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

PubMed

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

2018-01-04

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

Visualization of usability and functionality of a professional website through web-mining.

PubMed

Jones, Josette F; Mahoui, Malika; Gopa, Venkata Devi Pragna

2007-10-11

Functional interface design requires understanding of the information system structure and the user. Web logs record user interactions with the interface, and thus provide some insight into user search behavior and efficiency of the search process. The present study uses a data-mining approach with techniques such as association rules, clustering and classification, to visualize the usability and functionality of a digital library through in depth analyses of web logs.

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

NASA Astrophysics Data System (ADS)

Mack, P.

2003-05-01

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

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

PubMed Central

Muin, Michael; Fontelo, Paul

2006-01-01

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

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

ERIC Educational Resources Information Center

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

2008-01-01

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

A Web Tool for Research in Nonlinear Optics

NASA Astrophysics Data System (ADS)

Prikhod'ko, Nikolay V.; Abramovsky, Viktor A.; Abramovskaya, Natalia V.; Demichev, Andrey P.; Kryukov, Alexandr P.; Polyakov, Stanislav P.

2016-02-01

This paper presents a project of developing the web platform called WebNLO for computer modeling of nonlinear optics phenomena. We discuss a general scheme of the platform and a model for interaction between the platform modules. The platform is built as a set of interacting RESTful web services (SaaS approach). Users can interact with the platform through a web browser or command line interface. Such a resource has no analogues in the field of nonlinear optics and will be created for the first time therefore allowing researchers to access high-performance computing resources that will significantly reduce the cost of the research and development process.

BindML/BindML+: Detecting Protein-Protein Interaction Interface Propensity from Amino Acid Substitution Patterns.

PubMed

Wei, Qing; La, David; Kihara, Daisuke

2017-01-01

Prediction of protein-protein interaction sites in a protein structure provides important information for elucidating the mechanism of protein function and can also be useful in guiding a modeling or design procedures of protein complex structures. Since prediction methods essentially assess the propensity of amino acids that are likely to be part of a protein docking interface, they can help in designing protein-protein interactions. Here, we introduce BindML and BindML+ protein-protein interaction sites prediction methods. BindML predicts protein-protein interaction sites by identifying mutation patterns found in known protein-protein complexes using phylogenetic substitution models. BindML+ is an extension of BindML for distinguishing permanent and transient types of protein-protein interaction sites. We developed an interactive web-server that provides a convenient interface to assist in structural visualization of protein-protein interactions site predictions. The input data for the web-server are a tertiary structure of interest. BindML and BindML+ are available at http://kiharalab.org/bindml/ and http://kiharalab.org/bindml/plus/ .

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

PubMed Central

2015-01-01

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

A new reference implementation of the PSICQUIC web service.

PubMed

del-Toro, Noemi; Dumousseau, Marine; Orchard, Sandra; Jimenez, Rafael C; Galeota, Eugenia; Launay, Guillaume; Goll, Johannes; Breuer, Karin; Ono, Keiichiro; Salwinski, Lukasz; Hermjakob, Henning

2013-07-01

The Proteomics Standard Initiative Common QUery InterfaCe (PSICQUIC) specification was created by the Human Proteome Organization Proteomics Standards Initiative (HUPO-PSI) to enable computational access to molecular-interaction data resources by means of a standard Web Service and query language. Currently providing >150 million binary interaction evidences from 28 servers globally, the PSICQUIC interface allows the concurrent search of multiple molecular-interaction information resources using a single query. Here, we present an extension of the PSICQUIC specification (version 1.3), which has been released to be compliant with the enhanced standards in molecular interactions. The new release also includes a new reference implementation of the PSICQUIC server available to the data providers. It offers augmented web service capabilities and improves the user experience. PSICQUIC has been running for almost 5 years, with a user base growing from only 4 data providers to 28 (April 2013) allowing access to 151 310 109 binary interactions. The power of this web service is shown in PSICQUIC View web application, an example of how to simultaneously query, browse and download results from the different PSICQUIC servers. This application is free and open to all users with no login requirement (http://www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml).

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

NASA Astrophysics Data System (ADS)

Demir, I.

2015-12-01

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

Internet Technology in Magnetic Resonance: A Common Gateway Interface Program for the World-Wide Web NMR Spectrometer

NASA Astrophysics Data System (ADS)

Buszko, Marian L.; Buszko, Dominik; Wang, Daniel C.

1998-04-01

A custom-written Common Gateway Interface (CGI) program for remote control of an NMR spectrometer using a World Wide Web browser has been described. The program, running on a UNIX workstation, uses multiple processes to handle concurrent tasks of interacting with the user and with the spectrometer. The program's parent process communicates with the browser and sends out commands to the spectrometer; the child process is mainly responsible for data acquisition. Communication between the processes is via the shared memory mechanism. The WWW pages that have been developed for the system make use of the frames feature of web browsers. The CGI program provides an intuitive user interface to the NMR spectrometer, making, in effect, a complex system an easy-to-use Web appliance.

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.

Effective Levels of Adaptation to Different Types of Users in Interactive Museum Systems.

ERIC Educational Resources Information Center

Paterno, F.; Mancini, C.

2000-01-01

Discusses user interaction with museum application interfaces and emphasizes the importance of adaptable and adaptive interfaces to meet differing user needs. Considers levels of support that can be given to different users during navigation of museum hypermedia information, using examples from the Web site for the Marble Museum (Italy).…

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

PubMed Central

Turner, Brian; Razick, Sabry; Turinsky, Andrei L.; Vlasblom, James; Crowdy, Edgard K.; Cho, Emerson; Morrison, Kyle; Wodak, Shoshana J.

2010-01-01

We present iRefWeb, a web interface to protein interaction data consolidated from 10 public databases: BIND, BioGRID, CORUM, DIP, IntAct, HPRD, MINT, MPact, MPPI and OPHID. iRefWeb enables users to examine aggregated interactions for a protein of interest, and presents various statistical summaries of the data across databases, such as the number of organism-specific interactions, proteins and cited publications. Through links to source databases and supporting evidence, researchers may gauge the reliability of an interaction using simple criteria, such as the detection methods, the scale of the study (high- or low-throughput) or the number of cited publications. Furthermore, iRefWeb compares the information extracted from the same publication by different databases, and offers means to follow-up possible inconsistencies. We provide an overview of the consolidated protein–protein interaction landscape and show how it can be automatically cropped to aid the generation of meaningful organism-specific interactomes. iRefWeb can be accessed at: http://wodaklab.org/iRefWeb. Database URL: http://wodaklab.org/iRefWeb/ PMID:20940177

Open Technology Approaches to Geospatial Interface Design

NASA Astrophysics Data System (ADS)

Crevensten, B.; Simmons, D.; Alaska Satellite Facility

2011-12-01

What problems do you not want your software developers to be solving? Choosing open technologies across the entire stack of software development-from low-level shared libraries to high-level user interaction implementations-is a way to help ensure that customized software yields innovative and valuable tools for Earth Scientists. This demonstration will review developments in web application technologies and the recurring patterns of interaction design regarding exploration and discovery of geospatial data through the Vertex: ASF's Dataportal interface, a project utilizing current open web application standards and technologies including HTML5, jQueryUI, Backbone.js and the Jasmine unit testing framework.

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

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

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

PubMed

Blin, Kai; Wohlleben, Wolfgang; Weber, Tilmann

2018-05-02

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

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

PubMed

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

2010-05-01

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

Internet Technology in Magnetic Resonance: A Common Gateway Interface Program for the World-Wide Web NMR Spectrometer

PubMed

Buszko; Buszko; Wang

1998-04-01

A custom-written Common Gateway Interface (CGI) program for remote control of an NMR spectrometer using a World Wide Web browser has been described. The program, running on a UNIX workstation, uses multiple processes to handle concurrent tasks of interacting with the user and with the spectrometer. The program's parent process communicates with the browser and sends out commands to the spectrometer; the child process is mainly responsible for data acquisition. Communication between the processes is via the shared memory mechanism. The WWW pages that have been developed for the system make use of the frames feature of web browsers. The CGI program provides an intuitive user interface to the NMR spectrometer, making, in effect, a complex system an easy-to-use Web appliance. Copyright 1998 Academic Press.

Information Architecture for the Web: The IA Matrix Approach to Designing Children's Portals.

ERIC Educational Resources Information Center

Large, Andrew; Beheshti, Jamshid; Cole, Charles

2002-01-01

Presents a matrix that can serve as a tool for designing the information architecture of a Web portal in a logical and systematic manner. Highlights include interfaces; metaphors; navigation; interaction; information retrieval; and an example of a children's Web portal to provide access to museum information. (Author/LRW)

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…

Sign language Web pages.

PubMed

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

2006-01-01

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

Web accessibility and open source software.

PubMed

Obrenović, Zeljko

2009-07-01

A Web browser provides a uniform user interface to different types of information. Making this interface universally accessible and more interactive is a long-term goal still far from being achieved. Universally accessible browsers require novel interaction modalities and additional functionalities, for which existing browsers tend to provide only partial solutions. Although functionality for Web accessibility can be found as open source and free software components, their reuse and integration is complex because they were developed in diverse implementation environments, following standards and conventions incompatible with the Web. To address these problems, we have started several activities that aim at exploiting the potential of open-source software for Web accessibility. The first of these activities is the development of Adaptable Multi-Interface COmmunicator (AMICO):WEB, an infrastructure that facilitates efficient reuse and integration of open source software components into the Web environment. The main contribution of AMICO:WEB is in enabling the syntactic and semantic interoperability between Web extension mechanisms and a variety of integration mechanisms used by open source and free software components. Its design is based on our experiences in solving practical problems where we have used open source components to improve accessibility of rich media Web applications. The second of our activities involves improving education, where we have used our platform to teach students how to build advanced accessibility solutions from diverse open-source software. We are also partially involved in the recently started Eclipse projects called Accessibility Tools Framework (ACTF), the aim of which is development of extensible infrastructure, upon which developers can build a variety of utilities that help to evaluate and enhance the accessibility of applications and content for people with disabilities. In this article we briefly report on these activities.

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.

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2014-07-01

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

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

Chao, Tian-Jy; Kim, Younghun

An end-to-end interoperability and workflows from building architecture design to one or more simulations, in one aspect, may comprise establishing a BIM enablement platform architecture. A data model defines data entities and entity relationships for enabling the interoperability and workflows. A data definition language may be implemented that defines and creates a table schema of a database associated with the data model. Data management services and/or application programming interfaces may be implemented for interacting with the data model. Web services may also be provided for interacting with the data model via the Web. A user interface may be implemented thatmore » communicates with users and uses the BIM enablement platform architecture, the data model, the data definition language, data management services and application programming interfaces to provide functions to the users to perform work related to building information management.« less

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.

Lost in Interaction in IMS Learning Design Runtime Environments

ERIC Educational Resources Information Center

Derntl, Michael; Neumann, Susanne; Oberhuemer, Petra

2014-01-01

Educators are exploiting the advantages of advanced web-based collaboration technologies and massive online interactions. Interactions between learners and human or nonhuman resources therefore play an increasingly important pedagogical role, and the way these interactions are expressed in the user interface of virtual learning environments is…

Development of Web Interfaces for Analysis Codes

NASA Astrophysics Data System (ADS)

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

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

Web-based metabolic network visualization with a zooming user interface

PubMed Central

2011-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-07-01

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

3dRPC: a web server for 3D RNA-protein structure prediction.

PubMed

Huang, Yangyu; Li, Haotian; Xiao, Yi

2018-04-01

RNA-protein interactions occur in many biological processes. To understand the mechanism of these interactions one needs to know three-dimensional (3D) structures of RNA-protein complexes. 3dRPC is an algorithm for prediction of 3D RNA-protein complex structures and consists of a docking algorithm RPDOCK and a scoring function 3dRPC-Score. RPDOCK is used to sample possible complex conformations of an RNA and a protein by calculating the geometric and electrostatic complementarities and stacking interactions at the RNA-protein interface according to the features of atom packing of the interface. 3dRPC-Score is a knowledge-based potential that uses the conformations of nucleotide-amino-acid pairs as statistical variables and that is used to choose the near-native complex-conformations obtained from the docking method above. Recently, we built a web server for 3dRPC. The users can easily use 3dRPC without installing it locally. RNA and protein structures in PDB (Protein Data Bank) format are the only needed input files. It can also incorporate the information of interface residues or residue-pairs obtained from experiments or theoretical predictions to improve the prediction. The address of 3dRPC web server is http://biophy.hust.edu.cn/3dRPC. yxiao@hust.edu.cn.

Solar Irradiance Data Products at the LASP Interactive Solar IRradiance Datacenter (LISIRD)

NASA Astrophysics Data System (ADS)

Lindholm, D. M.; Ware DeWolfe, A.; Wilson, A.; Pankratz, C. K.; Snow, M. A.; Woods, T. N.

2011-12-01

The Laboratory for Atmospheric and Space Physics (LASP) has developed the LASP Interactive Solar IRradiance Datacenter (LISIRD, http://lasp.colorado.edu/lisird/) web site to provide access to a comprehensive set of solar irradiance measurements and related datasets. Current data holdings include products from NASA missions SORCE, UARS, SME, and TIMED-SEE. The data provided covers a wavelength range from soft X-ray (XUV) at 0.1 nm up to the near infrared (NIR) at 2400 nm, as well as Total Solar Irradiance (TSI). Other datasets include solar indices, spectral and flare models, solar images, and more. The LISIRD web site features updated plotting, browsing, and download capabilities enabled by dygraphs, JavaScript, and Ajax calls to the LASP Time Series Server (LaTiS). In addition to the web browser interface, most of the LISIRD datasets can be accessed via the LaTiS web service interface that supports the OPeNDAP standard. OPeNDAP clients and other programming APIs are available for making requests that subset, aggregate, or filter data on the server before it is transported to the user. This poster provides an overview of the LISIRD system, summarizes the datasets currently available, and provides details on how to access solar irradiance data products through LISIRD's interfaces.

Universities and Libraries Move to the Mobile Web

ERIC Educational Resources Information Center

Aldrich, Alan W.

2010-01-01

The convergence of web-enabled smartphones, the applications designed for smartphone interfaces, and cloud computing is rapidly changing how people interact with each other and with their environments. The commercial sector has taken the lead in creating mobile websites that leverage the capacities of smartphones, and the academic community has…

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.

PRince: a web server for structural and physicochemical analysis of protein-RNA interface.

PubMed

Barik, Amita; Mishra, Abhishek; Bahadur, Ranjit Prasad

2012-07-01

We have developed a web server, PRince, which analyzes the structural features and physicochemical properties of the protein-RNA interface. Users need to submit a PDB file containing the atomic coordinates of both the protein and the RNA molecules in complex form (in '.pdb' format). They should also mention the chain identifiers of interacting protein and RNA molecules. The size of the protein-RNA interface is estimated by measuring the solvent accessible surface area buried in contact. For a given protein-RNA complex, PRince calculates structural, physicochemical and hydration properties of the interacting surfaces. All these parameters generated by the server are presented in a tabular format. The interacting surfaces can also be visualized with software plug-in like Jmol. In addition, the output files containing the list of the atomic coordinates of the interacting protein, RNA and interface water molecules can be downloaded. The parameters generated by PRince are novel, and users can correlate them with the experimentally determined biophysical and biochemical parameters for better understanding the specificity of the protein-RNA recognition process. This server will be continuously upgraded to include more parameters. PRince is publicly accessible and free for use. Available at http://www.facweb.iitkgp.ernet.in/~rbahadur/prince/home.html.

End-to-end interoperability and workflows from building architecture design to one or more simulations

DOEpatents

Chao, Tian-Jy; Kim, Younghun

2015-02-10

An end-to-end interoperability and workflows from building architecture design to one or more simulations, in one aspect, may comprise establishing a BIM enablement platform architecture. A data model defines data entities and entity relationships for enabling the interoperability and workflows. A data definition language may be implemented that defines and creates a table schema of a database associated with the data model. Data management services and/or application programming interfaces may be implemented for interacting with the data model. Web services may also be provided for interacting with the data model via the Web. A user interface may be implemented that communicates with users and uses the BIM enablement platform architecture, the data model, the data definition language, data management services and application programming interfaces to provide functions to the users to perform work related to building information management.

An Interactive Medical Knowledge Assistant

NASA Astrophysics Data System (ADS)

Czejdo, Bogdan D.; Baszun, Mikolaj

This paper describes an interactive medical knowledge assistant that can help a doctor or a patient in making important health related decisions. The system is Web based and consists of several modules, including a medical knowledge base, a doctor interface module, patient interface module and a the main module of the medical knowledge assistant. The medical assistant is designed to help interpret the fuzzy data using rough sets approach. The patient interface includes sub-system for real time monitoring of patients' health parameters and sending them to the main module of the medical knowledge assistant.

WMI2, the Student's On-Line Symbolic Calculator

ERIC Educational Resources Information Center

Kovacs, Zoltan

2011-01-01

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

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

NASA Astrophysics Data System (ADS)

Demir, I.; Krajewski, W. F.

2012-04-01

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

ESTminer: a Web interface for mining EST contig and cluster databases.

PubMed

Huang, Yecheng; Pumphrey, Janie; Gingle, Alan R

2005-03-01

ESTminer is a Web application and database schema for interactive mining of expressed sequence tag (EST) contig and cluster datasets. The Web interface contains a query frame that allows the selection of contigs/clusters with specific cDNA library makeup or a threshold number of members. The results are displayed as color-coded tree nodes, where the color indicates the fractional size of each cDNA library component. The nodes are expandable, revealing library statistics as well as EST or contig members, with links to sequence data, GenBank records or user configurable links. Also, the interface allows 'queries within queries' where the result set of a query is further filtered by the subsequent query. ESTminer is implemented in Java/JSP and the package, including MySQL and Oracle schema creation scripts, is available from http://cggc.agtec.uga.edu/Data/download.asp agingle@uga.edu.

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

NASA Astrophysics Data System (ADS)

Manaud, N.; Gonzalez, J.

2014-04-01

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

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

NASA Technical Reports Server (NTRS)

Day, B; Law, Emily S.

2017-01-01

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

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

NASA Astrophysics Data System (ADS)

Day, B.; Law, E.

2017-09-01

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

The Monash University Interactive Simple Climate Model

NASA Astrophysics Data System (ADS)

Dommenget, D.

2013-12-01

The Monash university interactive simple climate model is a web-based interface that allows students and the general public to explore the physical simulation of the climate system with a real global climate model. It is based on the Globally Resolved Energy Balance (GREB) model, which is a climate model published by Dommenget and Floeter [2011] in the international peer review science journal Climate Dynamics. The model simulates most of the main physical processes in the climate system in a very simplistic way and therefore allows very fast and simple climate model simulations on a normal PC computer. Despite its simplicity the model simulates the climate response to external forcings, such as doubling of the CO2 concentrations very realistically (similar to state of the art climate models). The Monash simple climate model web-interface allows you to study the results of more than a 2000 different model experiments in an interactive way and it allows you to study a number of tutorials on the interactions of physical processes in the climate system and solve some puzzles. By switching OFF/ON physical processes you can deconstruct the climate and learn how all the different processes interact to generate the observed climate and how the processes interact to generate the IPCC predicted climate change for anthropogenic CO2 increase. The presentation will illustrate how this web-base tool works and what are the possibilities in teaching students with this tool are.

ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites.

PubMed

Konc, Janez; Miller, Benjamin T; Štular, Tanja; Lešnik, Samo; Woodcock, H Lee; Brooks, Bernard R; Janežič, Dušanka

2015-11-23

Proteins often exist only as apo structures (unligated) in the Protein Data Bank, with their corresponding holo structures (with ligands) unavailable. However, apoproteins may not represent the amino-acid residue arrangement upon ligand binding well, which is especially problematic for molecular docking. We developed the ProBiS-CHARMMing web interface by connecting the ProBiS ( http://probis.cmm.ki.si ) and CHARMMing ( http://www.charmming.org ) web servers into one functional unit that enables prediction of protein-ligand complexes and allows for their geometry optimization and interaction energy calculation. The ProBiS web server predicts ligands (small compounds, proteins, nucleic acids, and single-atom ligands) that may bind to a query protein. This is achieved by comparing its surface structure against a nonredundant database of protein structures and finding those that have binding sites similar to that of the query protein. Existing ligands found in the similar binding sites are then transposed to the query according to predictions from ProBiS. The CHARMMing web server enables, among other things, minimization and potential energy calculation for a wide variety of biomolecular systems, and it is used here to optimize the geometry of the predicted protein-ligand complex structures using the CHARMM force field and to calculate their interaction energies with the corresponding query proteins. We show how ProBiS-CHARMMing can be used to predict ligands and their poses for a particular binding site, and minimize the predicted protein-ligand complexes to obtain representations of holoproteins. The ProBiS-CHARMMing web interface is freely available for academic users at http://probis.nih.gov.

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

NASA Technical Reports Server (NTRS)

Lin, Risheng; Afjeh, Abdollah A.

2003-01-01

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

IntegratedMap: a Web interface for integrating genetic map data.

PubMed

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

2005-05-01

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

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

PubMed

Olechnovič, Kliment; Venclovas, Ceslovas

2014-07-01

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

Interactive Web-based Floodplain Simulation System for Realistic Experiments of Flooding and Flood Damage

NASA Astrophysics Data System (ADS)

Demir, I.

2013-12-01

Recent developments in web technologies make it easy to manage and visualize large data sets with general public. Novel visualization techniques and dynamic user interfaces allow users to create realistic environments, and interact with data to gain insight from simulations and environmental observations. The floodplain simulation system is a web-based 3D interactive flood simulation environment to create real world flooding scenarios. The simulation systems provides a visually striking platform with realistic terrain information, and water simulation. Students can create and modify predefined scenarios, control environmental parameters, and evaluate flood mitigation techniques. The web-based simulation system provides an environment to children and adults learn about the flooding, flood damage, and effects of development and human activity in the floodplain. The system provides various scenarios customized to fit the age and education level of the users. This presentation provides an overview of the web-based flood simulation system, and demonstrates the capabilities of the system for various flooding and land use scenarios.

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

PubMed

Madadkar-Sobhani, Armin; Guallar, Victor

2013-07-01

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

41 CFR 102-33.400 - How must we report to FAIRS?

Code of Federal Regulations, 2013 CFR

2013-07-01

... a secure Web interface to the FAIRS application on the Internet. For information on becoming a FAIRS... GOVERNMENT AIRCRAFT Reporting Information on Government Aircraft Federal Aviation Interactive Reporting...

41 CFR 102-33.400 - How must we report to FAIRS?

Code of Federal Regulations, 2012 CFR

2012-01-01

... a secure Web interface to the FAIRS application on the Internet. For information on becoming a FAIRS... GOVERNMENT AIRCRAFT Reporting Information on Government Aircraft Federal Aviation Interactive Reporting...

41 CFR 102-33.400 - How must we report to FAIRS?

Code of Federal Regulations, 2014 CFR

2014-01-01

... a secure Web interface to the FAIRS application on the Internet. For information on becoming a FAIRS... GOVERNMENT AIRCRAFT Reporting Information on Government Aircraft Federal Aviation Interactive Reporting...

41 CFR 102-33.400 - How must we report to FAIRS?

Code of Federal Regulations, 2011 CFR

2011-01-01

... a secure Web interface to the FAIRS application on the Internet. For information on becoming a FAIRS... GOVERNMENT AIRCRAFT Reporting Information on Government Aircraft Federal Aviation Interactive Reporting...

Making Your Tools Useful to a Broader Audience

NASA Astrophysics Data System (ADS)

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

2006-12-01

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

The OGC Sensor Web Enablement framework

NASA Astrophysics Data System (ADS)

Cox, S. J.; Botts, M.

2006-12-01

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

Nuclear data made easily accessible through the Notre Dame Nuclear Database

NASA Astrophysics Data System (ADS)

Khouw, Timothy; Lee, Kevin; Fasano, Patrick; Mumpower, Matthew; Aprahamian, Ani

2014-09-01

In 1994, the NNDC revolutionized nuclear research by providing a colorful, clickable, searchable database over the internet. Over the last twenty years, web technology has evolved dramatically. Our project, the Notre Dame Nuclear Database, aims to provide a more comprehensive and broadly searchable interactive body of data. The database can be searched by an array of filters which includes metadata such as the facility where a measurement is made, the author(s), or date of publication for the datum of interest. The user interface takes full advantage of HTML, a web markup language, CSS (cascading style sheets to define the aesthetics of the website), and JavaScript, a language that can process complex data. A command-line interface is supported that interacts with the database directly on a user's local machine which provides single command access to data. This is possible through the use of a standardized API (application programming interface) that relies upon well-defined filtering variables to produce customized search results. We offer an innovative chart of nuclides utilizing scalable vector graphics (SVG) to deliver users an unsurpassed level of interactivity supported on all computers and mobile devices. We will present a functional demo of our database at the conference.

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.

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.

DESCQA: Synthetic Sky Catalog Validation Framework

NASA Astrophysics Data System (ADS)

Mao, Yao-Yuan; Uram, Thomas D.; Zhou, Rongpu; Kovacs, Eve; Ricker, Paul M.; Kalmbach, J. Bryce; Padilla, Nelson; Lanusse, François; Zu, Ying; Tenneti, Ananth; Vikraman, Vinu; DeRose, Joseph

2018-04-01

The DESCQA framework provides rigorous validation protocols for assessing the quality of high-quality simulated sky catalogs in a straightforward and comprehensive way. DESCQA enables the inspection, validation, and comparison of an inhomogeneous set of synthetic catalogs via the provision of a common interface within an automated framework. An interactive web interface is also available at portal.nersc.gov/project/lsst/descqa.

The use of haptic interfaces and web services in crystallography: an application for a `screen to beam' interface

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

Bruno, Andrew E.; Soares, Alexei S.; Owen, Robin L.

Haptic interfaces have become common in consumer electronics. They enable easy interaction and information entry without the use of a mouse or keyboard. Our work illustrates the application of a haptic interface to crystallization screening in order to provide a natural means for visualizing and selecting results. By linking this to a cloud-based database and web-based application program interface, the same application shifts the approach from `point and click' to `touch and share', where results can be selected, annotated and discussed collaboratively. Furthermore, in the crystallographic application, given a suitable crystallization plate, beamline and robotic end effector, the resulting informationmore » can be used to close the loop between screening and X-ray analysis, allowing a direct and efficient `screen to beam' approach. The application is not limited to the area of crystallization screening; `touch and share' can be used by any information-rich scientific analysis and geographically distributed collaboration.« less

The use of haptic interfaces and web services in crystallography: an application for a `screen to beam' interface

DOE PAGES

Bruno, Andrew E.; Soares, Alexei S.; Owen, Robin L.; ...

2016-11-11

Haptic interfaces have become common in consumer electronics. They enable easy interaction and information entry without the use of a mouse or keyboard. Our work illustrates the application of a haptic interface to crystallization screening in order to provide a natural means for visualizing and selecting results. By linking this to a cloud-based database and web-based application program interface, the same application shifts the approach from `point and click' to `touch and share', where results can be selected, annotated and discussed collaboratively. Furthermore, in the crystallographic application, given a suitable crystallization plate, beamline and robotic end effector, the resulting informationmore » can be used to close the loop between screening and X-ray analysis, allowing a direct and efficient `screen to beam' approach. The application is not limited to the area of crystallization screening; `touch and share' can be used by any information-rich scientific analysis and geographically distributed collaboration.« less

A Randomized Trial Comparing Classical Participatory Design to VandAID, an Interactive CrowdSourcing Platform to Facilitate User-centered Design.

PubMed

Dufendach, Kevin R; Koch, Sabine; Unertl, Kim M; Lehmann, Christoph U

2017-10-26

Early involvement of stakeholders in the design of medical software is particularly important due to the need to incorporate complex knowledge and actions associated with clinical work. Standard user-centered design methods include focus groups and participatory design sessions with individual stakeholders, which generally limit user involvement to a small number of individuals due to the significant time investments from designers and end users. The goal of this project was to reduce the effort for end users to participate in co-design of a software user interface by developing an interactive web-based crowdsourcing platform. In a randomized trial, we compared a new web-based crowdsourcing platform to standard participatory design sessions. We developed an interactive, modular platform that allows responsive remote customization and design feedback on a visual user interface based on user preferences. The responsive canvas is a dynamic HTML template that responds in real time to user preference selections. Upon completion, the design team can view the user's interface creations through an administrator portal and download the structured selections through a REDCap interface. We have created a software platform that allows users to customize a user interface and see the results of that customization in real time, receiving immediate feedback on the impact of their design choices. Neonatal clinicians used the new platform to successfully design and customize a neonatal handoff tool. They received no specific instruction and yet were able to use the software easily and reported high usability. VandAID, a new web-based crowdsourcing platform, can involve multiple users in user-centered design simultaneously and provides means of obtaining design feedback remotely. The software can provide design feedback at any stage in the design process, but it will be of greatest utility for specifying user requirements and evaluating iterative designs with multiple options.

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

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…

KFC Server: interactive forecasting of protein interaction hot spots.

PubMed

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

2008-07-01

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

KFC Server: interactive forecasting of protein interaction hot spots

PubMed Central

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

2008-01-01

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

Web-based health services and clinical decision support.

PubMed

Jegelevicius, Darius; Marozas, Vaidotas; Lukosevicius, Arunas; Patasius, Martynas

2004-01-01

The purpose of this study was the development of a Web-based e-health service for comprehensive assistance and clinical decision support. The service structure consists of a Web server, a PHP-based Web interface linked to a clinical SQL database, Java applets for interactive manipulation and visualization of signals and a Matlab server linked with signal and data processing algorithms implemented by Matlab programs. The service ensures diagnostic signal- and image analysis-sbased clinical decision support. By using the discussed methodology, a pilot service for pathology specialists for automatic calculation of the proliferation index has been developed. Physicians use a simple Web interface for uploading the pictures under investigation to the server; subsequently a Java applet interface is used for outlining the region of interest and, after processing on the server, the requested proliferation index value is calculated. There is also an "expert corner", where experts can submit their index estimates and comments on particular images, which is especially important for system developers. These expert evaluations are used for optimization and verification of automatic analysis algorithms. Decision support trials have been conducted for ECG and ophthalmology ultrasonic investigations of intraocular tumor differentiation. Data mining algorithms have been applied and decision support trees constructed. These services are under implementation by a Web-based system too. The study has shown that the Web-based structure ensures more effective, flexible and accessible services compared with standalone programs and is very convenient for biomedical engineers and physicians, especially in the development phase.

Dosvox Usability: recommendations for improving interaction of blind people with the web using the system.

PubMed

de Souza, Edson Rufino; de Freitas, Sydney Fernandes

2012-01-01

At present, it is recognized that the Internet plays key role in universalization of opportunities in society in which we live. For people with disabilities, the content must be accessible in all websites, but the assistive technologies used must be adequate to the specific needs of people with disabilities. Dosvox is a free system developed in the Universidade Federal do Rio de Janeiro (UFRJ) specially designed for blind people and used by them in the performance of their tasks with the use of computers. Previously, through exploratory research based on the observation of the interaction of blind students with the Web, usability problems were identified in the Dosvox interface and in the Webvox, the Web browser included in the system, and these problems were related to the fact that the interface is designed in accordance with the mental model of these Information Technology professionals. This study consolidate the problems in earlier phases of the research, link the results with usability heuristics of Nielsen and propose several improvements to Dosvox and its development process.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Wireless, Web-Based Interactive Control of Optical Coherence Tomography with Mobile Devices.

PubMed

Mehta, Rajvi; Nankivil, Derek; Zielinski, David J; Waterman, Gar; Keller, Brenton; Limkakeng, Alexander T; Kopper, Regis; Izatt, Joseph A; Kuo, Anthony N

2017-01-01

Optical coherence tomography (OCT) is widely used in ophthalmology clinics and has potential for more general medical settings and remote diagnostics. In anticipation of remote applications, we developed wireless interactive control of an OCT system using mobile devices. A web-based user interface (WebUI) was developed to interact with a handheld OCT system. The WebUI consisted of key OCT displays and controls ported to a webpage using HTML and JavaScript. Client-server relationships were created between the WebUI and the OCT system computer. The WebUI was accessed on a cellular phone mounted to the handheld OCT probe to wirelessly control the OCT system. Twenty subjects were imaged using the WebUI to assess the system. System latency was measured using different connection types (wireless 802.11n only, wireless to remote virtual private network [VPN], and cellular). Using a cellular phone, the WebUI was successfully used to capture posterior eye OCT images in all subjects. Simultaneous interactivity by a remote user on a laptop was also demonstrated. On average, use of the WebUI added only 58, 95, and 170 ms to the system latency using wireless only, wireless to VPN, and cellular connections, respectively. Qualitatively, operator usage was not affected. Using a WebUI, we demonstrated wireless and remote control of an OCT system with mobile devices. The web and open source software tools used in this project make it possible for any mobile device to potentially control an OCT system through a WebUI. This platform can be a basis for remote, teleophthalmology applications using OCT.

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.

User-Interface Design Characteristics of Fortune 500 B2C E-Commerce Sites and Industry Differences

ERIC Educational Resources Information Center

Zhao, Jensen J.; Truell, Allen D.; Alexander, Melody W.

