layered system, with each layer exposing a web service API: wmt-db: database of component, model, and simulation metadata and output wmt-api: configure and connect components wmt-exe: launch simulations on remote execution servers The database server provides, as JSON-encoded messages, the metadata for users to couple model components, including descriptions of component exchange items, uses and provides ports, and input parameters. Execution servers are network-accessible computational resources, ranging from HPC systems to desktop computers, containing the CSDMS software stack for running a simulation. Once a simulation completes, its output, in NetCDF, is packaged and uploaded to a data server where it is stored and from which a user can download it as a single compressed archive file.

Systems Engineering Model and Training Application for Desktop Environment

NASA Technical Reports Server (NTRS)

May, Jeffrey T.

2010-01-01

Provide a graphical user interface based simulator for desktop training, operations and procedure development and system reference. This simulator allows for engineers to train and further understand the dynamics of their system from their local desktops. It allows the users to train and evaluate their system at a pace and skill level based on the user's competency and from a perspective based on the user's need. The simulator will not require any special resources to execute and should generally be available for use. The interface is based on a concept of presenting the model of the system in ways that best suits the user's application or training needs. The three levels of views are Component View, the System View (overall system), and the Console View (monitor). These views are portals into a single model, so changing the model from one view or from a model manager Graphical User Interface will be reflected on all other views.

WebTOP: A 3D Interactive System for Teaching and Learning Optics

ERIC Educational Resources Information Center

Mzoughi, Taha; Herring, S. Davis; Foley, John T.; Morris, Matthew J.; Gilbert, Peter J.

2007-01-01

WebTOP is a three-dimensional, Web-based, interactive computer graphics system that helps instructors teach and students learn about waves and optics. Current subject areas include waves, geometrical optics, reflection and refraction, polarization, interference, diffraction, lasers, and scattering. Some of the topics covered are suited for…

Mfold web server for nucleic acid folding and hybridization prediction

PubMed Central

Zuker, Michael

2003-01-01

The abbreviated name, ‘mfold web server’, describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software. Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and ‘energy dot plots’, are available for the folding of single sequences. A variety of ‘bulk’ servers give less information, but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as ‘MFOLDROOT’. PMID:12824337

Managing research and surveillance projects in real-time with a novel open-source eManagement tool designed for under-resourced countries.

PubMed

Steiner, Andreas; Hella, Jerry; Grüninger, Servan; Mhalu, Grace; Mhimbira, Francis; Cercamondi, Colin I; Doulla, Basra; Maire, Nicolas; Fenner, Lukas

2016-09-01

A software tool is developed to facilitate data entry and to monitor research projects in under-resourced countries in real-time. The eManagement tool "odk_planner" is written in the scripting languages PHP and Python. The odk_planner is lightweight and uses minimal internet resources. It was designed to be used with the open source software Open Data Kit (ODK). The users can easily configure odk_planner to meet their needs, and the online interface displays data collected from ODK forms in a graphically informative way. The odk_planner also allows users to upload pictures and laboratory results and sends text messages automatically. User-defined access rights protect data and privacy. We present examples from four field applications in Tanzania successfully using the eManagement tool: 1) clinical trial; 2) longitudinal Tuberculosis (TB) Cohort Study with a complex visit schedule, where it was used to graphically display missing case report forms, upload digitalized X-rays, and send text message reminders to patients; 3) intervention study to improve TB case detection, carried out at pharmacies: a tablet-based electronic referral system monitored referred patients, and sent automated messages to remind pharmacy clients to visit a TB Clinic; and 4) TB retreatment case monitoring designed to improve drug resistance surveillance: clinicians at four public TB clinics and lab technicians at the TB reference laboratory used a smartphone-based application that tracked sputum samples, and collected clinical and laboratory data. The user friendly, open source odk_planner is a simple, but multi-functional, Web-based eManagement tool with add-ons that helps researchers conduct studies in under-resourced countries. © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

X based interactive computer graphics applications for aerodynamic design and education

NASA Technical Reports Server (NTRS)

Benson, Thomas J.; Higgs, C. Fred, III

1995-01-01

Six computer applications packages have been developed to solve a variety of aerodynamic problems in an interactive environment on a single workstation. The packages perform classical one dimensional analysis under the control of a graphical user interface and can be used for preliminary design or educational purposes. The programs were originally developed on a Silicon Graphics workstation and used the GL version of the FORMS library as the graphical user interface. These programs have recently been converted to the XFORMS library of X based graphics widgets and have been tested on SGI, IBM, Sun, HP and PC-Lunix computers. The paper will show results from the new VU-DUCT program as a prime example. VU-DUCT has been developed as an educational package for the study of subsonic open and closed loop wind tunnels.

Distributed 3D Information Visualization - Towards Integration of the Dynamic 3D Graphics and Web Services

NASA Astrophysics Data System (ADS)

Vucinic, Dean; Deen, Danny; Oanta, Emil; Batarilo, Zvonimir; Lacor, Chris

This paper focuses on visualization and manipulation of graphical content in distributed network environments. The developed graphical middleware and 3D desktop prototypes were specialized for situational awareness. This research was done in the LArge Scale COllaborative decision support Technology (LASCOT) project, which explored and combined software technologies to support human-centred decision support system for crisis management (earthquake, tsunami, flooding, airplane or oil-tanker incidents, chemical, radio-active or other pollutants spreading, etc.). The performed state-of-the-art review did not identify any publicly available large scale distributed application of this kind. Existing proprietary solutions rely on the conventional technologies and 2D representations. Our challenge was to apply the "latest" available technologies, such Java3D, X3D and SOAP, compatible with average computer graphics hardware. The selected technologies are integrated and we demonstrate: the flow of data, which originates from heterogeneous data sources; interoperability across different operating systems and 3D visual representations to enhance the end-users interactions.

Web-Based Learning in the Computer-Aided Design Curriculum.

ERIC Educational Resources Information Center

Sung, Wen-Tsai; Ou, S. C.

2002-01-01

Applies principles of constructivism and virtual reality (VR) to computer-aided design (CAD) curriculum, particularly engineering, by integrating network, VR and CAD technologies into a Web-based learning environment that expands traditional two-dimensional computer graphics into a three-dimensional real-time simulation that enhances user…

A web portal for hydrodynamical, cosmological simulations

NASA Astrophysics Data System (ADS)

Ragagnin, A.; Dolag, K.; Biffi, V.; Cadolle Bel, M.; Hammer, N. J.; Krukau, A.; Petkova, M.; Steinborn, D.

2017-07-01

This article describes a data centre hosting a web portal for accessing and sharing the output of large, cosmological, hydro-dynamical simulations with a broad scientific community. It also allows users to receive related scientific data products by directly processing the raw simulation data on a remote computing cluster. The data centre has a multi-layer structure: a web portal, a job control layer, a computing cluster and a HPC storage system. The outer layer enables users to choose an object from the simulations. Objects can be selected by visually inspecting 2D maps of the simulation data, by performing highly compounded and elaborated queries or graphically by plotting arbitrary combinations of properties. The user can run analysis tools on a chosen object. These services allow users to run analysis tools on the raw simulation data. The job control layer is responsible for handling and performing the analysis jobs, which are executed on a computing cluster. The innermost layer is formed by a HPC storage system which hosts the large, raw simulation data. The following services are available for the users: (I) CLUSTERINSPECT visualizes properties of member galaxies of a selected galaxy cluster; (II) SIMCUT returns the raw data of a sub-volume around a selected object from a simulation, containing all the original, hydro-dynamical quantities; (III) SMAC creates idealized 2D maps of various, physical quantities and observables of a selected object; (IV) PHOX generates virtual X-ray observations with specifications of various current and upcoming instruments.

Lightweight application for generating clinical research information systems: MAGIC.

PubMed

Leskošek, Brane; Pajntar, Marjan

2015-12-01

Our purpose was to build and test a lightweight solution for generating clinical research information systems (CRIS) that would allow non-IT professionals with basic knowledge of computer usage to quickly define and build a ready-to-use, safe and secure web-based clinical research system for data management. We use the acronym MAGIC (Medical Application Generator InteraCtive) for the system. The generated CRIS should be very easy to build and use, so a common LAMP (Linux Apache MySQL Perl) platform was used, which also enables short development cycles. The application was built and tested using eXtreme Programming (XP) principles by a small development team consisting of one informatics specialist, one physician and one graphical designer/programmer. The parameter and graphical user interface (GUI) definitions for the CRIS can be made by non-IT professionals using an intuitive English-language-like formalism called application definition language (ADL). From these definitions, the MAGIC builds an end-user CRIS that can be used on a wide variety of platforms (from standard workstations to hand-held devices). A working example of a national health-care-quality assessment program is presented to illustrate this process. The lightweight application for generating CRIS (MAGIC) has proven to be useful for both clinical and analytical users in real working environment. To achieve better performance and interoperability, we are planning to recompile the application using XML schemas (XSD) in HL7 CDA or openEHR archetypes formats used for parameters definition and for data interchange between different information systems.

LookSeq: a browser-based viewer for deep sequencing data.

PubMed

Manske, Heinrich Magnus; Kwiatkowski, Dominic P

2009-11-01

Sequencing a genome to great depth can be highly informative about heterogeneity within an individual or a population. Here we address the problem of how to visualize the multiple layers of information contained in deep sequencing data. We propose an interactive AJAX-based web viewer for browsing large data sets of aligned sequence reads. By enabling seamless browsing and fast zooming, the LookSeq program assists the user to assimilate information at different levels of resolution, from an overview of a genomic region to fine details such as heterogeneity within the sample. A specific problem, particularly if the sample is heterogeneous, is how to depict information about structural variation. LookSeq provides a simple graphical representation of paired sequence reads that is more revealing about potential insertions and deletions than are conventional methods.

Developing Web Services for Technology Education. The Graphic Communication Electronic Publishing Project.

ERIC Educational Resources Information Center

Sanders, Mark

1999-01-01

Graphic Communication Electronic Publishing Project supports a Web site (http://TechEd.vt.edu/gcc/) for graphic communication teachers and students, providing links to Web materials, conversion of print materials to electronic formats, and electronic products and services including job listings, resume posting service, and a listserv. (SK)

MuffinInfo: HTML5-Based Statistics Extractor from Next-Generation Sequencing Data.

PubMed

Alic, Andy S; Blanquer, Ignacio

2016-09-01

Usually, the information known a priori about a newly sequenced organism is limited. Even resequencing the same organism can generate unpredictable output. We introduce MuffinInfo, a FastQ/Fasta/SAM information extractor implemented in HTML5 capable of offering insights into next-generation sequencing (NGS) data. Our new tool can run on any software or hardware environment, in command line or graphically, and in browser or standalone. It presents information such as average length, base distribution, quality scores distribution, k-mer histogram, and homopolymers analysis. MuffinInfo improves upon the existing extractors by adding the ability to save and then reload the results obtained after a run as a navigable file (also supporting saving pictures of the charts), by supporting custom statistics implemented by the user, and by offering user-adjustable parameters involved in the processing, all in one software. At the moment, the extractor works with all base space technologies such as Illumina, Roche, Ion Torrent, Pacific Biosciences, and Oxford Nanopore. Owing to HTML5, our software demonstrates the readiness of web technologies for mild intensive tasks encountered in bioinformatics.