2006-01-01

This study examined the user-interface design characteristics of 107 Fortune 500 B2C e-commerce Web sites and industry differences. Data were collected from corporate homepages, B2C product/service pages, B2C interactive shopping pages, as well as customer satisfaction of 321 online shoppers. The findings indicate that (a) to attract online…

Integrating DXplain into a clinical information system using the World Wide Web.

PubMed

Elhanan, G; Socratous, S A; Cimino, J J

1996-01-01

The World Wide Web(WWW) offers a cross-platform environment and standard protocols that enable integration of various applications available on the Internet. The authors use the Web to facilitate interaction between their Web-based Clinical Information System and a decision-support system-DXplain, at the Massachusetts General Hospital-using local architecture and Common Gateway Interface programs. The current application translates patients laboratory test results into DXplain's terms to generate diagnostic hypotheses. Two different access methods are utilized for this model; Hypertext Transfer Protocol (HTTP) and TCP/IP function calls. While clinical aspects cannot be evaluated as yet, the model demonstrates the potential of Web-based applications for interaction and integration and how local architecture, with a controlled vocabulary server, can further facilitate such integration. This model serves to demonstrate some of the limitations of the current WWW technology and identifies issues such as control over Web resources and their utilization and liability issues as possible obstacles for further integration.

On Building a Search Interface Discovery System

NASA Astrophysics Data System (ADS)

Shestakov, Denis

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

Wiki use in mental health practice: recognizing potential use of collaborative technology.

PubMed

Bastida, Richard; McGrath, Ian; Maude, Phil

2010-04-01

Web 2.0, the second-generation of the World Wide Web, differs to earlier versions of Web development and design in that it facilitates more user-friendly, interactive information sharing and mechanisms for greater collaboration between users. Examples of Web 2.0 include Web-based communities, hosted services, social networking sites, video sharing sites, blogs, mashups, and wikis. Users are able to interact with others across the world or to add to or change website content. This paper examines examples of wiki use in the Australian mental health sector. A wiki can be described as an online collaborative and interactive database that can be easily edited by users. They are accessed via a standard Web browser which has an interface similar to traditional Web pages, thus do not require special application or software for the user. Although there is a paucity of literature describing wiki use in mental health, other industries have developed uses, including a repository of knowledge, a platform for collaborative writing, a project management tool, and an alternative to traditional Web pages or Intranets. This paper discusses the application of wikis in other industries and offers suggestions by way of examples of how this technology could be used in the mental health sector.

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

PubMed

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

2018-06-05

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

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

PubMed

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

2018-06-13

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

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

NASA Astrophysics Data System (ADS)

Demir, I.; Krajewski, W. F.

2011-12-01

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

VirGO: A Visual Browser for the ESO Science Archive Facility

NASA Astrophysics Data System (ADS)

Hatziminaoglou, Evanthia; Chéreau, Fabien

2009-03-01

VirGO is the next generation Visual Browser for the ESO Science Archive Facility (SAF) developed in the Virtual Observatory Project Office. VirGO enables astronomers to discover and select data easily from millions of observations in a visual and intuitive way. It allows real-time access and the graphical display of a large number of observations by showing instrumental footprints and image previews, as well as their selection and filtering for subsequent download from the ESO SAF web interface. It also permits the loading of external FITS files or VOTables, as well as the superposition of Digitized Sky Survey images to be used as background. All data interfaces are based on Virtual Observatory (VO) standards that allow access to images and spectra from external data centres, and interaction with the ESO SAF web interface or any other VO applications.

A resource-oriented architecture for a Geospatial Web

NASA Astrophysics Data System (ADS)

Mazzetti, Paolo; Nativi, Stefano

2010-05-01

In this presentation we discuss some architectural issues on the design of an architecture for a Geospatial Web, that is an information system for sharing geospatial resources according to the Web paradigm. The success of the Web in building a multi-purpose information space, has raised questions about the possibility of adopting the same approach for systems dedicated to the sharing of more specific resources, such as the geospatial information, that is information characterized by spatial/temporal reference. To this aim an investigation on the nature of the Web and on the validity of its paradigm for geospatial resources is required. The Web was born in the early 90's to provide "a shared information space through which people and machines could communicate" [Berners-Lee 1996]. It was originally built around a small set of specifications (e.g. URI, HTTP, HTML, etc.); however, in the last two decades several other technologies and specifications have been introduced in order to extend its capabilities. Most of them (e.g. the SOAP family) actually aimed to transform the Web in a generic Distributed Computing Infrastructure. While these efforts were definitely successful enabling the adoption of service-oriented approaches for machine-to-machine interactions supporting complex business processes (e.g. for e-Government and e-Business applications), they do not fit in the original concept of the Web. In the year 2000, R. T. Fielding, one of the designers of the original Web specifications, proposes a new architectural style for distributed systems, called REST (Representational State Transfer), aiming to capture the fundamental characteristics of the Web as it was originally conceived [Fielding 2000]. In this view, the nature of the Web lies not so much in the technologies, as in the way they are used. Maintaining the Web architecture conform to the REST style would then assure the scalability, extensibility and low entry barrier of the original Web. On the contrary, systems using the same Web technologies and specifications but according to a different architectural style, despite their usefulness, should not be considered part of the Web. If the REST style captures the significant Web characteristics, then, in order to build a Geospatial Web it is necessary that its architecture satisfies all the REST constraints. One of them is of particular importance: the adoption of a Uniform Interface. It prescribes that all the geospatial resources must be accessed through the same interface; moreover according to the REST style this interface must satisfy four further constraints: a) identification of resources; b) manipulation of resources through representations; c) self-descriptive messages; and, d) hypermedia as the engine of application state. In the Web, the uniform interface provides basic operations which are meaningful for generic resources. They typically implement the CRUD pattern (Create-Retrieve-Update-Delete) which demonstrated to be flexible and powerful in several general-purpose contexts (e.g. filesystem management, SQL for database management systems, etc.). Restricting the scope to a subset of resources it would be possible to identify other generic actions which are meaningful for all of them. For example for geospatial resources, subsetting, resampling, interpolation and coordinate reference systems transformations functionalities are candidate functionalities for a uniform interface. However an investigation is needed to clarify the semantics of those actions for different resources, and consequently if they can really ascend the role of generic interface operation. Concerning the point a), (identification of resources), it is required that every resource addressable in the Geospatial Web has its own identifier (e.g. a URI). This allows to implement citation and re-use of resources, simply providing the URI. OPeNDAP and KVP encodings of OGC data access services specifications might provide a basis for it. Concerning point b) (manipulation of resources through representations), the Geospatial Web poses several issues. In fact, while the Web mainly handles semi-structured information, in the Geospatial Web the information is typically structured with several possible data models (e.g. point series, gridded coverages, trajectories, etc.) and encodings. A possibility would be to simplify the interchange formats, choosing to support a subset of data models and format(s). This is what actually the Web designers did choosing to define a common format for hypermedia (HTML), although the underlying protocol would be generic. Concerning point c), self-descriptive messages, the exchanged messages should describe themselves and their content. This would not be actually a major issue considering the effort put in recent years on geospatial metadata models and specifications. The point d), hypermedia as the engine of application state, is actually where the Geospatial Web would mainly differ from existing geospatial information sharing systems. In fact the existing systems typically adopt a service-oriented architecture, where applications are built as a single service or as a workflow of services. On the other hand, in the Geospatial Web, applications should be built following the path between interconnected resources. The link between resources should be made explicit as hyperlinks. The adoption of Semantic Web solutions would allow to define not only the existence of a link between two resources, but also the nature of the link. The implementation of a Geospatial Web would allow to build an information system with the same characteristics of the Web sharing its points-of-strength and weaknesses. The main advantages would be the following: • The user would interact with the Geospatial Web according to the well-known Web navigation paradigm. This would lower the barrier to the access to geospatial applications for non-specialists (e.g. the success of Google Maps and other Web mapping applications); • Successful Web and Web 2.0 applications - search engines, feeds, social network - could be integrated/replicated in the Geospatial Web; The main drawbacks would be the following: • The Uniform Interface simplifies the overall system architecture (e.g. no service registry, and service descriptors required), but moves the complexity to the data representation. Moreover since the interface must stay generic, it results really simple and therefore complex interactions would require several transfers. • In the geospatial domain one of the most valuable resources are processes (e.g. environmental models). How they can be modeled as resources accessed through the common interface is an open issue. Taking into account advantages and drawback it seems that a Geospatial Web would be useful, but its use would be limited to specific use-cases not covering all the possible applications. The Geospatial Web architecture could be partly based on existing specifications, while other aspects need investigation. References [Berners-Lee 1996] T. Berners-Lee, "WWW: Past, present, and future". IEEE Computer, 29(10), Oct. 1996, pp. 69-77. [Fielding 2000] Fielding, R. T. 2000. Architectural styles and the design of network-based software architectures. PhD Dissertation. Dept. of Information and Computer Science, University of California, Irvine

SIMAP—the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage

PubMed Central

Arnold, Roland; Goldenberg, Florian; Mewes, Hans-Werner; Rattei, Thomas

2014-01-01

The Similarity Matrix of Proteins (SIMAP, http://mips.gsf.de/simap/) database has been designed to massively accelerate computationally expensive protein sequence analysis tasks in bioinformatics. It provides pre-calculated sequence similarities interconnecting the entire known protein sequence universe, complemented by pre-calculated protein features and domains, similarity clusters and functional annotations. SIMAP covers all major public protein databases as well as many consistently re-annotated metagenomes from different repositories. As of September 2013, SIMAP contains >163 million proteins corresponding to ∼70 million non-redundant sequences. SIMAP uses the sensitive FASTA search heuristics, the Smith–Waterman alignment algorithm, the InterPro database of protein domain models and the BLAST2GO functional annotation algorithm. SIMAP assists biologists by facilitating the interactive exploration of the protein sequence universe. Web-Service and DAS interfaces allow connecting SIMAP with any other bioinformatic tool and resource. All-against-all protein sequence similarity matrices of project-specific protein collections are generated on request. Recent improvements allow SIMAP to cover the rapidly growing sequenced protein sequence universe. New Web-Service interfaces enhance the connectivity of SIMAP. Novel tools for interactive extraction of protein similarity networks have been added. Open access to SIMAP is provided through the web portal; the portal also contains instructions and links for software access and flat file downloads. PMID:24165881

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.

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

PubMed Central

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

2012-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

CREDO: a structural interactomics database for drug discovery

PubMed Central

Schreyer, Adrian M.; Blundell, Tom L.

2013-01-01

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

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.

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

PubMed Central

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

2012-01-01

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

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

PubMed

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

2012-07-01

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

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.

RAPID and HTML5's potential

NASA Technical Reports Server (NTRS)

Torosyan, David

2012-01-01

Just as important as the engineering that goes into building a robot is the method of interaction, or how human users will use the machine. As part of the Human-System Interactions group (Conductor) at JPL, I explored using a web interface to interact with ATHLETE, a prototype lunar rover. I investigated the usefulness of HTML 5 and Javascript as a telemetry viewer as well as the feasibility of having a rover communicate with a web server. To test my ideas I built a mobile-compatible website and designed primarily for an Android tablet. The website took input from ATHLETE engineers, and upon its completion I conducted a user test to assess its effectiveness.

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

NASA Technical Reports Server (NTRS)

Ponyik, Joseph G.; York, David W.

2002-01-01

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

Wireless, Web-Based Interactive Control of Optical Coherence Tomography with Mobile Devices

PubMed Central

Mehta, Rajvi; Nankivil, Derek; Zielinski, David J.; Waterman, Gar; Keller, Brenton; Limkakeng, Alexander T.; Kopper, Regis; Izatt, Joseph A.; Kuo, Anthony N.

2017-01-01

Purpose Optical coherence tomography (OCT) is widely used in ophthalmology clinics and has potential for more general medical settings and remote diagnostics. In anticipation of remote applications, we developed wireless interactive control of an OCT system using mobile devices. Methods A web-based user interface (WebUI) was developed to interact with a handheld OCT system. The WebUI consisted of key OCT displays and controls ported to a webpage using HTML and JavaScript. Client–server relationships were created between the WebUI and the OCT system computer. The WebUI was accessed on a cellular phone mounted to the handheld OCT probe to wirelessly control the OCT system. Twenty subjects were imaged using the WebUI to assess the system. System latency was measured using different connection types (wireless 802.11n only, wireless to remote virtual private network [VPN], and cellular). Results Using a cellular phone, the WebUI was successfully used to capture posterior eye OCT images in all subjects. Simultaneous interactivity by a remote user on a laptop was also demonstrated. On average, use of the WebUI added only 58, 95, and 170 ms to the system latency using wireless only, wireless to VPN, and cellular connections, respectively. Qualitatively, operator usage was not affected. Conclusions Using a WebUI, we demonstrated wireless and remote control of an OCT system with mobile devices. Translational Relevance The web and open source software tools used in this project make it possible for any mobile device to potentially control an OCT system through a WebUI. This platform can be a basis for remote, teleophthalmology applications using OCT. PMID:28138415

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

PubMed

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

2016-07-08

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

iELM—a web server to explore short linear motif-mediated interactions

PubMed Central

Weatheritt, Robert J.; Jehl, Peter; Dinkel, Holger; Gibson, Toby J.

2012-01-01

The recent expansion in our knowledge of protein–protein interactions (PPIs) has allowed the annotation and prediction of hundreds of thousands of interactions. However, the function of many of these interactions remains elusive. The interactions of Eukaryotic Linear Motif (iELM) web server provides a resource for predicting the function and positional interface for a subset of interactions mediated by short linear motifs (SLiMs). The iELM prediction algorithm is based on the annotated SLiM classes from the Eukaryotic Linear Motif (ELM) resource and allows users to explore both annotated and user-generated PPI networks for SLiM-mediated interactions. By incorporating the annotated information from the ELM resource, iELM provides functional details of PPIs. This can be used in proteomic analysis, for example, to infer whether an interaction promotes complex formation or degradation. Furthermore, details of the molecular interface of the SLiM-mediated interactions are also predicted. This information is displayed in a fully searchable table, as well as graphically with the modular architecture of the participating proteins extracted from the UniProt and Phospho.ELM resources. A network figure is also presented to aid the interpretation of results. The iELM server supports single protein queries as well as large-scale proteomic submissions and is freely available at http://i.elm.eu.org. PMID:22638578

JSME: a free molecule editor in JavaScript.

PubMed

Bienfait, Bruno; Ertl, Peter

2013-01-01

A molecule editor, i.e. a program facilitating graphical input and interactive editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. Today, when a web browser has become the universal scientific user interface, a tool to edit molecules directly within the web browser is essential. One of the most popular tools for molecular structure input on the web is the JME applet. Since its release nearly 15 years ago, however the web environment has changed and Java applets are facing increasing implementation hurdles due to their maintenance and support requirements, as well as security issues. This prompted us to update the JME editor and port it to a modern Internet programming language - JavaScript. The actual molecule editing Java code of the JME editor was translated into JavaScript with help of the Google Web Toolkit compiler and a custom library that emulates a subset of the GUI features of the Java runtime environment. In this process, the editor was enhanced by additional functionalities including a substituent menu, copy/paste, drag and drop and undo/redo capabilities and an integrated help. In addition to desktop computers, the editor supports molecule editing on touch devices, including iPhone, iPad and Android phones and tablets. In analogy to JME the new editor is named JSME. This new molecule editor is compact, easy to use and easy to incorporate into web pages. A free molecule editor written in JavaScript was developed and is released under the terms of permissive BSD license. The editor is compatible with JME, has practically the same user interface as well as the web application programming interface. The JSME editor is available for download from the project web page http://peter-ertl.com/jsme/

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.

Web-based Visual Analytics for Extreme Scale Climate Science

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

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

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

Interactive Visualization of Computational Fluid Dynamics using Mosaic

NASA Technical Reports Server (NTRS)

Clucas, Jean; Watson, Velvin; Chancellor, Marisa K. (Technical Monitor)

1994-01-01

The Web provides new Methods for accessing Information world-wide, but the current text-and-pictures approach neither utilizes all the Web's possibilities not provides for its limitations. While the inclusion of pictures and animations in a paper communicates more effectively than text alone, It Is essentially an extension of the concept of "publication." Also, as use of the Web increases putting images and animations online will quickly load even the "Information Superhighway." We need to find forms of communication that take advantage of the special nature of the Web. This paper presents one approach: the use of the Internet and the Mosaic interface for data sharing and collaborative analysis. We will describe (and In the presentation, demonstrate) our approach: using FAST (Flow Analysis Software Toolkit), a scientific visualization package, as a data viewer and interactive tool called from MOSAIC. Our intent is to stimulate the development of other tools that utilize the unique nature of electronic communication.

WebProtégé: A Collaborative Ontology Editor and Knowledge Acquisition Tool for the Web

PubMed Central

Tudorache, Tania; Nyulas, Csongor; Noy, Natalya F.; Musen, Mark A.

2012-01-01

In this paper, we present WebProtégé—a lightweight ontology editor and knowledge acquisition tool for the Web. With the wide adoption of Web 2.0 platforms and the gradual adoption of ontologies and Semantic Web technologies in the real world, we need ontology-development tools that are better suited for the novel ways of interacting, constructing and consuming knowledge. Users today take Web-based content creation and online collaboration for granted. WebProtégé integrates these features as part of the ontology development process itself. We tried to lower the entry barrier to ontology development by providing a tool that is accessible from any Web browser, has extensive support for collaboration, and a highly customizable and pluggable user interface that can be adapted to any level of user expertise. The declarative user interface enabled us to create custom knowledge-acquisition forms tailored for domain experts. We built WebProtégé using the existing Protégé infrastructure, which supports collaboration on the back end side, and the Google Web Toolkit for the front end. The generic and extensible infrastructure allowed us to easily deploy WebProtégé in production settings for several projects. We present the main features of WebProtégé and its architecture and describe briefly some of its uses for real-world projects. WebProtégé is free and open source. An online demo is available at http://webprotege.stanford.edu. PMID:23807872

MOSAIC: a chemical-genetic interaction data repository and web resource for exploring chemical modes of action.

PubMed

Nelson, Justin; Simpkins, Scott W; Safizadeh, Hamid; Li, Sheena C; Piotrowski, Jeff S; Hirano, Hiroyuki; Yashiroda, Yoko; Osada, Hiroyuki; Yoshida, Minoru; Boone, Charles; Myers, Chad L

2018-04-01

Chemical-genomic approaches that map interactions between small molecules and genetic perturbations offer a promising strategy for functional annotation of uncharacterized bioactive compounds. We recently developed a new high-throughput platform for mapping chemical-genetic (CG) interactions in yeast that can be scaled to screen large compound collections, and we applied this system to generate CG interaction profiles for more than 13 000 compounds. When integrated with the existing global yeast genetic interaction network, CG interaction profiles can enable mode-of-action prediction for previously uncharacterized compounds as well as discover unexpected secondary effects for known drugs. To facilitate future analysis of these valuable data, we developed a public database and web interface named MOSAIC. The website provides a convenient interface for querying compounds, bioprocesses (Gene Ontology terms) and genes for CG information including direct CG interactions, bioprocesses and gene-level target predictions. MOSAIC also provides access to chemical structure information of screened molecules, chemical-genomic profiles and the ability to search for compounds sharing structural and functional similarity. This resource will be of interest to chemical biologists for discovering new small molecule probes with specific modes-of-action as well as computational biologists interested in analysing CG interaction networks. MOSAIC is available at http://mosaic.cs.umn.edu. hisyo@riken.jp, yoshidam@riken.jp, charlie.boone@utoronto.ca or chadm@umn.edu. Supplementary data are available at Bioinformatics online.

DIANA-microT web server: elucidating microRNA functions through target prediction.

PubMed

Maragkakis, M; Reczko, M; Simossis, V A; Alexiou, P; Papadopoulos, G L; Dalamagas, T; Giannopoulos, G; Goumas, G; Koukis, E; Kourtis, K; Vergoulis, T; Koziris, N; Sellis, T; Tsanakas, P; Hatzigeorgiou, A G

2009-07-01

Computational microRNA (miRNA) target prediction is one of the key means for deciphering the role of miRNAs in development and disease. Here, we present the DIANA-microT web server as the user interface to the DIANA-microT 3.0 miRNA target prediction algorithm. The web server provides extensive information for predicted miRNA:target gene interactions with a user-friendly interface, providing extensive connectivity to online biological resources. Target gene and miRNA functions may be elucidated through automated bibliographic searches and functional information is accessible through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The web server offers links to nomenclature, sequence and protein databases, and users are facilitated by being able to search for targeted genes using different nomenclatures or functional features, such as the genes possible involvement in biological pathways. The target prediction algorithm supports parameters calculated individually for each miRNA:target gene interaction and provides a signal-to-noise ratio and a precision score that helps in the evaluation of the significance of the predicted results. Using a set of miRNA targets recently identified through the pSILAC method, the performance of several computational target prediction programs was assessed. DIANA-microT 3.0 achieved there with 66% the highest ratio of correctly predicted targets over all predicted targets. The DIANA-microT web server is freely available at www.microrna.gr/microT.

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

PubMed

Li, Yan; Andrade, Jorge

2017-01-01

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

The online Tabloid Proteome: an annotated database of protein associations

PubMed Central

Turan, Demet; Tavernier, Jan

2018-01-01

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

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

DOE PAGES

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

2016-08-31

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

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

PubMed

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

2016-08-31

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

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

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

Peng, Jiajie; Li, Hongxiang; Liu, Yongzhuang

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

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

NASA Astrophysics Data System (ADS)

Ye, Mengxuan; Wei, Shuangfeng; Zhang, Dongmei

2016-11-01

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

Space Physics Data Facility Web Services

NASA Technical Reports Server (NTRS)

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

2005-01-01

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

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

HippDB: a database of readily targeted helical protein-protein interactions.

PubMed

Bergey, Christina M; Watkins, Andrew M; Arora, Paramjit S

2013-11-01

HippDB catalogs every protein-protein interaction whose structure is available in the Protein Data Bank and which exhibits one or more helices at the interface. The Web site accepts queries on variables such as helix length and sequence, and it provides computational alanine scanning and change in solvent-accessible surface area values for every interfacial residue. HippDB is intended to serve as a starting point for structure-based small molecule and peptidomimetic drug development. HippDB is freely available on the web at http://www.nyu.edu/projects/arora/hippdb. The Web site is implemented in PHP, MySQL and Apache. Source code freely available for download at http://code.google.com/p/helidb, implemented in Perl and supported on Linux. arora@nyu.edu.

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

PubMed

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

2009-11-01

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

Maximizing Impact: Pairing interactive web visualizations with traditional print media

NASA Astrophysics Data System (ADS)

Read, E. K.; Appling, A.; Carr, L.; De Cicco, L.; Read, J. S.; Walker, J. I.; Winslow, L. A.

2016-12-01

Our Nation's rapidly growing store of environmental data makes new demands on researchers: to take on increasingly broad-scale, societally relevant analyses and to rapidly communicate findings to the public. Interactive web-based data visualizations now commonly supplement or comprise journalism, and science journalism has followed suit. To maximize the impact of US Geological Survey (USGS) science, the USGS Office of Water Information Data Science team builds tools and products that combine traditional static research products (e.g., print journal articles) with web-based, interactive data visualizations that target non-scientific audiences. We developed a lightweight, open-source framework for web visualizations to reduce time to production. The framework provides templates for a data visualization workflow and the packaging of text, interactive figures, and images into an appealing web interface with standardized look and feel, usage tracking, and responsiveness. By partnering with subject matter experts to focus on timely, societally relevant issues, we use these tools to produce appealing visual stories targeting specific audiences, including managers, the general public, and scientists, on diverse topics including drought, microplastic pollution, and fisheries response to climate change. We will describe the collaborative and technical methodologies used; describe some examples of how it's worked; and challenges and opportunities for the future.

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.

Web-based interactive drone control using hand gesture

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Web-based interactive drone control using hand gesture.

PubMed

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

2018-01-01

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

Exploring JavaScript and ROOT technologies to create Web-based ATLAS analysis and monitoring tools

NASA Astrophysics Data System (ADS)

Sánchez Pineda, A.

2015-12-01

We explore the potential of current web applications to create online interfaces that allow the visualization, interaction and real cut-based physics analysis and monitoring of processes through a web browser. The project consists in the initial development of web- based and cloud computing services to allow students and researchers to perform fast and very useful cut-based analysis on a browser, reading and using real data and official Monte- Carlo simulations stored in ATLAS computing facilities. Several tools are considered: ROOT, JavaScript and HTML. Our study case is the current cut-based H → ZZ → llqq analysis of the ATLAS experiment. Preliminary but satisfactory results have been obtained online.

Oyster Fisheries App

NASA Technical Reports Server (NTRS)

Perez Guerrero, Geraldo A.; Armstrong, Duane; Underwood, Lauren

2015-01-01

This project is creating a cloud-enabled, HTML 5 web application to help oyster fishermen and state agencies apply Earth science to improve the management of this important natural and economic resource. The Oyster Fisheries app gathers and analyzes environmental and water quality information, and alerts fishermen and resources managers about problems in oyster fishing waters. An intuitive interface based on Google Maps displays the geospatial information and provides familiar interactive controls to the users. Alerts can be tailored to notify users when conditions in specific leases or public fishing areas require attention. The app is hosted on the Amazon Web Services cloud. It is being developed and tested using some of the latest web development tools such as web components and Polymer.

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

NASA Astrophysics Data System (ADS)

Ruegg, C. S.

2011-12-01

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

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.

Usability evaluation of an experimental text summarization system and three search engines: implications for the reengineering of health care interfaces.

PubMed

Kushniruk, Andre W; Kan, Min-Yem; McKeown, Kathleen; Klavans, Judith; Jordan, Desmond; LaFlamme, Mark; Patel, Vimia L

2002-01-01

This paper describes the comparative evaluation of an experimental automated text summarization system, Centrifuser and three conventional search engines - Google, Yahoo and About.com. Centrifuser provides information to patients and families relevant to their questions about specific health conditions. It then produces a multidocument summary of articles retrieved by a standard search engine, tailored to the user's question. Subjects, consisting of friends or family of hospitalized patients, were asked to "think aloud" as they interacted with the four systems. The evaluation involved audio- and video recording of subject interactions with the interfaces in situ at a hospital. Results of the evaluation show that subjects found Centrifuser's summarization capability useful and easy to understand. In comparing Centrifuser to the three search engines, subjects' ratings varied; however, specific interface features were deemed useful across interfaces. We conclude with a discussion of the implications for engineering Web-based retrieval systems.

EcoCyc: a comprehensive database resource for Escherichia coli

PubMed Central

Keseler, Ingrid M.; Collado-Vides, Julio; Gama-Castro, Socorro; Ingraham, John; Paley, Suzanne; Paulsen, Ian T.; Peralta-Gil, Martín; Karp, Peter D.

2005-01-01

The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli. Through ongoing manual curation, extensive information such as summary comments, regulatory information, literature citations and evidence types has been extracted from 8862 publications and added to Version 8.5 of the EcoCyc database. The EcoCyc database can be accessed through a World Wide Web interface, while the downloadable Pathway Tools software and data files enable computational exploration of the data and provide enhanced querying capabilities that web interfaces cannot support. For example, EcoCyc contains carefully curated information that can be used as training sets for bioinformatics prediction of entities such as promoters, operons, genetic networks, transcription factor binding sites, metabolic pathways, functionally related genes, protein complexes and protein–ligand interactions. PMID:15608210

Environmental Models as a Service: Enabling Interoperability ...

EPA Pesticide Factsheets

Achieving interoperability in environmental modeling has evolved as software technology has progressed. The recent rise of cloud computing and proliferation of web services initiated a new stage for creating interoperable systems. Scientific programmers increasingly take advantage of streamlined deployment processes and affordable cloud access to move algorithms and data to the web for discoverability and consumption. In these deployments, environmental models can become available to end users through RESTful web services and consistent application program interfaces (APIs) that consume, manipulate, and store modeling data. RESTful modeling APIs also promote discoverability and guide usability through self-documentation. Embracing the RESTful paradigm allows models to be accessible via a web standard, and the resulting endpoints are platform- and implementation-agnostic while simultaneously presenting significant computational capabilities for spatial and temporal scaling. RESTful APIs present data in a simple verb-noun web request interface: the verb dictates how a resource is consumed using HTTP methods (e.g., GET, POST, and PUT) and the noun represents the URL reference of the resource on which the verb will act. The RESTful API can self-document in both the HTTP response and an interactive web page using the Open API standard. This lets models function as an interoperable service that promotes sharing, documentation, and discoverability. Here, we discuss the

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

PubMed

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

2012-07-01

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

P1198: software for tracing decision behavior in lending to small businesses.

PubMed

Andersson, P

2001-05-01

This paper describes a process-tracing software program specially designed to capture decision behavior in lending to small businesses. The source code was written in Lotus Notes. The software runs in a Web browser and consists of two interacting systems: a database and a user interface. The database includes three realistic loan applications. The user interface consists of different but interacting screens that enable the participant to operate the software. Log files register the decision behavior of the participant. An empirical example is presented in order to show the software's potential in providing insights into judgment and decision making. The implications of the software are discussed.

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

Biotool2Web: creating simple Web interfaces for bioinformatics applications.

PubMed

Shahid, Mohammad; Alam, Intikhab; Fuellen, Georg

2006-01-01

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

Intranets: Considerations for the Information Services Manager.

ERIC Educational Resources Information Center

Blackmore, Paul

1997-01-01

This article identifies benefits of using Internet technologies in an organization's intranet or internal information system: ease-of-use, one interface, implementation cost, access, information services (flat content and interactive intranets), support desks (via Web services and e-mail), document management. Discusses the impact of intranets on…

Resource Discovery within the Networked "Hybrid" Library.

ERIC Educational Resources Information Center

Leigh, Sally-Anne

This paper focuses on the development, adoption, and integration of resource discovery, knowledge management, and/or knowledge sharing interfaces such as interactive portals, and the use of the library's World Wide Web presence to increase the availability and usability of information services. The introduction addresses changes in library…

Understanding the Requirements for Open Source Software

DTIC Science & Technology

2009-06-17

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

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

PubMed Central

Lin, Yi-Jung; Speedie, Stuart

2003-01-01

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

The DIMA web resource--exploring the protein domain network.

PubMed

Pagel, Philipp; Oesterheld, Matthias; Stümpflen, Volker; Frishman, Dmitrij

2006-04-15

Conserved domains represent essential building blocks of most known proteins. Owing to their role as modular components carrying out specific functions they form a network based both on functional relations and direct physical interactions. We have previously shown that domain interaction networks provide substantially novel information with respect to networks built on full-length protein chains. In this work we present a comprehensive web resource for exploring the Domain Interaction MAp (DIMA), interactively. The tool aims at integration of multiple data sources and prediction techniques, two of which have been implemented so far: domain phylogenetic profiling and experimentally demonstrated domain contacts from known three-dimensional structures. A powerful yet simple user interface enables the user to compute, visualize, navigate and download domain networks based on specific search criteria. http://mips.gsf.de/genre/proj/dima

Caching strategies for improving performance of web-based Geographic applications

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

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

PubMed

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

2015-02-03

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

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

PubMed

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

2017-02-01

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

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

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

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

E-Homebook System: A Web-Based Interactive Education Interface

ERIC Educational Resources Information Center

Chen, Hsi-mei; Yu, Cris; Chang, Cheng-sian

2007-01-01

Children's academic performance and social competence in school is positively associated with parent involvement. However, the researches about educational learning models often ignore the parent part. Moreover, Internet forms a new paradigm, education and communication approach is more complicated than ever. In this paper, we would like to…

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

PubMed

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

2018-06-25

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

The THOSE remote interface

NASA Astrophysics Data System (ADS)

Klawon, Kevin; Gold, Josh; Bachman, Kristen

2013-05-01

The DIA, in conjunction with the Army Research Lab (ARL), wants to create an Unmanned Ground Sensor (UGS) controller that is (a) interoperable across all controller platforms, (b) capable of easily adding new sensors, radios, and processes and (c) backward compatible with existing UGS systems. To achieve this, a Terra Harvest controller was created that used Java JRE 1.6 and an Open Services Gateway initiative (OSGi) platform, named Terra Harvest Open Software Environment (THOSE). OSGi is an extensible framework that provides a modularized environment for deploying functionality in "bundles". These bundles can publish, discover, and share services available from other external bundles or bundles provided by the controller core. With the addition of a web GUI used for interacting with THOSE, a natural step was then to create a common remote interface that allows 3rd party real-time interaction with the controller. This paper provides an overview of the THOSE system and its components as well as a description of the architectural structure of the remote interface, highlighting the interactions occurring between the controller and the remote interface and its role in providing a positive user experience for managing UGSS functions.

Web-phreeq: a WWW instructional tool for modeling the distribution of chemical species in water

NASA Astrophysics Data System (ADS)

Saini-Eidukat, Bernhardt; Yahin, Andrew

1999-05-01

A WWW-based tool, WEB-PHREEQ, was developed for classroom teaching and for routine calculation of low temperature aqueous speciation. Accessible with any computer that has an internet-connected forms-capable WWW-browser, WEB-PHREEQ provides user interface and other support for modeling, creates a properly formatted input file, passes it to the public domain program PHREEQC and returns the output to the WWW browser. Users can calculate the equilibrium speciation of a solution over a range of temperatures or can react solid minerals or gases with a particular water and examine the resulting chemistry. WEB-PHREEQ is one of a number of interactive distributed-computing programs available on the WWW that are of interest to geoscientists.