In silico modeling for tumor growth visualization.

PubMed

Jeanquartier, Fleur; Jean-Quartier, Claire; Cemernek, David; Holzinger, Andreas

2016-08-08

Cancer is a complex disease. Fundamental cellular based studies as well as modeling provides insight into cancer biology and strategies to treatment of the disease. In silico models complement in vivo models. Research on tumor growth involves a plethora of models each emphasizing isolated aspects of benign and malignant neoplasms. Biologists and clinical scientists are often overwhelmed by the mathematical background knowledge necessary to grasp and to apply a model to their own research. We aim to provide a comprehensive and expandable simulation tool to visualizing tumor growth. This novel Web-based application offers the advantage of a user-friendly graphical interface with several manipulable input variables to correlate different aspects of tumor growth. By refining model parameters we highlight the significance of heterogeneous intercellular interactions on tumor progression. Within this paper we present the implementation of the Cellular Potts Model graphically presented through Cytoscape.js within a Web application. The tool is available under the MIT license at https://github.com/davcem/cpm-cytoscape and http://styx.cgv.tugraz.at:8080/cpm-cytoscape/ . In-silico methods overcome the lack of wet experimental possibilities and as dry method succeed in terms of reduction, refinement and replacement of animal experimentation, also known as the 3R principles. Our visualization approach to simulation allows for more flexible usage and easy extension to facilitate understanding and gain novel insight. We believe that biomedical research in general and research on tumor growth in particular will benefit from the systems biology perspective.

"One-Stop Shopping" for Ocean Remote-Sensing and Model Data

NASA Technical Reports Server (NTRS)

Li, P. Peggy; Vu, Quoc; Chao, Yi; Li, Zhi-Jin; Choi, Jei-Kook

2006-01-01

OurOcean Portal 2.0 (http:// ourocean.jpl.nasa.gov) is a software system designed to enable users to easily gain access to ocean observation data, both remote-sensing and in-situ, configure and run an Ocean Model with observation data assimilated on a remote computer, and visualize both the observation data and the model outputs. At present, the observation data and models focus on the California coastal regions and Prince William Sound in Alaska. This system can be used to perform both real-time and retrospective analyses of remote-sensing data and model outputs. OurOcean Portal 2.0 incorporates state-of-the-art information technologies (IT) such as MySQL database, Java Web Server (Apache/Tomcat), Live Access Server (LAS), interactive graphics with Java Applet at the Client site and MatLab/GMT at the server site, and distributed computing. OurOcean currently serves over 20 real-time or historical ocean data products. The data are served in pre-generated plots or their native data format. For some of the datasets, users can choose different plotting parameters and produce customized graphics. OurOcean also serves 3D Ocean Model outputs generated by ROMS (Regional Ocean Model System) using LAS. The Live Access Server (LAS) software, developed by the Pacific Marine Environmental Laboratory (PMEL) of the National Oceanic and Atmospheric Administration (NOAA), is a configurable Web-server program designed to provide flexible access to geo-referenced scientific data. The model output can be views as plots in horizontal slices, depth profiles or time sequences, or can be downloaded as raw data in different data formats, such as NetCDF, ASCII, Binary, etc. The interactive visualization is provided by graphic software, Ferret, also developed by PMEL. In addition, OurOcean allows users with minimal computing resources to configure and run an Ocean Model with data assimilation on a remote computer. Users may select the forcing input, the data to be assimilated, the simulation period, and the output variables and submit the model to run on a backend parallel computer. When the run is complete, the output will be added to the LAS server for

Installation of the National Transport Code Collaboration Data Server at the ITPA International Multi-tokamak Confinement Profile Database

NASA Astrophysics Data System (ADS)

Roach, Colin; Carlsson, Johan; Cary, John R.; Alexander, David A.

2002-11-01

The National Transport Code Collaboration (NTCC) has developed an array of software, including a data client/server. The data server, which is written in C++, serves local data (in the ITER Profile Database format) as well as remote data (by accessing one or several MDS+ servers). The client, a web-invocable Java applet, provides a uniform, intuitive, user-friendly, graphical interface to the data server. The uniformity of the interface relieves the user from the trouble of mastering the differences between different data formats and lets him/her focus on the essentials: plotting and viewing the data. The user runs the client by visiting a web page using any Java capable Web browser. The client is automatically downloaded and run by the browser. A reference to the data server is then retrieved via the standard Web protocol (HTTP). The communication between the client and the server is then handled by the mature, industry-standard CORBA middleware. CORBA has bindings for all common languages and many high-quality implementations are available (both Open Source and commercial). The NTCC data server has been installed at the ITPA International Multi-tokamak Confinement Profile Database, which is hosted by the UKAEA at Culham Science Centre. The installation of the data server is protected by an Internet firewall. To make it accessible to clients outside the firewall some modifications of the server were required. The working version of the ITPA confinement profile database is not open to the public. Authentification of legitimate users is done utilizing built-in Java security features to demand a password to download the client. We present an overview of the NTCC data client/server and some details of how the CORBA firewall-traversal issues were resolved and how the user authentification is implemented.

PBEQ-Solver for online visualization of electrostatic potential of biomolecules.

PubMed

Jo, Sunhwan; Vargyas, Miklos; Vasko-Szedlar, Judit; Roux, Benoît; Im, Wonpil

2008-07-01

PBEQ-Solver provides a web-based graphical user interface to read biomolecular structures, solve the Poisson-Boltzmann (PB) equations and interactively visualize the electrostatic potential. PBEQ-Solver calculates (i) electrostatic potential and solvation free energy, (ii) protein-protein (DNA or RNA) electrostatic interaction energy and (iii) pKa of a selected titratable residue. All the calculations can be performed in both aqueous solvent and membrane environments (with a cylindrical pore in the case of membrane). PBEQ-Solver uses the PBEQ module in the biomolecular simulation program CHARMM to solve the finite-difference PB equation of molecules specified by users. Users can interactively inspect the calculated electrostatic potential on the solvent-accessible surface as well as iso-electrostatic potential contours using a novel online visualization tool based on MarvinSpace molecular visualization software, a Java applet integrated within CHARMM-GUI (http://www.charmm-gui.org). To reduce the computational time on the server, and to increase the efficiency in visualization, all the PB calculations are performed with coarse grid spacing (1.5 A before and 1 A after focusing). PBEQ-Solver suggests various physical parameters for PB calculations and users can modify them if necessary. PBEQ-Solver is available at http://www.charmm-gui.org/input/pbeqsolver.

PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface.

PubMed

Uszkoreit, Julian; Maerkens, Alexandra; Perez-Riverol, Yasset; Meyer, Helmut E; Marcus, Katrin; Stephan, Christian; Kohlbacher, Oliver; Eisenacher, Martin

2015-07-02

Protein inference connects the peptide spectrum matches (PSMs) obtained from database search engines back to proteins, which are typically at the heart of most proteomics studies. Different search engines yield different PSMs and thus different protein lists. Analysis of results from one or multiple search engines is often hampered by different data exchange formats and lack of convenient and intuitive user interfaces. We present PIA, a flexible software suite for combining PSMs from different search engine runs and turning these into consistent results. PIA can be integrated into proteomics data analysis workflows in several ways. A user-friendly graphical user interface can be run either locally or (e.g., for larger core facilities) from a central server. For automated data processing, stand-alone tools are available. PIA implements several established protein inference algorithms and can combine results from different search engines seamlessly. On several benchmark data sets, we show that PIA can identify a larger number of proteins at the same protein FDR when compared to that using inference based on a single search engine. PIA supports the majority of established search engines and data in the mzIdentML standard format. It is implemented in Java and freely available at https://github.com/mpc-bioinformatics/pia.

An Early-Warning System for Volcanic Ash Dispersal: The MAFALDA Procedure

NASA Astrophysics Data System (ADS)

Barsotti, S.; Nannipieri, L.; Neri, A.

2006-12-01

Forecasts of the dispersal of volcanic ash is a fundamental goal in order to mitigate its potential impact on urbanized areas and transport routes surrounding explosive volcanoes. To this aim we developed an early- warning procedure named MAFALDA (Modeling And Forecasting Ash Loading and Dispersal in the Atmosphere). Such tool is able to quantitatively forecast the atmospheric concentration of ash as well as the ground deposition as a function of time over a 3D spatial domain.\\The main features of MAFALDA are: (1) the use of the hybrid Lagrangian-Eulerian code VOL-CALPUFF able to describe both the rising column phase and the atmospheric dispersal as a function of weather conditions, (2) the use of high-resolution weather forecasting data, (3) the short execution time that allows to analyse a set of scenarios and (4) the web-based CGI software application (written in Perl programming language) that shows the results in a standard graphical web interface and makes it suitable as an early-warning system during volcanic crises.\\MAFALDA is composed by a computational part that simulates the ash cloud dynamics and a graphical interface for visualizing the modelling results. The computational part includes the codes for elaborating the meteorological data, the dispersal code and the post-processing programs. These produces hourly 2D maps of aerial ash concentration at several vertical levels, extension of "threat" area on air and 2D maps of ash deposit on the ground, in addition to graphs of hourly variations of column height.\\The processed results are available on the web by the graphical interface and the users can choose, by drop-down menu, which data to visualize. \\A first partial application of the procedure has been carried out for Mt. Etna (Italy). In this case, the procedure simulates four volcanological scenarios characterized by different plume intensities and uses 48-hrs weather forecasting data with a resolution of 7 km provided by the Italian Air Force.

Augmented Reality 2.0

NASA Astrophysics Data System (ADS)

Schmalstieg, Dieter; Langlotz, Tobias; Billinghurst, Mark

Augmented Reality (AR) was first demonstrated in the 1960s, but only recently have technologies emerged that can be used to easily deploy AR applications to many users. Camera-equipped cell phones with significant processing power and graphics abilities provide an inexpensive and versatile platform for AR applications, while the social networking technology of Web 2.0 provides a large-scale infrastructure for collaboratively producing and distributing geo-referenced AR content. This combination of widely used mobile hardware and Web 2.0 software allows the development of a new type of AR platform that can be used on a global scale. In this paper we describe the Augmented Reality 2.0 concept and present existing work on mobile AR and web technologies that could be used to create AR 2.0 applications.

CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison

PubMed Central

Castrignanò, Tiziana; Canali, Alessandro; Grillo, Giorgio; Liuni, Sabino; Mignone, Flavio; Pesole, Graziano

2004-01-01

The identification and characterization of genome tracts that are highly conserved across species during evolution may contribute significantly to the functional annotation of whole-genome sequences. Indeed, such sequences are likely to correspond to known or unknown coding exons or regulatory motifs. Here, we present a web server implementing a previously developed algorithm that, by comparing user-submitted genome sequences, is able to identify statistically significant conserved blocks and assess their coding or noncoding nature through the measure of a coding potential score. The web tool, available at http://www.caspur.it/CSTminer/, is dynamically interconnected with the Ensembl genome resources and produces a graphical output showing a map of detected conserved sequences and annotated gene features. PMID:15215464

Magnetic Fields for All: The GPIPS Community Web-Access Portal

NASA Astrophysics Data System (ADS)

Carveth, Carol; Clemens, D. P.; Pinnick, A.; Pavel, M.; Jameson, K.; Taylor, B.

2007-12-01

The new GPIPS website portal provides community users with an intuitive and powerful interface to query the data products of the Galactic Plane Infrared Polarization Survey. The website, which was built using PHP for the front end and MySQL for the database back end, allows users to issue queries based on galactic or equatorial coordinates, GPIPS-specific identifiers, polarization information, magnitude information, and several other attributes. The returns are presented in HTML tables, with the added option of either downloading or being emailed an ASCII file including the same or more information from the database. Other functionalities of the website include providing details of the status of the Survey (which fields have been observed or are planned to be observed), techniques involved in data collection and analysis, and descriptions of the database contents and names. For this initial launch of the website, users may access the GPIPS polarization point source catalog and the deep coadd photometric point source catalog. Future planned developments include a graphics-based method for querying the database, as well as tools to combine neighboring GPIPS images into larger image files for both polarimetry and photometry. This work is partially supported by NSF grant AST-0607500.

SVGenes: a library for rendering genomic features in scalable vector graphic format.

PubMed

Etherington, Graham J; MacLean, Daniel

2013-08-01

Drawing genomic features in attractive and informative ways is a key task in visualization of genomics data. Scalable Vector Graphics (SVG) format is a modern and flexible open standard that provides advanced features including modular graphic design, advanced web interactivity and animation within a suitable client. SVGs do not suffer from loss of image quality on re-scaling and provide the ability to edit individual elements of a graphic on the whole object level independent of the whole image. These features make SVG a potentially useful format for the preparation of publication quality figures including genomic objects such as genes or sequencing coverage and for web applications that require rich user-interaction with the graphical elements. SVGenes is a Ruby-language library that uses SVG primitives to render typical genomic glyphs through a simple and flexible Ruby interface. The library implements a simple Page object that spaces and contains horizontal Track objects that in turn style, colour and positions features within them. Tracks are the level at which visual information is supplied providing the full styling capability of the SVG standard. Genomic entities like genes, transcripts and histograms are modelled in Glyph objects that are attached to a track and take advantage of SVG primitives to render the genomic features in a track as any of a selection of defined glyphs. The feature model within SVGenes is simple but flexible and not dependent on particular existing gene feature formats meaning graphics for any existing datasets can easily be created without need for conversion. The library is provided as a Ruby Gem from https://rubygems.org/gems/bio-svgenes under the MIT license, and open source code is available at https://github.com/danmaclean/bioruby-svgenes also under the MIT License. dan.maclean@tsl.ac.uk.

Interactive Maps on War and Peace: A WebGIS Application for Civic Education

NASA Astrophysics Data System (ADS)

Wirkus, Lars; Strunck, Alexander

2013-04-01

War and violent conflict are omnipresent-be it war in the Middle East, violent conflicts in failed states or increasing military expenditures and exports/ imports of military goods. To understand certain conflicts or peace processes and their possible interrelation, to conduct a well-founded political discussion and to support or influence decision-making, one matter is of special importance: easily accessible and, in particular, reliable data and information. Against this background, the Bonn International Center for Conversion (BICC) in close cooperation with the German Federal Agency for Civic Education (bpb) has been developing a map-based information portal on war and peace with various thematic modules for the latter's online service (http://sicherheitspolitik.bpb.de). The portal will eventually offer nine of such modules that are intended to give various target groups, such as interested members of the public, teachers and learners, policymakers and representatives of the media access to the required information in form of an interactive and country-based global overview or a comparison of different issues. Five thematic modules have been completed so far: War and conflict, peace and demobilization, military capacities, resources and conflict, conventional weapons. The portal offers a broad spectrum of different data processing and visualization tools. Its central feature is an interactive mapping component based on WebGIS and a relational database. Content and data provided through thematic maps in the form of WebGIS layers are generally supplemented by info graphics, data tables and short articles providing deeper knowledge on the respective issue. All modules and their sub-chapters are introduced by background texts. They put all interactive maps of a module into an appropriate context and help the users to also understand the interrelation between various layers. If a layer is selected, all corresponding texts and graphics are shown automatically below the map. Data tables are offered if the copyright of datasets allows such use. All data of all thematic modules is presented in country profiles in a consolidated manner. The portal has been created with Open Source Software. PostgreSQL and PostGIS, MapServer, OpenLayers, MapProxy and cmsmadesimple are combined to manipulate and transform global data sets into interactive thematic maps. A purpose-programmed layer selection menu enables users to select single layers or to combine up to three matching layers from all possible pre-set layer combinations. This applies both to fields of topics within a module and across various modules. Due to the complexity of the structure and visualization constraints, no more than three layers can be combined. The WebGIS-based information portal on war and peace is an excellent example of how GIS technologies can be used for education and outreach. Not only can they play a crucial role in supporting the educational mandate and mission of certain institutions. They can also directly support various target groups in obtaining the knowledge needed by providing a collection of straight forward designed, ready-to-use data, info graphics and maps.

Visual design for the user interface, Part 1: Design fundamentals.

PubMed

Lynch, P J

1994-01-01

Digital audiovisual media and computer-based documents will be the dominant forms of professional communication in both clinical medicine and the biomedical sciences. The design of highly interactive multimedia systems will shortly become a major activity for biocommunications professionals. The problems of human-computer interface design are intimately linked with graphic design for multimedia presentations and on-line document systems. This article outlines the history of graphic interface design and the theories that have influenced the development of today's major graphic user interfaces.

SEPHYDRO: An Integrated Multi-Filter Web-Based Tool for Baseflow Separation

NASA Astrophysics Data System (ADS)

Serban, D.; MacQuarrie, K. T. B.; Popa, A.

2017-12-01

Knowledge of baseflow contributions to streamflow is important for understanding watershed scale hydrology, including groundwater-surface water interactions, impact of geology and landforms on baseflow, estimation of groundwater recharge rates, etc. Baseflow (or hydrograph) separation methods can be used as supporting tools in many areas of environmental research, such as the assessment of the impact of agricultural practices, urbanization and climate change on surface water and groundwater. Over the past few decades various digital filtering and graphically-based methods have been developed in an attempt to improve the assessment of the dynamics of the various sources of streamflow (e.g. groundwater, surface runoff, subsurface flow); however, these methods are not available under an integrated platform and, individually, often require significant effort for implementation. Here we introduce SEPHYDRO, an open access, customizable web-based tool, which integrates 11 algorithms allowing for separation of streamflow hydrographs. The streamlined interface incorporates a reference guide as well as additional information that allows users to import their own data, customize the algorithms, and compare, visualise and export results. The tool includes one-, two- and three-parameter digital filters as well as graphical separation methods and has been successfully applied in Atlantic Canada, in studies dealing with nutrient loading to fresh water and coastal water ecosystems. Future developments include integration of additional separation algorithms as well as incorporation of geochemical separation methods. SEPHYDRO has been developed through a collaborative research effort between the Canadian Rivers Institute, University of New Brunswick (Fredericton, New Brunswick, Canada), Agriculture and Agri-Food Canada and Environment and Climate Change Canada and is currently available at http://canadianriversinstitute.com/tool/

KymoKnot: A web server and software package to identify and locate knots in trajectories of linear or circular polymers.

PubMed

Tubiana, Luca; Polles, Guido; Orlandini, Enzo; Micheletti, Cristian

2018-06-07

The KymoKnot software package and web server identifies and locates physical knots or proper knots in a series of polymer conformations. It is mainly intended as an analysis tool for trajectories of linear or circular polymers, but it can be used on single instances too, e.g. protein structures in PDB format. A key element of the software package is the so-called minimally interfering chain closure algorithm that is used to detect physical knots in open chains and to locate the knotted region in both open and closed chains. The web server offers a user-friendly graphical interface that identifies the knot type and highlights the knotted region on each frame of the trajectory, which the user can visualize interactively from various viewpoints. The dynamical evolution of the knotted region along the chain contour is presented as a kymograph. All data can be downloaded in text format. The KymoKnot package is licensed under the BSD 3-Clause licence. The server is publicly available at http://kymoknot.sissa.it/kymoknot/interactive.php .

A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0

PubMed Central

Bazinet, Adam L.; Zwickl, Derrick J.; Cummings, Michael P.

2014-01-01

We introduce molecularevolution.org, a publicly available gateway for high-throughput, maximum-likelihood phylogenetic analysis powered by grid computing. The gateway features a garli 2.0 web service that enables a user to quickly and easily submit thousands of maximum likelihood tree searches or bootstrap searches that are executed in parallel on distributed computing resources. The garli web service allows one to easily specify partitioned substitution models using a graphical interface, and it performs sophisticated post-processing of phylogenetic results. Although the garli web service has been used by the research community for over three years, here we formally announce the availability of the service, describe its capabilities, highlight new features and recent improvements, and provide details about how the grid system efficiently delivers high-quality phylogenetic results. [garli, gateway, grid computing, maximum likelihood, molecular evolution portal, phylogenetics, web service.] PMID:24789072

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

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

Bouckk John; Michael McLeod; Kim Worley

1999-09-10

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

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.

An Evaluation of the Interactive Query Expansion in an Online Library Catalogue with a Graphical User Interface.

ERIC Educational Resources Information Center

Hancock-Beaulieu, Micheline; And Others

1995-01-01

An online library catalog was used to evaluate an interactive query expansion facility based on relevance feedback for the Okapi, probabilistic, term weighting, retrieval system. A graphical user interface allowed searchers to select candidate terms extracted from relevant retrieved items to reformulate queries. Results suggested that the…

Young Children's Skill in Using a Mouse to Control a Graphical Computer Interface.

ERIC Educational Resources Information Center

Crook, Charles

1992-01-01

Describes a study that investigated the performance of preschoolers and children in the first three years of formal education on tasks that involved skills using a mouse-based control of a graphical computer interface. The children's performance is compared with that of novice adult users and expert users. (five references) (LRW)

User interface support

NASA Technical Reports Server (NTRS)

Lewis, Clayton; Wilde, Nick

1989-01-01

Space construction will require heavy investment in the development of a wide variety of user interfaces for the computer-based tools that will be involved at every stage of construction operations. Using today's technology, user interface development is very expensive for two reasons: (1) specialized and scarce programming skills are required to implement the necessary graphical representations and complex control regimes for high-quality interfaces; (2) iteration on prototypes is required to meet user and task requirements, since these are difficult to anticipate with current (and foreseeable) design knowledge. We are attacking this problem by building a user interface development tool based on extensions to the spreadsheet model of computation. The tool provides high-level support for graphical user interfaces and permits dynamic modification of interfaces, without requiring conventional programming concepts and skills.

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

PubMed

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

2014-05-05

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

The Protein Disease Database of human body fluids: II. Computer methods and data issues.

PubMed

Lemkin, P F; Orr, G A; Goldstein, M P; Creed, G J; Myrick, J E; Merril, C R

1995-01-01

The Protein Disease Database (PDD) is a relational database of proteins and diseases. With this database it is possible to screen for quantitative protein abnormalities associated with disease states. These quantitative relationships use data drawn from the peer-reviewed biomedical literature. Assays may also include those observed in high-resolution electrophoretic gels that offer the potential to quantitate many proteins in a single test as well as data gathered by enzymatic or immunologic assays. We are using the Internet World Wide Web (WWW) and the Web browser paradigm as an access method for wide distribution and querying of the Protein Disease Database. The WWW hypertext transfer protocol and its Common Gateway Interface make it possible to build powerful graphical user interfaces that can support easy-to-use data retrieval using query specification forms or images. The details of these interactions are totally transparent to the users of these forms. Using a client-server SQL relational database, user query access, initial data entry and database maintenance are all performed over the Internet with a Web browser. We discuss the underlying design issues, mapping mechanisms and assumptions that we used in constructing the system, data entry, access to the database server, security, and synthesis of derived two-dimensional gel image maps and hypertext documents resulting from SQL database searches.