Iconic hyperlinks on e-commerce websites.

PubMed

Cheng, Hong-In; Patterson, Patrick E

2007-01-01

The proper use of iconic interfaces reduces system complexity and helps users interact with systems more easily. However, due to carelessness, inadequate research, and the web's relatively short history, the icons used on web sites often are ambiguous. Because non-identifiable icons may convey meanings other than those intended, designers must consider whether icons are easily identifiable when creating web sites. In this study, visual icons used on e-business web sites were examined by population stereotypy and categorized into three groups: identifiable, medium, and vague. Representative icons from each group were tested by comparing selection performance in groups of student volunteers, with identifiable and medium icons improving performance. We found that only easily identifiable icons can reduce complexity and increase system usability.

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.

Web-Based Geospatial Visualization of GPM Data with CesiumJS

NASA Technical Reports Server (NTRS)

Lammers, Matt

2018-01-01

Advancements in the capabilities of JavaScript frameworks and web browsing technology have made online visualization of large geospatial datasets such as those coming from precipitation satellites viable. These data benefit from being visualized on and above a three-dimensional surface. The open-source JavaScript framework CesiumJS (http://cesiumjs.org), developed by Analytical Graphics, Inc., leverages the WebGL protocol to do just that. This presentation will describe how CesiumJS has been used in three-dimensional visualization products developed as part of the NASA Precipitation Processing System (PPS) STORM data-order website. Existing methods of interacting with Global Precipitation Measurement (GPM) Mission data primarily focus on two-dimensional static images, whether displaying vertical slices or horizontal surface/height-level maps. These methods limit interactivity with the robust three-dimensional data coming from the GPM core satellite. Integrating the data with CesiumJS in a web-based user interface has allowed us to create the following products. We have linked with the data-order interface an on-the-fly visualization tool for any GPM/partner satellite orbit. A version of this tool also focuses on high-impact weather events. It enables viewing of combined radar and microwave-derived precipitation data on mobile devices and in a way that can be embedded into other websites. We also have used CesiumJS to visualize a method of integrating gridded precipitation data with modeled wind speeds that animates over time. Emphasis in the presentation will be placed on how a variety of technical methods were used to create these tools, and how the flexibility of the CesiumJS framework facilitates creative approaches to interact with the data.

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

PubMed Central

2014-01-01

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

Are Pretty Interfaces Worth the Time? The Effects of User Interface Types on Web-Based Instruction

ERIC Educational Resources Information Center

Cheon, Jongpil; Grant, Michael M.

2009-01-01

The purpose of this study was to examine the effectiveness of three different interface types on Web-based instruction: a text-based interface, a graphical interface and a metaphorical interface. In order to determine differences among three interface groups, we compared learning performance, cognitive load, usability, and appeal with various data…

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.

An overview of emerging technologies in contemporary decision support system development

NASA Astrophysics Data System (ADS)

Nursal, Ahmad Taufik; Omar, Mohd Faizal; Nawi, Mohd Nasrun Mohd

2014-12-01

The rapid development of Web technology has opened a new approach to Decision Support System (DSS) development. For instance, Social Media is one of the Web 2.0 digital platforms that allow the creation and exchanges of user-generate content through an interactive interface, high user control and mass participation. The concept and characteristics of Web 2.0 such as remote, platform-independent, context-rich and easy to use, which is fulfill the concept and purpose of DSS. This paper outlines some of the elementary concepts of Web 2.0 and social media technology which can be potentially integrated within DSS to enhance the decision-making process. Our initial investigation indicates that there is limited study attempt to embed Web 2.0 into DSS. Thus, this paper highlights the importance of Web 2.0 technology in order to foster the betterment of DSS development and its usability.

VisGets: coordinated visualizations for web-based information exploration and discovery.

PubMed

Dörk, Marian; Carpendale, Sheelagh; Collins, Christopher; Williamson, Carey

2008-01-01

In common Web-based search interfaces, it can be difficult to formulate queries that simultaneously combine temporal, spatial, and topical data filters. We investigate how coordinated visualizations can enhance search and exploration of information on the World Wide Web by easing the formulation of these types of queries. Drawing from visual information seeking and exploratory search, we introduce VisGets--interactive query visualizations of Web-based information that operate with online information within a Web browser. VisGets provide the information seeker with visual overviews of Web resources and offer a way to visually filter the data. Our goal is to facilitate the construction of dynamic search queries that combine filters from more than one data dimension. We present a prototype information exploration system featuring three linked VisGets (temporal, spatial, and topical), and used it to visually explore news items from online RSS feeds.

Wilber 3: A Python-Django Web Application For Acquiring Large-scale Event-oriented Seismic Data

NASA Astrophysics Data System (ADS)

Newman, R. L.; Clark, A.; Trabant, C. M.; Karstens, R.; Hutko, A. R.; Casey, R. E.; Ahern, T. K.

2013-12-01

Since 2001, the IRIS Data Management Center (DMC) WILBER II system has provided a convenient web-based interface for locating seismic data related to a particular event, and requesting a subset of that data for download. Since its launch, both the scale of available data and the technology of web-based applications have developed significantly. Wilber 3 is a ground-up redesign that leverages a number of public and open-source projects to provide an event-oriented data request interface with a high level of interactivity and scalability for multiple data types. Wilber 3 uses the IRIS/Federation of Digital Seismic Networks (FDSN) web services for event data, metadata, and time-series data. Combining a carefully optimized Google Map with the highly scalable SlickGrid data API, the Wilber 3 client-side interface can load tens of thousands of events or networks/stations in a single request, and provide instantly responsive browsing, sorting, and filtering of event and meta data in the web browser, without further reliance on the data service. The server-side of Wilber 3 is a Python-Django application, one of over a dozen developed in the last year at IRIS, whose common framework, components, and administrative overhead represent a massive savings in developer resources. Requests for assembled datasets, which may include thousands of data channels and gigabytes of data, are queued and executed using the Celery distributed Python task scheduler, giving Wilber 3 the ability to operate in parallel across a large number of nodes.

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.

WebGL-enabled 3D visualization of a Solar Flare Simulation

NASA Astrophysics Data System (ADS)

Chen, A.; Cheung, C. M. M.; Chintzoglou, G.

2016-12-01

The visualization of magnetohydrodynamic (MHD) simulations of astrophysical systems such as solar flares often requires specialized software packages (e.g. Paraview and VAPOR). A shortcoming of using such software packages is the inability to share our findings with the public and scientific community in an interactive and engaging manner. By using the javascript-based WebGL application programming interface (API) and the three.js javascript package, we create an online in-browser experience for rendering solar flare simulations that will be interactive and accessible to the general public. The WebGL renderer displays objects such as vector flow fields, streamlines and textured isosurfaces. This allows the user to explore the spatial relation between the solar coronal magnetic field and the thermodynamic structure of the plasma in which the magnetic field is embedded. Plans for extending the features of the renderer will also be presented.

A WebGL Tool for Visualizing the Topology of the Sun's Coronal Magnetic Field

NASA Astrophysics Data System (ADS)

Duffy, A.; Cheung, C.; DeRosa, M. L.

2012-12-01

We present a web-based, topology-viewing tool that allows users to visualize the geometry and topology of the Sun's 3D coronal magnetic field in an interactive manner. The tool is implemented using, open-source, mature, modern web technologies including WebGL, jQuery, HTML 5, and CSS 3, which are compatible with nearly all modern web browsers. As opposed to the traditional method of visualization, which involves the downloading and setup of various software packages-proprietary and otherwise-the tool presents a clean interface that allows the user to easily load and manipulate the model, while also offering great power to choose which topological features are displayed. The tool accepts data encoded in the JSON open format that has libraries available for nearly every major programming language, making it simple to generate the data.

Sharing Human-Generated Observations by Integrating HMI and the Semantic Sensor Web

PubMed Central

Sigüenza, Álvaro; Díaz-Pardo, David; Bernat, Jesús; Vancea, Vasile; Blanco, José Luis; Conejero, David; Gómez, Luis Hernández

2012-01-01

Current “Internet of Things” concepts point to a future where connected objects gather meaningful information about their environment and share it with other objects and people. In particular, objects embedding Human Machine Interaction (HMI), such as mobile devices and, increasingly, connected vehicles, home appliances, urban interactive infrastructures, etc., may not only be conceived as sources of sensor information, but, through interaction with their users, they can also produce highly valuable context-aware human-generated observations. We believe that the great promise offered by combining and sharing all of the different sources of information available can be realized through the integration of HMI and Semantic Sensor Web technologies. This paper presents a technological framework that harmonizes two of the most influential HMI and Sensor Web initiatives: the W3C's Multimodal Architecture and Interfaces (MMI) and the Open Geospatial Consortium (OGC) Sensor Web Enablement (SWE) with its semantic extension, respectively. Although the proposed framework is general enough to be applied in a variety of connected objects integrating HMI, a particular development is presented for a connected car scenario where drivers' observations about the traffic or their environment are shared across the Semantic Sensor Web. For implementation and evaluation purposes an on-board OSGi (Open Services Gateway Initiative) architecture was built, integrating several available HMI, Sensor Web and Semantic Web technologies. A technical performance test and a conceptual validation of the scenario with potential users are reported, with results suggesting the approach is sound. PMID:22778643

Sharing human-generated observations by integrating HMI and the Semantic Sensor Web.

PubMed

Sigüenza, Alvaro; Díaz-Pardo, David; Bernat, Jesús; Vancea, Vasile; Blanco, José Luis; Conejero, David; Gómez, Luis Hernández

2012-01-01

Current "Internet of Things" concepts point to a future where connected objects gather meaningful information about their environment and share it with other objects and people. In particular, objects embedding Human Machine Interaction (HMI), such as mobile devices and, increasingly, connected vehicles, home appliances, urban interactive infrastructures, etc., may not only be conceived as sources of sensor information, but, through interaction with their users, they can also produce highly valuable context-aware human-generated observations. We believe that the great promise offered by combining and sharing all of the different sources of information available can be realized through the integration of HMI and Semantic Sensor Web technologies. This paper presents a technological framework that harmonizes two of the most influential HMI and Sensor Web initiatives: the W3C's Multimodal Architecture and Interfaces (MMI) and the Open Geospatial Consortium (OGC) Sensor Web Enablement (SWE) with its semantic extension, respectively. Although the proposed framework is general enough to be applied in a variety of connected objects integrating HMI, a particular development is presented for a connected car scenario where drivers' observations about the traffic or their environment are shared across the Semantic Sensor Web. For implementation and evaluation purposes an on-board OSGi (Open Services Gateway Initiative) architecture was built, integrating several available HMI, Sensor Web and Semantic Web technologies. A technical performance test and a conceptual validation of the scenario with potential users are reported, with results suggesting the approach is sound.

INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species.

PubMed

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

2018-05-09

Proteins perform biological functions through cascading interactions with each other by forming protein complexes. As a result, interactions among proteins, called protein-protein interactions (PPIs) are not completely free from selection constraint during evolution. Therefore, the identification and analysis of PPI changes during evolution can give us new insight into the evolution of functions. Although many algorithms, databases and websites have been developed to help the study of PPIs, most of them are limited to visualize the structure and features of PPIs in a chosen single species with limited functions in the visualization perspective. This leads to difficulties in the identification of different patterns of PPIs in different species and their functional consequences. To resolve these issues, we developed a web application, called INTER-Species Protein Interaction Analysis (INTERSPIA). Given a set of proteins of user's interest, INTERSPIA first discovers additional proteins that are functionally associated with the input proteins and searches for different patterns of PPIs in multiple species through a server-side pipeline, and second visualizes the dynamics of PPIs in multiple species using an easy-to-use web interface. INTERSPIA is freely available at http://bioinfo.konkuk.ac.kr/INTERSPIA/.

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.

Web based tools for data manipulation, visualisation and validation with interactive georeferenced graphs

NASA Astrophysics Data System (ADS)

Ivankovic, D.; Dadic, V.

2009-04-01

Some of oceanographic parameters have to be manually inserted into database; some (for example data from CTD probe) are inserted from various files. All this parameters requires visualization, validation and manipulation from research vessel or scientific institution, and also public presentation. For these purposes is developed web based system, containing dynamic sql procedures and java applets. Technology background is Oracle 10g relational database, and Oracle application server. Web interfaces are developed using PL/SQL stored database procedures (mod PL/SQL). Additional parts for data visualization include use of Java applets and JavaScript. Mapping tool is Google maps API (javascript) and as alternative java applet. Graph is realized as dynamically generated web page containing java applet. Mapping tool and graph are georeferenced. That means that click on some part of graph, automatically initiate zoom or marker onto location where parameter was measured. This feature is very useful for data validation. Code for data manipulation and visualization are partially realized with dynamic SQL and that allow as to separate data definition and code for data manipulation. Adding new parameter in system requires only data definition and description without programming interface for this kind of data.

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.

Seeing the System through the End Users' Eyes: Shadow Expert Technique for Evaluating the Consistency of a Learning Management System

NASA Astrophysics Data System (ADS)

Holzinger, Andreas; Stickel, Christian; Fassold, Markus; Ebner, Martin

Interface consistency is an important basic concept in web design and has an effect on performance and satisfaction of end users. Consistency also has significant effects on the learning performance of both expert and novice end users. Consequently, the evaluation of consistency within a e-learning system and the ensuing eradication of irritating discrepancies in the user interface redesign is a big issue. In this paper, we report of our experiences with the Shadow Expert Technique (SET) during the evaluation of the consistency of the user interface of a large university learning management system. The main objective of this new usability evaluation method is to understand the interaction processes of end users with a specific system interface. Two teams of usability experts worked independently from each other in order to maximize the objectivity of the results. The outcome of this SET method is a list of recommended changes to improve the user interaction processes, hence to facilitate high consistency.

Spaces of the Hilltop: A Case Study of Community/Academic Interaction

ERIC Educational Resources Information Center

Knochel, Aaron; Selfe, Dickie

2012-01-01

The mapping imagery of the web interface is an attempt to illustrate the surprising element of the Hilltop project. The map is not "accurate." It shows real streets and highways in, around, and in-between the Ohio State University and the Hilltop community, but it is not intended to provide directions.

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

PubMed Central

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

2015-01-01

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

eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.

PubMed

Kinoshita, Kengo; Murakami, Yoichi; Nakamura, Haruki

2007-07-01

We have developed a method to predict ligand-binding sites in a new protein structure by searching for similar binding sites in the Protein Data Bank (PDB). The similarities are measured according to the shapes of the molecular surfaces and their electrostatic potentials. A new web server, eF-seek, provides an interface to our search method. It simply requires a coordinate file in the PDB format, and generates a prediction result as a virtual complex structure, with the putative ligands in a PDB format file as the output. In addition, the predicted interacting interface is displayed to facilitate the examination of the virtual complex structure on our own applet viewer with the web browser (URL: http://eF-site.hgc.jp/eF-seek).

P43-S Computational Biology Applications Suite for High-Performance Computing (BioHPC.net)

PubMed Central

Pillardy, J.

2007-01-01

One of the challenges of high-performance computing (HPC) is user accessibility. At the Cornell University Computational Biology Service Unit, which is also a Microsoft HPC institute, we have developed a computational biology application suite that allows researchers from biological laboratories to submit their jobs to the parallel cluster through an easy-to-use Web interface. Through this system, we are providing users with popular bioinformatics tools including BLAST, HMMER, InterproScan, and MrBayes. The system is flexible and can be easily customized to include other software. It is also scalable; the installation on our servers currently processes approximately 8500 job submissions per year, many of them requiring massively parallel computations. It also has a built-in user management system, which can limit software and/or database access to specified users. TAIR, the major database of the plant model organism Arabidopsis, and SGN, the international tomato genome database, are both using our system for storage and data analysis. The system consists of a Web server running the interface (ASP.NET C#), Microsoft SQL server (ADO.NET), compute cluster running Microsoft Windows, ftp server, and file server. Users can interact with their jobs and data via a Web browser, ftp, or e-mail. The interface is accessible at http://cbsuapps.tc.cornell.edu/.

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

PubMed Central

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

2017-01-01

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

Interactive Webmap-Based Science Planning for BepiColombo

NASA Astrophysics Data System (ADS)

McAuliffe, J.; Martinez, S.; Ortiz de Landaluce, I.; de la Fuente, S.

2015-10-01

For BepiColombo, ESA's Mission to Mercury, we will build a web-based, map-based interface to the Science Planning System. This interface will allow the mission's science teams to visually define targets for observations and interactively specify what operations will make up the given observation. This will be a radical departure from previous ESA mission planning methods. Such an interface will rely heavily on GIS technologies. This interface will provide footprint coverage of all existing archived data for Mercury, including a set of built-in basemaps. This will allow the science teams to analyse their planned observations and operational constraints with relevant contextual information from their own instrument, other BepiColombo instruments or from previous missions. The interface will allow users to import and export data in commonly used GIS formats, such that it can be visualised together with the latest planning information (e.g. import custom basemaps) or analysed in other GIS software. The interface will work with an object-oriented concept of an observation that will be a key characteristic of the overall BepiColombo scienceplanning concept. Observation templates or classes will be tracked right through the planning-executionprocessing- archiving cycle to the final archived science products. By using an interface that synthesises all relevant available information, the science teams will have a better understanding of the operational environment; it will enhance their ability to plan efficiently minimising or removing manual planning. Interactive 3D visualisation of the planned, scheduled and executed observations, simulation of the viewing conditions and interactive modification of the observation parameters are also being considered.

PMD2HD--a web tool aligning a PubMed search results page with the local German Cancer Research Centre library collection.

PubMed

Bohne-Lang, Andreas; Lang, Elke; Taube, Anke

2005-06-27

Web-based searching is the accepted contemporary mode of retrieving relevant literature, and retrieving as many full text articles as possible is a typical prerequisite for research success. In most cases only a proportion of references will be directly accessible as digital reprints through displayed links. A large number of references, however, have to be verified in library catalogues and, depending on their availability, are accessible as print holdings or by interlibrary loan request. The problem of verifying local print holdings from an initial retrieval set of citations can be solved using Z39.50, an ANSI protocol for interactively querying library information systems. Numerous systems include Z39.50 interfaces and therefore can process Z39.50 interactive requests. However, the programmed query interaction command structure is non-intuitive and inaccessible to the average biomedical researcher. For the typical user, it is necessary to implement the protocol within a tool that hides and handles Z39.50 syntax, presenting a comfortable user interface. PMD2HD is a web tool implementing Z39.50 to provide an appropriately functional and usable interface to integrate into the typical workflow that follows an initial PubMed literature search, providing users with an immediate asset to assist in the most tedious step in literature retrieval, checking for subscription holdings against a local online catalogue. PMD2HD can facilitate literature access considerably with respect to the time and cost of manual comparisons of search results with local catalogue holdings. The example presented in this article is related to the library system and collections of the German Cancer Research Centre. However, the PMD2HD software architecture and use of common Z39.50 protocol commands allow for transfer to a broad range of scientific libraries using Z39.50-compatible library information systems.

Using JavaScript and the FDSN web service to create an interactive earthquake information system

NASA Astrophysics Data System (ADS)

Fischer, Kasper D.

2015-04-01

The FDSN web service provides a web interface to access earthquake meta-data (e. g. event or station information) and waveform date over the internet. Requests are send to a server as URLs and the output is either XML or miniSEED. This makes it hard to read by humans but easy to process with different software. Different data centers are already supporting the FDSN web service, e. g. USGS, IRIS, ORFEUS. The FDSN web service is also part of the Seiscomp3 (http://www.seiscomp3.org) software. The Seismological Observatory of the Ruhr-University switched to Seiscomp3 as the standard software for the analysis of mining induced earthquakes at the beginning of 2014. This made it necessary to create a new web-based earthquake information service for the publication of results to the general public. This has be done by processing the output of a FDSN web service query by javascript running in a standard browser. The result is an interactive map presenting the observed events and further information of events and stations on a single web page as a table and on a map. In addition the user can download event information, waveform data and station data in different formats like miniSEED, quakeML or FDSNxml. The developed code and all used libraries are open source and freely available.

The RING 2.0 web server for high quality residue interaction networks.

PubMed

Piovesan, Damiano; Minervini, Giovanni; Tosatto, Silvio C E

2016-07-08

Residue interaction networks (RINs) are an alternative way of representing protein structures where nodes are residues and arcs physico-chemical interactions. RINs have been extensively and successfully used for analysing mutation effects, protein folding, domain-domain communication and catalytic activity. Here we present RING 2.0, a new version of the RING software for the identification of covalent and non-covalent bonds in protein structures, including π-π stacking and π-cation interactions. RING 2.0 is extremely fast and generates both intra and inter-chain interactions including solvent and ligand atoms. The generated networks are very accurate and reliable thanks to a complex empirical re-parameterization of distance thresholds performed on the entire Protein Data Bank. By default, RING output is generated with optimal parameters but the web server provides an exhaustive interface to customize the calculation. The network can be visualized directly in the browser or in Cytoscape. Alternatively, the RING-Viz script for Pymol allows visualizing the interactions at atomic level in the structure. The web server and RING-Viz, together with an extensive help and tutorial, are available from URL: http://protein.bio.unipd.it/ring. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Intelligent Visualization of Geo-Information on the Future Web

NASA Astrophysics Data System (ADS)

Slusallek, P.; Jochem, R.; Sons, K.; Hoffmann, H.

2012-04-01

Visualization is a key component of the "Observation Web" and will become even more important in the future as geo data becomes more widely accessible. The common statement that "Data that cannot be seen, does not exist" is especially true for non-experts, like most citizens. The Web provides the most interesting platform for making data easily and widely available. However, today's Web is not well suited for the interactive visualization and exploration that is often needed for geo data. Support for 3D data was added only recently and at an extremely low level (WebGL), but even the 2D visualization capabilities of HTML e.g. (images, canvas, SVG) are rather limited, especially regarding interactivity. We have developed XML3D as an extension to HTML-5. It allows for compactly describing 2D and 3D data directly as elements of an HTML-5 document. All graphics elements are part of the Document Object Model (DOM) and can be manipulated via the same set of DOM events and methods that millions of Web developers use on a daily basis. Thus, XML3D makes highly interactive 2D and 3D visualization easily usable, not only for geo data. XML3D is supported by any WebGL-capable browser but we also provide native implementations in Firefox and Chromium. As an example, we show how OpenStreetMap data can be mapped directly to XML3D and visualized interactively in any Web page. We show how this data can be easily augmented with additional data from the Web via a few lines of Javascript. We also show how embedded semantic data (via RDFa) allows for linking the visualization back to the data's origin, thus providing an immersive interface for interacting with and modifying the original data. XML3D is used as key input for standardization within the W3C Community Group on "Declarative 3D for the Web" chaired by the DFKI and has recently been selected as one of the Generic Enabler for the EU Future Internet initiative.

TreePlus: interactive exploration of networks with enhanced tree layouts.

PubMed

Lee, Bongshin; Parr, Cynthia S; Plaisant, Catherine; Bederson, Benjamin B; Veksler, Vladislav D; Gray, Wayne D; Kotfila, Christopher

2006-01-01

Despite extensive research, it is still difficult to produce effective interactive layouts for large graphs. Dense layout and occlusion make food webs, ontologies, and social networks difficult to understand and interact with. We propose a new interactive Visual Analytics component called TreePlus that is based on a tree-style layout. TreePlus reveals the missing graph structure with visualization and interaction while maintaining good readability. To support exploration of the local structure of the graph and gathering of information from the extensive reading of labels, we use a guiding metaphor of "Plant a seed and watch it grow." It allows users to start with a node and expand the graph as needed, which complements the classic overview techniques that can be effective at (but often limited to) revealing clusters. We describe our design goals, describe the interface, and report on a controlled user study with 28 participants comparing TreePlus with a traditional graph interface for six tasks. In general, the advantage of TreePlus over the traditional interface increased as the density of the displayed data increased. Participants also reported higher levels of confidence in their answers with TreePlus and most of them preferred TreePlus.

Social Circles: A 3D User Interface for Facebook

NASA Astrophysics Data System (ADS)

Rodrigues, Diego; Oakley, Ian

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

Open Astronomy Catalogs API

NASA Astrophysics Data System (ADS)

Guillochon, James; Cowperthwaite, Philip S.

2018-05-01

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

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

PubMed

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

2014-12-12

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

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.

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

NASA Astrophysics Data System (ADS)

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

2014-06-01

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

Improving Conceptual Design for Launch Vehicles

NASA Technical Reports Server (NTRS)

Olds, John R.

1998-01-01

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

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

NASA Astrophysics Data System (ADS)

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

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

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

NASA Astrophysics Data System (ADS)

Bartsch, H.; Erlebacher, G.

2003-12-01

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

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.

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.

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

PubMed Central

2016-01-01

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

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

PubMed

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

2016-08-05

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

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.

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

NASA Astrophysics Data System (ADS)

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

2005-12-01

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

A Framework for Integrating Oceanographic Data Repositories

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

78 FR 79434 - Notice of Technical Conference

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-30

...: one that will allow EQR users to file through a web interface on the Commission's Web site, and a... the conference, staff will demonstrate how to make a filing using both the XML and web interface... Calendar of Events on the Commission's Web site, www.ferc.gov . A free webcast of the conference will be...

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

NASA Astrophysics Data System (ADS)

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

2000-04-01

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

Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models

PubMed Central

2014-01-01

Background Logos are commonly used in molecular biology to provide a compact graphical representation of the conservation pattern of a set of sequences. They render the information contained in sequence alignments or profile hidden Markov models by drawing a stack of letters for each position, where the height of the stack corresponds to the conservation at that position, and the height of each letter within a stack depends on the frequency of that letter at that position. Results We present a new tool and web server, called Skylign, which provides a unified framework for creating logos for both sequence alignments and profile hidden Markov models. In addition to static image files, Skylign creates a novel interactive logo plot for inclusion in web pages. These interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position. Conclusion Skylign is available as a website, a scriptable web service with a RESTful interface, and as a software package for download. Skylign’s interactive logos are easily incorporated into a web page with just a few lines of HTML markup. Skylign may be found at http://skylign.org. PMID:24410852

Systemic Vulnerabilities in Customer-Premises Equipment (CPE) Routers

DTIC Science & Technology

2017-07-01

equipment (CPE),1 specifically small office/home office (SOHO) routers, has become ubiquitous. CPE routers are notorious for their web interface...and enabling remote management, although all settings controllable over the web -management interface can be manipulated. • 85% (11 of 13) of...specifically small office/home office (SOHO) routers— has become ubiquitous. CPE routers are notorious for their web interface vulnerabilities, old ver- sions

VirGO: A Visual Browser for the ESO Science Archive Facility

NASA Astrophysics Data System (ADS)

Chéreau, Fabien

2012-04-01

VirGO is the next generation Visual Browser for the ESO Science Archive Facility developed by the Virtual Observatory (VO) Systems Department. It is a plug-in for the popular open source software Stellarium adding capabilities for browsing professional astronomical data. VirGO gives astronomers the possibility to easily discover and select data from millions of observations in a new visual and intuitive way. Its main feature is to perform real-time access and graphical display of a large number of observations by showing instrumental footprints and image previews, and to allow their selection and filtering for subsequent download from the ESO SAF web interface. It also allows the loading of external FITS files or VOTables, the superimposition of Digitized Sky Survey (DSS) background images, and the visualization of the sky in a `real life' mode as seen from the main ESO sites. All data interfaces are based on Virtual Observatory standards which allow access to images and spectra from external data centers, and interaction with the ESO SAF web interface or any other VO applications supporting the PLASTIC messaging system.

Multiple scavengers respond rapidly to pulsed carrion resources at the land-ocean interface

NASA Astrophysics Data System (ADS)

Schlacher, Thomas A.; Strydom, Simone; Connolly, Rod M.

2013-04-01

Sandy beaches are the globe's longest interface region between the oceans and the continents, forming highly permeable boundaries across which matter flows readily. Stranded marine carrion supplies a high-quality food source to scavengers, but the role of animal carcasses is generally under-reported in sandy-beach food webs. We examined the response of scavengers to pulsed subsidies in the form of experimental additions of fish carcasses to the dune-beach interface in eastern Australia. Ghost crabs (Ocypode spp.) are the dominant invertebrate scavengers in these habitats and they responded strongly and consistently to changed resource availability: densities increased significantly within days of carrion augmentations. Carcasses added experimentally also formed local nuclei for a diversity of vertebrate scavengers that aggregated at food falls; these included large lizards, several species of birds (including raptors), and foxes. Consumption of fish carrion by the vertebrate scavengers was rapid and often complete. There is also evidence for higher-order interactions, where responses of invertebrate scavengers became depressed in plots where vertebrate scavenger activity was intense. Our findings emphasize that carrion can be a pivotal component of beach food webs.

LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands

PubMed Central

Dodda, Leela S.

2017-01-01

Abstract The accurate calculation of protein/nucleic acid–ligand interactions or condensed phase properties by force field-based methods require a precise description of the energetics of intermolecular interactions. Despite the progress made in force fields, small molecule parameterization remains an open problem due to the magnitude of the chemical space; the most critical issue is the estimation of a balanced set of atomic charges with the ability to reproduce experimental properties. The LigParGen web server provides an intuitive interface for generating OPLS-AA/1.14*CM1A(-LBCC) force field parameters for organic ligands, in the formats of commonly used molecular dynamics and Monte Carlo simulation packages. This server has high value for researchers interested in studying any phenomena based on intermolecular interactions with ligands via molecular mechanics simulations. It is free and open to all at jorgensenresearch.com/ligpargen, and has no login requirements. PMID:28444340

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

PubMed Central

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

2014-01-01

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

UCbase 2.0: ultraconserved sequences database (2014 update)

PubMed Central

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

2014-01-01

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

VirHostNet 2.0: surfing on the web of virus/host molecular interactions data.

PubMed

Guirimand, Thibaut; Delmotte, Stéphane; Navratil, Vincent

2015-01-01

VirHostNet release 2.0 (http://virhostnet.prabi.fr) is a knowledgebase dedicated to the network-based exploration of virus-host protein-protein interactions. Since the previous VirhostNet release (2009), a second run of manual curation was performed to annotate the new torrent of high-throughput protein-protein interactions data from the literature. This resource is shared publicly, in PSI-MI TAB 2.5 format, using a PSICQUIC web service. The new interface of VirHostNet 2.0 is based on Cytoscape web library and provides a user-friendly access to the most complete and accurate resource of virus-virus and virus-host protein-protein interactions as well as their projection onto their corresponding host cell protein interaction networks. We hope that the VirHostNet 2.0 system will facilitate systems biology and gene-centered analysis of infectious diseases and will help to identify new molecular targets for antiviral drugs design. This resource will also continue to help worldwide scientists to improve our knowledge on molecular mechanisms involved in the antiviral response mediated by the cell and in the viral strategies selected by viruses to hijack the host immune system. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

WheatGenome.info: A Resource for Wheat Genomics Resource.

PubMed

Lai, Kaitao

2016-01-01

An integrated database with a variety of Web-based systems named WheatGenome.info hosting wheat genome and genomic data has been developed to support wheat research and crop improvement. The resource includes multiple Web-based applications, which are implemented as a variety of Web-based systems. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This portal provides links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/ .

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.

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

PubMed

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

2016-11-01

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

AnnoLnc: a web server for systematically annotating novel human lncRNAs.

PubMed

Hou, Mei; Tang, Xing; Tian, Feng; Shi, Fangyuan; Liu, Fenglin; Gao, Ge

2016-11-16

Long noncoding RNAs (lncRNAs) have been shown to play essential roles in almost every important biological process through multiple mechanisms. Although the repertoire of human lncRNAs has rapidly expanded, their biological function and regulation remain largely elusive, calling for a systematic and integrative annotation tool. Here we present AnnoLnc ( http://annolnc.cbi.pku.edu.cn ), a one-stop portal for systematically annotating novel human lncRNAs. Based on more than 700 data sources and various tool chains, AnnoLnc enables a systematic annotation covering genomic location, secondary structure, expression patterns, transcriptional regulation, miRNA interaction, protein interaction, genetic association and evolution. An intuitive web interface is available for interactive analysis through both desktops and mobile devices, and programmers can further integrate AnnoLnc into their pipeline through standard JSON-based Web Service APIs. To the best of our knowledge, AnnoLnc is the only web server to provide on-the-fly and systematic annotation for newly identified human lncRNAs. Compared with similar tools, the annotation generated by AnnoLnc covers a much wider spectrum with intuitive visualization. Case studies demonstrate the power of AnnoLnc in not only rediscovering known functions of human lncRNAs but also inspiring novel hypotheses.

Web-Based Interface for Command and Control of Network Sensors

NASA Technical Reports Server (NTRS)

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

2010-01-01

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

3Dmol.js: molecular visualization with WebGL.

PubMed

Rego, Nicholas; Koes, David

2015-04-15

3Dmol.js is a modern, object-oriented JavaScript library that uses the latest web technologies to provide interactive, hardware-accelerated three-dimensional representations of molecular data without the need to install browser plugins or Java. 3Dmol.js provides a full featured API for developers as well as a straightforward declarative interface that lets users easily share and embed molecular data in websites. 3Dmol.js is distributed under the permissive BSD open source license. Source code and documentation can be found at http://3Dmol.csb.pitt.edu dkoes@pitt.edu. © The Author 2014. Published by Oxford University Press.