Web usability testing with a Hispanic medically underserved population.

PubMed

Moore, Mary; Bias, Randolph G; Prentice, Katherine; Fletcher, Robin; Vaughn, Terry

2009-04-01

Skilled website developers value usability testing to assure user needs are met. When the target audience differs substantially from the developers, it becomes essential to tailor both design and evaluation methods. In this study, researchers carried out a multifaceted usability evaluation of a website (Healthy Texas) designed for Hispanic audiences with lower computer literacy and lower health literacy. METHODS INCLUDED: (1) heuristic evaluation by a usability engineer, (2) remote end-user testing using WebEx software; and (3) face-to-face testing in a community center where use of the website was likely. Researchers found standard usability testing methods needed to be modified to provide interpreters, increased flexibility for time on task, presence of a trusted intermediary such as a librarian, and accommodation for family members who accompanied participants. Participants offered recommendations for website redesign, including simplified language, engaging and relevant graphics, culturally relevant examples, and clear navigation. User-centered design is especially important when website developers are not representative of the target audience. Failure to conduct appropriate usability testing with a representative audience can substantially reduce use and value of the website. This thorough course of usability testing identified improvements that benefit all users but become crucial when trying to reach an underserved audience.

Visual Design Principles Applied To World Wide Web Construction.

ERIC Educational Resources Information Center

Luck, Donald D.; Hunter, J. Mark

This paper describes basic types of World Wide Web pages and presents design criteria for page layout based on principles of visual literacy. Discussion focuses on pages that present information in the following styles: billboard; directory/index; textual; and graphics. Problems and solutions in Web page construction are explored according to…

Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data

PubMed Central

Zhao, Zheng; Bai, Jing; Wu, Aiwei; Wang, Yuan; Zhang, Jinwen; Wang, Zishan; Li, Yongsheng; Xu, Juan; Li, Xia

2015-01-01

Long non-coding RNAs (lncRNAs) are emerging as key regulators of diverse biological processes and diseases. However, the combinatorial effects of these molecules in a specific biological function are poorly understood. Identifying co-expressed protein-coding genes of lncRNAs would provide ample insight into lncRNA functions. To facilitate such an effort, we have developed Co-LncRNA, which is a web-based computational tool that allows users to identify GO annotations and KEGG pathways that may be affected by co-expressed protein-coding genes of a single or multiple lncRNAs. LncRNA co-expressed protein-coding genes were first identified in publicly available human RNA-Seq datasets, including 241 datasets across 6560 total individuals representing 28 tissue types/cell lines. Then, the lncRNA combinatorial effects in a given GO annotations or KEGG pathways are taken into account by the simultaneous analysis of multiple lncRNAs in user-selected individual or multiple datasets, which is realized by enrichment analysis. In addition, this software provides a graphical overview of pathways that are modulated by lncRNAs, as well as a specific tool to display the relevant networks between lncRNAs and their co-expressed protein-coding genes. Co-LncRNA also supports users in uploading their own lncRNA and protein-coding gene expression profiles to investigate the lncRNA combinatorial effects. It will be continuously updated with more human RNA-Seq datasets on an annual basis. Taken together, Co-LncRNA provides a web-based application for investigating lncRNA combinatorial effects, which could shed light on their biological roles and could be a valuable resource for this community. Database URL: http://www.bio-bigdata.com/Co-LncRNA/ PMID:26363020

GAIA virtual observatory - development and practices

NASA Astrophysics Data System (ADS)

Syrjäsuo, Mikko; Marple, Steve

2010-05-01

The Global Auroral Imaging Access, or GAIA, is a virtual observatory providing quick access to summary data from satellite and ground-based instruments that remote sense auroral precipitation (http://gaia-vxo.org). This web-based service facilitates locating data relevant to particular events by simultaneously displaying summary images from various data sets around the world. At the moment, there are GAIA server nodes in Canada, Finland, Norway and the UK. The development is an international effort and the software and metadata are freely available. The GAIA system is based on a relational database which is queried by a dedicated software suite that also creates the graphical end-user interface if such is needed. Most commonly, the virtual observatory is used interactively by using a web browser: the user provides the date and the type of data of interest. As the summary data from multiple instruments are displayed simultaneously, the user can conveniently explore the recorded data. The virtual observatory provides essentially instant access to the images originating from all major auroral instrument networks including THEMIS, NORSTAR, GLORIA and MIRACLE. The scientific, educational and outreach use is limited by creativity rather than access. The first version of the GAIA was developed at the University of Calgary (Alberta, Canada) in 2004-2005. This proof-of-concept included mainly THEMIS and MIRACLE data, which comprised of millions of summary plots and thumbnail images. However, it was soon realised that a complete re-design was necessary to increase flexibility. In the presentation, we will discuss the early history and motivation of GAIA as well as how the development continued towards the current version. The emphasis will be on practical problems and their solutions. Relevant design choices will also be highlighted.

Access Control of Web- and Java-Based Applications

NASA Technical Reports Server (NTRS)

Tso, Kam S.; Pajevski, Michael J.

2013-01-01

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

Autoplot: a Browser for Science Data on the Web

NASA Astrophysics Data System (ADS)

Faden, J.; Weigel, R. S.; West, E. E.; Merka, J.

2008-12-01

Autoplot (www.autoplot.org) is software for plotting data from many different sources and in many different file formats. Data from CDF, CEF, Fits, NetCDF, and OpenDAP can be plotted, along with many other sources such as ASCII tables and Excel spreadsheets. This is done by adapting these various data formats and APIs into a common data model that borrows from the netCDF and CDF data models. Autoplot uses a web browser metaphor to simplify use. The user specifies a parameter URL, for example a CDF file accessible via http with a parameter name appended, and the file resource is downloaded and the parameter is rendered in a scientifically meaningful way. When data span multiple files, the user can use a file name template in the URL to aggregate (combine) a set of remote files. So the problem of aggregating data across file boundaries is handled on the client side, allowing simple web servers to be used. The das2 graphics library provides rich controls for exploring the data. Scripting is supported through Python, providing not just programmatic control, but for calculating new parameters in a language that will look familiar to IDL and Matlab users. Autoplot is Java-based software, and will run on most computers without a burdensome installation process. It can also used as an applet or as a servlet that serves static images. Autoplot was developed as part of the Virtual Radiation Belt Observatory (ViRBO) project, and is also being used for the Virtual Magnetospheric Observatory (VMO). It is expected that this flexible, general-purpose plotting tool will be useful for allowing a data provider to add instant visualization capabilities to a directory of files or for general use in the Virtual Observatory environment.

EarthServer - 3D Visualization on the Web

NASA Astrophysics Data System (ADS)

Wagner, Sebastian; Herzig, Pasquale; Bockholt, Ulrich; Jung, Yvonne; Behr, Johannes

2013-04-01

EarthServer (www.earthserver.eu), funded by the European Commission under its Seventh Framework Program, is a project to enable the management, access and exploration of massive, multi-dimensional datasets using Open GeoSpatial Consortium (OGC) query and processing language standards like WCS 2.0 and WCPS. To this end, a server/client architecture designed to handle Petabyte/Exabyte volumes of multi-dimensional data is being developed and deployed. As an important part of the EarthServer project, six Lighthouse Applications, major scientific data exploitation initiatives, are being established to make cross-domain, Earth Sciences related data repositories available in an open and unified manner, as service endpoints based on solutions and infrastructure developed within the project. Clients technology developed and deployed in EarthServer ranges from mobile and web clients to immersive virtual reality systems, all designed to interact with a physically and logically distributed server infrastructure using exclusively OGC standards. In this contribution, we would like to present our work on a web-based 3D visualization and interaction client for Earth Sciences data using only technology found in standard web browsers without requiring the user to install plugins or addons. Additionally, we are able to run the earth data visualization client on a wide range of different platforms with very different soft- and hardware requirements such as smart phones (e.g. iOS, Android), different desktop systems etc. High-quality, hardware-accelerated visualization of 3D and 4D content in standard web browsers can be realized now and we believe it will become more and more common to use this fast, lightweight and ubiquitous platform to provide insights into big datasets without requiring the user to set up a specialized client first. With that in mind, we will also point out some of the limitations we encountered using current web technologies. Underlying the EarthServer web client and on top of HTML5, WebGL and JavaScript we have developed the X3DOM framework (www.x3dom.org), which makes possible to embed declarative X3D scenegraphs, an ISO standard XML-based file format for representing 3D computer graphics, directly within HTML, thus enabling developers to rapidly design 3D content that blends seamlessly into HTML interfaces using Javascript. This approach (commonly referred to as a polyfill layer) is used to mimic native web browser support for declarative 3D content and is an important component in our web client architecture.

Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel pores.

PubMed

Lee, Kyu Il; Jo, Sunhwan; Rui, Huan; Egwolf, Bernhard; Roux, Benoît; Pastor, Richard W; Im, Wonpil

2012-01-30

Brownian dynamics (BD) based on accurate potential of mean force is an efficient and accurate method for simulating ion transport through wide ion channels. Here, a web-based graphical user interface (GUI) is presented for carrying out grand canonical Monte Carlo (GCMC) BD simulations of channel proteins: http://www.charmm-gui.org/input/gcmcbd. The webserver is designed to help users avoid most of the technical difficulties and issues encountered in setting up and simulating complex pore systems. GCMC/BD simulation results for three proteins, the voltage dependent anion channel (VDAC), α-Hemolysin (α-HL), and the protective antigen pore of the anthrax toxin (PA), are presented to illustrate the system setup, input preparation, and typical output (conductance, ion density profile, ion selectivity, and ion asymmetry). Two models for the input diffusion constants for potassium and chloride ions in the pore are compared: scaling of the bulk diffusion constants by 0.5, as deduced from previous all-atom molecular dynamics simulations of VDAC, and a hydrodynamics based model (HD) of diffusion through a tube. The HD model yields excellent agreement with experimental conductances for VDAC and α-HL, while scaling bulk diffusion constants by 0.5 leads to underestimates of 10-20%. For PA, simulated ion conduction values overestimate experimental values by a factor of 1.5-7 (depending on His protonation state and the transmembrane potential), implying that the currently available computational model of this protein requires further structural refinement. Copyright © 2011 Wiley Periodicals, Inc.

ReVeaLD: a user-driven domain-specific interactive search platform for biomedical research.