An Overview of ARL’s Multimodal Signatures Database and Web Interface

DTIC Science & Technology

2007-12-01

ActiveX components, which hindered distribution due to license agreements and run-time license software to use such components. g. Proprietary...Overview The database consists of multimodal signature data files in the HDF5 format. Generally, each signature file contains all the ancillary...only contains information in the database, Web interface, and signature files that is releasable to the public. The Web interface consists of static

Network Science Research Laboratory (NSRL) Telemetry Warehouse

DTIC Science & Technology

2016-06-01

Functionality and architecture of the NSRL Telemetry Warehouse are also described as well as the web interface, data structure, security aspects, and...Experiment Controller 6 4.5 Telemetry Sensors 7 4.6 Custom Data Processing Nodes 7 5. Web Interface 8 6. Data Structure 8 6.1 Measurements 8...telemetry in comma-separated value (CSV) format from the web interface or via custom applications developed by researchers using the client application

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

NASA Astrophysics Data System (ADS)

Fragkoulis, Marios; Spinellis, Diomidis; Louridas, Panos

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

MCSDSS: A Multi-Criteria Decision Support System for Merging Geoscience Information with Natural User Interfaces, Preference Ranking, and Interactive Data Utilities

NASA Astrophysics Data System (ADS)

Pierce, S. A.; Gentle, J.

2015-12-01

The multi-criteria decision support system (MCSDSS) is a newly completed application for touch-enabled group decision support that uses D3 data visualization tools, a geojson conversion utility that we developed, and Paralelex to create an interactive tool. The MCSDSS is a prototype system intended to demonstrate the potential capabilities of a single page application (SPA) running atop a web and cloud based architecture utilizing open source technologies. The application is implemented on current web standards while supporting human interface design that targets both traditional mouse/keyboard interactions and modern touch/gesture enabled interactions. The technology stack for MCSDSS was selected with the goal of creating a robust and dynamic modular codebase that can be adjusted to fit many use cases and scale to support usage loads that range between simple data display to complex scientific simulation-based modelling and analytics. The application integrates current frameworks for highly performant agile development with unit testing, statistical analysis, data visualization, mapping technologies, geographic data manipulation, and cloud infrastructure while retaining support for traditional HTML5/CSS3 web standards. The software lifecylcle for MCSDSS has following best practices to develop, share, and document the codebase and application. Code is documented and shared via an online repository with the option for programmers to see, contribute, or fork the codebase. Example data files and tutorial documentation have been shared with clear descriptions and data object identifiers. And the metadata about the application has been incorporated into an OntoSoft entry to ensure that MCSDSS is searchable and clearly described. MCSDSS is a flexible platform that allows for data fusion and inclusion of large datasets in an interactive front-end application capable of connecting with other science-based applications and advanced computing resources. In addition, MCSDSS offers functionality that enables communication with non-technical users for policy, education, or engagement with groups around scientific topics with societal relevance.

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

NASA Astrophysics Data System (ADS)

Siarto, J.

2014-12-01

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

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

NASA Astrophysics Data System (ADS)

Stoltz, Peter; Veitzer, Seth

2008-04-01

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

Web of Pseudostreamer and Streamer Belts and their Interplanetary Signatures

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

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

MDB: the Metalloprotein Database and Browser at The Scripps Research Institute

PubMed Central

Castagnetto, Jesus M.; Hennessy, Sean W.; Roberts, Victoria A.; Getzoff, Elizabeth D.; Tainer, John A.; Pique, Michael E.

2002-01-01

The Metalloprotein Database and Browser (MDB; http://metallo.scripps.edu) at The Scripps Research Institute is a web-accessible resource for metalloprotein research. It offers the scientific community quantitative information on geometrical parameters of metal-binding sites in protein structures available from the Protein Data Bank (PDB). The MDB also offers analytical tools for the examination of trends or patterns in the indexed metal-binding sites. A user can perform interactive searches, metal-site structure visualization (via a Java applet), and analysis of the quantitative data by accessing the MDB through a web browser without requiring an external application or platform-dependent plugin. The MDB also has a non-interactive interface with which other web sites and network-aware applications can seamlessly incorporate data or statistical analysis results from metal-binding sites. The information contained in the MDB is periodically updated with automated algorithms that find and index metal sites from new protein structures released by the PDB. PMID:11752342

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

PubMed Central

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

2003-01-01

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

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

PubMed

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

2018-06-05

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

Graph Visualization for RDF Graphs with SPARQL-EndPoints

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

Sukumar, Sreenivas R; Bond, Nathaniel

2014-07-11

RDF graphs are hard to visualize as triples. This software module is a web interface that connects to a SPARQL endpoint and retrieves graph data that the user can explore interactively and seamlessly. The software written in python and JavaScript has been tested to work on screens as little as the smart phones to large screens such as EVEREST.

The Influence of Online Comments on Perceptions of Antimarijuana Public Service Announcements on YouTube

ERIC Educational Resources Information Center

Walther, Joseph B.; DeAndrea, David; Kim, Jinsuk; Anthony, James C.

2010-01-01

Web-based media often present multiple sources of influence, such as mass media and peers, within one interface. When individuals identify with peers who are visually anonymous and with whom they do not directly interact, they should be susceptible to social influence from that group. This study examined the interplay among antimarijuana public…

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

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.

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.

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

PubMed

Basu, M K

2001-06-01

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

Interface Psychology: Touchscreens Change Attribute Importance, Decision Criteria, and Behavior in Online Choice

PubMed Central

Gips, James

2015-01-01

Abstract As the rise of tablets and smartphones move the dominant interface for digital content from mouse or trackpad to direct touchscreen interaction, work is needed to explore the role of interfaces in shaping psychological reactions to online content. This research explores the role of direct-touch interfaces in product search and choice, and isolates the touch element from other form factor changes such as screen size. Results from an experimental study using a travel recommendation Web site show that a direct-touch interface (vs. a more traditional mouse interface) increases the number of alternatives searched, and biases evaluations toward tangible attributes such as décor and furniture over intangible attributes such as WiFi and employee demeanor. Direct-touch interfaces also elevate the importance of internal and subjective satisfaction metrics such as instinct over external and objective metrics such as reviews, which in turn increases anticipated satisfaction metrics. Findings suggest that interfaces can strongly affect how online content is explored, perceived, remembered, and acted on, and further work in interface psychology could be as fruitful as research exploring the content itself. PMID:26348814

Interface Psychology: Touchscreens Change Attribute Importance, Decision Criteria, and Behavior in Online Choice.

PubMed

Brasel, S Adam; Gips, James

2015-09-01

As the rise of tablets and smartphones move the dominant interface for digital content from mouse or trackpad to direct touchscreen interaction, work is needed to explore the role of interfaces in shaping psychological reactions to online content. This research explores the role of direct-touch interfaces in product search and choice, and isolates the touch element from other form factor changes such as screen size. Results from an experimental study using a travel recommendation Web site show that a direct-touch interface (vs. a more traditional mouse interface) increases the number of alternatives searched, and biases evaluations toward tangible attributes such as décor and furniture over intangible attributes such as WiFi and employee demeanor. Direct-touch interfaces also elevate the importance of internal and subjective satisfaction metrics such as instinct over external and objective metrics such as reviews, which in turn increases anticipated satisfaction metrics. Findings suggest that interfaces can strongly affect how online content is explored, perceived, remembered, and acted on, and further work in interface psychology could be as fruitful as research exploring the content itself.

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

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

Wong, Pak C.

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

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

PubMed

Gordon, Paul M K; Sensen, Christoph W

2007-06-18

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

Seahawk: moving beyond HTML in Web-based bioinformatics analysis

PubMed Central

Gordon, Paul MK; Sensen, Christoph W

2007-01-01

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

Stiffener-skin interactions in pressure-loaded composite panels

NASA Technical Reports Server (NTRS)

Loup, D. C.; Hyer, M. W.; Starnes, J. H., Jr.

1986-01-01

The effects of flange thickness, web height, and skin stiffness on the strain distributions in the skin-stiffener interface region of pressure-loaded graphite-epoxy panels, stiffened by the type-T stiffener, were examined at pressure levels up to one atmosphere. The results indicate that at these pressures geometric nonlinearities are important, and that the overall stiffener stiffness has a significant effect on panel response, particularly on the out-of-plane deformation or pillowing of the skin. The strain gradients indicated that the interface between the skin and the stiffener experiences two components of shear stress, in addition to a normal (peel) stress. Thus, the skin-stiffener interface problem is a three-dimensional problem rather than a two-dimensional one, as is often assumed.

Ontology-Driven Search and Triage: Design of a Web-Based Visual Interface for MEDLINE.

PubMed

Demelo, Jonathan; Parsons, Paul; Sedig, Kamran

2017-02-02

Diverse users need to search health and medical literature to satisfy open-ended goals such as making evidence-based decisions and updating their knowledge. However, doing so is challenging due to at least two major difficulties: (1) articulating information needs using accurate vocabulary and (2) dealing with large document sets returned from searches. Common search interfaces such as PubMed do not provide adequate support for exploratory search tasks. Our objective was to improve support for exploratory search tasks by combining two strategies in the design of an interactive visual interface by (1) using a formal ontology to help users build domain-specific knowledge and vocabulary and (2) providing multi-stage triaging support to help mitigate the information overload problem. We developed a Web-based tool, Ontology-Driven Visual Search and Triage Interface for MEDLINE (OVERT-MED), to test our design ideas. We implemented a custom searchable index of MEDLINE, which comprises approximately 25 million document citations. We chose a popular biomedical ontology, the Human Phenotype Ontology (HPO), to test our solution to the vocabulary problem. We implemented multistage triaging support in OVERT-MED, with the aid of interactive visualization techniques, to help users deal with large document sets returned from searches. Formative evaluation suggests that the design features in OVERT-MED are helpful in addressing the two major difficulties described above. Using a formal ontology seems to help users articulate their information needs with more accurate vocabulary. In addition, multistage triaging combined with interactive visualizations shows promise in mitigating the information overload problem. Our strategies appear to be valuable in addressing the two major problems in exploratory search. Although we tested OVERT-MED with a particular ontology and document collection, we anticipate that our strategies can be transferred successfully to other contexts. ©Jonathan Demelo, Paul Parsons, Kamran Sedig. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 02.02.2017.

Ontology-Driven Search and Triage: Design of a Web-Based Visual Interface for MEDLINE

PubMed Central

2017-01-01

Background Diverse users need to search health and medical literature to satisfy open-ended goals such as making evidence-based decisions and updating their knowledge. However, doing so is challenging due to at least two major difficulties: (1) articulating information needs using accurate vocabulary and (2) dealing with large document sets returned from searches. Common search interfaces such as PubMed do not provide adequate support for exploratory search tasks. Objective Our objective was to improve support for exploratory search tasks by combining two strategies in the design of an interactive visual interface by (1) using a formal ontology to help users build domain-specific knowledge and vocabulary and (2) providing multi-stage triaging support to help mitigate the information overload problem. Methods We developed a Web-based tool, Ontology-Driven Visual Search and Triage Interface for MEDLINE (OVERT-MED), to test our design ideas. We implemented a custom searchable index of MEDLINE, which comprises approximately 25 million document citations. We chose a popular biomedical ontology, the Human Phenotype Ontology (HPO), to test our solution to the vocabulary problem. We implemented multistage triaging support in OVERT-MED, with the aid of interactive visualization techniques, to help users deal with large document sets returned from searches. Results Formative evaluation suggests that the design features in OVERT-MED are helpful in addressing the two major difficulties described above. Using a formal ontology seems to help users articulate their information needs with more accurate vocabulary. In addition, multistage triaging combined with interactive visualizations shows promise in mitigating the information overload problem. Conclusions Our strategies appear to be valuable in addressing the two major problems in exploratory search. Although we tested OVERT-MED with a particular ontology and document collection, we anticipate that our strategies can be transferred successfully to other contexts. PMID:28153818

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

PubMed Central

2011-01-01

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

Embedded Web Technology: Internet Technology Applied to Real-Time System Control

NASA Technical Reports Server (NTRS)

Daniele, Carl J.

1998-01-01

The NASA Lewis Research Center is developing software tools to bridge the gap between the traditionally non-real-time Internet technology and the real-time, embedded-controls environment for space applications. Internet technology has been expanding at a phenomenal rate. The simple World Wide Web browsers (such as earlier versions of Netscape, Mosaic, and Internet Explorer) that resided on personal computers just a few years ago only enabled users to log into and view a remote computer site. With current browsers, users not only view but also interact with remote sites. In addition, the technology now supports numerous computer platforms (PC's, MAC's, and Unix platforms), thereby providing platform independence.In contrast, the development of software to interact with a microprocessor (embedded controller) that is used to monitor and control a space experiment has generally been a unique development effort. For each experiment, a specific graphical user interface (GUI) has been developed. This procedure works well for a single-user environment. However, the interface for the International Space Station (ISS) Fluids and Combustion Facility will have to enable scientists throughout the world and astronauts onboard the ISS, using different computer platforms, to interact with their experiments in the Fluids and Combustion Facility. Developing a specific GUI for all these users would be cost prohibitive. An innovative solution to this requirement, developed at Lewis, is to use Internet technology, where the general problem of platform independence has already been partially solved, and to leverage this expanding technology as new products are developed. This approach led to the development of the Embedded Web Technology (EWT) program at Lewis, which has the potential to significantly reduce software development costs for both flight and ground software.

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

PubMed

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

2011-03-08

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

Automatic geospatial information Web service composition based on ontology interface matching

NASA Astrophysics Data System (ADS)

Xu, Xianbin; Wu, Qunyong; Wang, Qinmin

2008-10-01

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

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application.

PubMed

Hanwell, Marcus D; de Jong, Wibe A; Harris, Christopher J

2017-10-30

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction-connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platform with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web-going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

DOE PAGES

Hanwell, Marcus D.; de Jong, Wibe A.; Harris, Christopher J.

2017-10-30

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction - connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platformmore » with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web - going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.« less

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

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

Hanwell, Marcus D.; de Jong, Wibe A.; Harris, Christopher J.

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction - connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platformmore » with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web - going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.« less

Web OPAC Interfaces: An Overview.

ERIC Educational Resources Information Center

Babu, B. Ramesh; O'Brien, Ann

2000-01-01

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

WARCProcessor: An Integrative Tool for Building and Management of Web Spam Corpora.

PubMed

Callón, Miguel; Fdez-Glez, Jorge; Ruano-Ordás, David; Laza, Rosalía; Pavón, Reyes; Fdez-Riverola, Florentino; Méndez, Jose Ramón

2017-12-22

In this work we present the design and implementation of WARCProcessor, a novel multiplatform integrative tool aimed to build scientific datasets to facilitate experimentation in web spam research. The developed application allows the user to specify multiple criteria that change the way in which new corpora are generated whilst reducing the number of repetitive and error prone tasks related with existing corpus maintenance. For this goal, WARCProcessor supports up to six commonly used data sources for web spam research, being able to store output corpus in standard WARC format together with complementary metadata files. Additionally, the application facilitates the automatic and concurrent download of web sites from Internet, giving the possibility of configuring the deep of the links to be followed as well as the behaviour when redirected URLs appear. WARCProcessor supports both an interactive GUI interface and a command line utility for being executed in background.

VizieR Data Extraction Disseminated through Widgets

NASA Astrophysics Data System (ADS)

Landais, G.; Boch, T.; Ochsenbein, F.; Simon, A.-C.

2015-09-01

The CDS widgets are a collection of web applications easily embeddable in web pages. The Apache Shindig framework, relying on OpenSocial specification, enables to reuse code in any web page by giving interactive output and broadcasting capabilities: for instance to use the result of a search widget to populate other widgets. Some of these widgets are already used in the VizieR web application. The “plot widget” is used to illustrate associated data like time-series or spectra coming from publications. The data extracted with a SQL-like language (which can operate with different type of resources like FITS, ASCII files, etc.) are then disseminated in a “plot widge” that is ergonomic and contains evolved customization capabilities. The VizieR photometry viewer is the result of filter gathering and pipeline automatization: the interface use a dedicated widget that integrates three linked views: a photometry point, a sky chart and the VizieR tabular data.

Credibility judgments in web page design - a brief review.

PubMed

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

2016-01-01

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

Credibility judgments in web page design – a brief review

PubMed Central

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

2016-01-01

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

WARCProcessor: An Integrative Tool for Building and Management of Web Spam Corpora

PubMed Central

Callón, Miguel; Fdez-Glez, Jorge; Ruano-Ordás, David; Laza, Rosalía; Pavón, Reyes; Méndez, Jose Ramón

2017-01-01

In this work we present the design and implementation of WARCProcessor, a novel multiplatform integrative tool aimed to build scientific datasets to facilitate experimentation in web spam research. The developed application allows the user to specify multiple criteria that change the way in which new corpora are generated whilst reducing the number of repetitive and error prone tasks related with existing corpus maintenance. For this goal, WARCProcessor supports up to six commonly used data sources for web spam research, being able to store output corpus in standard WARC format together with complementary metadata files. Additionally, the application facilitates the automatic and concurrent download of web sites from Internet, giving the possibility of configuring the deep of the links to be followed as well as the behaviour when redirected URLs appear. WARCProcessor supports both an interactive GUI interface and a command line utility for being executed in background. PMID:29271913

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Climate Model Diagnostic Analyzer Web Service System

NASA Astrophysics Data System (ADS)

Lee, S.; Pan, L.; Zhai, C.; Tang, B.; Jiang, J. H.

2014-12-01

We have developed a cloud-enabled web-service system that empowers physics-based, multi-variable model performance evaluations and diagnoses through the comprehensive and synergistic use of multiple observational data, reanalysis data, and model outputs. We have developed a methodology to transform an existing science application code into a web service using a Python wrapper interface and Python web service frameworks. The web-service system, called Climate Model Diagnostic Analyzer (CMDA), currently supports (1) all the observational datasets from Obs4MIPs and a few ocean datasets from NOAA and Argo, which can serve as observation-based reference data for model evaluation, (2) many of CMIP5 model outputs covering a broad range of atmosphere, ocean, and land variables from the CMIP5 specific historical runs and AMIP runs, and (3) ECMWF reanalysis outputs for several environmental variables in order to supplement observational datasets. Analysis capabilities currently supported by CMDA are (1) the calculation of annual and seasonal means of physical variables, (2) the calculation of time evolution of the means in any specified geographical region, (3) the calculation of correlation between two variables, (4) the calculation of difference between two variables, and (5) the conditional sampling of one physical variable with respect to another variable. A web user interface is chosen for CMDA because it not only lowers the learning curve and removes the adoption barrier of the tool but also enables instantaneous use, avoiding the hassle of local software installation and environment incompatibility. CMDA will be used as an educational tool for the summer school organized by JPL's Center for Climate Science in 2014. In order to support 30+ simultaneous users during the school, we have deployed CMDA to the Amazon cloud environment. The cloud-enabled CMDA will provide each student with a virtual machine while the user interaction with the system will remain the same through web-browser interfaces. The summer school will serve as a valuable testbed for the tool development, preparing CMDA to serve its target community: Earth-science modeling and model-analysis community.

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.

Aladin Lite: Embed your Sky in the Browser

NASA Astrophysics Data System (ADS)

Boch, T.; Fernique, P.

2014-05-01

I will introduce and describe Aladin Lite1, a lightweight interactive sky viewer running natively in the browser. The past five years have seen the emergence of powerful and complex web applications, thanks to major improvements in JavaScript engines and the advent of HTML5. At the same time, browser plugins Java applets, Flash, Silverlight) that were commonly used to run rich Internet applications are declining and are not well suited for mobile devices. The Aladin team took this opportunity to develop Aladin Lite, a lightweight version of Aladin geared towards simple visualization of a sky region. Relying on the widely supported HTML5 canvas element, it provides an intuitive user interface running on desktops and tablets. This first version allows one to interactively visualize multi-resolution HEALPix image and superimpose tabular data and footprints. Aladin Lite is easily embeddable on any web page and may be of interest for data providers which will be able to use it as an interactive previewer for their own image surveys, previously pre-processed as explained in details in the poster "Create & publish your Hierarchical Progressive Survey". I will present the main features of Aladin Lite as well as the JavaScript API which gives the building blocks to create rich interactions between a web page and Aladin Lite.

Building a semi-automatic ontology learning and construction system for geosciences

NASA Astrophysics Data System (ADS)

Babaie, H. A.; Sunderraman, R.; Zhu, Y.

2013-12-01

We are developing an ontology learning and construction framework that allows continuous, semi-automatic knowledge extraction, verification, validation, and maintenance by potentially a very large group of collaborating domain experts in any geosciences field. The system brings geoscientists from the side-lines to the center stage of ontology building, allowing them to collaboratively construct and enrich new ontologies, and merge, align, and integrate existing ontologies and tools. These constantly evolving ontologies can more effectively address community's interests, purposes, tools, and change. The goal is to minimize the cost and time of building ontologies, and maximize the quality, usability, and adoption of ontologies by the community. Our system will be a domain-independent ontology learning framework that applies natural language processing, allowing users to enter their ontology in a semi-structured form, and a combined Semantic Web and Social Web approach that lets direct participation of geoscientists who have no skill in the design and development of their domain ontologies. A controlled natural language (CNL) interface and an integrated authoring and editing tool automatically convert syntactically correct CNL text into formal OWL constructs. The WebProtege-based system will allow a potentially large group of geoscientists, from multiple domains, to crowd source and participate in the structuring of their knowledge model by sharing their knowledge through critiquing, testing, verifying, adopting, and updating of the concept models (ontologies). We will use cloud storage for all data and knowledge base components of the system, such as users, domain ontologies, discussion forums, and semantic wikis that can be accessed and queried by geoscientists in each domain. We will use NoSQL databases such as MongoDB as a service in the cloud environment. MongoDB uses the lightweight JSON format, which makes it convenient and easy to build Web applications using just HTML5 and Javascript, thereby avoiding cumbersome server side coding present in the traditional approaches. The JSON format used in MongoDB is also suitable for storing and querying RDF data. We will store the domain ontologies and associated linked data in JSON/RDF formats. Our Web interface will be built upon the open source and configurable WebProtege ontology editor. We will develop a simplified mobile version of our user interface which will automatically detect the hosting device and adjust the user interface layout to accommodate different screen sizes. We will also use the Semantic Media Wiki that allows the user to store and query the data within the wiki pages. By using HTML 5, JavaScript, and WebGL, we aim to create an interactive, dynamic, and multi-dimensional user interface that presents various geosciences data sets in a natural and intuitive way.

PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides.

PubMed

Sarkar, Anita; Pérez, Serge

2012-11-14

Polysaccharides are ubiquitously present in the living world. Their structural versatility makes them important and interesting components in numerous biological and technological processes ranging from structural stabilization to a variety of immunologically important molecular recognition events. The knowledge of polysaccharide three-dimensional (3D) structure is important in studying carbohydrate-mediated host-pathogen interactions, interactions with other bio-macromolecules, drug design and vaccine development as well as material science applications or production of bio-ethanol. PolySac3DB is an annotated database that contains the 3D structural information of 157 polysaccharide entries that have been collected from an extensive screening of scientific literature. They have been systematically organized using standard names in the field of carbohydrate research into 18 categories representing polysaccharide families. Structure-related information includes the saccharides making up the repeat unit(s) and their glycosidic linkages, the expanded 3D representation of the repeat unit, unit cell dimensions and space group, helix type, diffraction diagram(s) (when applicable), experimental and/or simulation methods used for structure description, link to the abstract of the publication, reference and the atomic coordinate files for visualization and download. The database is accompanied by a user-friendly graphical user interface (GUI). It features interactive displays of polysaccharide structures and customized search options for beginners and experts, respectively. The site also serves as an information portal for polysaccharide structure determination techniques. The web-interface also references external links where other carbohydrate-related resources are available. PolySac3DB is established to maintain information on the detailed 3D structures of polysaccharides. All the data and features are available via the web-interface utilizing the search engine and can be accessed at http://polysac3db.cermav.cnrs.fr.

WebVR: an interactive web browser for virtual environments

NASA Astrophysics Data System (ADS)

Barsoum, Emad; Kuester, Falko

2005-03-01

The pervasive nature of web-based content has lead to the development of applications and user interfaces that port between a broad range of operating systems and databases, while providing intuitive access to static and time-varying information. However, the integration of this vast resource into virtual environments has remained elusive. In this paper we present an implementation of a 3D Web Browser (WebVR) that enables the user to search the internet for arbitrary information and to seamlessly augment this information into virtual environments. WebVR provides access to the standard data input and query mechanisms offered by conventional web browsers, with the difference that it generates active texture-skins of the web contents that can be mapped onto arbitrary surfaces within the environment. Once mapped, the corresponding texture functions as a fully integrated web-browser that will respond to traditional events such as the selection of links or text input. As a result, any surface within the environment can be turned into a web-enabled resource that provides access to user-definable data. In order to leverage from the continuous advancement of browser technology and to support both static as well as streamed content, WebVR uses ActiveX controls to extract the desired texture skin from industry strength browsers, providing a unique mechanism for data fusion and extensibility.

modPDZpep: a web resource for structure based analysis of human PDZ-mediated interaction networks.

PubMed

Sain, Neetu; Mohanty, Debasisa

2016-09-21

PDZ domains recognize short sequence stretches usually present in C-terminal of their interaction partners. Because of the involvement of PDZ domains in many important biological processes, several attempts have been made for developing bioinformatics tools for genome-wide identification of PDZ interaction networks. Currently available tools for prediction of interaction partners of PDZ domains utilize machine learning approach. Since, they have been trained using experimental substrate specificity data for specific PDZ families, their applicability is limited to PDZ families closely related to the training set. These tools also do not allow analysis of PDZ-peptide interaction interfaces. We have used a structure based approach to develop modPDZpep, a program to predict the interaction partners of human PDZ domains and analyze structural details of PDZ interaction interfaces. modPDZpep predicts interaction partners by using structural models of PDZ-peptide complexes and evaluating binding energy scores using residue based statistical pair potentials. Since, it does not require training using experimental data on peptide binding affinity, it can predict substrates for diverse PDZ families. Because of the use of simple scoring function for binding energy, it is also fast enough for genome scale structure based analysis of PDZ interaction networks. Benchmarking using artificial as well as real negative datasets indicates good predictive power with ROC-AUC values in the range of 0.7 to 0.9 for a large number of human PDZ domains. Another novel feature of modPDZpep is its ability to map novel PDZ mediated interactions in human protein-protein interaction networks, either by utilizing available experimental phage display data or by structure based predictions. In summary, we have developed modPDZpep, a web-server for structure based analysis of human PDZ domains. It is freely available at http://www.nii.ac.in/modPDZpep.html or http://202.54.226.235/modPDZpep.html . This article was reviewed by Michael Gromiha and Zoltán Gáspári.

SLIM: an alternative Web interface for MEDLINE/PubMed searches – a preliminary study

PubMed Central

Muin, Michael; Fontelo, Paul; Liu, Fang; Ackerman, Michael

2005-01-01

Background With the rapid growth of medical information and the pervasiveness of the Internet, online search and retrieval systems have become indispensable tools in medicine. The progress of Web technologies can provide expert searching capabilities to non-expert information seekers. The objective of the project is to create an alternative search interface for MEDLINE/PubMed searches using JavaScript slider bars. SLIM, or Slider Interface for MEDLINE/PubMed searches, was developed with PHP and JavaScript. Interactive slider bars in the search form controlled search parameters such as limits, filters and MeSH terminologies. Connections to PubMed were done using the Entrez Programming Utilities (E-Utilities). Custom scripts were created to mimic the automatic term mapping process of Entrez. Page generation times for both local and remote connections were recorded. Results Alpha testing by developers showed SLIM to be functionally stable. Page generation times to simulate loading times were recorded the first week of alpha and beta testing. Average page generation times for the index page, previews and searches were 2.94 milliseconds, 0.63 seconds and 3.84 seconds, respectively. Eighteen physicians from the US, Australia and the Philippines participated in the beta testing and provided feedback through an online survey. Most users found the search interface user-friendly and easy to use. Information on MeSH terms and the ability to instantly hide and display abstracts were identified as distinctive features. Conclusion SLIM can be an interactive time-saving tool for online medical literature research that improves user control and capability to instantly refine and refocus search strategies. With continued development and by integrating search limits, methodology filters, MeSH terms and levels of evidence, SLIM may be useful in the practice of evidence-based medicine. PMID:16321145

SLIM: an alternative Web interface for MEDLINE/PubMed searches - a preliminary study.

PubMed

Muin, Michael; Fontelo, Paul; Liu, Fang; Ackerman, Michael

2005-12-01

With the rapid growth of medical information and the pervasiveness of the Internet, online search and retrieval systems have become indispensable tools in medicine. The progress of Web technologies can provide expert searching capabilities to non-expert information seekers. The objective of the project is to create an alternative search interface for MEDLINE/PubMed searches using JavaScript slider bars. SLIM, or Slider Interface for MEDLINE/PubMed searches, was developed with PHP and JavaScript. Interactive slider bars in the search form controlled search parameters such as limits, filters and MeSH terminologies. Connections to PubMed were done using the Entrez Programming Utilities (E-Utilities). Custom scripts were created to mimic the automatic term mapping process of Entrez. Page generation times for both local and remote connections were recorded. Alpha testing by developers showed SLIM to be functionally stable. Page generation times to simulate loading times were recorded the first week of alpha and beta testing. Average page generation times for the index page, previews and searches were 2.94 milliseconds, 0.63 seconds and 3.84 seconds, respectively. Eighteen physicians from the US, Australia and the Philippines participated in the beta testing and provided feedback through an online survey. Most users found the search interface user-friendly and easy to use. Information on MeSH terms and the ability to instantly hide and display abstracts were identified as distinctive features. SLIM can be an interactive time-saving tool for online medical literature research that improves user control and capability to instantly refine and refocus search strategies. With continued development and by integrating search limits, methodology filters, MeSH terms and levels of evidence, SLIM may be useful in the practice of evidence-based medicine.

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.

g:Profiler-a web server for functional interpretation of gene lists (2016 update).

PubMed

Reimand, Jüri; Arak, Tambet; Adler, Priit; Kolberg, Liis; Reisberg, Sulev; Peterson, Hedi; Vilo, Jaak

2016-07-08

Functional enrichment analysis is a key step in interpreting gene lists discovered in diverse high-throughput experiments. g:Profiler studies flat and ranked gene lists and finds statistically significant Gene Ontology terms, pathways and other gene function related terms. Translation of hundreds of gene identifiers is another core feature of g:Profiler. Since its first publication in 2007, our web server has become a popular tool of choice among basic and translational researchers. Timeliness is a major advantage of g:Profiler as genome and pathway information is synchronized with the Ensembl database in quarterly updates. g:Profiler supports 213 species including mammals and other vertebrates, plants, insects and fungi. The 2016 update of g:Profiler introduces several novel features. We have added further functional datasets to interpret gene lists, including transcription factor binding site predictions, Mendelian disease annotations, information about protein expression and complexes and gene mappings of human genetic polymorphisms. Besides the interactive web interface, g:Profiler can be accessed in computational pipelines using our R package, Python interface and BioJS component. g:Profiler is freely available at http://biit.cs.ut.ee/gprofiler/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

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…

A Web Service and Interface for Remote Electronic Device Characterization

ERIC Educational Resources Information Center

Dutta, S.; Prakash, S.; Estrada, D.; Pop, E.

2011-01-01

A lightweight Web Service and a Web site interface have been developed, which enable remote measurements of electronic devices as a "virtual laboratory" for undergraduate engineering classes. Using standard browsers without additional plugins (such as Internet Explorer, Firefox, or even Safari on an iPhone), remote users can control a Keithley…

The impact of visual layout factors on performance in Web pages: a cross-language study.

PubMed

Parush, Avi; Shwarts, Yonit; Shtub, Avy; Chandra, M Jeya

2005-01-01

Visual layout has a strong impact on performance and is a critical factor in the design of graphical user interfaces (GUIs) and Web pages. Many design guidelines employed in Web page design were inherited from human performance literature and GUI design studies and practices. However, few studies have investigated the more specific patterns of performance with Web pages that may reflect some differences between Web page and GUI design. We investigated interactions among four visual layout factors in Web page design (quantity of links, alignment, grouping indications, and density) in two experiments: one with pages in Hebrew, entailing right-to-left reading, and the other with English pages, entailing left-to-right reading. Some performance patterns (measured by search times and eye movements) were similar between languages. Performance was particularly poor in pages with many links and variable densities, but it improved with the presence of uniform density. Alignment was not shown to be a performance-enhancing factor. The findings are discussed in terms of the similarities and differences in the impact of layout factors between GUIs and Web pages. Actual or potential applications of this research include specific guidelines for Web page design.

Web service activities at the IRIS DMC to support federated and multidisciplinary access

NASA Astrophysics Data System (ADS)

Trabant, Chad; Ahern, Timothy K.

2013-04-01

At the IRIS Data Management Center (DMC) we have developed a suite of web service interfaces to access our large archive of, primarily seismological, time series data and related metadata. The goals of these web services include providing: a) next-generation and easily used access interfaces for our current users, b) access to data holdings in a form usable for non-seismologists, c) programmatic access to facilitate integration into data processing workflows and d) a foundation for participation in federated data discovery and access systems. To support our current users, our services provide access to the raw time series data and metadata or conversions of the raw data to commonly used formats. Our services also support simple, on-the-fly signal processing options that are common first steps in many workflows. Additionally, high-level data products derived from raw data are available via service interfaces. To support data access by researchers unfamiliar with seismic data we offer conversion of the data to broadly usable formats (e.g. ASCII text) and data processing to convert the data to Earth units. By their very nature, web services are programmatic interfaces. Combined with ubiquitous support for web technologies in programming & scripting languages and support in many computing environments, web services are very well suited for integrating data access into data processing workflows. As programmatic interfaces that can return data in both discipline-specific and broadly usable formats, our services are also well suited for participation in federated and brokered systems either specific to seismology or multidisciplinary. Working within the International Federation of Digital Seismograph Networks, the DMC collaborated on the specification of standardized web service interfaces for use at any seismological data center. These data access interfaces, when supported by multiple data centers, will form a foundation on which to build discovery and access mechanisms for data sets spanning multiple centers. To promote the adoption of these standardized services the DMC has developed portable implementations of the software needed to host these interfaces, minimizing the work required at each data center. Within the COOPEUS project framework, the DMC is working with EU partners to install web services implementations at multiple data centers in Europe.

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.

The GLIMS Glacier Database

NASA Astrophysics Data System (ADS)

Raup, B. H.; Khalsa, S. S.; Armstrong, R.

2007-12-01

The Global Land Ice Measurements from Space (GLIMS) project has built a geospatial and temporal database of glacier data, composed of glacier outlines and various scalar attributes. These data are being derived primarily from satellite imagery, such as from ASTER and Landsat. Each "snapshot" of a glacier is from a specific time, and the database is designed to store multiple snapshots representative of different times. We have implemented two web-based interfaces to the database; one enables exploration of the data via interactive maps (web map server), while the other allows searches based on text-field constraints. The web map server is an Open Geospatial Consortium (OGC) compliant Web Map Server (WMS) and Web Feature Server (WFS). This means that other web sites can display glacier layers from our site over the Internet, or retrieve glacier features in vector format. All components of the system are implemented using Open Source software: Linux, PostgreSQL, PostGIS (geospatial extensions to the database), MapServer (WMS and WFS), and several supporting components such as Proj.4 (a geographic projection library) and PHP. These tools are robust and provide a flexible and powerful framework for web mapping applications. As a service to the GLIMS community, the database contains metadata on all ASTER imagery acquired over glacierized terrain. Reduced-resolution of the images (browse imagery) can be viewed either as a layer in the MapServer application, or overlaid on the virtual globe within Google Earth. The interactive map application allows the user to constrain by time what data appear on the map. For example, ASTER or glacier outlines from 2002 only, or from Autumn in any year, can be displayed. The system allows users to download their selected glacier data in a choice of formats. The results of a query based on spatial selection (using a mouse) or text-field constraints can be downloaded in any of these formats: ESRI shapefiles, KML (Google Earth), MapInfo, GML (Geography Markup Language) and GMT (Generic Mapping Tools). This "clip-and-ship" function allows users to download only the data they are interested in. Our flexible web interfaces to the database, which includes various support layers (e.g. a layer to help collaborators identify satellite imagery over their region of expertise) will facilitate enhanced analysis to be undertaken on glacier systems, their distribution, and their impacts on other Earth systems.

hPDI: a database of experimental human protein-DNA interactions.

PubMed

Xie, Zhi; Hu, Shaohui; Blackshaw, Seth; Zhu, Heng; Qian, Jiang

2010-01-15

The human protein DNA Interactome (hPDI) database holds experimental protein-DNA interaction data for humans identified by protein microarray assays. The unique characteristics of hPDI are that it contains consensus DNA-binding sequences not only for nearly 500 human transcription factors but also for >500 unconventional DNA-binding proteins, which are completely uncharacterized previously. Users can browse, search and download a subset or the entire data via a web interface. This database is freely accessible for any academic purposes. http://bioinfo.wilmer.jhu.edu/PDI/.

MyGeoHub: A Collaborative Geospatial Research and Education Platform

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803.

PubMed

Kim, Woo-Yeon; Kang, Sungsoo; Kim, Byoung-Chul; Oh, Jeehyun; Cho, Seongwoong; Bhak, Jong; Choi, Jong-Soon

2008-01-01

Cyanobacteria are model organisms for studying photosynthesis, carbon and nitrogen assimilation, evolution of plant plastids, and adaptability to environmental stresses. Despite many studies on cyanobacteria, there is no web-based database of their regulatory and signaling protein-protein interaction networks to date. We report a database and website SynechoNET that provides predicted protein-protein interactions. SynechoNET shows cyanobacterial domain-domain interactions as well as their protein-level interactions using the model cyanobacterium, Synechocystis sp. PCC 6803. It predicts the protein-protein interactions using public interaction databases that contain mutually complementary and redundant data. Furthermore, SynechoNET provides information on transmembrane topology, signal peptide, and domain structure in order to support the analysis of regulatory membrane proteins. Such biological information can be queried and visualized in user-friendly web interfaces that include the interactive network viewer and search pages by keyword and functional category. SynechoNET is an integrated protein-protein interaction database designed to analyze regulatory membrane proteins in cyanobacteria. It provides a platform for biologists to extend the genomic data of cyanobacteria by predicting interaction partners, membrane association, and membrane topology of Synechocystis proteins. SynechoNET is freely available at http://synechocystis.org/ or directly at http://bioportal.kobic.kr/SynechoNET/.

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.

VirGO: A Visual Browser for the ESO Science Archive Facility

NASA Astrophysics Data System (ADS)

Chéreau, F.

2008-08-01

VirGO is the next generation Visual Browser for the ESO Science Archive Facility developed by the Virtual Observatory (VO) Systems Department. It is a plug-in for the popular open source software Stellarium adding capabilities for browsing professional astronomical data. VirGO gives astronomers the possibility to easily discover and select data from millions of observations in a new visual and intuitive way. Its main feature is to perform real-time access and graphical display of a large number of observations by showing instrumental footprints and image previews, and to allow their selection and filtering for subsequent download from the ESO SAF web interface. It also allows the loading of external FITS files or VOTables, the superimposition of Digitized Sky Survey (DSS) background images, and the visualization of the sky in a `real life' mode as seen from the main ESO sites. All data interfaces are based on Virtual Observatory standards which allow access to images and spectra from external data centers, and interaction with the ESO SAF web interface or any other VO applications supporting the PLASTIC messaging system. The main website for VirGO is at http://archive.eso.org/cms/virgo.

Designing an information search interface for younger and older adults.

PubMed

Pak, Richard; Price, Margaux M

2008-08-01

The present study examined Web-based information retrieval as a function of age for two information organization schemes: hierarchical organization and one organized around tags or keywords. Older adults' performance in information retrieval tasks has traditionally been lower compared with younger adults'. The current study examined the degree to which information organization moderated age-related performance differences on an information retrieval task. The theory of fluid and crystallized intelligence may provide insight into different kinds of information architectures that may reduce age-related differences in computer-based information retrieval performance. Fifty younger (18-23 years of age) and 50 older (55-76 years of age) participants browsed a Web site for answers to specific questions. Half of the participants browsed the hierarchically organized system (taxonomy), which maintained a one-to-one relationship between menu link and page, whereas the other half browsed the tag-based interface, with a many-to-one relationship between menu and page. This difference was expected to interact with age-related differences in fluid and crystallized intelligence. Age-related differences in information retrieval performance persisted; however, a tag-based retrieval interface reduced age-related differences, as compared with a taxonomical interface. Cognitive aging theory can lead to interface interventions that reduce age-related differences in performance with technology. In an information retrieval paradigm, older adults may be able to leverage their increased crystallized intelligence to offset fluid intelligence declines in a computer-based information search task. More research is necessary, but the results suggest that information retrieval interfaces organized around keywords may reduce age-related differences in performance.

Mars Data analysis and visualization with Marsoweb

NASA Astrophysics Data System (ADS)

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

2003-04-01

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

A service-based framework for pharmacogenomics data integration

NASA Astrophysics Data System (ADS)

Wang, Kun; Bai, Xiaoying; Li, Jing; Ding, Cong

2010-08-01

Data are central to scientific research and practices. The advance of experiment methods and information retrieval technologies leads to explosive growth of scientific data and databases. However, due to the heterogeneous problems in data formats, structures and semantics, it is hard to integrate the diversified data that grow explosively and analyse them comprehensively. As more and more public databases are accessible through standard protocols like programmable interfaces and Web portals, Web-based data integration becomes a major trend to manage and synthesise data that are stored in distributed locations. Mashup, a Web 2.0 technique, presents a new way to compose content and software from multiple resources. The paper proposes a layered framework for integrating pharmacogenomics data in a service-oriented approach using the mashup technology. The framework separates the integration concerns from three perspectives including data, process and Web-based user interface. Each layer encapsulates the heterogeneous issues of one aspect. To facilitate the mapping and convergence of data, the ontology mechanism is introduced to provide consistent conceptual models across different databases and experiment platforms. To support user-interactive and iterative service orchestration, a context model is defined to capture information of users, tasks and services, which can be used for service selection and recommendation during a dynamic service composition process. A prototype system is implemented and cases studies are presented to illustrate the promising capabilities of the proposed approach.

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.

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

NASA Technical Reports Server (NTRS)

Liszka, Kathy J.; Holtz, Allen P.

2004-01-01

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

An HTML Tool for Production of Interactive Stereoscopic Compositions.

PubMed

Chistyakov, Alexey; Soto, Maria Teresa; Martí, Enric; Carrabina, Jordi

2016-12-01

The benefits of stereoscopic vision in medical applications were appreciated and have been thoroughly studied for more than a century. The usage of the stereoscopic displays has a proven positive impact on performance in various medical tasks. At the same time the market of 3D-enabled technologies is blooming. New high resolution stereo cameras, TVs, projectors, monitors, and head mounted displays become available. This equipment, completed with a corresponding application program interface (API), could be relatively easy implemented in a system. Such complexes could open new possibilities for medical applications exploiting the stereoscopic depth. This work proposes a tool for production of interactive stereoscopic graphical user interfaces, which could represent a software layer for web-based medical systems facilitating the stereoscopic effect. Further the tool's operation mode and the results of the conducted subjective and objective performance tests will be exposed.

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

NASA Astrophysics Data System (ADS)

Polkowski, Marcin; Grad, Marek

2016-04-01

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

LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis.

PubMed

Nagraj, V P; Magee, Neal E; Sheffield, Nathan C

2018-06-06

The past few years have seen an explosion of interest in understanding the role of regulatory DNA. This interest has driven large-scale production of functional genomics data and analytical methods. One popular analysis is to test for enrichment of overlaps between a query set of genomic regions and a database of region sets. In this way, new genomic data can be easily connected to annotations from external data sources. Here, we present an interactive interface for enrichment analysis of genomic locus overlaps using a web server called LOLAweb. LOLAweb accepts a set of genomic ranges from the user and tests it for enrichment against a database of region sets. LOLAweb renders results in an R Shiny application to provide interactive visualization features, enabling users to filter, sort, and explore enrichment results dynamically. LOLAweb is built and deployed in a Linux container, making it scalable to many concurrent users on our servers and also enabling users to download and run LOLAweb locally.

FASTQ quality control dashboard

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

2016-07-25

FQCDB builds up existing open source software, FastQC, implementing a modern web interface for across parsed output of FastQC. In addition, FQCDB is extensible as a web service to include additional plots of type line, boxplot, or heatmap, across data formatted according to guidelines. The interface is also configurable via more readable JSON format, enabling customization by non-web programmers.

Tags Extarction from Spatial Documents in Search Engines

NASA Astrophysics Data System (ADS)

Borhaninejad, S.; Hakimpour, F.; Hamzei, E.

2015-12-01

Nowadays the selective access to information on the Web is provided by search engines, but in the cases which the data includes spatial information the search task becomes more complex and search engines require special capabilities. The purpose of this study is to extract the information which lies in spatial documents. To that end, we implement and evaluate information extraction from GML documents and a retrieval method in an integrated approach. Our proposed system consists of three components: crawler, database and user interface. In crawler component, GML documents are discovered and their text is parsed for information extraction; storage. The database component is responsible for indexing of information which is collected by crawlers. Finally the user interface component provides the interaction between system and user. We have implemented this system as a pilot system on an Application Server as a simulation of Web. Our system as a spatial search engine provided searching capability throughout the GML documents and thus an important step to improve the efficiency of search engines has been taken.

UCbase 2.0: ultraconserved sequences database (2014 update).

PubMed

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

2014-01-01

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

Subcellular object quantification with Squassh3C and SquasshAnalyst.

PubMed

Rizk, Aurélien; Mansouri, Maysam; Ballmer-Hofer, Kurt; Berger, Philipp

2015-11-01

Quantitative image analysis plays an important role in contemporary biomedical research. Squassh is a method for automatic detection, segmentation, and quantification of subcellular structures and analysis of their colocalization. Here we present the applications Squassh3C and SquasshAnalyst. Squassh3C extends the functionality of Squassh to three fluorescence channels and live-cell movie analysis. SquasshAnalyst is an interactive web interface for the analysis of Squassh3C object data. It provides segmentation image overview and data exploration, figure generation, object and image filtering, and a statistical significance test in an easy-to-use interface. The overall procedure combines the Squassh3C plug-in for the free biological image processing program ImageJ and a web application working in conjunction with the free statistical environment R, and it is compatible with Linux, MacOS X, or Microsoft Windows. Squassh3C and SquasshAnalyst are available for download at www.psi.ch/lbr/SquasshAnalystEN/SquasshAnalyst.zip.

FwWebViewPlus: integration of web technologies into WinCC OA based Human-Machine Interfaces at CERN

NASA Astrophysics Data System (ADS)

Golonka, Piotr; Fabian, Wojciech; Gonzalez-Berges, Manuel; Jasiun, Piotr; Varela-Rodriguez, Fernando

2014-06-01

The rapid growth in popularity of web applications gives rise to a plethora of reusable graphical components, such as Google Chart Tools and JQuery Sparklines, implemented in JavaScript and run inside a web browser. In the paper we describe the tool that allows for seamless integration of web-based widgets into WinCC Open Architecture, the SCADA system used commonly at CERN to build complex Human-Machine Interfaces. Reuse of widely available widget libraries and pushing the development efforts to a higher abstraction layer based on a scripting language allow for significant reduction in maintenance of the code in multi-platform environments compared to those currently used in C++ visualization plugins. Adequately designed interfaces allow for rapid integration of new web widgets into WinCC OA. At the same time, the mechanisms familiar to HMI developers are preserved, making the use of new widgets "native". Perspectives for further integration between the realms of WinCC OA and Web development are also discussed.

Neuron-Like Networks Between Ribosomal Proteins Within the Ribosome

NASA Astrophysics Data System (ADS)

Poirot, Olivier; Timsit, Youri

2016-05-01

From brain to the World Wide Web, information-processing networks share common scale invariant properties. Here, we reveal the existence of neural-like networks at a molecular scale within the ribosome. We show that with their extensions, ribosomal proteins form complex assortative interaction networks through which they communicate through tiny interfaces. The analysis of the crystal structures of 50S eubacterial particles reveals that most of these interfaces involve key phylogenetically conserved residues. The systematic observation of interactions between basic and aromatic amino acids at the interfaces and along the extension provides new structural insights that may contribute to decipher the molecular mechanisms of signal transmission within or between the ribosomal proteins. Similar to neurons interacting through “molecular synapses”, ribosomal proteins form a network that suggest an analogy with a simple molecular brain in which the “sensory-proteins” innervate the functional ribosomal sites, while the “inter-proteins” interconnect them into circuits suitable to process the information flow that circulates during protein synthesis. It is likely that these circuits have evolved to coordinate both the complex macromolecular motions and the binding of the multiple factors during translation. This opens new perspectives on nanoscale information transfer and processing.

A Web Based Approach to Integrate Space Culture and Education

NASA Astrophysics Data System (ADS)

Gerla, F.

2002-01-01

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

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2015-01-01

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

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 .

Access to Space Interactive Design Web Site

NASA Technical Reports Server (NTRS)

Leon, John; Cutlip, William; Hametz, Mark

2000-01-01

The Access To Space (ATS) Group at NASA's Goddard Space Flight Center (GSFC) supports the science and technology community at GSFC by facilitating frequent and affordable opportunities for access to space. Through partnerships established with access mode suppliers, the ATS Group has developed an interactive Mission Design web site. The ATS web site provides both the information and the tools necessary to assist mission planners in selecting and planning their ride to space. This includes the evaluation of single payloads vs. ride-sharing opportunities to reduce the cost of access to space. Features of this site include the following: (1) Mission Database. Our mission database contains a listing of missions ranging from proposed missions to manifested. Missions can be entered by our user community through data input tools. Data is then accessed by users through various search engines: orbit parameters, ride-share opportunities, spacecraft parameters, other mission notes, launch vehicle, and contact information. (2) Launch Vehicle Toolboxes. The launch vehicle toolboxes provide the user a full range of information on vehicle classes and individual configurations. Topics include: general information, environments, performance, payload interface, available volume, and launch sites.

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

Flexible software architecture for user-interface and machine control in laboratory automation.

PubMed

Arutunian, E B; Meldrum, D R; Friedman, N A; Moody, S E

1998-10-01

We describe a modular, layered software architecture for automated laboratory instruments. The design consists of a sophisticated user interface, a machine controller and multiple individual hardware subsystems, each interacting through a client-server architecture built entirely on top of open Internet standards. In our implementation, the user-interface components are built as Java applets that are downloaded from a server integrated into the machine controller. The user-interface client can thereby provide laboratory personnel with a familiar environment for experiment design through a standard World Wide Web browser. Data management and security are seamlessly integrated at the machine-controller layer using QNX, a real-time operating system. This layer also controls hardware subsystems through a second client-server interface. This architecture has proven flexible and relatively easy to implement and allows users to operate laboratory automation instruments remotely through an Internet connection. The software architecture was implemented and demonstrated on the Acapella, an automated fluid-sample-processing system that is under development at the University of Washington.

MaROS Strategic Relay Planning and Coordination Interfaces

NASA Technical Reports Server (NTRS)

Allard, Daniel A.

2010-01-01

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

Flight Planning in the Cloud

NASA Technical Reports Server (NTRS)

Flores, Sarah L.; Chapman, Bruce D.; Tung, Waye W.; Zheng, Yang

2011-01-01

This new interface will enable Principal Investigators (PIs), as well as UAVSAR (Uninhabited Aerial Vehicle Synthetic Aperture Radar) members to do their own flight planning and time estimation without having to request flight lines through the science coordinator. It uses an all-in-one Google Maps interface, a JPL hosted database, and PI flight requirements to design an airborne flight plan. The application will enable users to see their own flight plan being constructed interactively through a map interface, and then the flight planning software will generate all the files necessary for the flight. Afterward, the UAVSAR team can then complete the flight request, including calendaring and supplying requisite flight request files in the expected format for processing by NASA s airborne science program. Some of the main features of the interface include drawing flight lines on the map, nudging them, adding them to the current flight plan, and reordering them. The user can also search and select takeoff, landing, and intermediate airports. As the flight plan is constructed, all of its components are constantly being saved to the database, and the estimated flight times are updated. Another feature is the ability to import flight lines from previously saved flight plans. One of the main motivations was to make this Web application as simple and intuitive as possible, while also being dynamic and robust. This Web application can easily be extended to support other airborne instruments.

An Application Programming Interface for Synthetic Snowflake Particle Structure and Scattering Data

NASA Technical Reports Server (NTRS)

Lammers, Matthew; Kuo, Kwo-Sen

2017-01-01

The work by Kuo and colleagues on growing synthetic snowflakes and calculating their single-scattering properties has demonstrated great potential to improve the retrievals of snowfall. To grant colleagues flexible and targeted access to their large collection of sizes and shapes at fifteen (15) microwave frequencies, we have developed a web-based Application Programming Interface (API) integrated with NASA Goddard's Precipitation Processing System (PPS) Group. It is our hope that the API will enable convenient programmatic utilization of the database. To help users better understand the API's capabilities, we have developed an interactive web interface called the OpenSSP API Query Builder, which implements an intuitive system of mechanisms for selecting shapes, sizes, and frequencies to generate queries, with which the API can then extract and return data from the database. The Query Builder also allows for the specification of normalized particle size distributions by setting pertinent parameters, with which the API can also return mean geometric and scattering properties for each size bin. Additionally, the Query Builder interface enables downloading of raw scattering and particle structure data packages. This presentation will describe some of the challenges and successes associated with developing such an API. Examples of its usage will be shown both through downloading output and pulling it into a spreadsheet, as well as querying the API programmatically and working with the output in code.

HomPPI: a class of sequence homology based protein-protein interface prediction methods

PubMed Central

2011-01-01

Background Although homology-based methods are among the most widely used methods for predicting the structure and function of proteins, the question as to whether interface sequence conservation can be effectively exploited in predicting protein-protein interfaces has been a subject of debate. Results We studied more than 300,000 pair-wise alignments of protein sequences from structurally characterized protein complexes, including both obligate and transient complexes. We identified sequence similarity criteria required for accurate homology-based inference of interface residues in a query protein sequence. Based on these analyses, we developed HomPPI, a class of sequence homology-based methods for predicting protein-protein interface residues. We present two variants of HomPPI: (i) NPS-HomPPI (Non partner-specific HomPPI), which can be used to predict interface residues of a query protein in the absence of knowledge of the interaction partner; and (ii) PS-HomPPI (Partner-specific HomPPI), which can be used to predict the interface residues of a query protein with a specific target protein. Our experiments on a benchmark dataset of obligate homodimeric complexes show that NPS-HomPPI can reliably predict protein-protein interface residues in a given protein, with an average correlation coefficient (CC) of 0.76, sensitivity of 0.83, and specificity of 0.78, when sequence homologs of the query protein can be reliably identified. NPS-HomPPI also reliably predicts the interface residues of intrinsically disordered proteins. Our experiments suggest that NPS-HomPPI is competitive with several state-of-the-art interface prediction servers including those that exploit the structure of the query proteins. The partner-specific classifier, PS-HomPPI can, on a large dataset of transient complexes, predict the interface residues of a query protein with a specific target, with a CC of 0.65, sensitivity of 0.69, and specificity of 0.70, when homologs of both the query and the target can be reliably identified. The HomPPI web server is available at http://homppi.cs.iastate.edu/. Conclusions Sequence homology-based methods offer a class of computationally efficient and reliable approaches for predicting the protein-protein interface residues that participate in either obligate or transient interactions. For query proteins involved in transient interactions, the reliability of interface residue prediction can be improved by exploiting knowledge of putative interaction partners. PMID:21682895

Collaborative Interactive Visualization Exploratory Concept

DTIC Science & Technology

2015-06-01

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

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

PubMed

Kozma, Dániel; Tusnády, Gábor E

2015-09-17

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

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

PubMed

Vali, Faisal; Hong, Robert

2007-10-11

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

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

ERIC Educational Resources Information Center

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

1998-01-01

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

OpenSearch technology for geospatial resources discovery

NASA Astrophysics Data System (ADS)

Papeschi, Fabrizio; Enrico, Boldrini; Mazzetti, Paolo

2010-05-01

In 2005, the term Web 2.0 has been coined by Tim O'Reilly to describe a quickly growing set of Web-based applications that share a common philosophy of "mutually maximizing collective intelligence and added value for each participant by formalized and dynamic information sharing". Around this same period, OpenSearch a new Web 2.0 technology, was developed. More properly, OpenSearch is a collection of technologies that allow publishing of search results in a format suitable for syndication and aggregation. It is a way for websites and search engines to publish search results in a standard and accessible format. Due to its strong impact on the way the Web is perceived by users and also due its relevance for businesses, Web 2.0 has attracted the attention of both mass media and the scientific community. This explosive growth in popularity of Web 2.0 technologies like OpenSearch, and practical applications of Service Oriented Architecture (SOA) resulted in an increased interest in similarities, convergence, and a potential synergy of these two concepts. SOA is considered as the philosophy of encapsulating application logic in services with a uniformly defined interface and making these publicly available via discovery mechanisms. Service consumers may then retrieve these services, compose and use them according to their current needs. A great degree of similarity between SOA and Web 2.0 may be leading to a convergence between the two paradigms. They also expose divergent elements, such as the Web 2.0 support to the human interaction in opposition to the typical SOA machine-to-machine interaction. According to these considerations, the Geospatial Information (GI) domain, is also moving first steps towards a new approach of data publishing and discovering, in particular taking advantage of the OpenSearch technology. A specific GI niche is represented by the OGC Catalog Service for Web (CSW) that is part of the OGC Web Services (OWS) specifications suite, which provides a set of services for discovery, access, and processing of geospatial resources in a SOA framework. GI-cat is a distributed CSW framework implementation developed by the ESSI Lab of the Italian National Research Council (CNR-IMAA) and the University of Florence. It provides brokering and mediation functionalities towards heterogeneous resources and inventories, exposing several standard interfaces for query distribution. This work focuses on a new GI-cat interface which allows the catalog to be queried according to the OpenSearch syntax specification, thus filling the gap between the SOA architectural design of the CSW and the Web 2.0. At the moment, there is no OGC standard specification about this topic, but an official change request has been proposed in order to enable the OGC catalogues to support OpenSearch queries. In this change request, an OpenSearch extension is proposed providing a standard mechanism to query a resource based on temporal and geographic extents. Two new catalog operations are also proposed, in order to publish a suitable OpenSearch interface. This extended interface is implemented by the modular GI-cat architecture adding a new profiling module called "OpenSearch profiler". Since GI-cat also acts as a clearinghouse catalog, another component called "OpenSearch accessor" is added in order to access OpenSearch compliant services. An important role in the GI-cat extension, is played by the adopted mapping strategy. Two different kind of mappings are required: query, and response elements mapping. Query mapping is provided in order to fit the simple OpenSearch query syntax to the complex CSW query expressed by the OGC Filter syntax. GI-cat internal data model is based on the ISO-19115 profile, that is more complex than the simple XML syndication formats, such as RSS 2.0 and Atom 1.0, suggested by OpenSearch. Once response elements are available, in order to be presented, they need to be translated from the GI-cat internal data model, to the above mentioned syndication formats; the mapping processing, is bidirectional. When GI-cat is used to access OpenSearch compliant services, the CSW query must be mapped to the OpenSearch query, and the response elements, must be translated according to the GI-cat internal data model. As results of such extensions, GI-cat provides a user friendly facade to the complex CSW interface, thus enabling it to be queried, for example, using a browser toolbar.

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.

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

NASA Astrophysics Data System (ADS)

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

2015-03-01

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

[Stress and information-communication technologies: from videoterminal to web].

PubMed

Tomei, G; Ciarrocca, M; De Sio, S; Suppi, A; Sinibaldi, F; Di Pastena, C; Scala, B; Corbosiero, P; De Angelis, A; Prenna, A; Tomei, F; Sancini, A

2012-07-01

The relationship between stress and new technologies has always been a vexed question. Sociologists and philosophers say technology is a double edged sword, on one hand it increases the potential of human senses, while on the other hand it forces man to adopt rhythms and conditions not natural but artificial, with consequences for his physical and mental health. Modern Cognitive Ergonomic tries to analyze to technology, interacting with mental functions, causes stress and it tries to offer the most appropriate technological solutions for human work. From our analysis it emerges that the old media have an influence on mood causing episodes of insomnia, irritability, anxiety, etc., even if in a way that cannot be completely evaluated. Contrariwise, a controlled use of the web can improve the communication and the interacting abilities in patients with psychosocial distress and low social skills. Nielsen's Heuristics are a great tool to value methods of informatical and media interfaces.

CASAS: Cancer Survival Analysis Suite, a web based application

PubMed Central

Rupji, Manali; Zhang, Xinyan; Kowalski, Jeanne

2017-01-01

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

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

PubMed

Rupji, Manali; Zhang, Xinyan; Kowalski, Jeanne

2017-01-01

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

A web-portal for interactive data exploration, visualization, and hypothesis testing

PubMed Central

Bartsch, Hauke; Thompson, Wesley K.; Jernigan, Terry L.; Dale, Anders M.

2014-01-01

Clinical research studies generate data that need to be shared and statistically analyzed by their participating institutions. The distributed nature of research and the different domains involved present major challenges to data sharing, exploration, and visualization. The Data Portal infrastructure was developed to support ongoing research in the areas of neurocognition, imaging, and genetics. Researchers benefit from the integration of data sources across domains, the explicit representation of knowledge from domain experts, and user interfaces providing convenient access to project specific data resources and algorithms. The system provides an interactive approach to statistical analysis, data mining, and hypothesis testing over the lifetime of a study and fulfills a mandate of public sharing by integrating data sharing into a system built for active data exploration. The web-based platform removes barriers for research and supports the ongoing exploration of data. PMID:24723882

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

PubMed

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

2006-02-01

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

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

NASA Astrophysics Data System (ADS)

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

2014-07-01

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

C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms

PubMed Central

Alam, Zaid; Peddinti, Gopal

2017-01-01

Abstract The advent of polypharmacology paradigm in drug discovery calls for novel chemoinformatic tools for analyzing compounds’ multi-targeting activities. Such tools should provide an intuitive representation of the chemical space through capturing and visualizing underlying patterns of compound similarities linked to their polypharmacological effects. Most of the existing compound-centric chemoinformatics tools lack interactive options and user interfaces that are critical for the real-time needs of chemical biologists carrying out compound screening experiments. Toward that end, we introduce C-SPADE, an open-source exploratory web-tool for interactive analysis and visualization of drug profiling assays (biochemical, cell-based or cell-free) using compound-centric similarity clustering. C-SPADE allows the users to visually map the chemical diversity of a screening panel, explore investigational compounds in terms of their similarity to the screening panel, perform polypharmacological analyses and guide drug-target interaction predictions. C-SPADE requires only the raw drug profiling data as input, and it automatically retrieves the structural information and constructs the compound clusters in real-time, thereby reducing the time required for manual analysis in drug development or repurposing applications. The web-tool provides a customizable visual workspace that can either be downloaded as figure or Newick tree file or shared as a hyperlink with other users. C-SPADE is freely available at http://cspade.fimm.fi/. PMID:28472495

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

The Virtual Brain: a simulator of primate brain network dynamics.

PubMed

Sanz Leon, Paula; Knock, Stuart A; Woodman, M Marmaduke; Domide, Lia; Mersmann, Jochen; McIntosh, Anthony R; Jirsa, Viktor

2013-01-01

We present The Virtual Brain (TVB), a neuroinformatics platform for full brain network simulations using biologically realistic connectivity. This simulation environment enables the model-based inference of neurophysiological mechanisms across different brain scales that underlie the generation of macroscopic neuroimaging signals including functional MRI (fMRI), EEG and MEG. Researchers from different backgrounds can benefit from an integrative software platform including a supporting framework for data management (generation, organization, storage, integration and sharing) and a simulation core written in Python. TVB allows the reproduction and evaluation of personalized configurations of the brain by using individual subject data. This personalization facilitates an exploration of the consequences of pathological changes in the system, permitting to investigate potential ways to counteract such unfavorable processes. The architecture of TVB supports interaction with MATLAB packages, for example, the well known Brain Connectivity Toolbox. TVB can be used in a client-server configuration, such that it can be remotely accessed through the Internet thanks to its web-based HTML5, JS, and WebGL graphical user interface. TVB is also accessible as a standalone cross-platform Python library and application, and users can interact with the scientific core through the scripting interface IDLE, enabling easy modeling, development and debugging of the scientific kernel. This second interface makes TVB extensible by combining it with other libraries and modules developed by the Python scientific community. In this article, we describe the theoretical background and foundations that led to the development of TVB, the architecture and features of its major software components as well as potential neuroscience applications.

The Virtual Brain: a simulator of primate brain network dynamics

PubMed Central

Sanz Leon, Paula; Knock, Stuart A.; Woodman, M. Marmaduke; Domide, Lia; Mersmann, Jochen; McIntosh, Anthony R.; Jirsa, Viktor

2013-01-01

We present The Virtual Brain (TVB), a neuroinformatics platform for full brain network simulations using biologically realistic connectivity. This simulation environment enables the model-based inference of neurophysiological mechanisms across different brain scales that underlie the generation of macroscopic neuroimaging signals including functional MRI (fMRI), EEG and MEG. Researchers from different backgrounds can benefit from an integrative software platform including a supporting framework for data management (generation, organization, storage, integration and sharing) and a simulation core written in Python. TVB allows the reproduction and evaluation of personalized configurations of the brain by using individual subject data. This personalization facilitates an exploration of the consequences of pathological changes in the system, permitting to investigate potential ways to counteract such unfavorable processes. The architecture of TVB supports interaction with MATLAB packages, for example, the well known Brain Connectivity Toolbox. TVB can be used in a client-server configuration, such that it can be remotely accessed through the Internet thanks to its web-based HTML5, JS, and WebGL graphical user interface. TVB is also accessible as a standalone cross-platform Python library and application, and users can interact with the scientific core through the scripting interface IDLE, enabling easy modeling, development and debugging of the scientific kernel. This second interface makes TVB extensible by combining it with other libraries and modules developed by the Python scientific community. In this article, we describe the theoretical background and foundations that led to the development of TVB, the architecture and features of its major software components as well as potential neuroscience applications. PMID:23781198

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.

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.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

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.