PubMed

Kamdar, Maulik R; Zeginis, Dimitris; Hasnain, Ali; Decker, Stefan; Deus, Helena F

2014-02-01

Bioinformatics research relies heavily on the ability to discover and correlate data from various sources. The specialization of life sciences over the past decade, coupled with an increasing number of biomedical datasets available through standardized interfaces, has created opportunities towards new methods in biomedical discovery. Despite the popularity of semantic web technologies in tackling the integrative bioinformatics challenge, there are many obstacles towards its usage by non-technical research audiences. In particular, the ability to fully exploit integrated information needs using improved interactive methods intuitive to the biomedical experts. In this report we present ReVeaLD (a Real-time Visual Explorer and Aggregator of Linked Data), a user-centered visual analytics platform devised to increase intuitive interaction with data from distributed sources. ReVeaLD facilitates query formulation using a domain-specific language (DSL) identified by biomedical experts and mapped to a self-updated catalogue of elements from external sources. ReVeaLD was implemented in a cancer research setting; queries included retrieving data from in silico experiments, protein modeling and gene expression. ReVeaLD was developed using Scalable Vector Graphics and JavaScript and a demo with explanatory video is available at http://www.srvgal78.deri.ie:8080/explorer. A set of user-defined graphic rules controls the display of information through media-rich user interfaces. Evaluation of ReVeaLD was carried out as a game: biomedical researchers were asked to assemble a set of 5 challenge questions and time and interactions with the platform were recorded. Preliminary results indicate that complex queries could be formulated under less than two minutes by unskilled researchers. The results also indicate that supporting the identification of the elements of a DSL significantly increased intuitiveness of the platform and usability of semantic web technologies by domain users. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

User Interface Design in Medical Distributed Web Applications.

PubMed

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

2016-01-01

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

Application of open source standards and technologies in the http://climate4impact.eu/ portal

NASA Astrophysics Data System (ADS)

Plieger, Maarten; Som de Cerff, Wim; Pagé, Christian; Tatarinova, Natalia

2015-04-01

This presentation will demonstrate how to calculate and visualize the climate indice SU (number of summer days) on the climate4impact portal. The following topics will be covered during the demonstration: - Security: Login using OpenID for access to the Earth System Grid Fedeation (ESGF) data nodes. The ESGF works in conjunction with several external websites and systems. The climate4impact portal uses X509 based short lived credentials, generated on behalf of the user with a MyProxy service. Single Sign-on (SSO) is used to make these websites and systems work together. - Discovery: Facetted search based on e.g. variable name, model and institute using the ESGF search services. A catalog browser allows for browsing through CMIP5 and any other climate model data catalogues (e.g. ESSENCE, EOBS, UNIDATA). - Processing using Web Processing Services (WPS): Transform data, subset, export into other formats, and perform climate indices calculations using Web Processing Services implemented by PyWPS, based on NCAR NCPP OpenClimateGIS and IS-ENES2 ICCLIM. - Visualization using Web Map Services (WMS): Visualize data from ESGF data nodes using ADAGUC Web Map Services. The aim of climate4impact is to enhance the use of Climate Research Data and to enhance the interaction with climate effect/impact communities. The portal is based on 21 impact use cases from 5 different European countries, and is evaluated by a user panel consisting of use case owners. It has been developed within the European projects IS-ENES and IS-ENES2 for more than 5 years, and its development currently continues within IS-ENES2 and CLIPC. As the climate impact community is very broad, the focus is mainly on the scientific impact community. This work has resulted in the ENES portal interface for climate impact communities and can be visited at http://climate4impact.eu/ The current main objectives for climate4impact can be summarized in two objectives. The first one is to work on a web interface which automatically generates a graphical user interface on WPS endpoints. The WPS calculates climate indices and subset data using OpenClimateGIS/ICCLIM on data stored in ESGF data nodes. Data is then transmitted from ESGF nodes over secured OpenDAP and becomes available in a new, per user, secured OpenDAP server. The results can then be visualized again using ADAGUC WMS. Dedicated wizards for processing of climate indices will be developed in close collaboration with users. The second one is to expose climate4impact services, so as to offer standardized services which can be used by other portals. This has the advantage to add interoperability between several portals, as well as to enable the design of specific portals aimed at different impact communities, either thematic or national, for example.

Patch Finder Plus (PFplus): a web server for extracting and displaying positive electrostatic patches on protein surfaces.

PubMed

Shazman, Shula; Celniker, Gershon; Haber, Omer; Glaser, Fabian; Mandel-Gutfreund, Yael

2007-07-01

Positively charged electrostatic patches on protein surfaces are usually indicative of nucleic acid binding interfaces. Interestingly, many proteins which are not involved in nucleic acid binding possess large positive patches on their surface as well. In some cases, the positive patches on the protein are related to other functional properties of the protein family. PatchFinderPlus (PFplus) http://pfp.technion.ac.il is a web-based tool for extracting and displaying continuous electrostatic positive patches on protein surfaces. The input required for PFplus is either a four letter PDB code or a protein coordinate file in PDB format, provided by the user. PFplus computes the continuum electrostatics potential and extracts the largest positive patch for each protein chain in the PDB file. The server provides an output file in PDB format including a list of the patch residues. In addition, the largest positive patch is displayed on the server by a graphical viewer (Jmol), using a simple color coding.

Patch Finder Plus (PFplus): A web server for extracting and displaying positive electrostatic patches on protein surfaces

PubMed Central

Shazman, Shula; Celniker, Gershon; Haber, Omer; Glaser, Fabian; Mandel-Gutfreund, Yael

2007-01-01

Positively charged electrostatic patches on protein surfaces are usually indicative of nucleic acid binding interfaces. Interestingly, many proteins which are not involved in nucleic acid binding possess large positive patches on their surface as well. In some cases, the positive patches on the protein are related to other functional properties of the protein family. PatchFinderPlus (PFplus) http://pfp.technion.ac.il is a web-based tool for extracting and displaying continuous electrostatic positive patches on protein surfaces. The input required for PFplus is either a four letter PDB code or a protein coordinate file in PDB format, provided by the user. PFplus computes the continuum electrostatics potential and extracts the largest positive patch for each protein chain in the PDB file. The server provides an output file in PDB format including a list of the patch residues. In addition, the largest positive patch is displayed on the server by a graphical viewer (Jmol), using a simple color coding. PMID:17537808

SVGMap: configurable image browser for experimental data.

PubMed

Rafael-Palou, Xavier; Schroeder, Michael P; Lopez-Bigas, Nuria

2012-01-01

Spatial data visualization is very useful to represent biological data and quickly interpret the results. For instance, to show the expression pattern of a gene in different tissues of a fly, an intuitive approach is to draw the fly with the corresponding tissues and color the expression of the gene in each of them. However, the creation of these visual representations may be a burdensome task. Here we present SVGMap, a java application that automatizes the generation of high-quality graphics for singular data items (e.g. genes) and biological conditions. SVGMap contains a browser that allows the user to navigate the different images created and can be used as a web-based results publishing tool. SVGMap is freely available as precompiled java package as well as source code at http://bg.upf.edu/svgmap. It requires Java 6 and any recent web browser with JavaScript enabled. The software can be run on Linux, Mac OS X and Windows systems. nuria.lopez@upf.edu

Support of US CLIVAR Project Office 2012

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

Cummings, Donna

Director of JOSS, supervised the U.S. CLIVAR Project Office Director and helped direct the officer to enhance the goals and objectives of the U.S. CLIVAR Project and budget. Financial Manager of JOSS, worked to complete proposals and monitor compliance with award requirements and funding limitations and ensure the U.S. CLIVAR Project Office complied with UCAR policies and procedures. Project Coordinator administered the funding for the U.S. CLIVAR Project Office and was responsible for coordinating special projects that required additional support from JOSS technical staff. These projects included activities such as website updates, technology upgrades, production of printed reports, and developmentmore » of graphic elements like logos. Web Developer worked both on web development and graphic work and the work consisted of the following: Maintaining the site ? installing updates to Drupal CMS (Content Management System). Creating new templates for webpages and styling them with CSS and JavaScript/jQuery code. Fixing the styling on webpages that the content contributor/manager (Jenn Mays) created and has had trouble with. Creating new web forms for abstract uploading, subscriptions, and meeting registrations. Created 4 webpages for the ?ASP: Key Uncertainties in the Global Carbon-Cycle? meeting. Developed a document review form, instruction webpages, login redirect, dynamic table with form submissions for the US CLIVAR SSC Science Plan Document Review. This was open to the public from June 12, 2013 until July 10, 2013. During this time the user accounts had to be checked (daily) that were created by the public, to delete any spam ones. Graphics work: preparing images for general use on webpages, webpage banners, and for meeting name badges, creating a US CLIVAR letterhead, redesigning the US AMOC logo. System Administrator spent time working on the migration of the US CLIVAR site from the USGCRP office to UCAR here Boulder. This was done to increase the general speed of the site & to allow the web developer to work in it more efficiently. Main tasks were to Archive the old Site, create new development site for web developer, and move web address to new website when web developer was finished with development. There are no patients or equipment related to this proposals« less

Sharing and reusing cardiovascular anatomical models over the Web: a step towards the implementation of the virtual physiological human project.

PubMed

Gianni, Daniele; McKeever, Steve; Yu, Tommy; Britten, Randall; Delingette, Hervé; Frangi, Alejandro; Hunter, Peter; Smith, Nicolas

2010-06-28

Sharing and reusing anatomical models over the Web offers a significant opportunity to progress the investigation of cardiovascular diseases. However, the current sharing methodology suffers from the limitations of static model delivery (i.e. embedding static links to the models within Web pages) and of a disaggregated view of the model metadata produced by publications and cardiac simulations in isolation. In the context of euHeart--a research project targeting the description and representation of cardiovascular models for disease diagnosis and treatment purposes--we aim to overcome the above limitations with the introduction of euHeartDB, a Web-enabled database for anatomical models of the heart. The database implements a dynamic sharing methodology by managing data access and by tracing all applications. In addition to this, euHeartDB establishes a knowledge link with the physiome model repository by linking geometries to CellML models embedded in the simulation of cardiac behaviour. Furthermore, euHeartDB uses the exFormat--a preliminary version of the interoperable FieldML data format--to effectively promote reuse of anatomical models, and currently incorporates Continuum Mechanics, Image Analysis, Signal Processing and System Identification Graphical User Interface (CMGUI), a rendering engine, to provide three-dimensional graphical views of the models populating the database. Currently, euHeartDB stores 11 cardiac geometries developed within the euHeart project consortium.

Student Research Projects

NASA Technical Reports Server (NTRS)

Yeske, Lanny A.

1998-01-01

Numerous FY1998 student research projects were sponsored by the Mississippi State University Center for Air Sea Technology. This technical note describes these projects which include research on: (1) Graphical User Interfaces, (2) Master Environmental Library, (3) Database Management Systems, (4) Naval Interactive Data Analysis System, (5) Relocatable Modeling Environment, (6) Tidal Models, (7) Book Inventories, (8) System Analysis, (9) World Wide Web Development, (10) Virtual Data Warehouse, (11) Enterprise Information Explorer, (12) Equipment Inventories, (13) COADS, and (14) JavaScript Technology.

Web-Based Media Contents Editor for UCC Websites

NASA Astrophysics Data System (ADS)

Kim, Seoksoo

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

Univariate Probability Distributions

ERIC Educational Resources Information Center

Leemis, Lawrence M.; Luckett, Daniel J.; Powell, Austin G.; Vermeer, Peter E.

2012-01-01

We describe a web-based interactive graphic that can be used as a resource in introductory classes in mathematical statistics. This interactive graphic presents 76 common univariate distributions and gives details on (a) various features of the distribution such as the functional form of the probability density function and cumulative distribution…

Transportable Applications Environment (TAE) Plus: A NASA tool used to develop and manage graphical user interfaces

NASA Technical Reports Server (NTRS)

Szczur, Martha R.