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

NASA Astrophysics Data System (ADS)

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

2011-03-01

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

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site

PubMed Central

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

2015-01-01

Protein–peptide interactions play a key role in cell functions. Their structural characterization, though challenging, is important for the discovery of new drugs. The CABS-dock web server provides an interface for modeling protein–peptide interactions using a highly efficient protocol for the flexible docking of peptides to proteins. While other docking algorithms require pre-defined localization of the binding site, CABS-dock does not require such knowledge. Given a protein receptor structure and a peptide sequence (and starting from random conformations and positions of the peptide), CABS-dock performs simulation search for the binding site allowing for full flexibility of the peptide and small fluctuations of the receptor backbone. This protocol was extensively tested over the largest dataset of non-redundant protein–peptide interactions available to date (including bound and unbound docking cases). For over 80% of bound and unbound dataset cases, we obtained models with high or medium accuracy (sufficient for practical applications). Additionally, as optional features, CABS-dock can exclude user-selected binding modes from docking search or to increase the level of flexibility for chosen receptor fragments. CABS-dock is freely available as a web server at http://biocomp.chem.uw.edu.pl/CABSdock. PMID:25943545

NaviCom: a web application to create interactive molecular network portraits using multi-level omics data.

PubMed

Dorel, Mathurin; Viara, Eric; Barillot, Emmanuel; Zinovyev, Andrei; Kuperstein, Inna

2017-01-01

Human diseases such as cancer are routinely characterized by high-throughput molecular technologies, and multi-level omics data are accumulated in public databases at increasing rate. Retrieval and visualization of these data in the context of molecular network maps can provide insights into the pattern of regulation of molecular functions reflected by an omics profile. In order to make this task easy, we developed NaviCom, a Python package and web platform for visualization of multi-level omics data on top of biological network maps. NaviCom is bridging the gap between cBioPortal, the most used resource of large-scale cancer omics data and NaviCell, a data visualization web service that contains several molecular network map collections. NaviCom proposes several standardized modes of data display on top of molecular network maps, allowing addressing specific biological questions. We illustrate how users can easily create interactive network-based cancer molecular portraits via NaviCom web interface using the maps of Atlas of Cancer Signalling Network (ACSN) and other maps. Analysis of these molecular portraits can help in formulating a scientific hypothesis on the molecular mechanisms deregulated in the studied disease. NaviCom is available at https://navicom.curie.fr. © The Author(s) 2017. Published by Oxford University Press.

Integrating Radar Image Data with Google Maps

NASA Technical Reports Server (NTRS)

Chapman, Bruce D.; Gibas, Sarah

2010-01-01

A public Web site has been developed as a method for displaying the multitude of radar imagery collected by NASA s Airborne Synthetic Aperture Radar (AIRSAR) instrument during its 16-year mission. Utilizing NASA s internal AIRSAR site, the new Web site features more sophisticated visualization tools that enable the general public to have access to these images. The site was originally maintained at NASA on six computers: one that held the Oracle database, two that took care of the software for the interactive map, and three that were for the Web site itself. Several tasks were involved in moving this complicated setup to just one computer. First, the AIRSAR database was migrated from Oracle to MySQL. Then the back-end of the AIRSAR Web site was updated in order to access the MySQL database. To do this, a few of the scripts needed to be modified; specifically three Perl scripts that query that database. The database connections were then updated from Oracle to MySQL, numerous syntax errors were corrected, and a query was implemented that replaced one of the stored Oracle procedures. Lastly, the interactive map was designed, implemented, and tested so that users could easily browse and access the radar imagery through the Google Maps interface.

Experiment Software and Projects on the Web with VISPA

NASA Astrophysics Data System (ADS)

Erdmann, M.; Fischer, B.; Fischer, R.; Geiser, E.; Glaser, C.; Müller, G.; Rieger, M.; Urban, M.; von Cube, R. F.; Welling, C.

2017-10-01

The Visual Physics Analysis (VISPA) project defines a toolbox for accessing software via the web. It is based on latest web technologies and provides a powerful extension mechanism that enables to interface a wide range of applications. Beyond basic applications such as a code editor, a file browser, or a terminal, it meets the demands of sophisticated experiment-specific use cases that focus on physics data analyses and typically require a high degree of interactivity. As an example, we developed a data inspector that is capable of browsing interactively through event content of several data formats, e.g., MiniAOD which is utilized by the CMS collaboration. The VISPA extension mechanism can also be used to embed external web-based applications that benefit from dynamic allocation of user-defined computing resources via SSH. For example, by wrapping the JSROOT project, ROOT files located on any remote machine can be inspected directly through a VISPA server instance. We introduced domains that combine groups of users and role-based permissions. Thereby, tailored projects are enabled, e.g. for teaching where access to student’s homework is restricted to a team of tutors, or for experiment-specific data that may only be accessible for members of the collaboration. We present the extension mechanism including corresponding applications and give an outlook onto the new permission system.

Search of the Deep and Dark Web via DARPA Memex

NASA Astrophysics Data System (ADS)

Mattmann, C. A.

2015-12-01

Search has progressed through several stages due to the increasing size of the Web. Search engines first focused on text and its rate of occurrence; then focused on the notion of link analysis and citation then on interactivity and guided search; and now on the use of social media - who we interact with, what we comment on, and who we follow (and who follows us). The next stage, referred to as "deep search," requires solutions that can bring together text, images, video, importance, interactivity, and social media to solve this challenging problem. The Apache Nutch project provides an open framework for large-scale, targeted, vertical search with capabilities to support all past and potential future search engine foci. Nutch is a flexible infrastructure allowing open access to ranking; URL selection and filtering approaches, to the link graph generated from search, and Nutch has spawned entire sub communities including Apache Hadoop and Apache Tika. It addresses many current needs with the capability to support new technologies such as image and video. On the DARPA Memex project, we are creating create specific extensions to Nutch that will directly improve its overall technological superiority for search and that will directly allow us to address complex search problems including human trafficking. We are integrating state-of-the-art algorithms developed by Kitware for IARPA Aladdin combined with work by Harvard to provide image and video understanding support allowing automatic detection of people and things and massive deployment via Nutch. We are expanding Apache Tika for scene understanding, object/person detection and classification in images/video. We are delivering an interactive and visual interface for initiating Nutch crawls. The interface uses Python technologies to expose Nutch data and to provide a domain specific language for crawls. With the Bokeh visualization library the interface we are delivering simple interactive crawl visualization and plotting techniques for exploring crawled information. The platform classifies, identify, and thwart predators, help to find victims and to identify buyers in human trafficking and will deliver technological superiority in search engines for DARPA. We are already transitioning the technologies into Geo and Planetary Science, and Bioinformatics.

NASA Webworldwind: Multidimensional Virtual Globe for Geo Big Data Visualization

NASA Astrophysics Data System (ADS)

Brovelli, M. A.; Hogan, P.; Prestifilippo, G.; Zamboni, G.

2016-06-01

In this paper, we presented a web application created using the NASA WebWorldWind framework. The application is capable of visualizing n-dimensional data using a Voxel model. In this case study, we handled social media data and Call Detailed Records (CDR) of telecommunication networks. These were retrieved from the "BigData Challenge 2015" of Telecom Italia. We focused on the visualization process for a suitable way to show this geo-data in a 3D environment, incorporating more than three dimensions. This engenders an interactive way to browse the data in their real context and understand them quickly. Users will be able to handle several varieties of data, import their dataset using a particular data structure, and then mash them up in the WebWorldWind virtual globe. A broad range of public use this tool for diverse purposes is possible, without much experience in the field, thanks to the intuitive user-interface of this web app.

GLobal Integrated Design Environment (GLIDE): A Concurrent Engineering Application

NASA Technical Reports Server (NTRS)

McGuire, Melissa L.; Kunkel, Matthew R.; Smith, David A.

2010-01-01

The GLobal Integrated Design Environment (GLIDE) is a client-server software application purpose-built to mitigate issues associated with real time data sharing in concurrent engineering environments and to facilitate discipline-to-discipline interaction between multiple engineers and researchers. GLIDE is implemented in multiple programming languages utilizing standardized web protocols to enable secure parameter data sharing between engineers and researchers across the Internet in closed and/or widely distributed working environments. A well defined, HyperText Transfer Protocol (HTTP) based Application Programming Interface (API) to the GLIDE client/server environment enables users to interact with GLIDE, and each other, within common and familiar tools. One such common tool, Microsoft Excel (Microsoft Corporation), paired with its add-in API for GLIDE, is discussed in this paper. The top-level examples given demonstrate how this interface improves the efficiency of the design process of a concurrent engineering study while reducing potential errors associated with manually sharing information between study participants.

WebEAV: automatic metadata-driven generation of web interfaces to entity-attribute-value databases.

PubMed

Nadkarni, P M; Brandt, C M; Marenco, L

2000-01-01

The task of creating and maintaining a front end to a large institutional entity-attribute-value (EAV) database can be cumbersome when using traditional client-server technology. Switching to Web technology as a delivery vehicle solves some of these problems but introduces others. In particular, Web development environments tend to be primitive, and many features that client-server developers take for granted are missing. WebEAV is a generic framework for Web development that is intended to streamline the process of Web application development for databases having a significant EAV component. It also addresses some challenging user interface issues that arise when any complex system is created. The authors describe the architecture of WebEAV and provide an overview of its features with suitable examples.

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.

PubMed

Katayama, Toshiaki; Wilkinson, Mark D; Micklem, Gos; Kawashima, Shuichi; Yamaguchi, Atsuko; Nakao, Mitsuteru; Yamamoto, Yasunori; Okamoto, Shinobu; Oouchida, Kenta; Chun, Hong-Woo; Aerts, Jan; Afzal, Hammad; Antezana, Erick; Arakawa, Kazuharu; Aranda, Bruno; Belleau, Francois; Bolleman, Jerven; Bonnal, Raoul Jp; Chapman, Brad; Cock, Peter Ja; Eriksson, Tore; Gordon, Paul Mk; Goto, Naohisa; Hayashi, Kazuhiro; Horn, Heiko; Ishiwata, Ryosuke; Kaminuma, Eli; Kasprzyk, Arek; Kawaji, Hideya; Kido, Nobuhiro; Kim, Young Joo; Kinjo, Akira R; Konishi, Fumikazu; Kwon, Kyung-Hoon; Labarga, Alberto; Lamprecht, Anna-Lena; Lin, Yu; Lindenbaum, Pierre; McCarthy, Luke; Morita, Hideyuki; Murakami, Katsuhiko; Nagao, Koji; Nishida, Kozo; Nishimura, Kunihiro; Nishizawa, Tatsuya; Ogishima, Soichi; Ono, Keiichiro; Oshita, Kazuki; Park, Keun-Joon; Prins, Pjotr; Saito, Taro L; Samwald, Matthias; Satagopam, Venkata P; Shigemoto, Yasumasa; Smith, Richard; Splendiani, Andrea; Sugawara, Hideaki; Taylor, James; Vos, Rutger A; Withers, David; Yamasaki, Chisato; Zmasek, Christian M; Kawamoto, Shoko; Okubo, Kosaku; Asai, Kiyoshi; Takagi, Toshihisa

2013-02-11

BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

PubMed Central

2013-01-01

Background BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. Results The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. Conclusion We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer. PMID:23398680

The New LASP Interactive Solar IRradiance Datacenter (LISIRD)

NASA Astrophysics Data System (ADS)

Baltzer, T.; Wilson, A.; Lindholm, D. M.; Snow, M. A.; Woodraska, D.; Pankratz, C. K.

2017-12-01

The New LASP Interactive Solar IRradiance Datacenter (LISIRD) The University of Colorado at Boulder's Laboratory for Atmospheric and Space Physics (LASP) has a long history of providing state of the art Solar instrumentation and datasets to the community. In 2005, LASP created a web interface called LISIRD which provided plotting of and access to a number of Solar Irradiance measured and modeled datasets, and it has been used extensively by members of the community both within and outside of LASP. In August of 2017, LASP is set to release a new version of LISIRD for use by anyone interested in viewing and downloading the datasets it serves. This talk will describe the new LISIRD with emphasis on features enabled by it to include: New and more functional plotting interfaces Better dataset browse and search capabilities More datasets Easier to add datasets from a wider array of resources Cleaner interface with better use of screen real estate Much easier to update metadata describing each dataset Much of this capability is leveraged off new infrastructure that will also be touched upon.

A web-based platform for virtual screening.

PubMed

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

2003-09-01

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

SCHeMA web-based observation data information system

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

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

PubMed

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

2008-07-01

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

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.

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.

Design for Connecting Spatial Data Infrastructures with Sensor Web (sensdi)

NASA Astrophysics Data System (ADS)

Bhattacharya, D.; M., M.

2016-06-01

Integrating Sensor Web With Spatial Data Infrastructures (SENSDI) aims to extend SDIs with sensor web enablement, converging geospatial and built infrastructure, and implement test cases with sensor data and SDI. It is about research to harness the sensed environment by utilizing domain specific sensor data to create a generalized sensor webframework. The challenges being semantic enablement for Spatial Data Infrastructures, and connecting the interfaces of SDI with interfaces of Sensor Web. The proposed research plan is to Identify sensor data sources, Setup an open source SDI, Match the APIs and functions between Sensor Web and SDI, and Case studies like hazard applications, urban applications etc. We take up co-operative development of SDI best practices to enable a new realm of a location enabled and semantically enriched World Wide Web - the "Geospatial Web" or "Geosemantic Web" by setting up one to one correspondence between WMS, WFS, WCS, Metadata and 'Sensor Observation Service' (SOS); 'Sensor Planning Service' (SPS); 'Sensor Alert Service' (SAS); a service that facilitates asynchronous message interchange between users and services, and between two OGC-SWE services, called the 'Web Notification Service' (WNS). Hence in conclusion, it is of importance to geospatial studies to integrate SDI with Sensor Web. The integration can be done through merging the common OGC interfaces of SDI and Sensor Web. Multi-usability studies to validate integration has to be undertaken as future research.

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

NASA Astrophysics Data System (ADS)

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

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

cPath: open source software for collecting, storing, and querying biological pathways.

PubMed

Cerami, Ethan G; Bader, Gary D; Gross, Benjamin E; Sander, Chris

2006-11-13

Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling.

A resource oriented webs service for environmental modeling

NASA Astrophysics Data System (ADS)

Ferencik, Ioan

2013-04-01

Environmental modeling is a largely adopted practice in the study of natural phenomena. Environmental models can be difficult to build and use and thus sharing them within the community is an important aspect. The most common approach to share a model is to expose it as a web service. In practice the interaction with this web service is cumbersome due to lack of standardized contract and the complexity of the model being exposed. In this work we investigate the use of a resource oriented approach in exposing environmental models as web services. We view a model as a layered resource build atop the object concept from Object Oriented Programming, augmented with persistence capabilities provided by an embedded object database to keep track of its state and implementing the four basic principles of resource oriented architectures: addressability, statelessness, representation and uniform interface. For implementation we use exclusively open source software: Django framework, dyBase object oriented database and Python programming language. We developed a generic framework of resources structured into a hierarchy of types and consequently extended this typology with recurses specific to the domain of environmental modeling. To test our web service we used cURL, a robust command-line based web client.

CMCC Data Distribution Centre

NASA Astrophysics Data System (ADS)

Aloisio, Giovanni; Fiore, Sandro; Negro, A.

2010-05-01

The CMCC Data Distribution Centre (DDC) is the primary entry point (web gateway) to the CMCC. It is a Data Grid Portal providing a ubiquitous and pervasive way to ease data publishing, climate metadata search, datasets discovery, metadata annotation, data access, data aggregation, sub-setting, etc. The grid portal security model includes the use of HTTPS protocol for secure communication with the client (based on X509v3 certificates that must be loaded into the browser) and secure cookies to establish and maintain user sessions. The CMCC DDC is now in a pre-production phase and it is currently used only by internal users (CMCC researchers and climate scientists). The most important component already available in the CMCC DDC is the Search Engine which allows users to perform, through web interfaces, distributed search and discovery activities by introducing one or more of the following search criteria: horizontal extent (which can be specified by interacting with a geographic map), vertical extent, temporal extent, keywords, topics, creation date, etc. By means of this page the user submits the first step of the query process on the metadata DB, then, she can choose one or more datasets retrieving and displaying the complete XML metadata description (from the browser). This way, the second step of the query process is carried out by accessing to a specific XML document of the metadata DB. Finally, through the web interface, the user can access to and download (partially or totally) the data stored on the storage device accessing to OPeNDAP servers and to other available grid storage interfaces. Requests concerning datasets stored in deep storage will be served asynchronously.

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

DTIC Science & Technology

2013-09-01

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

SAFOD Brittle Microstructure and Mechanics Knowledge Base (BM2KB)

NASA Astrophysics Data System (ADS)

Babaie, Hassan A.; Broda Cindi, M.; Hadizadeh, Jafar; Kumar, Anuj

2013-07-01

Scientific drilling near Parkfield, California has established the San Andreas Fault Observatory at Depth (SAFOD), which provides the solid earth community with short range geophysical and fault zone material data. The BM2KB ontology was developed in order to formalize the knowledge about brittle microstructures in the fault rocks sampled from the SAFOD cores. A knowledge base, instantiated from this domain ontology, stores and presents the observed microstructural and analytical data with respect to implications for brittle deformation and mechanics of faulting. These data can be searched on the knowledge base‧s Web interface by selecting a set of terms (classes, properties) from different drop-down lists that are dynamically populated from the ontology. In addition to this general search, a query can also be conducted to view data contributed by a specific investigator. A search by sample is done using the EarthScope SAFOD Core Viewer that allows a user to locate samples on high resolution images of core sections belonging to different runs and holes. The class hierarchy of the BM2KB ontology was initially designed using the Unified Modeling Language (UML), which was used as a visual guide to develop the ontology in OWL applying the Protégé ontology editor. Various Semantic Web technologies such as the RDF, RDFS, and OWL ontology languages, SPARQL query language, and Pellet reasoning engine, were used to develop the ontology. An interactive Web application interface was developed through Jena, a java based framework, with AJAX technology, jsp pages, and java servlets, and deployed via an Apache tomcat server. The interface allows the registered user to submit data related to their research on a sample of the SAFOD core. The submitted data, after initial review by the knowledge base administrator, are added to the extensible knowledge base and become available in subsequent queries to all types of users. The interface facilitates inference capabilities in the ontology, supports SPARQL queries, allows for modifications based on successive discoveries, and provides an accessible knowledge base on the Web.

Innovative Approaches for the Dissemination of Near Real-time Geostationary Satellite Data for Terrestrial and Space Weather Applications

NASA Astrophysics Data System (ADS)

Jedlovec, G.; McGrath, K.; Meyer, P. J.; Berndt, E.

2017-12-01

A GOES-R series receiving station has been installed at the NASA Marshall Space Flight Center (MSFC) to support GOES-16 transition-to-operations projects of NASA's Earth science program and provide a community portal for GOES-16 data access. This receiving station is comprised of a 6.5-meter dish; motor-driven positioners; Quorum feed and demodulator; and three Linux workstations for ingest, processing, display, and subsequent product generation. The Community Satellite Processing Package (CSPP) is used to process GOES Rebroadcast data from the Advanced Baseline Imager (ABI), Geostationary Lightning Mapper (GLM), Solar Ultraviolet Imager (SUVI), Extreme Ultraviolet and X-ray Irradiance Sensors (EXIS), and Space Environment In-Situ Suite (SEISS) into Level 1b and Level 2 files. GeoTIFFs of the imagery from several of these instruments are ingested into an Esri Arc Enterprise Web Map Service (WMS) server with tiled imagery displayable through a web browser interface or by connecting directly to the WMS with a Geographic Information System software package. These data also drive a basic web interface where users can manually zoom to and animate regions of interest or acquire similar results using a published Application Program Interface. While not as interactive as a WMS-driven interface, this system is much more expeditious with generating and distributing requested imagery. The legacy web capability enacted for the predecessor GOES Imager currently supports approximately 500,000 unique visitors each month. Dissemination capabilities have been refined to support a significantly larger number of anticipated users. The receiving station also supports NASA's Short-term Prediction, Research, and Transition Center's (SPoRT) project activities to dissemination near real-time ABI RGB products to National Weather Service National Centers, including the Satellite Analysis Branch, National Hurricane Center, Ocean Prediction Center, and Weather Prediction Center, where they are displayed in N-AWIPS and AWIPS II. The multitude of additional real-time data users include the U.S. Coast Guard, Federal Aviation Administration, and The Weather Company. A second antenna is being installed for the ingest, processing, and dissemination of GOES-S data.

OxfordGrid: a web interface for pairwise comparative map views.

PubMed

Yang, Hongyu; Gingle, Alan R

2005-12-01

OxfordGrid is a web application and database schema for storing and interactively displaying genetic map data in a comparative, dot-plot, fashion. Its display is composed of a matrix of cells, each representing a pairwise comparison of mapped probe data for two linkage groups or chromosomes. These are arranged along the axes with one forming grid columns and the other grid rows with the degree and pattern of synteny/colinearity between the two linkage groups manifested in the cell's dot density and structure. A mouse click over the selected grid cell launches an image map-based display for the selected cell. Both individual and linear groups of mapped probes can be selected and displayed. Also, configurable links can be used to access other web resources for mapped probe information. OxfordGrid is implemented in C#/ASP.NET and the package, including MySQL schema creation scripts, is available at ftp://cggc.agtec.uga.edu/OxfordGrid/.

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

PubMed

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

2017-08-01

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

Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots

PubMed Central

Xayaphoummine, A.; Bucher, T.; Isambert, H.

2005-01-01

The Kinefold web server provides a web interface for stochastic folding simulations of nucleic acids on second to minute molecular time scales. Renaturation or co-transcriptional folding paths are simulated at the level of helix formation and dissociation in agreement with the seminal experimental results. Pseudoknots and topologically ‘entangled’ helices (i.e. knots) are efficiently predicted taking into account simple geometrical and topological constraints. To encourage interactivity, simulations launched as immediate jobs are automatically stopped after a few seconds and return adapted recommendations. Users can then choose to continue incomplete simulations using the batch queuing system or go back and modify suggested options in their initial query. Detailed output provide (i) a series of low free energy structures, (ii) an online animated folding path and (iii) a programmable trajectory plot focusing on a few helices of interest to each user. The service can be accessed at . PMID:15980546

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

PubMed Central

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

2009-01-01

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

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

PubMed

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

2009-11-01

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

A RESTful interface to pseudonymization services in modern web applications.

PubMed

Lablans, Martin; Borg, Andreas; Ückert, Frank

2015-02-07

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

JetWeb: A WWW interface and database for Monte Carlo tuning and validation

NASA Astrophysics Data System (ADS)

Butterworth, J. M.; Butterworth, S.

2003-06-01

A World Wide Web interface to a Monte Carlo tuning facility is described. The aim of the package is to allow rapid and reproducible comparisons to be made between detailed measurements at high-energy physics colliders and general physics simulation packages. The package includes a relational database, a Java servlet query and display facility, and clean interfaces to simulation packages and their parameters.

A spatial web/agent-based model to support stakeholders' negotiation regarding land development.

PubMed

Pooyandeh, Majeed; Marceau, Danielle J

2013-11-15

Decision making in land management can be greatly enhanced if the perspectives of concerned stakeholders are taken into consideration. This often implies negotiation in order to reach an agreement based on the examination of multiple alternatives. This paper describes a spatial web/agent-based modeling system that was developed to support the negotiation process of stakeholders regarding land development in southern Alberta, Canada. This system integrates a fuzzy analytic hierarchy procedure within an agent-based model in an interactive visualization environment provided through a web interface to facilitate the learning and negotiation of the stakeholders. In the pre-negotiation phase, the stakeholders compare their evaluation criteria using linguistic expressions. Due to the uncertainty and fuzzy nature of such comparisons, a fuzzy Analytic Hierarchy Process is then used to prioritize the criteria. The negotiation starts by a development plan being submitted by a user (stakeholder) through the web interface. An agent called the proposer, which represents the proposer of the plan, receives this plan and starts negotiating with all other agents. The negotiation is conducted in a step-wise manner where the agents change their attitudes by assigning a new set of weights to their criteria. If an agreement is not achieved, a new location for development is proposed by the proposer agent. This process is repeated until a location is found that satisfies all agents to a certain predefined degree. To evaluate the performance of the model, the negotiation was simulated with four agents, one of which being the proposer agent, using two hypothetical development plans. The first plan was selected randomly; the other one was chosen in an area that is of high importance to one of the agents. While the agents managed to achieve an agreement about the location of the land development after three rounds of negotiation in the first scenario, seven rounds were required in the second scenario. The proposed web/agent-based model facilitates the interaction and learning among stakeholders when facing multiple alternatives. Copyright © 2013 Elsevier Ltd. All rights reserved.

The LandCarbon Web Application: Advanced Geospatial Data Delivery and Visualization Tools for Communication about Ecosystem Carbon Sequestration and Greenhouse Gas Fluxes

NASA Astrophysics Data System (ADS)

Thomas, N.; Galey, B.; Zhu, Z.; Sleeter, B. M.; Lehmer, E.

2015-12-01

The LandCarbon web application (http://landcarbon.org) is a collaboration between the U.S. Geological Survey and U.C. Berkeley's Geospatial Innovation Facility (GIF). The LandCarbon project is a national assessment focused on improved understanding of carbon sequestration and greenhouse gas fluxes in and out of ecosystems related to land use, using scientific capabilities from USGS and other organizations. The national assessment is conducted at a regional scale, covers all 50 states, and incorporates data from remote sensing, land change studies, aquatic and wetland data, hydrological and biogeochemical modeling, and wildfire mapping to estimate baseline and future potential carbon storage and greenhouse gas fluxes. The LandCarbon web application is a geospatial portal that allows for a sophisticated data delivery system as well as a suite of engaging tools that showcase the LandCarbon data using interactive web based maps and charts. The web application was designed to be flexible and accessible to meet the needs of a variety of users. Casual users can explore the input data and results of the assessment for a particular area of interest in an intuitive and interactive map, without the need for specialized software. Users can view and interact with maps, charts, and statistics that summarize the baseline and future potential carbon storage and fluxes for U.S. Level 2 Ecoregions for 3 IPCC emissions scenarios. The application allows users to access the primary data sources and assessment results for viewing and download, and also to learn more about the assessment's objectives, methods, and uncertainties through published reports and documentation. The LandCarbon web application is built on free and open source libraries including Django and D3. The GIF has developed the Django-Spillway package, which facilitates interactive visualization and serialization of complex geospatial raster data. The underlying LandCarbon data is available through an open application programming interface (API), which will allow other organizations to build their own custom applications and tools. New features such as finer scale aggregation and an online carbon calculator are being added to the LandCarbon web application to continue to make the site interactive, visually compelling, and useful for a wide range of users.

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").

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

NASA Technical Reports Server (NTRS)

Shiffman, Smadar; Degani, Asaf; Heymann, Michael

2004-01-01

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

Aided generation of search interfaces to astronomical archives

NASA Astrophysics Data System (ADS)

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

2016-07-01

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

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

PubMed

Stocker, Gernot; Rieder, Dietmar; Trajanoski, Zlatko

2004-03-22

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

Construction of a Linux based chemical and biological information system.

PubMed

Molnár, László; Vágó, István; Fehér, András

2003-01-01

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

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

PubMed

Harris, M; Jones, T A

2001-08-01

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

A database for TMT interface control documents

NASA Astrophysics Data System (ADS)

Gillies, Kim; Roberts, Scott; Brighton, Allan; Rogers, John

2016-08-01

The TMT Software System consists of software components that interact with one another through a software infrastructure called TMT Common Software (CSW). CSW consists of software services and library code that is used by developers to create the subsystems and components that participate in the software system. CSW also defines the types of components that can be constructed and their roles. The use of common component types and shared middleware services allows standardized software interfaces for the components. A software system called the TMT Interface Database System was constructed to support the documentation of the interfaces for components based on CSW. The programmer describes a subsystem and each of its components using JSON-style text files. A command interface file describes each command a component can receive and any commands a component sends. The event interface files describe status, alarms, and events a component publishes and status and events subscribed to by a component. A web application was created to provide a user interface for the required features. Files are ingested into the software system's database. The user interface allows browsing subsystem interfaces, publishing versions of subsystem interfaces, and constructing and publishing interface control documents that consist of the intersection of two subsystem interfaces. All published subsystem interfaces and interface control documents are versioned for configuration control and follow the standard TMT change control processes. Subsystem interfaces and interface control documents can be visualized in the browser or exported as PDF files.

Deep Interactive Learning with Sharkzor

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

None

Sharkzor is a web application for machine-learning assisted image sort and summary. Deep learning algorithms are leveraged to infer, augment, and automate the user’s mental model. Initially, images uploaded by the user are spread out on a canvas. The user then interacts with the images to impute their mental model into the applications algorithmic underpinnings. Methods of interaction within Sharkzor’s user interface and user experience support three primary user tasks: triage, organize and automate. The user triages the large pile of overlapping images by moving images of interest into proximity. The user then organizes said images into meaningful groups. Aftermore » interacting with the images and groups, deep learning helps to automate the user’s interactions. The loop of interaction, automation, and response by the user allows the system to quickly make sense of large amounts of data.« less

Towards a framework for geospatial tangible user interfaces in collaborative urban planning

NASA Astrophysics Data System (ADS)

Maquil, Valérie; Leopold, Ulrich; De Sousa, Luís Moreira; Schwartz, Lou; Tobias, Eric

2018-04-01

The increasing complexity of urban planning projects today requires new approaches to better integrate stakeholders with different professional backgrounds throughout a city. Traditional tools used in urban planning are designed for experts and offer little opportunity for participation and collaborative design. This paper introduces the concept of geospatial tangible user interfaces (GTUI) and reports on the design and implementation as well as the usability of such a GTUI to support stakeholder participation in collaborative urban planning. The proposed system uses physical objects to interact with large digital maps and geospatial data projected onto a tabletop. It is implemented using a PostGIS database, a web map server providing OGC web services, the computer vision framework reacTIVision, a Java-based TUIO client, and GeoTools. We describe how a GTUI has be instantiated and evaluated within the scope of two case studies related to real world collaborative urban planning scenarios. Our results confirm the feasibility of our proposed GTUI solutions to (a) instantiate different urban planning scenarios, (b) support collaboration, and (c) ensure an acceptable usability.

Towards a framework for geospatial tangible user interfaces in collaborative urban planning

NASA Astrophysics Data System (ADS)

Maquil, Valérie; Leopold, Ulrich; De Sousa, Luís Moreira; Schwartz, Lou; Tobias, Eric

2018-03-01

The increasing complexity of urban planning projects today requires new approaches to better integrate stakeholders with different professional backgrounds throughout a city. Traditional tools used in urban planning are designed for experts and offer little opportunity for participation and collaborative design. This paper introduces the concept of geospatial tangible user interfaces (GTUI) and reports on the design and implementation as well as the usability of such a GTUI to support stakeholder participation in collaborative urban planning. The proposed system uses physical objects to interact with large digital maps and geospatial data projected onto a tabletop. It is implemented using a PostGIS database, a web map server providing OGC web services, the computer vision framework reacTIVision, a Java-based TUIO client, and GeoTools. We describe how a GTUI has be instantiated and evaluated within the scope of two case studies related to real world collaborative urban planning scenarios. Our results confirm the feasibility of our proposed GTUI solutions to (a) instantiate different urban planning scenarios, (b) support collaboration, and (c) ensure an acceptable usability.

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

PubMed Central

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

2010-01-01

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

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

PubMed

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

2010-07-01

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

Information System through ANIS at CeSAM

NASA Astrophysics Data System (ADS)

Moreau, C.; Agneray, F.; Gimenez, S.

2015-09-01

ANIS (AstroNomical Information System) is a web generic tool developed at CeSAM to facilitate and standardize the implementation of astronomical data of various kinds through private and/or public dedicated Information Systems. The architecture of ANIS is composed of a database server which contains the project data, a web user interface template which provides high level services (search, extract and display imaging and spectroscopic data using a combination of criteria, an object list, a sql query module or a cone search interfaces), a framework composed of several packages, and a metadata database managed by a web administration entity. The process to implement a new ANIS instance at CeSAM is easy and fast : the scientific project has to submit data or a data secure access, the CeSAM team installs the new instance (web interface template and the metadata database), and the project administrator can configure the instance with the web ANIS-administration entity. Currently, the CeSAM offers through ANIS a web access to VO compliant Information Systems for different projects (HeDaM, HST-COSMOS, CFHTLS-ZPhots, ExoDAT,...).

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.

A Search Engine Features Comparison.

ERIC Educational Resources Information Center

Vorndran, Gerald

Until recently, the World Wide Web (WWW) public access search engines have not included many of the advanced commands, options, and features commonly available with the for-profit online database user interfaces, such as DIALOG. This study evaluates the features and characteristics common to both types of search interfaces, examines the Web search…

Evaluation of expert system application based on usability aspects

NASA Astrophysics Data System (ADS)

Munaiseche, C. P. C.; Liando, O. E. S.

2016-04-01

Usability usually defined as a point of human acceptance to a product or a system based on understands and right reaction to an interface. The performance of web application has been influence by the quality of the interface of that web to supporting information transfer process. Preferably, before the applications of expert systems were installed in the operational environment, these applications must be evaluated first by usability testing. This research aimed to measure the usability of the expert system application using tasks as interaction media. This study uses an expert system application to diagnose skin disease in human using questionnaire method which utilize the tasks as interaction media in measuring the usability. Certain tasks were executed by the participants in observing usability value of the application. The usability aspects observed were learnability, efficiency, memorability, errors, and satisfaction. Each questionnaire question represent aspects of usability. The results present the usability value for each aspect and the total average merit for all the five-usability aspect was 4.28, this indicated that the tested expert system application is in the range excellent for the usability level, so the application can be implemented as the operated system by user. The main contribution of the study is the research became the first step in using task model in the usability evaluation for the expert system application software.