1992-01-01

The Transportable Applications Environment (TAE) Plus was built to support the construction of graphical user interfaces (GUI's) for highly interactive applications, such as real-time processing systems and scientific analysis systems. It is a general purpose portable tool that includes a 'What You See Is What You Get' WorkBench that allows user interface designers to layout and manipulate windows and interaction objects. The WorkBench includes both user entry objects (e.g., radio buttons, menus) and data-driven objects (e.g., dials, gages, stripcharts), which dynamically change based on values of realtime data. Discussed here is what TAE Plus provides, how the implementation has utilized state-of-the-art technologies within graphic workstations, and how it has been used both within and without NASA.

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

PubMed

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

2014-01-01

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

ASK-LDT 2.0: A Web-Based Graphical Tool for Authoring Learning Designs

ERIC Educational Resources Information Center

Zervas, Panagiotis; Fragkos, Konstantinos; Sampson, Demetrios G.

2013-01-01

During the last decade, Open Educational Resources (OERs) have gained increased attention for their potential to support open access, sharing and reuse of digital educational resources. Therefore, a large amount of digital educational resources have become available worldwide through web-based open access repositories which are referred to as…

Towards a Taxonomy of Metaphorical Graphical User Interfaces: Demands and Implementations.

ERIC Educational Resources Information Center

Cates, Ward Mitchell

The graphical user interface (GUI) has become something of a standard for instructional programs in recent years. One type of GUI is the metaphorical type. For example, the Macintosh GUI is based on the "desktop" metaphor where objects one manipulates within the GUI are implied to be objects one might find in a real office's desktop.…

VISL: A Virtual Ice Sheet Laboratory For Outreach and K-12 Education

NASA Astrophysics Data System (ADS)

Halkides, D. J.; Larour, E. Y.; Cheng, D. L.; Perez, G.; Romero, V.; Saks, O.

2014-12-01

We present a prototype Virtual Ice Sheet Laboratory (VISL) geared to K-12 classrooms and the general public, with the goal of improving climate literacy, especially in regards to the crucial role of the polar ice sheets in Earth's climate and sea level. VISL will allow users to perform guided experiments using the Ice Sheet System Model (ISSM), a state-of-the-art ice flow model developed at NASA's Jet Propulsion Laboratory and UC Irvine that simulates the near-term evolution of the ice sheets on Greenland and Antarctica. VISL users will access ISSM via a graphical interface that can be launched from a web browser on a computer, tablet or smart phone. Users select climate conditions and run time by moving graphic sliders then watch how a given region evolves in time under those conditions. Lesson plans will include conceptual background, instructions for table top experiments related to the concepts addressed in a given lesson, and a guide for performing model experiments and interpreting their results. Activities with different degrees of complexity will aim for consistency with NGSS Physical Science criteria for different grade bands (K-2, 3-5, 6-8, and 9-12), although they will not be labeled as such to encourage a broad user base. Activities will emphasize the development of physical intuition and critical thinking skills, understanding conceptual and computational models, as well as observation recording, concept articulation, hypothesis formulation and testing, and mathematical analysis. At our present phase of development, we seek input from the greater science education and outreach communities regarding VISL's planned content, as well as additional features and topic areas that educators and students would find useful.

VISL: A Virtual Ice Sheet Laboratory For Outreach and K-12 Education

NASA Astrophysics Data System (ADS)

Cheng, D. L. C.; Halkides, D. J.; Larour, E. Y.; Moore, J.; Dunn, S.; Perez, G.

2015-12-01

We present an update on our developing Virtual Ice Sheet Laboratory (VISL). Geared to K-12 classrooms and the general public, VISL's main goal is to improve climate literacy, especially in regards to the crucial role of the polar ice sheets in Earth's climate and sea level. VISL will allow users to perform guided experiments using the Ice Sheet System Model (ISSM), a state-of-the-art ice flow model developed at NASA's Jet Propulsion Laboratory and UC Irvine that simulates the near-term evolution of the ice sheets on Greenland and Antarctica. VISL users will access ISSM via a graphical interface that can be launched from a web browser on a computer, tablet or smart phone. Users select climate conditions and run time by moving graphic sliders then watch how a given region evolves in time under those conditions. Lesson plans will include conceptual background, instructions for table top experiments related to the concepts addressed in a given lesson, and a guide for performing model experiments and interpreting their results. Activities with different degrees of complexity will aim for consistency with NGSS Physical Science criteria for different grade bands (K-2, 3-5, 6-8, and 9-12), although they will not be labeled as such to encourage a broad user base. Activities will emphasize the development of physical intuition and critical thinking skills, understanding conceptual and computational models, as well as observation recording, concept articulation, hypothesis formulation and testing, and mathematical analysis. At our present phase of development, we seek input from the greater science education and outreach communities regarding VISL's planned content, as well as additional features and topic areas that educators and students would find useful.

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.

Rational analyses of information foraging on the web.

PubMed

Pirolli, Peter

2005-05-06

This article describes rational analyses and cognitive models of Web users developed within information foraging theory. This is done by following the rational analysis methodology of (a) characterizing the problems posed by the environment, (b) developing rational analyses of behavioral solutions to those problems, and (c) developing cognitive models that approach the realization of those solutions. Navigation choice is modeled as a random utility model that uses spreading activation mechanisms that link proximal cues (information scent) that occur in Web browsers to internal user goals. Web-site leaving is modeled as an ongoing assessment by the Web user of the expected benefits of continuing at a Web site as opposed to going elsewhere. These cost-benefit assessments are also based on spreading activation models of information scent. Evaluations include a computational model of Web user behavior called Scent-Based Navigation and Information Foraging in the ACT Architecture, and the Law of Surfing, which characterizes the empirical distribution of the length of paths of visitors at a Web site. 2005 Lawrence Erlbaum Associates, Inc.

Development of a Web-based financial application System

NASA Astrophysics Data System (ADS)

Hasan, M. R.; Ibrahimy, M. I.; Motakabber, S. M. A.; Ferdaus, M. M.; Khan, M. N. H.; Mostafa, M. G.

2013-12-01

The paper describes a technique to develop a web based financial system, following latest technology and business needs. In the development of web based application, the user friendliness and technology both are very important. It is used ASP .NET MVC 4 platform and SQL 2008 server for development of web based financial system. It shows the technique for the entry system and report monitoring of the application is user friendly. This paper also highlights the critical situations of development, which will help to develop the quality product.

ToTem: a tool for variant calling pipeline optimization.

PubMed

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

2018-06-26

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

TileDCS web system

NASA Astrophysics Data System (ADS)

Maidantchik, C.; Ferreira, F.; Grael, F.; Atlas Tile Calorimeter Community

2010-04-01

The web system described here provides features to monitor the ATLAS Detector Control System (DCS) acquired data. The DCS is responsible for overseeing the coherent and safe operation of the ATLAS experiment hardware. In the context of the Hadronic Tile Calorimeter Detector (TileCal), it controls the power supplies of the readout electronics acquiring voltages, currents, temperatures and coolant pressure measurements. The physics data taking requires the stable operation of the power sources. The TileDCS Web System retrieves automatically data and extracts the statistics for given periods of time. The mean and standard deviation outcomes are stored as XML files and are compared to preset thresholds. Further, a graphical representation of the TileCal cylinders indicates the state of the supply system of each detector drawer. Colors are designated for each kind of state. In this way problems are easier to find and the collaboration members can focus on them. The user selects a module and the system presents detailed information. It is possible to verify the statistics and generate charts of the parameters over the time. The TileDCS Web System also presents information about the power supplies latest status. One wedge is colored green whenever the system is on. Otherwise it is colored red. Furthermore, it is possible to perform customized analysis. It provides search interfaces where the user can set the module, parameters, and the time period of interest. The system also produces the output of the retrieved data as charts, XML files, CSV and ROOT files according to the user's choice.

Alignment-Annotator web server: rendering and annotating sequence alignments.

PubMed

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-07-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Alignment-Annotator web server: rendering and annotating sequence alignments

PubMed Central

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-01-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. Availability: http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. PMID:24813445

Broadening the interface bandwidth in simulation based training

NASA Technical Reports Server (NTRS)

Somers, Larry E.

1989-01-01

Currently most computer based simulations rely exclusively on computer generated graphics to create the simulation. When training is involved, the method almost exclusively used to display information to the learner is text displayed on the cathode ray tube. MICROEXPERT Systems is concentrating on broadening the communications bandwidth between the computer and user by employing a novel approach to video image storage combined with sound and voice output. An expert system is used to combine and control the presentation of analog video, sound, and voice output with computer based graphics and text. Researchers are currently involved in the development of several graphics based user interfaces for NASA, the U.S. Army, and the U.S. Navy. Here, the focus is on the human factors considerations, software modules, and hardware components being used to develop these interfaces.

Analysis and visualization of disease courses in a semantically-enabled cancer registry.

PubMed

Esteban-Gil, Angel; Fernández-Breis, Jesualdo Tomás; Boeker, Martin

2017-09-29

Regional and epidemiological cancer registries are important for cancer research and the quality management of cancer treatment. Many technological solutions are available to collect and analyse data for cancer registries nowadays. However, the lack of a well-defined common semantic model is a problem when user-defined analyses and data linking to external resources are required. The objectives of this study are: (1) design of a semantic model for local cancer registries; (2) development of a semantically-enabled cancer registry based on this model; and (3) semantic exploitation of the cancer registry for analysing and visualising disease courses. Our proposal is based on our previous results and experience working with semantic technologies. Data stored in a cancer registry database were transformed into RDF employing a process driven by OWL ontologies. The semantic representation of the data was then processed to extract semantic patient profiles, which were exploited by means of SPARQL queries to identify groups of similar patients and to analyse the disease timelines of patients. Based on the requirements analysis, we have produced a draft of an ontology that models the semantics of a local cancer registry in a pragmatic extensible way. We have implemented a Semantic Web platform that allows transforming and storing data from cancer registries in RDF. This platform also permits users to formulate incremental user-defined queries through a graphical user interface. The query results can be displayed in several customisable ways. The complex disease timelines of individual patients can be clearly represented. Different events, e.g. different therapies and disease courses, are presented according to their temporal and causal relations. The presented platform is an example of the parallel development of ontologies and applications that take advantage of semantic web technologies in the medical field. The semantic structure of the representation renders it easy to analyse key figures of the patients and their evolution at different granularity levels.

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

Web-Compatible Graphics Visualization Framework for Online Instruction and Assessment of Hardware Concepts

ERIC Educational Resources Information Center

Chandramouli, Magesh; Chittamuru, Siva-Teja

2016-01-01

This paper explains the design of a graphics-based virtual environment for instructing computer hardware concepts to students, especially those at the beginner level. Photorealistic visualizations and simulations are designed and programmed with interactive features allowing students to practice, explore, and test themselves on computer hardware…

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

ERIC Educational Resources Information Center

Usip, Ebenge E.; Bee, Richard H.

1998-01-01

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

RGG: A general GUI Framework for R scripts

PubMed Central

Visne, Ilhami; Dilaveroglu, Erkan; Vierlinger, Klemens; Lauss, Martin; Yildiz, Ahmet; Weinhaeusel, Andreas; Noehammer, Christa; Leisch, Friedrich; Kriegner, Albert

2009-01-01

Background R is the leading open source statistics software with a vast number of biostatistical and bioinformatical analysis packages. To exploit the advantages of R, extensive scripting/programming skills are required. Results We have developed a software tool called R GUI Generator (RGG) which enables the easy generation of Graphical User Interfaces (GUIs) for the programming language R by adding a few Extensible Markup Language (XML) – tags. RGG consists of an XML-based GUI definition language and a Java-based GUI engine. GUIs are generated in runtime from defined GUI tags that are embedded into the R script. User-GUI input is returned to the R code and replaces the XML-tags. RGG files can be developed using any text editor. The current version of RGG is available as a stand-alone software (RGGRunner) and as a plug-in for JGR. Conclusion RGG is a general GUI framework for R that has the potential to introduce R statistics (R packages, built-in functions and scripts) to users with limited programming skills and helps to bridge the gap between R developers and GUI-dependent users. RGG aims to abstract the GUI development from individual GUI toolkits by using an XML-based GUI definition language. Thus RGG can be easily integrated in any software. The RGG project further includes the development of a web-based repository for RGG-GUIs. RGG is an open source project licensed under the Lesser General Public License (LGPL) and can be downloaded freely at PMID:19254356

Graphics interfaces and numerical simulations: Mexican Virtual Solar Observatory

NASA Astrophysics Data System (ADS)

Hernández, L.; González, A.; Salas, G.; Santillán, A.

2007-08-01

Preliminary results associated to the computational development and creation of the Mexican Virtual Solar Observatory (MVSO) are presented. Basically, the MVSO prototype consists of two parts: the first, related to observations that have been made during the past ten years at the Solar Observation Station (EOS) and at the Carl Sagan Observatory (OCS) of the Universidad de Sonora in Mexico. The second part is associated to the creation and manipulation of a database produced by numerical simulations related to solar phenomena, we are using the MHD ZEUS-3D code. The development of this prototype was made using mysql, apache, java and VSO 1.2. based GNU and `open source philosophy'. A graphic user interface (GUI) was created in order to make web-based, remote numerical simulations. For this purpose, Mono was used, because it is provides the necessary software to develop and run .NET client and server applications on Linux. Although this project is still under development, we hope to have access, by means of this portal, to other virtual solar observatories and to be able to count on a database created through numerical simulations or, given the case, perform simulations associated to solar phenomena.

NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores.

PubMed

Ryu, Hyojung; Lim, GyuTae; Sung, Bong Hyun; Lee, Jinhyuk

2016-02-15

Protein structure refinement is a necessary step for the study of protein function. In particular, some nuclear magnetic resonance (NMR) structures are of lower quality than X-ray crystallographic structures. Here, we present NMRe, a web-based server for NMR structure refinement. The previously developed knowledge-based energy function STAP (Statistical Torsion Angle Potential) was used for NMRe refinement. With STAP, NMRe provides two refinement protocols using two types of distance restraints. If a user provides NOE (Nuclear Overhauser Effect) data, the refinement is performed with the NOE distance restraints as a conventional NMR structure refinement. Additionally, NMRe generates NOE-like distance restraints based on the inter-hydrogen distances derived from the input structure. The efficiency of NMRe refinement was validated on 20 NMR structures. Most of the quality assessment scores of the refined NMR structures were better than those of the original structures. The refinement results are provided as a three-dimensional structure view, a secondary structure scheme, and numerical and graphical structure validation scores. NMRe is available at http://psb.kobic.re.kr/nmre/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Shared virtual environments for telerehabilitation.

PubMed

Popescu, George V; Burdea, Grigore; Boian, Rares

2002-01-01

Current VR telerehabilitation systems use offline remote monitoring from the clinic and patient-therapist videoconferencing. Such "store and forward" and video-based systems cannot implement medical services involving patient therapist direct interaction. Real-time telerehabilitation applications (including remote therapy) can be developed using a shared Virtual Environment (VE) architecture. We developed a two-user shared VE for hand telerehabilitation. Each site has a telerehabilitation workstation with a videocamera and a Rutgers Master II (RMII) force feedback glove. Each user can control a virtual hand and interact hapticly with virtual objects. Simulated physical interactions between therapist and patient are implemented using hand force feedback. The therapist's graphic interface contains several virtual panels, which allow control over the rehabilitation process. These controls start a videoconferencing session, collect patient data, or apply therapy. Several experimental telerehabilitation scenarios were successfully tested on a LAN. A Web-based approach to "real-time" patient telemonitoring--the monitoring portal for hand telerehabilitation--was also developed. The therapist interface is implemented as a Java3D applet that monitors patient hand movement. The monitoring portal gives real-time performance on off-the-shelf desktop workstations.

A National Solar Digital Observatory

NASA Astrophysics Data System (ADS)

Hill, F.

2000-05-01

The continuing development of the Internet as a research tool, combined with an improving funding climate, has sparked new interest in the development of Internet-linked astronomical data bases and analysis tools. Here I outline a concept for a National Solar Digital Observatory (NSDO), a set of data archives and analysis tools distributed in physical location at sites which already host such systems. A central web site would be implemented from which a user could search all of the component archives, select and download data, and perform analyses. Example components include NSO's Digital Library containing its synoptic and GONG data, and the forthcoming SOLIS archive. Several other archives, in various stages of development, also exist. Potential analysis tools include content-based searches, visualized programming tools, and graphics routines. The existence of an NSDO would greatly facilitate solar physics research, as a user would no longer need to have detailed knowledge of all solar archive sites. It would also improve public outreach efforts. The National Solar Observatory is operated by AURA, Inc. under a cooperative agreement with the National Science Foundation.

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

Engineering designer transcription activator-like effector nucleases (TALENs) by REAL or REAL-Fast assembly.

PubMed

Reyon, Deepak; Khayter, Cyd; Regan, Maureen R; Joung, J Keith; Sander, Jeffry D

2012-10-01

Engineered transcription activator-like effector nucleases (TALENs) are broadly useful tools for performing targeted genome editing in a wide variety of organisms and cell types including plants, zebrafish, C. elegans, rat, human somatic cells, and human pluripotent stem cells. Here we describe detailed protocols for the serial, hierarchical assembly of TALENs that require neither PCR nor specialized multi-fragment ligations and that can be implemented by any laboratory. These restriction enzyme and ligation (REAL)-based protocols can be practiced using plasmid libraries and user-friendly, Web-based software that both identifies target sites in sequences of interest and generates printable graphical guides that facilitate assembly of TALENs. With the described platform of reagents, protocols, and software, researchers can easily engineer multiple TALENs within 2 weeks using standard cloning techniques. 2012 by John Wiley & Sons, Inc.

DOE SBIR Phase II Final Technical Report - Assessing Climate Change Effects on Wind Energy

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

Whiteman, Cameron; Capps, Scott

Specialized Vertum Partners software tools were prototyped, tested and commercialized to allow wind energy stakeholders to assess the uncertainties of climate change on wind power production and distribution. This project resulted in three commercially proven products and a marketing tool. The first was a Weather Research and Forecasting Model (WRF) based resource evaluation system. The second was a web-based service providing global 10m wind data from multiple sources to wind industry subscription customers. The third product addressed the needs of our utility clients looking at climate change effects on electricity distribution. For this we collaborated on the Santa Ana Wildfiremore » Threat Index (SAWTi), which was released publicly last quarter. Finally to promote these products and educate potential users we released “Gust or Bust”, a graphic-novel styled marketing publication.« less

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

PubMed

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

2015-08-06

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

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

NASA Astrophysics Data System (ADS)

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

1999-07-01

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

Data Discovery and Access via the Heliophysics Events Knowledgebase (HEK)

NASA Astrophysics Data System (ADS)

Somani, A.; Hurlburt, N. E.; Schrijver, C. J.; Cheung, M.; Freeland, S.; Slater, G. L.; Seguin, R.; Timmons, R.; Green, S.; Chang, L.; Kobashi, A.; Jaffey, A.

2011-12-01

The HEK is a integrated system which helps direct scientists to solar events and data from a variety of providers. The system is fully operational and adoption of HEK has been growing since the launch of NASA's SDO mission. In this presentation we describe the different components that comprise HEK. The Heliophysics Events Registry (HER) and Heliophysics Coverage Registry (HCR) form the two major databases behind the system. The HCR allows the user to search on coverage event metadata for a variety of instruments. The HER allows the user to search on annotated event metadata for a variety of instruments. Both the HCR and HER are accessible via a web API which can return search results in machine readable formats (e.g. XML and JSON). A variety of SolarSoft services are also provided to allow users to search the HEK as well as obtain and manipulate data. Other components include - the Event Detection System (EDS) continually runs feature finding algorithms on SDO data to populate the HER with relevant events, - A web form for users to request SDO data cutouts for multiple AIA channels as well as HMI line-of-sight magnetograms, - iSolSearch, which allows a user to browse events in the HER and search for specific events over a specific time interval, all within a graphical web page, - Panorama, which is the software tool used for rapid visualization of large volumes of solar image data in multiple channels/wavelengths. The user can also easily create WYSIWYG movies and launch the Annotator tool to describe events and features. - EVACS, which provides a JOGL powered client for the HER and HCR. EVACS displays the searched for events on a full disk magnetogram of the sun while displaying more detailed information for events.

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

PubMed

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

2011-07-20

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

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

ERIC Educational Resources Information Center

Huang, Kuo Hung

2011-01-01

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

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

PubMed

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

2017-01-01

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

Continuation of research into language concepts for the mission support environment

NASA Technical Reports Server (NTRS)

1991-01-01

A concept for a more intuitive and graphically based Computation (Comp) Builder was developed. The Graphical Comp Builder Prototype was developed, which is an X Window based graphical tool that allows the user to build Comps using graphical symbols. Investigation was conducted to determine the availability and suitability of the Ada programming language for the development of future control center type software. The Space Station Freedom Project identified Ada as the desirable programming language for the development of Space Station Control Center software systems.

Design and Implementation of a Tool for Teaching Programming.

ERIC Educational Resources Information Center

Goktepe, Mesut; And Others

1989-01-01

Discussion of the use of computers in education focuses on a graphics-based system for teaching the Pascal programing language for problem solving. Topics discussed include user interface; notification based systems; communication processes; object oriented programing; workstations; graphics architecture; and flowcharts. (18 references) (LRW)

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

PubMed Central

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

2013-01-01

Motivation: Easily visualization of complex data features is a necessary step to conduct studies on next-generation sequencing (NGS) data. We developed STAR, an integrated web application that enables online management, visualization and track-based analysis of NGS data. Results: STAR is a multilayer web service system. On the client side, STAR leverages JavaScript, HTML5 Canvas and asynchronous communications to deliver a smoothly scrolling desktop-like graphical user interface with a suite of in-browser analysis tools that range from providing simple track configuration controls to sophisticated feature detection within datasets. On the server side, STAR supports private session state retention via an account management system and provides data management modules that enable collection, visualization and analysis of third-party sequencing data from the public domain with over thousands of tracks hosted to date. Overall, STAR represents a next-generation data exploration solution to match the requirements of NGS data, enabling both intuitive visualization and dynamic analysis of data. Availability and implementation: STAR browser system is freely available on the web at http://wanglab.ucsd.edu/star/browser and https://github.com/angell1117/STAR-genome-browser. Contact: wei-wang@ucsd.edu PMID:24078702

3D virtual environment of Taman Mini Indonesia Indah in a web

NASA Astrophysics Data System (ADS)

Wardijono, B. A.; Wardhani, I. P.; Chandra, Y. I.; Pamungkas, B. U. G.