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

NASA Astrophysics Data System (ADS)

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

2003-12-01

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

Biowep: a workflow enactment portal for bioinformatics applications.

PubMed

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

2007-03-08

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

Biowep: a workflow enactment portal for bioinformatics applications

PubMed Central

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

2007-01-01

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

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

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

DTIC Science & Technology

2012-03-01

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

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

NASA Astrophysics Data System (ADS)

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

2008-12-01

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

RAIN: RNA–protein Association and Interaction Networks

PubMed Central

Junge, Alexander; Refsgaard, Jan C.; Garde, Christian; Pan, Xiaoyong; Santos, Alberto; Alkan, Ferhat; Anthon, Christian; von Mering, Christian; Workman, Christopher T.; Jensen, Lars Juhl; Gorodkin, Jan

2017-01-01

Protein association networks can be inferred from a range of resources including experimental data, literature mining and computational predictions. These types of evidence are emerging for non-coding RNAs (ncRNAs) as well. However, integration of ncRNAs into protein association networks is challenging due to data heterogeneity. Here, we present a database of ncRNA–RNA and ncRNA–protein interactions and its integration with the STRING database of protein–protein interactions. These ncRNA associations cover four organisms and have been established from curated examples, experimental data, interaction predictions and automatic literature mining. RAIN uses an integrative scoring scheme to assign a confidence score to each interaction. We demonstrate that RAIN outperforms the underlying microRNA-target predictions in inferring ncRNA interactions. RAIN can be operated through an easily accessible web interface and all interaction data can be downloaded. Database URL: http://rth.dk/resources/rain PMID:28077569

Protecting clinical data on Web client computers: the PCASSO approach.

PubMed Central

Masys, D. R.; Baker, D. B.

1998-01-01

The ubiquity and ease of use of the Web have made it an increasingly popular medium for communication of health-related information. Web interfaces to commercially available clinical information systems are now available or under development by most major vendors. To the extent that such interfaces involve the use of unprotected operating systems, they are vulnerable to security limitations of Web client software environments. The Patient Centered Access to Secure Systems Online (PCASSO) project extends the protections for person-identifiable health data on Web client computers. PCASSO uses several approaches, including physical protection of authentication information, execution containment, graphical displays, and monitoring the client system for intrusions and co-existing programs that may compromise security. PMID:9929243

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

PubMed

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

2014-07-01

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

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2016-01-14

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

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

PubMed Central

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

2016-01-01

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

DNA Data Visualization (DDV): Software for Generating Web-Based Interfaces Supporting Navigation and Analysis of DNA Sequence Data of Entire Genomes.

PubMed

Neugebauer, Tomasz; Bordeleau, Eric; Burrus, Vincent; Brzezinski, Ryszard

2015-01-01

Data visualization methods are necessary during the exploration and analysis activities of an increasingly data-intensive scientific process. There are few existing visualization methods for raw nucleotide sequences of a whole genome or chromosome. Software for data visualization should allow the researchers to create accessible data visualization interfaces that can be exported and shared with others on the web. Herein, novel software developed for generating DNA data visualization interfaces is described. The software converts DNA data sets into images that are further processed as multi-scale images to be accessed through a web-based interface that supports zooming, panning and sequence fragment selection. Nucleotide composition frequencies and GC skew of a selected sequence segment can be obtained through the interface. The software was used to generate DNA data visualization of human and bacterial chromosomes. Examples of visually detectable features such as short and long direct repeats, long terminal repeats, mobile genetic elements, heterochromatic segments in microbial and human chromosomes, are presented. The software and its source code are available for download and further development. The visualization interfaces generated with the software allow for the immediate identification and observation of several types of sequence patterns in genomes of various sizes and origins. The visualization interfaces generated with the software are readily accessible through a web browser. This software is a useful research and teaching tool for genetics and structural genomics.

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

PubMed

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

2013-02-01

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

The visualCMAT: A web-server to select and interpret correlated mutations/co-evolving residues in protein families.

PubMed

Suplatov, Dmitry; Sharapova, Yana; Timonina, Daria; Kopylov, Kirill; Švedas, Vytas

2018-04-01

The visualCMAT web-server was designed to assist experimental research in the fields of protein/enzyme biochemistry, protein engineering, and drug discovery by providing an intuitive and easy-to-use interface to the analysis of correlated mutations/co-evolving residues. Sequence and structural information describing homologous proteins are used to predict correlated substitutions by the Mutual information-based CMAT approach, classify them into spatially close co-evolving pairs, which either form a direct physical contact or interact with the same ligand (e.g. a substrate or a crystallographic water molecule), and long-range correlations, annotate and rank binding sites on the protein surface by the presence of statistically significant co-evolving positions. The results of the visualCMAT are organized for a convenient visual analysis and can be downloaded to a local computer as a content-rich all-in-one PyMol session file with multiple layers of annotation corresponding to bioinformatic, statistical and structural analyses of the predicted co-evolution, or further studied online using the built-in interactive analysis tools. The online interactivity is implemented in HTML5 and therefore neither plugins nor Java are required. The visualCMAT web-server is integrated with the Mustguseal web-server capable of constructing large structure-guided sequence alignments of protein families and superfamilies using all available information about their structures and sequences in public databases. The visualCMAT web-server can be used to understand the relationship between structure and function in proteins, implemented at selecting hotspots and compensatory mutations for rational design and directed evolution experiments to produce novel enzymes with improved properties, and employed at studying the mechanism of selective ligand's binding and allosteric communication between topologically independent sites in protein structures. The web-server is freely available at https://biokinet.belozersky.msu.ru/visualcmat and there are no login requirements.

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.

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

NASA Astrophysics Data System (ADS)

Thanh, B.

2016-12-01

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

Changing learning with new interactive and media-rich instruction environments: virtual labs case study report.

PubMed

Huang, Camillan

2003-01-01

Technology has created a new dimension for visual teaching and learning with web-delivered interactive media. The Virtual Labs Project has embraced this technology with instructional design and evaluation methodologies behind the simPHYSIO suite of simulation-based, online interactive teaching modules in physiology for the Stanford students. In addition, simPHYSIO provides the convenience of anytime web-access and a modular structure that allows for personalization and customization of the learning material. This innovative tool provides a solid delivery and pedagogical backbone that can be applied to developing an interactive simulation-based training tool for the use and management of the Picture Archiving and Communication System (PACS) image information system. The disparity in the knowledge between health and IT professionals can be bridged by providing convenient modular teaching tools to fill the gaps in knowledge. An innovative teaching method in the whole PACS is deemed necessary for its successful implementation and operation since it has become widely distributed with many interfaces, components, and customizations. This paper will discuss the techniques for developing an interactive-based teaching tool, a case study of its implementation, and a perspective for applying this approach to an online PACS training tool. Copyright 2002 Elsevier Science Ltd.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

LightWAVE: Waveform and Annotation Viewing and Editing in a Web Browser.

PubMed

Moody, George B

2013-09-01

This paper describes LightWAVE, recently-developed open-source software for viewing ECGs and other physiologic waveforms and associated annotations (event markers). It supports efficient interactive creation and modification of annotations, capabilities that are essential for building new collections of physiologic signals and time series for research. LightWAVE is constructed of components that interact in simple ways, making it straightforward to enhance or replace any of them. The back end (server) is a common gateway interface (CGI) application written in C for speed and efficiency. It retrieves data from its data repository (PhysioNet's open-access PhysioBank archives by default, or any set of files or web pages structured as in PhysioBank) and delivers them in response to requests generated by the front end. The front end (client) is a web application written in JavaScript. It runs within any modern web browser and does not require installation on the user's computer, tablet, or phone. Finally, LightWAVE's scribe is a tiny CGI application written in Perl, which records the user's edits in annotation files. LightWAVE's data repository, back end, and front end can be located on the same computer or on separate computers. The data repository may be split across multiple computers. For compatibility with the standard browser security model, the front end and the scribe must be loaded from the same domain.

A demanding web-based PACS supported by web services technology

NASA Astrophysics Data System (ADS)

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

2006-03-01

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

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site.

PubMed

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

2015-07-01

Protein-peptide interactions play a key role in cell functions. Their structural characterization, though challenging, is important for the discovery of new drugs. The CABS-dock web server provides an interface for modeling protein-peptide interactions using a highly efficient protocol for the flexible docking of peptides to proteins. While other docking algorithms require pre-defined localization of the binding site, CABS-dock does not require such knowledge. Given a protein receptor structure and a peptide sequence (and starting from random conformations and positions of the peptide), CABS-dock performs simulation search for the binding site allowing for full flexibility of the peptide and small fluctuations of the receptor backbone. This protocol was extensively tested over the largest dataset of non-redundant protein-peptide interactions available to date (including bound and unbound docking cases). For over 80% of bound and unbound dataset cases, we obtained models with high or medium accuracy (sufficient for practical applications). Additionally, as optional features, CABS-dock can exclude user-selected binding modes from docking search or to increase the level of flexibility for chosen receptor fragments. CABS-dock is freely available as a web server at http://biocomp.chem.uw.edu.pl/CABSdock. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-25

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

Does Interface Matter? A Study of Web Authoring and Editing by Inexperienced Web Writers

ERIC Educational Resources Information Center

Dick, Rodney F.

2006-01-01

This study explores the complicated nature of the interface as a mediational tool for inexperienced writers as they composed hypertext documents. Because technology can become so quickly and inextricably connected to people's everyday lives, it is essential to explore the effects on these technologies before they become invisible. Because…

A Simple and Customizable Web Interface to the Virtual Solar Observatory

NASA Astrophysics Data System (ADS)

Hughitt, V. Keith; Hourcle, J.; Suarez-Sola, I.; Davey, A.

2010-05-01

As the variety and number of solar data sources continue to increase at a rapid rate, the importance of providing methods to search through these sources becomes increasingly important. By taking advantage of the power of modern JavaScript libraries, a new version of the Virtual Solar Observatory's web interface aims to provide a significantly faster and simpler way to explore the multitude of data repositories available. Querying asynchroniously serves not only to eliminates bottlenecks resulting from slow or unresponsive data providers, but also allows for displaying of results as soon as they are returned. Implicit pagination and post-query filtering enables users to work with large result-sets, while a more modular and customizable UI provides a mechanism for customizing both the look-and-feel and behavior of the VSO web interface. Finally, the new web interface features a custom widget system capable of displaying additional tools and information along-side of the standard VSO search form. Interested users can also write their own widgets and submit them for future incorporation into VSO.

Quantifying medical student clinical experiences via an ICD Code Logging App.

PubMed

Rawlins, Fred; Sumpter, Cameron; Sutphin, Dean; Garner, Harold R

2018-03-01

The logging of ICD Diagnostic, Procedure and Drug codes is one means of tracking the experience of medical students' clinical rotations. The goal is to create a web-based computer and mobile application to track the progress of trainees, monitor the effectiveness of their training locations and be a means of sampling public health status. We have developed a web-based app in which medical trainees make entries via a simple and quick interface optimized for both mobile devices and personal computers. For each patient interaction, users enter ICD diagnostic, procedure, and drug codes via a hierarchical or search entry interface, as well as patient demographics (age range and gender, but no personal identifiers), and free-text notes. Users and administrators can review and edit input via a series of output interfaces. The user interface and back-end database are provided via dual redundant failover Linux servers. Students master the interface in ten minutes, and thereafter complete entries in less than one minute. Five hundred-forty 3rd year VCOM students each averaged 100 entries in the first four week clinical rotation. Data accumulated in various Appalachian clinics and Central American medical mission trips has demonstrated the public health surveillance utility of the application. PC and mobile apps can be used to collect medical trainee experience in real time or near real-time, quickly, and efficiently. This system has collected 75,596 entries to date, less than 2% of trainees have needed assistance to become proficient, and medical school administrators are using the various summaries to evaluate students and compare different rotation sites. Copyright © 2017. Published by Elsevier B.V.

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

PubMed

Christen, Victor; Hartung, Michael; Groß, Anika

2015-01-01

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

Interactive Visualization of Large-Scale Hydrological Data using Emerging Technologies in Web Systems and Parallel Programming

NASA Astrophysics Data System (ADS)

Demir, I.; Krajewski, W. F.

2013-12-01

As geoscientists are confronted with increasingly massive datasets from environmental observations to simulations, one of the biggest challenges is having the right tools to gain scientific insight from the data and communicate the understanding to stakeholders. Recent developments in web technologies make it easy to manage, visualize and share large data sets with general public. Novel visualization techniques and dynamic user interfaces allow users to interact with data, and modify the parameters to create custom views of the data to gain insight from simulations and environmental observations. This requires developing new data models and intelligent knowledge discovery techniques to explore and extract information from complex computational simulations or large data repositories. Scientific visualization will be an increasingly important component to build comprehensive environmental information platforms. This presentation provides an overview of the trends and challenges in the field of scientific visualization, and demonstrates information visualization and communication tools developed within the light of these challenges.

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

PubMed

Xie, Yang; Ying, Jinyong; Xie, Dexuan

2017-03-30

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

The World-Wide Web and Mosaic: An Overview for Librarians.

ERIC Educational Resources Information Center

Morgan, Eric Lease

1994-01-01

Provides an overview of the Internet's World-Wide Web (Web), a hypertext system. Highlights include the client/server model; Uniform Resource Locator; examples of software; Web servers versus Gopher servers; HyperText Markup Language (HTML); converting files; Common Gateway Interface; organizing Web information; and the role of librarians in…

Cool Apps: Building Cryospheric Data Applications With Standards-Based Service Oriented Architecture

NASA Astrophysics Data System (ADS)

Collins, J. A.; Truslove, I.; Billingsley, B. W.; Oldenburg, J.; Brodzik, M.; Lewis, S.; Liu, M.

2012-12-01

The National Snow and Ice Data Center (NSIDC) holds a large collection of cryospheric data, and is involved in a number of informatics research and development projects aimed at improving the discoverability and accessibility of these data. To develop high-quality software in a timely manner, we have adopted a Service-Oriented Architecture (SOA) approach for our core technical infrastructure development. Data services at NSIDC are internally exposed to other tools and applications through standards-based service interfaces. These standards include OAI-PMH (Open Archives Initiative Protocol for Metadata Harvesting), various OGC (Open Geospatial Consortium) standards including WMS (Web Map Service) and WFS (Web Feature Service), ESIP (Federation of Earth Sciences Information Partners) OpenSearch, and NSIDC-specific RESTful services. By taking a standards-based approach, we are able to use off-the-shelf tools and libraries to consume, translate and broker these data services, and thus develop applications faster. Additionally, by exposing public interfaces to these services we provide valuable data services to technical collaborators; for example, NASA Reverb (http://reverb.echo.nasa.gov) uses NSIDC's WMS services. Our latest generation of web applications consume these data services directly. The most complete example of this is the Operation IceBridge Data Portal (http://nsidc.org/icebridge/portal) which depends on many of the aforementioned services, and clearly exhibits many of the advantages of building applications atop a service-oriented architecture. This presentation outlines the architectural approach and components and open standards and protocols adopted at NSIDC, demonstrates the interactions and uses of public and internal service interfaces currently powering applications including the IceBridge Data Portal, and outlines the benefits and challenges of this approach.

cPath: open source software for collecting, storing, and querying biological pathways

PubMed Central

Cerami, Ethan G; Bader, Gary D; Gross, Benjamin E; Sander, Chris

2006-01-01

Background Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. Results We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. Conclusion cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling. PMID:17101041

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

PubMed

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

2016-01-01

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

The CDS at the Age of Multitouch Interfaces and Mobility

NASA Astrophysics Data System (ADS)

Schaaff, A.; Boch, T.; Fernique, P.; Kaestlé, V.

2012-09-01

Currently, we are witnessing a rapid evolution of new human-machine interfaces based on the widespread use of multitouch screens. This evolution is not just a replacement of the mouse-keyboard couple but requires a recast of the interfaces to take advantage of the new features (example: simultaneous selections in different parts of the screen). Traditional operating systems (mostly Windows and Linux) are also moving towards the integration of multitouch. It is possible in Windows7, also in Ubuntu (since release 10.10). The user interfaces of existing applications should be deeply impacted, as it is not just an adaptation of the existing ones: it is a transition from a selection in menus, click on button, to an intuitive based interaction. In this context the use of the semantics could help to understand what the user wants to do and to simplify the interfaces. The number of mobile devices (Smartphones based on iPhoneOS, AndroidOS and others, tablet computers (iPad, Galaxy Tab, etc.) is growing exponentially with a sustained frequency of replacement (18 months for a device). Smartphones provide an access to Web services but also to dedicated applications (available on App Store, Android Market, etc.). Investment in human resources to provide services on mobile devices could be limited in the first case (a simple adaptation of existing Web pages), but is higher in the case of dedicated applications (software development for a given operating system and the porting to other systems to achieve sufficient diffusion). Following this step, we have developed an Aladin Allsky lite application for Android, SkySurveys. This application is based on HEALPix and it was a real challenge to provide a tool with good display performances on a basic hardware device compared to a desktop or a laptop. We are now focusing the study on the use of HTML5, an emerging technology supported by recent versions of Internet browsers, which can provide rich content. HTML5 has the advantage of allowing developments independent of the mobile platform (‘write once, run everywhere’). We also expect broadening of the user of the services to new audiences and in particular to the educational community through new interface user-friendlier in terms of usability and interaction.

CartograTree: connecting tree genomes, phenotypes and environment.

PubMed

Vasquez-Gross, Hans A; Yu, John J; Figueroa, Ben; Gessler, Damian D G; Neale, David B; Wegrzyn, Jill L

2013-05-01

Today, researchers spend a tremendous amount of time gathering, formatting, filtering and visualizing data collected from disparate sources. Under the umbrella of forest tree biology, we seek to provide a platform and leverage modern technologies to connect biotic and abiotic data. Our goal is to provide an integrated web-based workspace that connects environmental, genomic and phenotypic data via geo-referenced coordinates. Here, we connect the genomic query web-based workspace, DiversiTree and a novel geographical interface called CartograTree to data housed on the TreeGenes database. To accomplish this goal, we implemented Simple Semantic Web Architecture and Protocol to enable the primary genomics database, TreeGenes, to communicate with semantic web services regardless of platform or back-end technologies. The novelty of CartograTree lies in the interactive workspace that allows for geographical visualization and engagement of high performance computing (HPC) resources. The application provides a unique tool set to facilitate research on the ecology, physiology and evolution of forest tree species. CartograTree can be accessed at: http://dendrome.ucdavis.edu/cartogratree. © 2013 Blackwell Publishing Ltd.

Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry.

PubMed

Wandy, Joe; Zhu, Yunfeng; van der Hooft, Justin J J; Daly, Rónán; Barrett, Michael P; Rogers, Simon

2017-09-14

We recently published MS2LDA, a method for the decomposition of sets of molecular fragment data derived from large metabolomics experiments. To make the method more widely available to the community, here we present ms2lda.org, a web application that allows users to upload their data, run MS2LDA analyses and explore the results through interactive visualisations. Ms2lda.org takes tandem mass spectrometry data in many standard formats and allows the user to infer the sets of fragment and neutral loss features that co-occur together (Mass2Motifs). As an alternative workflow, the user can also decompose a dataset onto predefined Mass2Motifs. This is accomplished through the web interface or programmatically from our web service. The website can be found at http://ms2lda.org , while the source code is available at https://github.com/sdrogers/ms2ldaviz under the MIT license. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Tower Mesonetwork Climatology and Interactive Display Tool

NASA Technical Reports Server (NTRS)

Case, Jonathan L.; Bauman, William H., III

2004-01-01

Forecasters at the 45th Weather Squadron and Spaceflight Meteorology Group use data from the tower network over the Kennedy Space Center (KSC) and Cape Canaveral Air Force Station (CCAFS) to evaluate Launch Commit Criteria, and issue and verify forecasts for ground operations. Systematic biases in these parameters could adversely affect an analysis, forecast, or verification. Also, substantial geographical variations in temperature and wind speed can occur under specific wind directions. To address these concerns, the Applied Meteorology Unit (AMU) developed a climatology of temperatures and winds from the tower network, and identified the geographical variation and significant tower biases. The mesoclimate is largely driven by the complex land-water interfaces across KSC/CCAFS. Towers with close proximity to water typically had much warmer nocturnal temperatures and higher wind speeds throughout the year. The strongest nocturnal wind speeds occurred from October to March whereas the strongest mean daytime wind speeds occurred from February to May. These results of this project can be viewed by forecasters through an interactive graphical user interface developed by the AMU. The web-based interface includes graphical and map displays of mean, standard deviation, bias, and data availability for any combination of towers, variables, months, hours, and wind directions.

Software Applications to Access Earth Science Data: Building an ECHO Client

NASA Astrophysics Data System (ADS)

Cohen, A.; Cechini, M.; Pilone, D.

2010-12-01

Historically, developing an ECHO (NASA’s Earth Observing System (EOS) ClearingHOuse) client required interaction with its SOAP API. SOAP, as a framework for web service communication has numerous advantages for Enterprise applications and Java/C# type programming languages. However, as interest has grown for quick development cycles and more intriguing “mashups,” ECHO has seen the SOAP API lose its appeal. In order to address these changing needs, ECHO has introduced two new interfaces facilitating simple access to its metadata holdings. The first interface is built upon the OpenSearch format and ESIP Federated Search framework. The second interface is built upon the Representational State Transfer (REST) architecture. Using the REST and OpenSearch APIs to access ECHO makes development with modern languages much more feasible and simpler. Client developers can leverage the simple interaction with ECHO to focus more of their time on the advanced functionality they are presenting to users. To demonstrate the simplicity of developing with the REST API, participants will be led through a hands-on experience where they will develop an ECHO client that performs the following actions: + Login + Provider discovery + Provider based dataset discovery + Dataset, Temporal, and Spatial constraint based Granule discovery + Online Data Access

Welcome to health information science and systems.

PubMed

Zhang, Yanchun

2013-01-01

Health Information Science and Systems is an exciting, new, multidisciplinary journal that aims to use technologies in computer science to assist in disease diagnoses, treatment, prediction and monitoring through the modeling, design, development, visualization, integration and management of health related information. These computer-science technologies include such as information systems, web technologies, data mining, image processing, user interaction and interface, sensors and wireless networking and are applicable to a wide range of health related information including medical data, biomedical data, bioinformatics data, public health data.

BioFET-SIM web interface: implementation and two applications.

PubMed

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

2012-01-01

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

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

NASA Technical Reports Server (NTRS)

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

2011-01-01

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

SnipViz: a compact and lightweight web site widget for display and dissemination of multiple versions of gene and protein sequences.

PubMed

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

2014-07-23

As high throughput sequencing continues to grow more commonplace, the need to disseminate the resulting data via web applications continues to grow. Particularly, there is a need to disseminate multiple versions of related gene and protein sequences simultaneously--whether they represent alleles present in a single species, variations of the same gene among different strains, or homologs among separate species. Often this is accomplished by displaying all versions of the sequence at once in a manner that is not intuitive or space-efficient and does not facilitate human understanding of the data. Web-based applications needing to disseminate multiple versions of sequences would benefit from a drop-in module designed to effectively disseminate these data. SnipViz is a client-side software tool designed to disseminate multiple versions of related gene and protein sequences on web sites. SnipViz has a space-efficient, interactive, and dynamic interface for navigating, analyzing and visualizing sequence data. It is written using standard World Wide Web technologies (HTML, Javascript, and CSS) and is compatible with most web browsers. SnipViz is designed as a modular client-side web component and may be incorporated into virtually any web site and be implemented without any programming. SnipViz is a drop-in client-side module for web sites designed to efficiently visualize and disseminate gene and protein sequences. SnipViz is open source and is freely available at https://github.com/yeastrc/snipviz.

SuperTarget goes quantitative: update on drug–target interactions

PubMed Central

Hecker, Nikolai; Ahmed, Jessica; von Eichborn, Joachim; Dunkel, Mathias; Macha, Karel; Eckert, Andreas; Gilson, Michael K.; Bourne, Philip E.; Preissner, Robert

2012-01-01

There are at least two good reasons for the on-going interest in drug–target interactions: first, drug-effects can only be fully understood by considering a complex network of interactions to multiple targets (so-called off-target effects) including metabolic and signaling pathways; second, it is crucial to consider drug-target-pathway relations for the identification of novel targets for drug development. To address this on-going need, we have developed a web-based data warehouse named SuperTarget, which integrates drug-related information associated with medical indications, adverse drug effects, drug metabolism, pathways and Gene Ontology (GO) terms for target proteins. At present, the updated database contains >6000 target proteins, which are annotated with >330 000 relations to 196 000 compounds (including approved drugs); the vast majority of interactions include binding affinities and pointers to the respective literature sources. The user interface provides tools for drug screening and target similarity inclusion. A query interface enables the user to pose complex queries, for example, to find drugs that target a certain pathway, interacting drugs that are metabolized by the same cytochrome P450 or drugs that target proteins within a certain affinity range. SuperTarget is available at http://bioinformatics.charite.de/supertarget. PMID:22067455

DNAproDB: an interactive tool for structural analysis of DNA–protein complexes

PubMed Central

Sagendorf, Jared M.

2017-01-01

Abstract Many biological processes are mediated by complex interactions between DNA and proteins. Transcription factors, various polymerases, nucleases and histones recognize and bind DNA with different levels of binding specificity. To understand the physical mechanisms that allow proteins to recognize DNA and achieve their biological functions, it is important to analyze structures of DNA–protein complexes in detail. DNAproDB is a web-based interactive tool designed to help researchers study these complexes. DNAproDB provides an automated structure-processing pipeline that extracts structural features from DNA–protein complexes. The extracted features are organized in structured data files, which are easily parsed with any programming language or viewed in a browser. We processed a large number of DNA–protein complexes retrieved from the Protein Data Bank and created the DNAproDB database to store this data. Users can search the database by combining features of the DNA, protein or DNA–protein interactions at the interface. Additionally, users can upload their own structures for processing privately and securely. DNAproDB provides several interactive and customizable tools for creating visualizations of the DNA–protein interface at different levels of abstraction that can be exported as high quality figures. All functionality is documented and freely accessible at http://dnaprodb.usc.edu. PMID:28431131

SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services

PubMed Central

Gessler, Damian DG; Schiltz, Gary S; May, Greg D; Avraham, Shulamit; Town, Christopher D; Grant, David; Nelson, Rex T

2009-01-01

Background SSWAP (Simple Semantic Web Architecture and Protocol; pronounced "swap") is an architecture, protocol, and platform for using reasoning to semantically integrate heterogeneous disparate data and services on the web. SSWAP was developed as a hybrid semantic web services technology to overcome limitations found in both pure web service technologies and pure semantic web technologies. Results There are currently over 2400 resources published in SSWAP. Approximately two dozen are custom-written services for QTL (Quantitative Trait Loci) and mapping data for legumes and grasses (grains). The remaining are wrappers to Nucleic Acids Research Database and Web Server entries. As an architecture, SSWAP establishes how clients (users of data, services, and ontologies), providers (suppliers of data, services, and ontologies), and discovery servers (semantic search engines) interact to allow for the description, querying, discovery, invocation, and response of semantic web services. As a protocol, SSWAP provides the vocabulary and semantics to allow clients, providers, and discovery servers to engage in semantic web services. The protocol is based on the W3C-sanctioned first-order description logic language OWL DL. As an open source platform, a discovery server running at (as in to "swap info") uses the description logic reasoner Pellet to integrate semantic resources. The platform hosts an interactive guide to the protocol at , developer tools at , and a portal to third-party ontologies at (a "swap meet"). Conclusion SSWAP addresses the three basic requirements of a semantic web services architecture (i.e., a common syntax, shared semantic, and semantic discovery) while addressing three technology limitations common in distributed service systems: i.e., i) the fatal mutability of traditional interfaces, ii) the rigidity and fragility of static subsumption hierarchies, and iii) the confounding of content, structure, and presentation. SSWAP is novel by establishing the concept of a canonical yet mutable OWL DL graph that allows data and service providers to describe their resources, to allow discovery servers to offer semantically rich search engines, to allow clients to discover and invoke those resources, and to allow providers to respond with semantically tagged data. SSWAP allows for a mix-and-match of terms from both new and legacy third-party ontologies in these graphs. PMID:19775460

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

PubMed

Pelz, Oliver; Gilsdorf, Moritz; Boutros, Michael

2010-04-12

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

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

PubMed

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

2014-03-01

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

Interactive web-based mapping: bridging technology and data for health.

PubMed

Highfield, Linda; Arthasarnprasit, Jutas; Ottenweller, Cecelia A; Dasprez, Arnaud

2011-12-23

The Community Health Information System (CHIS) online mapping system was first launched in 1998. Its overarching goal was to provide researchers, residents and organizations access to health related data reflecting the overall health and well-being of their communities within the Greater Houston area. In September 2009, initial planning and development began for the next generation of CHIS. The overarching goal for the new version remained to make health data easily accessible for a wide variety of research audiences. However, in the new version we specifically sought to make the CHIS truly interactive and give the user more control over data selection and reporting. In July 2011, a beta version of the next-generation of the application was launched. This next-generation is also a web based interactive mapping tool comprised of two distinct portals: the Breast Health Portal and Project Safety Net. Both are accessed via a Google mapping interface. Geographic coverage for the portals is currently an 8 county region centered on Harris County, Texas. Data accessed by the application include Census 2000, Census 2010 (underway), cancer incidence from the Texas Cancer Registry (TX Dept. of State Health Services), death data from Texas Vital Statistics, clinic locations for free and low-cost health services, along with service lists, hours of operation, payment options and languages spoken, uninsured and poverty data. The system features query on the fly technology, which means the data is not generated until the query is provided to the system. This allows users to interact in real-time with the databases and generate customized reports and maps. To the author's knowledge, the Breast Health Portal and Project Safety Net are the first local-scale interactive online mapping interfaces for public health data which allow users to control the data generated. For example, users may generate breast cancer incidence rates by Census tract, in real time, for women aged 40-64. Conversely, they could then generate the same rates for women aged 35-55. The queries are user controlled.

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

ERIC Educational Resources Information Center

Cheon, Jongpil; Grant, Michael M.

2012-01-01

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

The Common Gateway Interface (CGI) for Enhancing Access to Database Servers via the World Wide Web (WWW).

ERIC Educational Resources Information Center

Machovec, George S., Ed.

1995-01-01

Explains the Common Gateway Interface (CGI) protocol as a set of rules for passing information from a Web server to an external program such as a database search engine. Topics include advantages over traditional client/server solutions, limitations, sample library applications, and sources of information from the Internet. (LRW)

SCOWLP classification: Structural comparison and analysis of protein binding regions

PubMed Central

Teyra, Joan; Paszkowski-Rogacz, Maciej; Anders, Gerd; Pisabarro, M Teresa

2008-01-01

Background Detailed information about protein interactions is critical for our understanding of the principles governing protein recognition mechanisms. The structures of many proteins have been experimentally determined in complex with different ligands bound either in the same or different binding regions. Thus, the structural interactome requires the development of tools to classify protein binding regions. A proper classification may provide a general view of the regions that a protein uses to bind others and also facilitate a detailed comparative analysis of the interacting information for specific protein binding regions at atomic level. Such classification might be of potential use for deciphering protein interaction networks, understanding protein function, rational engineering and design. Description Protein binding regions (PBRs) might be ideally described as well-defined separated regions that share no interacting residues one another. However, PBRs are often irregular, discontinuous and can share a wide range of interacting residues among them. The criteria to define an individual binding region can be often arbitrary and may differ from other binding regions within a protein family. Therefore, the rational behind protein interface classification should aim to fulfil the requirements of the analysis to be performed. We extract detailed interaction information of protein domains, peptides and interfacial solvent from the SCOWLP database and we classify the PBRs of each domain family. For this purpose, we define a similarity index based on the overlapping of interacting residues mapped in pair-wise structural alignments. We perform our classification with agglomerative hierarchical clustering using the complete-linkage method. Our classification is calculated at different similarity cut-offs to allow flexibility in the analysis of PBRs, feature especially interesting for those protein families with conflictive binding regions. The hierarchical classification of PBRs is implemented into the SCOWLP database and extends the SCOP classification with three additional family sub-levels: Binding Region, Interface and Contacting Domains. SCOWLP contains 9,334 binding regions distributed within 2,561 families. In 65% of the cases we observe families containing more than one binding region. Besides, 22% of the regions are forming complex with more than one different protein family. Conclusion The current SCOWLP classification and its web application represent a framework for the study of protein interfaces and comparative analysis of protein family binding regions. This comparison can be performed at atomic level and allows the user to study interactome conservation and variability. The new SCOWLP classification may be of great utility for reconstruction of protein complexes, understanding protein networks and ligand design. SCOWLP will be updated with every SCOP release. The web application is available at . PMID:18182098

Evolving the Land Information System into a Cloud Computing Service

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

Houser, Paul R.