2018-05-01

Taman Mini Indonesia Indah known as TMII is a largest recreational park based on culture in Indonesia. This park has 250 acres that consist of houses from provinces in Indonesia. In TMII, there are traditional houses of the various provinces in Indonesia. The official website of TMII has informed the traditional houses, but the information was limited to public. To provide information more detail about TMII to the public, this research aims to create and develop virtual traditional houses as 3d graphics models and show it via website. The Virtual Reality (VR) technology was used to display the visualization of the TMII and the surrounding environment. This research used Blender software to create the 3D models and Unity3D software to make virtual reality models that can be showed on a web. This research has successfully created 33 virtual traditional houses of province in Indonesia. The texture of traditional house was taken from original to make the culture house realistic. The result of this research was the website of TMII including virtual culture houses that can be displayed through the web browser. The website consists of virtual environment scenes and internet user can walkthrough and navigates inside the scenes.

Dynamic assessment of microbial ecology (DAME): a web app for interactive analysis and visualization of microbial sequencing data.

PubMed

Piccolo, Brian D; Wankhade, Umesh D; Chintapalli, Sree V; Bhattacharyya, Sudeepa; Chunqiao, Luo; Shankar, Kartik

2018-03-15

Dynamic assessment of microbial ecology (DAME) is a Shiny-based web application for interactive analysis and visualization of microbial sequencing data. DAME provides researchers not familiar with R programming the ability to access the most current R functions utilized for ecology and gene sequencing data analyses. Currently, DAME supports group comparisons of several ecological estimates of α-diversity and β-diversity, along with differential abundance analysis of individual taxa. Using the Shiny framework, the user has complete control of all aspects of the data analysis, including sample/experimental group selection and filtering, estimate selection, statistical methods and visualization parameters. Furthermore, graphical and tabular outputs are supported by R packages using D3.js and are fully interactive. DAME was implemented in R but can be modified by Hypertext Markup Language (HTML), Cascading Style Sheets (CSS), and JavaScript. It is freely available on the web at https://acnc-shinyapps.shinyapps.io/DAME/. Local installation and source code are available through Github (https://github.com/bdpiccolo/ACNC-DAME). Any system with R can launch DAME locally provided the shiny package is installed. bdpiccolo@uams.edu.

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.

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

ERIC Educational Resources Information Center

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

2014-01-01

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

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

ERIC Educational Resources Information Center

Pomales-García, Cristina; Rivera-Nivar, Mericia

2015-01-01

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

Continuation of research into software for space operations support: Conversion of the display manager to X Windows/Motif, volume 2

NASA Technical Reports Server (NTRS)

Collier, Mark D.; Killough, Ronnie; Martin, Nancy L.

1990-01-01

NASA is currently using a set of applications called the Display Builder and Display Manager. They run on Concurrent systems and heavily depend on the Graphic Kernel System (GKS). At this time however, these two applications would more appropriately be developed in X Windows, in which a low X is used for all actual text and graphics display and a standard widget set (such as Motif) is used for the user interface. Use of the X Windows will increase performance, improve the user interface, enhance portability, and improve reliability. Prototype of X Window/Motif based Display Manager provides the following advantages over a GKS based application: improved performance by using a low level X Windows, display of graphic and text will be more efficient; improved user interface by using Motif; Improved portability by operating on both Concurrent and Sun workstations; and Improved reliability.

A Web platform for the interactive visualization and analysis of the 3D fractal dimension of MRI data.

PubMed

Jiménez, J; López, A M; Cruz, J; Esteban, F J; Navas, J; Villoslada, P; Ruiz de Miras, J

2014-10-01

This study presents a Web platform (http://3dfd.ujaen.es) for computing and analyzing the 3D fractal dimension (3DFD) from volumetric data in an efficient, visual and interactive way. The Web platform is specially designed for working with magnetic resonance images (MRIs) of the brain. The program estimates the 3DFD by calculating the 3D box-counting of the entire volume of the brain, and also of its 3D skeleton. All of this is done in a graphical, fast and optimized way by using novel technologies like CUDA and WebGL. The usefulness of the Web platform presented is demonstrated by its application in a case study where an analysis and characterization of groups of 3D MR images is performed for three neurodegenerative diseases: Multiple Sclerosis, Intrauterine Growth Restriction and Alzheimer's disease. To the best of our knowledge, this is the first Web platform that allows the users to calculate, visualize, analyze and compare the 3DFD from MRI images in the cloud. Copyright © 2014 Elsevier Inc. All rights reserved.

Observed and forecast flood-inundation mapping application-A pilot study of an eleven-mile reach of the White River, Indianapolis, Indiana

USGS Publications Warehouse

Kim, Moon H.; Morlock, Scott E.; Arihood, Leslie D.; Kiesler, James L.

2011-01-01

Near-real-time and forecast flood-inundation mapping products resulted from a pilot study for an 11-mile reach of the White River in Indianapolis. The study was done by the U.S. Geological Survey (USGS), Indiana Silver Jackets hazard mitigation taskforce members, the National Weather Service (NWS), the Polis Center, and Indiana University, in cooperation with the City of Indianapolis, the Indianapolis Museum of Art, the Indiana Department of Homeland Security, and the Indiana Department of Natural Resources, Division of Water. The pilot project showed that it is technically feasible to create a flood-inundation map library by means of a two-dimensional hydraulic model, use a map from the library to quickly complete a moderately detailed local flood-loss estimate, and automatically run the hydraulic model during a flood event to provide the maps and flood-damage information through a Web graphical user interface. A library of static digital flood-inundation maps was created by means of a calibrated two-dimensional hydraulic model. Estimated water-surface elevations were developed for a range of river stages referenced to a USGS streamgage and NWS flood forecast point colocated within the study reach. These maps were made available through the Internet in several formats, including geographic information system, Keyhole Markup Language, and Portable Document Format. A flood-loss estimate was completed for part of the study reach by using one of the flood-inundation maps from the static library. The Federal Emergency Management Agency natural disaster-loss estimation program HAZUS-MH, in conjunction with local building information, was used to complete a level 2 analysis of flood-loss estimation. A Service-Oriented Architecture-based dynamic flood-inundation application was developed and was designed to start automatically during a flood, obtain near real-time and forecast data (from the colocated USGS streamgage and NWS flood forecast point within the study reach), run the two-dimensional hydraulic model, and produce flood-inundation maps. The application used local building data and depth-damage curves to estimate flood losses based on the maps, and it served inundation maps and flood-loss estimates through a Web-based graphical user interface.

PyCorrFit-generic data evaluation for fluorescence correlation spectroscopy.

PubMed

Müller, Paul; Schwille, Petra; Weidemann, Thomas

2014-09-01

We present a graphical user interface (PyCorrFit) for the fitting of theoretical model functions to experimental data obtained by fluorescence correlation spectroscopy (FCS). The program supports many data file formats and features a set of tools specialized in FCS data evaluation. The Python source code is freely available for download from the PyCorrFit web page at http://pycorrfit.craban.de. We offer binaries for Ubuntu Linux, Mac OS X and Microsoft Windows. © The Author 2014. Published by Oxford University Press.

Graphic Enhancement of the Aircraft Penetration Model for Use as an Analytic Tool.

DTIC Science & Technology

1983-03-01

internal web of subroutines linked by a ’nervous sytem’ of labelled common blocks." [Ref. 23] Once the user prescribes the parameters for a particular...10 MI4 - ww (A~’ - 0 z . l J- 6,- L a-. 1- ’..u.. - V):LA r w iJ..W 0 d4- Z 9- wtv 4)Lj.J.44 I---M. .. j jU- Wix it 9I’-wku SAXw. Q.3 t- Vd I)4.J13v)v

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.

[Digital teaching archive. Concept, implementation, and experiences in a university setting].

PubMed

Trumm, C; Dugas, M; Wirth, S; Treitl, M; Lucke, A; Küttner, B; Pander, E; Clevert, D-A; Glaser, C; Reiser, M

2005-08-01

Film-based teaching files require a substantial investment in human, logistic, and financial resources. The combination of computer and network technology facilitates the workflow integration of distributing radiologic teaching cases within an institution (intranet) or via the World Wide Web (Internet). A digital teaching file (DTF) should include the following basic functions: image import from different sources and of different formats, editing of imported images, uniform case classification, quality control (peer review), a controlled access of different user groups (in-house and external), and an efficient retrieval strategy. The portable network graphics image format (PNG) is especially suitable for DTFs because of several features: pixel support, 2D-interlacing, gamma correction, and lossless compression. The American College of Radiology (ACR) "Index for Radiological Diagnoses" is hierarchically organized and thus an ideal classification system for a DTF. Computer-based training (CBT) in radiology is described in numerous publications, from supplementing traditional learning methods to certified education via the Internet. Attractiveness of a CBT application can be increased by integration of graphical and interactive elements but makes workflow integration of daily case input more difficult. Our DTF was built with established Internet instruments and integrated into a heterogeneous PACS/RIS environment. It facilitates a quick transfer (DICOM_Send) of selected images at the time of interpretation to the DTF and access to the DTF application at any time anywhere within the university hospital intranet employing a standard web browser. A DTF is a small but important building block in an institutional strategy of knowledge management.

Satellite-based virtual buoy system to monitor coastal water quality

NASA Astrophysics Data System (ADS)

Hu, Chuanmin; Barnes, Brian B.; Murch, Brock; Carlson, Paul

2014-05-01

There is a pressing need to assess coastal and estuarine water quality state and anomaly events to facilitate coastal management, but such a need is hindered by lack of resources to conduct frequent ship-based or buoy-based measurements. Here, we established a virtual buoy system (VBS) to facilitate satellite data visualization and interpretation of water quality assessment. The VBS is based on a virtual antenna system (VAS) that obtains low-level satellite data and generates higher-level data products using both National Aeronautics and Space Administration standard algorithms and regionally customized algorithms in near real time. The VB stations are predefined and carefully chosen to cover water quality gradients in estuaries and coastal waters, where multiyear time series at monthly and weekly intervals are extracted for the following parameters: sea surface temperature (°C), chlorophyll-a concentration (mg m-3), turbidity (NTU), diffuse light attenuation at 490 nm [Kd(490), m-1] or secchi disk depth (m), absorption coefficient of colored dissolved organic matter (m-1), and bottom available light (%). The time-series data are updated routinely and provided in both ASCII and graphical formats via a user-friendly web interface where all information is available to the user through a simple click. The VAS and VBS also provide necessary infrastructure to implement peer-reviewed regional algorithms to generate and share improved water quality data products with the user community.

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

PubMed Central

Davis, Ian W.; Leaver-Fay, Andrew; Chen, Vincent B.; Block, Jeremy N.; Kapral, Gary J.; Wang, Xueyi; Murray, Laura W.; Arendall, W. Bryan; Snoeyink, Jack; Richardson, Jane S.; Richardson, David C.

2007-01-01

MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu. PMID:17452350