The Land Information System (LIS) was developed to use advanced flexible land surface modeling and data assimilation frameworks to integrate extremely large satellite- and ground-based observations with advanced land surface models to produce continuous high-resolution fields of land surface states and fluxes. The resulting fields are extremely useful for drought and flood assessment, agricultural planning, disaster management, weather and climate forecasting, water resources assessment, and the like. We envisioned transforming the LIS modeling system into a scientific cloud computing-aware web and data service that would allow clients to easily setup and configure for use in addressing large water management issues.more » The focus of this Phase 1 project was to determine the scientific, technical, commercial merit and feasibility of the proposed LIS-cloud innovations that are currently barriers to broad LIS applicability. We (a) quantified the barriers to broad LIS utility and commercialization (high performance computing, big data, user interface, and licensing issues); (b) designed the proposed LIS-cloud web service, model-data interface, database services, and user interfaces; (c) constructed a prototype LIS user interface including abstractions for simulation control, visualization, and data interaction, (d) used the prototype to conduct a market analysis and survey to determine potential market size and competition, (e) identified LIS software licensing and copyright limitations and developed solutions, and (f) developed a business plan for development and marketing of the LIS-cloud innovation. While some significant feasibility issues were found in the LIS licensing, overall a high degree of LIS-cloud technical feasibility was found.« less

AplusB: A Web Application for Investigating A + B Designs for Phase I Cancer Clinical Trials.

PubMed

Wheeler, Graham M; Sweeting, Michael J; Mander, Adrian P

2016-01-01

In phase I cancer clinical trials, the maximum tolerated dose of a new drug is often found by a dose-escalation method known as the A + B design. We have developed an interactive web application, AplusB, which computes and returns exact operating characteristics of A + B trial designs. The application has a graphical user interface (GUI), requires no programming knowledge and is free to access and use on any device that can open an internet browser. A customised report is available for download for each design that contains tabulated operating characteristics and informative plots, which can then be compared with other dose-escalation methods. We present a step-by-step guide on how to use this application and provide several illustrative examples of its capabilities.

[Distance education: use of the WebCT as a support tool for teaching intravenous therapy in nursing undergraduate programs].

PubMed

Dias, Denise Costa; Cassiani, Silvia Helena De Bortoli

2003-01-01

This investigation focused on a learning environment via internet, through which Intravenous Therapy (IVT) was taught. Due to its complexity, Intravenous Therapy was chosen against numerous subjects to be taught through an e-learning environment, by comprising both technical procedures and conceptual aspects that can be discussed through a virtual learning environment. The objectives of this study were to develop educational material about Intravenous Therapy to guide students through the learning related to intravenous therapy, to have the related educational material evaluated by experts, and to evaluate the students' use of this material, considering difficulties and/or advantages, participation/interaction in this environment, and usability of its tools. The interface used for the internet-based training program was WebCT.

The ADAM project: a generic web interface for retrieval and display of ATLAS TDAQ information

NASA Astrophysics Data System (ADS)

Harwood, A.; Lehmann Miotto, G.; Magnoni, L.; Vandelli, W.; Savu, D.

2012-06-01

This paper describes a new approach to the visualization of information about the operation of the ATLAS Trigger and Data Acquisition system. ATLAS is one of the two general purpose detectors positioned along the Large Hadron Collider at CERN. Its data acquisition system consists of several thousand computers interconnected via multiple gigabit Ethernet networks, that are constantly monitored via different tools. Operational parameters ranging from the temperature of the computers to the network utilization are stored in several databases for later analysis. Although the ability to view these data-sets individually is already in place, currently there is no way to view this data together, in a uniform format, from one location. The ADAM project has been launched in order to overcome this limitation. It defines a uniform web interface to collect data from multiple providers that have different structures. It is capable of aggregating and correlating the data according to user defined criteria. Finally, it visualizes the collected data using a flexible and interactive front-end web system. Structurally, the project comprises of 3 main levels of the data collection cycle: The Level 0 represents the information sources within ATLAS. These providers do not store information in a uniform fashion. The first step of the project was to define a common interface with which to expose stored data. The interface designed for the project originates from the Google Data Protocol API. The idea is to allow read-only access to data providers, through HTTP requests similar in format to the SQL query structure. This provides a standardized way to access this different information sources within ATLAS. The Level 1 can be considered the engine of the system. The primary task of the Level 1 is to gather data from multiple data sources via the common interface, to correlate this data together, or over a defined time series, and expose the combined data as a whole to the Level 2 web interface. The Level 2 is designed to present the data in a similar style and aesthetic, despite the different data sources. Pages can be constructed, edited and personalized by users to suit the specific data being shown. Pages can show a collection of graphs displaying data potentially coming from multiple sources. The project as a whole has a great amount of scope thanks to the uniform approach chosen for exposing data, and the flexibility of the Level 2 in presenting results. The paper will describe in detail the design and implementation of this new tool. In particular we will go through the project architecture, the implementation choices and the examples of usage of the system in place within the ATLAS TDAQ infrastructure.

InterEvDock: a docking server to predict the structure of protein–protein interactions using evolutionary information

PubMed Central

Yu, Jinchao; Vavrusa, Marek; Andreani, Jessica; Rey, Julien; Tufféry, Pierre; Guerois, Raphaël

2016-01-01

The structural modeling of protein–protein interactions is key in understanding how cell machineries cross-talk with each other. Molecular docking simulations provide efficient means to explore how two unbound protein structures interact. InterEvDock is a server for protein docking based on a free rigid-body docking strategy. A systematic rigid-body docking search is performed using the FRODOCK program and the resulting models are re-scored with InterEvScore and SOAP-PP statistical potentials. The InterEvScore potential was specifically designed to integrate co-evolutionary information in the docking process. InterEvDock server is thus particularly well suited in case homologous sequences are available for both binding partners. The server returns 10 structures of the most likely consensus models together with 10 predicted residues most likely involved in the interface. In 91% of all complexes tested in the benchmark, at least one residue out of the 10 predicted is involved in the interface, providing useful guidelines for mutagenesis. InterEvDock is able to identify a correct model among the top10 models for 49% of the rigid-body cases with evolutionary information, making it a unique and efficient tool to explore structural interactomes under an evolutionary perspective. The InterEvDock web interface is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock/. PMID:27131368

A prototype web-GIS application for risk analysis of natural hazards in Switzerland

NASA Astrophysics Data System (ADS)

Aye, Zar Chi; Nicolet, Pierrick; Jaboyedoff, Michel; Derron, Marc-Henri; Gerber, Christian; Lévy, Sebastien

2016-04-01

Following changes in the system of Swiss subsidy in January 2008, the Swiss cantons and the Federal Office for the Environment (FOEN) were forced to prioritize different natural hazard protection projects based on their cost-effectiveness, as a response to limited financial resources (Bründl et al., 2009). For this purpose, applications such as EconoMe (OFEV, 2016) and Valdorisk (DGE, 2016) were developed for risk evaluation and prioritization of mitigation projects. These tools serve as a useful decision-making instrument to the community of practitioners and responsible authorities for natural hazard risk management in Switzerland. However, there are several aspects which could be improved, in particular, the integration and visualization of spatial information interactively through a web-GIS interface for better risk planning and evaluation. Therefore, in this study, we aim to develop an interactive web-GIS application based on the risk concepts applied in Switzerland. The purpose of this tool is to provide a rapid evaluation of risk before and after protection measures, and to test the efficiency of measures by using a simplified cost-benefit analysis within the context of different protection projects. This application allows to integrate different layers which are necessary to calculate risk, in particular, hazard intensity (vector) maps for different scenarios (such as 30, 100 and 300 years of return periods based on Swiss guidelines), exposed objects (such as buildings) and vulnerability information of these objects. Based on provided information and additional parameters, risk is calculated automatically and results are visualized within the web-GIS interface of the application. The users can modify these input information and parameters to create different risk scenarios. Based on the resultant risk scenarios, the users can propose and visualize (preliminary) risk reduction measures before realizing the actual design and dimensions of such protective measures in the area. After designing measures, the users can re-calculate risk by updating hazard intensity and object layers. This is achieved by manual editing of shape (vector) layers in the web-GIS interface interactively. Within the application, a cost-benefit analysis tool is also integrated to support the decision-making process for the selection of different protection measures. Finally, the resultant risk information (vector layers and data) can be exported in the form of shapefiles and excel sheets. A prototype application is realized using open-source geospatial software and technologies. Boundless framework with its client-side SDK environment is applied for the rapid prototyping. Free and open source components such as PostGIS spatial database, GeoServer and GeoWebCache, GeoExt and OpenLayers are used for the development of the platform. This developed prototype is demonstrated with a case study area located in Les Diablerets, Switzerland. This research work is carried out within a project funded by the Canton of Vaud, Switzerland. References: Bründl, M., Romang, H. E., Bischof, N., and Rheinberger, C. M.: The risk concept and its application in natural hazard risk management in Switzerland, Nat. Hazards Earth Syst. Sci., 9, 801-813, 2009. DGE: Valdorisk - Direction Générale de l'Environnement, www.vd.ch, accessed 9 January 2016, 2016. OFEV: EconoMe - Office fédéral de l'environnement, www.econome.admin.ch, accessed 9 January 2016, 2016.

Providing Web Interfaces to the NSF EarthScope USArray Transportable Array

NASA Astrophysics Data System (ADS)

Vernon, Frank; Newman, Robert; Lindquist, Kent

2010-05-01

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

Modern Technologies aspects for Oceanographic Data Management and Dissemination : The HNODC Implementation

NASA Astrophysics Data System (ADS)

Lykiardopoulos, A.; Iona, A.; Lakes, V.; Batis, A.; Balopoulos, E.

2009-04-01

The development of new technologies for the aim of enhancing Web Applications with Dynamically data access was the starting point for Geospatial Web Applications to developed at the same time as well. By the means of these technologies the Web Applications embed the capability of presenting Geographical representations of the Geo Information. The induction in nowadays, of the state of the art technologies known as Web Services, enforce the Web Applications to have interoperability among them i.e. to be able to process requests from each other via a network. In particular throughout the Oceanographic Community, modern Geographical Information systems based on Geospatial Web Services are now developed or will be developed shortly in the near future, with capabilities of managing the information itself fully through Web Based Geographical Interfaces. The exploitation of HNODC Data Base, through a Web Based Application enhanced with Web Services by the use of open source tolls may be consider as an ideal case of such implementation. Hellenic National Oceanographic Data Center (HNODC) as a National Public Oceanographic Data provider and at the same time a member of the International Net of Oceanographic Data Centers( IOC/IODE), owns a very big volume of Data and Relevant information about the Marine Ecosystem. For the efficient management and exploitation of these Data, a relational Data Base has been constructed with a storage of over 300.000 station data concerning, physical, chemical and biological Oceanographic information. The development of a modern Web Application for the End User worldwide to be able to explore and navigate throughout HNODC data via the use of an interface with the capability of presenting Geographical representations of the Geo Information, is today a fact. The application is constituted with State of the art software components and tools such as: • Geospatial and no Spatial Web Services mechanisms • Geospatial open source tools for the creation of Dynamic Geographical Representations. • Communication protocols (messaging mechanisms) in all Layers such as XML and GML together with SOAP protocol via Apache/Axis. At the same time the application may interact with any other SOA application either in sending or receiving Geospatial Data through Geographical Layers, since it inherits the big advantage of interoperability between Web Services systems. Roughly the Architecture can denoted as follows: • At the back End Open source PostgreSQL DBMS stands as the data storage mechanism with more than one Data Base Schemas cause of the separation of the Geospatial Data and the non Geospatial Data. • UMN Map Server and Geoserver are the mechanisms for: Represent Geospatial Data via Web Map Service (WMS) Querying and Navigating in Geospatial and Meta Data Information via Web Feature Service (WFS) oAnd in the near future Transacting and processing new or existing Geospatial Data via Web Processing Service (WPS) • Map Bender, a geospatial portal site management software for OGC and OWS architectures acts as the integration module between the Geospatial Mechanisms. Mapbender comes with an embedded data model capable to manage interfaces for displaying, navigating and querying OGC compliant web map and feature services (WMS and transactional WFS). • Apache and Tomcat stand again as the Web Service middle Layers • Apache Axis with it's embedded implementation of the SOAP protocol ("Simple Object Access Protocol") acts as the No spatial data Mechanism of Web Services. These modules of the platform are still under development but their implementation will be fulfilled in the near future. • And a new Web user Interface for the end user based on enhanced and customized version of a MapBender GUI, a powerful Web Services client. For HNODC the interoperability of Web Services is the big advantage of the developed platform since it is capable to act in the future as provider and consumer of Web Services in both ways: • Either as data products provider for external SOA platforms. • Or as consumer of data products from external SOA platforms for new applications to be developed or for existing applications to be enhanced. A great paradigm of Data Managenet integration and dissemination via the use of such technologies is the European's Union Research Project Seadatanet, with the main objective to develop a standardized distributed system for managing and disseminating the large and diverse data sets and to enhance the currently existing infrastructures with Web Services Further more and when the technology of Web Processing Service (WPS), will be mature enough and applicable for development, the derived data products will be able to have any kind of GIS functionality for consumers across the network. From this point of view HNODC, joins the global scientific community by providing and consuming application Independent data products.

DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions

PubMed Central

Kuang, Xingyan; Dhroso, Andi; Han, Jing Ginger; Shyu, Chi-Ren; Korkin, Dmitry

2016-01-01

Macromolecular interactions are formed between proteins, DNA and RNA molecules. Being a principle building block in macromolecular assemblies and pathways, the interactions underlie most of cellular functions. Malfunctioning of macromolecular interactions is also linked to a number of diseases. Structural knowledge of the macromolecular interaction allows one to understand the interaction’s mechanism, determine its functional implications and characterize the effects of genetic variations, such as single nucleotide polymorphisms, on the interaction. Unfortunately, until now the interactions mediated by different types of macromolecules, e.g. protein–protein interactions or protein–DNA interactions, are collected into individual and unrelated structural databases. This presents a significant obstacle in the analysis of macromolecular interactions. For instance, the homogeneous structural interaction databases prevent scientists from studying structural interactions of different types but occurring in the same macromolecular complex. Here, we introduce DOMMINO 2.0, a structural Database Of Macro-Molecular INteractiOns. Compared to DOMMINO 1.0, a comprehensive database on protein-protein interactions, DOMMINO 2.0 includes the interactions between all three basic types of macromolecules extracted from PDB files. DOMMINO 2.0 is automatically updated on a weekly basis. It currently includes ∼1 040 000 interactions between two polypeptide subunits (e.g. domains, peptides, termini and interdomain linkers), ∼43 000 RNA-mediated interactions, and ∼12 000 DNA-mediated interactions. All protein structures in the database are annotated using SCOP and SUPERFAMILY family annotation. As a result, protein-mediated interactions involving protein domains, interdomain linkers, C- and N- termini, and peptides are identified. Our database provides an intuitive web interface, allowing one to investigate interactions at three different resolution levels: whole subunit network, binary interaction and interaction interface. Database URL: http://dommino.org PMID:26827237

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.

Web-based volume slicer for 3D electron-microscopy data from EMDB

PubMed Central

Salavert-Torres, José; Iudin, Andrii; Lagerstedt, Ingvar; Sanz-García, Eduardo; Kleywegt, Gerard J.; Patwardhan, Ardan

2016-01-01

We describe the functionality and design of the Volume slicer – a web-based slice viewer for EMDB entries. This tool uniquely provides the facility to view slices from 3D EM reconstructions along the three orthogonal axes and to rapidly switch between them and navigate through the volume. We have employed multiple rounds of user-experience testing with members of the EM community to ensure that the interface is easy and intuitive to use and the information provided is relevant. The impetus to develop the Volume slicer has been calls from the EM community to provide web-based interactive visualisation of 2D slice data. This would be useful for quick initial checks of the quality of a reconstruction. Again in response to calls from the community, we plan to further develop the Volume slicer into a fully-fledged Volume browser that provides integrated visualisation of EMDB and PDB entries from the molecular to the cellular scale. PMID:26876163

Web Service Model for Plasma Simulations with Automatic Post Processing and Generation of Visual Diagnostics*

NASA Astrophysics Data System (ADS)

Exby, J.; Busby, R.; Dimitrov, D. A.; Bruhwiler, D.; Cary, J. R.

2003-10-01

We present our design and initial implementation of a web service model for running particle-in-cell (PIC) codes remotely from a web browser interface. PIC codes have grown significantly in complexity and now often require parallel execution on multiprocessor computers, which in turn requires sophisticated post-processing and data analysis. A significant amount of time and effort is required for a physicist to develop all the necessary skills, at the expense of actually doing research. Moreover, parameter studies with a computationally intensive code justify the systematic management of results with an efficient way to communicate them among a group of remotely located collaborators. Our initial implementation uses the OOPIC Pro code [1], Linux, Apache, MySQL, Python, and PHP. The Interactive Data Language is used for visualization. [1] D.L. Bruhwiler et al., Phys. Rev. ST-AB 4, 101302 (2001). * This work is supported by DOE grant # DE-FG02-03ER83857 and by Tech-X Corp. ** Also University of Colorado.

WheatGenome.info: an integrated database and portal for wheat genome information.

PubMed

Lai, Kaitao; Berkman, Paul J; Lorenc, Michal Tadeusz; Duran, Chris; Smits, Lars; Manoli, Sahana; Stiller, Jiri; Edwards, David

2012-02-01

Bread wheat (Triticum aestivum) is one of the most important crop plants, globally providing staple food for a large proportion of the human population. However, improvement of this crop has been limited due to its large and complex genome. Advances in genomics are supporting wheat crop improvement. We provide a variety of web-based systems hosting wheat genome and genomic data to support wheat research and crop improvement. WheatGenome.info is an integrated database resource which includes multiple web-based applications. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second-generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This system includes links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/.

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.

Web-based system for surgical planning and simulation

NASA Astrophysics Data System (ADS)

Eldeib, Ayman M.; Ahmed, Mohamed N.; Farag, Aly A.; Sites, C. B.

1998-10-01

The growing scientific knowledge and rapid progress in medical imaging techniques has led to an increasing demand for better and more efficient methods of remote access to high-performance computer facilities. This paper introduces a web-based telemedicine project that provides interactive tools for surgical simulation and planning. The presented approach makes use of client-server architecture based on new internet technology where clients use an ordinary web browser to view, send, receive and manipulate patients' medical records while the server uses the supercomputer facility to generate online semi-automatic segmentation, 3D visualization, surgical simulation/planning and neuroendoscopic procedures navigation. The supercomputer (SGI ONYX 1000) is located at the Computer Vision and Image Processing Lab, University of Louisville, Kentucky. This system is under development in cooperation with the Department of Neurological Surgery, Alliant Health Systems, Louisville, Kentucky. The server is connected via a network to the Picture Archiving and Communication System at Alliant Health Systems through a DICOM standard interface that enables authorized clients to access patients' images from different medical modalities.

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

PubMed

Li, Ping; Cunningham, Krystal

2005-05-01

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

Interface Between CDS/ISIS and the Web at the Library of the Cagliari Observatory

NASA Astrophysics Data System (ADS)

Mureddu, Leonardo; Denotti, Franca; Alvito, Gianni

The library catalog of the Cagliari Observatory was digitized some years ago, by using CDS/ISIS with a practical format named ``ASTCA'' derived from the well-known ``BIBLO''. Recently the observatory has put some effort into the creation and maintenance of a Web site; on that occasion the library database has been interfaced to the Web server by means of the software WWWISIS and a locally created search form. Both books and journals can be searched by remote users. Book searches can be made by authors, titles or keywords.

MScanner: a classifier for retrieving Medline citations

PubMed Central

Poulter, Graham L; Rubin, Daniel L; Altman, Russ B; Seoighe, Cathal

2008-01-01

Background Keyword searching through PubMed and other systems is the standard means of retrieving information from Medline. However, ad-hoc retrieval systems do not meet all of the needs of databases that curate information from literature, or of text miners developing a corpus on a topic that has many terms indicative of relevance. Several databases have developed supervised learning methods that operate on a filtered subset of Medline, to classify Medline records so that fewer articles have to be manually reviewed for relevance. A few studies have considered generalisation of Medline classification to operate on the entire Medline database in a non-domain-specific manner, but existing applications lack speed, available implementations, or a means to measure performance in new domains. Results MScanner is an implementation of a Bayesian classifier that provides a simple web interface for submitting a corpus of relevant training examples in the form of PubMed IDs and returning results ranked by decreasing probability of relevance. For maximum speed it uses the Medical Subject Headings (MeSH) and journal of publication as a concise document representation, and takes roughly 90 seconds to return results against the 16 million records in Medline. The web interface provides interactive exploration of the results, and cross validated performance evaluation on the relevant input against a random subset of Medline. We describe the classifier implementation, cross validate it on three domain-specific topics, and compare its performance to that of an expert PubMed query for a complex topic. In cross validation on the three sample topics against 100,000 random articles, the classifier achieved excellent separation of relevant and irrelevant article score distributions, ROC areas between 0.97 and 0.99, and averaged precision between 0.69 and 0.92. Conclusion MScanner is an effective non-domain-specific classifier that operates on the entire Medline database, and is suited to retrieving topics for which many features may indicate relevance. Its web interface simplifies the task of classifying Medline citations, compared to building a pre-filter and classifier specific to the topic. The data sets and open source code used to obtain the results in this paper are available on-line and as supplementary material, and the web interface may be accessed at . PMID:18284683

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.

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

NASA Technical Reports Server (NTRS)

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

1998-01-01

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

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.

PubMed

Côté, Richard G; Jones, Philip; Martens, Lennart; Kerrien, Samuel; Reisinger, Florian; Lin, Quan; Leinonen, Rasko; Apweiler, Rolf; Hermjakob, Henning

2007-10-18

Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. We have created the Protein Identifier Cross-Reference (PICR) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR interface, documentation and code examples are available at http://www.ebi.ac.uk/Tools/picr.

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases

PubMed Central

Côté, Richard G; Jones, Philip; Martens, Lennart; Kerrien, Samuel; Reisinger, Florian; Lin, Quan; Leinonen, Rasko; Apweiler, Rolf; Hermjakob, Henning

2007-01-01

Background Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. Results We have created the Protein Identifier Cross-Reference (PICR) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. Conclusion We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR interface, documentation and code examples are available at . PMID:17945017

SCSODC: Integrating Ocean Data for Visualization Sharing and Application

NASA Astrophysics Data System (ADS)

Xu, C.; Li, S.; Wang, D.; Xie, Q.

2014-02-01

The South China Sea Ocean Data Center (SCSODC) was founded in 2010 in order to improve collecting and managing of ocean data of the South China Sea Institute of Oceanology (SCSIO). The mission of SCSODC is to ensure the long term scientific stewardship of ocean data, information and products - collected through research groups, monitoring stations and observation cruises - and to facilitate the efficient use and distribution to possible users. However, data sharing and applications were limited due to the characteristics of distribution and heterogeneity that made it difficult to integrate the data. To surmount those difficulties, the Data Sharing System has been developed by the SCSODC using the most appropriate information management and information technology. The Data Sharing System uses open standards and tools to promote the capability to integrate ocean data and to interact with other data portals or users and includes a full range of processes such as data discovery, evaluation and access combining C/S and B/S mode. It provides a visualized management interface for the data managers and a transparent and seamless data access and application environment for users. Users are allowed to access data using the client software and to access interactive visualization application interface via a web browser. The architecture, key technologies and functionality of the system are discussed briefly in this paper. It is shown that the system of SCSODC is able to implement web visualization sharing and seamless access to ocean data in a distributed and heterogeneous environment.

BrainIACS: a system for web-based medical image processing

NASA Astrophysics Data System (ADS)

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

2009-02-01

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

The HydroShare Collaborative Repository for the Hydrology Community

NASA Astrophysics Data System (ADS)

Tarboton, D. G.; Idaszak, R.; Horsburgh, J. S.; Ames, D. P.; Goodall, J. L.; Couch, A.; Hooper, R. P.; Dash, P. K.; Stealey, M.; Yi, H.; Bandaragoda, C.; Castronova, A. M.

2017-12-01

HydroShare is an online, collaboration system for sharing of hydrologic data, analytical tools, and models. It supports the sharing of, and collaboration around, "resources" which are defined by standardized content types for data formats and models commonly used in hydrology. With HydroShare you can: Share your data and models with colleagues; Manage who has access to the content that you share; Share, access, visualize and manipulate a broad set of hydrologic data types and models; Use the web services application programming interface (API) to program automated and client access; Publish data and models and obtain a citable digital object identifier (DOI); Aggregate your resources into collections; Discover and access data and models published by others; Use web apps to visualize, analyze and run models on data in HydroShare. This presentation will describe the functionality and architecture of HydroShare highlighting our approach to making this system easy to use and serving the needs of the hydrology community represented by the Consortium of Universities for the Advancement of Hydrologic Sciences, Inc. (CUAHSI). Metadata for uploaded files is harvested automatically or captured using easy to use web user interfaces. Users are encouraged to add or create resources in HydroShare early in the data life cycle. To encourage this we allow users to share and collaborate on HydroShare resources privately among individual users or groups, entering metadata while doing the work. HydroShare also provides enhanced functionality for users through web apps that provide tools and computational capability for actions on resources. HydroShare's architecture broadly is comprised of: (1) resource storage, (2) resource exploration website, and (3) web apps for actions on resources. System components are loosely coupled and interact through APIs, which enhances robustness, as components can be upgraded and advanced relatively independently. The full power of this paradigm is the extensibility it supports. Web apps are hosted on separate servers, which may be 3rd party servers. They are registered in HydroShare using a web app resource that configures the connectivity for them to be discovered and launched directly from resource types they are associated with.

Timely Reporting and Interactive Visualization of Animal Health and Slaughterhouse Surveillance Data in Switzerland.

PubMed

Muellner, Ulrich J; Vial, Flavie; Wohlfender, Franziska; Hadorn, Daniela; Reist, Martin; Muellner, Petra

2015-01-01

The reporting of outputs from health surveillance systems should be done in a near real-time and interactive manner in order to provide decision makers with powerful means to identify, assess, and manage health hazards as early and efficiently as possible. While this is currently rarely the case in veterinary public health surveillance, reporting tools do exist for the visual exploration and interactive interrogation of health data. In this work, we used tools freely available from the Google Maps and Charts library to develop a web application reporting health-related data derived from slaughterhouse surveillance and from a newly established web-based equine surveillance system in Switzerland. Both sets of tools allowed entry-level usage without or with minimal programing skills while being flexible enough to cater for more complex scenarios for users with greater programing skills. In particular, interfaces linking statistical softwares and Google tools provide additional analytical functionality (such as algorithms for the detection of unusually high case occurrences) for inclusion in the reporting process. We show that such powerful approaches could improve timely dissemination and communication of technical information to decision makers and other stakeholders and could foster the early-warning capacity of animal health surveillance systems.

A collaborative platform for consensus sessions in pathology over Internet.

PubMed

Zapletal, Eric; Le Bozec, Christel; Degoulet, Patrice; Jaulent, Marie-Christine

2003-01-01

The design of valid databases in pathology faces the problem of diagnostic disagreement between pathologists. Organizing consensus sessions between experts to reduce the variability is a difficult task. The TRIDEM platform addresses the issue to organize consensus sessions in pathology over the Internet. In this paper, we present the basis to achieve such collaborative platform. On the one hand, the platform integrates the functionalities of the IDEM consensus module that alleviates the consensus task by presenting to pathologists preliminary computed consensus through ergonomic interfaces (automatic step). On the other hand, a set of lightweight interaction tools such as vocal annotations are implemented to ease the communication between experts as they discuss a case (interactive step). The architecture of the TRIDEM platform is based on a Java-Server-Page web server that communicate with the ObjectStore PSE/PRO database used for the object storage. The HTML pages generated by the web server run Java applets to perform the different steps (automatic and interactive) of the consensus. The current limitations of the platform is to only handle a synchronous process. Moreover, improvements like re-writing the consensus workflow with a protocol such as BPML are already forecast.

Inferring the microscopic surface energy of protein-protein interfaces from mutation data.

PubMed

Moal, Iain H; Dapkūnas, Justas; Fernández-Recio, Juan

2015-04-01

Mutations at protein-protein recognition sites alter binding strength by altering the chemical nature of the interacting surfaces. We present a simple surface energy model, parameterized with empirical ΔΔG values, yielding mean energies of -48 cal mol(-1) Å(-2) for interactions between hydrophobic surfaces, -51 to -80 cal mol(-1) Å(-2) for surfaces of complementary charge, and 66-83 cal mol(-1) Å(-2) for electrostatically repelling surfaces, relative to the aqueous phase. This places the mean energy of hydrophobic surface burial at -24 cal mol(-1) Å(-2) . Despite neglecting configurational entropy and intramolecular changes, the model correlates with empirical binding free energies of a functionally diverse set of rigid-body interactions (r = 0.66). When used to rerank docking poses, it can place near-native solutions in the top 10 for 37% of the complexes evaluated, and 82% in the top 100. The method shows that hydrophobic burial is the driving force for protein association, accounting for 50-95% of the cohesive energy. The model is available open-source from http://life.bsc.es/pid/web/surface_energy/ and via the CCharpPPI web server http://life.bsc.es/pid/ccharppi/. © 2015 Wiley Periodicals, Inc.

Towards democracy in spatial planning through spatial information built by communities: The investigation of spatial information built by citizens from participatory mapping to volunteered geographic information in Indonesia

NASA Astrophysics Data System (ADS)

Yudono, Adipandang

2017-06-01

Recently, crowd-sourced information is used to produce and improve collective knowledge and community capacity building. Triggered by broadening and expanding access to the Internet and cellular telephones, the utilisation of crowd-sourcing for policy advocacy, e-government and e-participation has increased globally [1]. Crowd-sourced information can conceivably support government’s or general social initiatives to inform, counsel, and cooperate, by engaging subjects and empowering decentralisation and democratization [2]. Crowd-sourcing has turned into a major technique for interactive mapping initiatives by urban or rural community because of its capability to incorporate a wide range of data. Continuously accumulated spatial data can be sorted, layered, and envisioned in ways that even beginners can comprehend with ease. Interactive spatial visualization has the possibility to be a useful democratic planning tool to empower citizens participating in spatial data provision and sharing in government programmes. Since the global emergence of World Wide Web (WWW) technology, the interaction between information providers and users has increased. Local communities are able to produce and share spatial data to produce web interfaces with territorial information in mapping application programming interfaces (APIs) public, such as Google maps, OSM and Wikimapia [3][4][5]. In terms of the democratic spatial planning action, Volunteered Geographic Information (VGI) is considered an effective voluntary method of helping people feel comfortable with the technology and other co-participants in order to shape coalitions of local knowledge. This paper has aim to investigate ‘How is spatial data created by citizens used in Indonesia?’ by discussing the characteristics of spatial data usage by citizens to support spatial policy formulation, starting with the history of participatory mapping to current VGI development in Indonesia.

Finding, Browsing and Getting Data Easily Using SPDF Web Services

NASA Technical Reports Server (NTRS)

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

A targeted e-learning program for surgical trainees to enhance patient safety in preventing surgical infection.

PubMed

McHugh, Seamus Mark; Corrigan, Mark; Dimitrov, Borislav; Cowman, Seamus; Tierney, Sean; Humphreys, Hilary; Hill, Arnold

2010-01-01

Surgical site infection accounts for 20% of all health care-associated infections (HCAIs); however, a program incorporating the education of surgeons has yet to be established across the specialty. An audit of surgical practice in infection prevention was carried out in Beaumont Hospital from July to November 2009. An educational Web site was developed targeting deficiencies highlighted in the audit. Interactive clinical cases were constructed using PHP coding, an HTML-embedded language, and then linked to a MySQL relational database. PowerPoint tutorials were produced as online Flash audiovisual movies. An online repository of streaming videos demonstrating best practice was made available, and weekly podcasts were made available on the iTunes© store for free download. Usage of the e-learning program was assessed quantitatively over 6 weeks in May and June 2010 using the commercial company Hitslink. During the 5-month audit, deficiencies in practice were highlighted, including the timing of surgical prophylaxis (33% noncompliance) and intravascular catheter care in surgical patients (38% noncompliance regarding necessity). Over the 6-week assessment of the educational material, the SurgInfection.com Web pages were accessed more than 8000 times; 77.9% of the visitors were from Ireland. The most commonly accessed modality was the repository with interactive clinical cases, accounting for 3463 (43%) of the Web site visits. The average user spent 57 minutes per visit, with 30% of them visiting the Web site multiple times. Interactive virtual cases mirroring real-life clinical scenarios are likely to be successful as an e-learning modality. User-friendly interfaces and 24-hour accessibility will increases uptake by surgical trainees.

Web-Based Course Management and Web Services

ERIC Educational Resources Information Center

Mandal, Chittaranjan; Sinha, Vijay Luxmi; Reade, Christopher M. P.

2004-01-01

The architecture of a web-based course management tool that has been developed at IIT [Indian Institute of Technology], Kharagpur and which manages the submission of assignments is discussed. Both the distributed architecture used for data storage and the client-server architecture supporting the web interface are described. Further developments…

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…

Software Tools to Support Research on Airport Departure Planning

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

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

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

PubMed Central

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

2003-01-01

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

Novel Scientific Visualization Interfaces for Interactive Information Visualization and Sharing

NASA Astrophysics Data System (ADS)

Demir, I.; Krajewski, W. F.

2012-12-01

As geoscientists are confronted with increasingly massive datasets from environmental observations to simulations, one of the biggest challenges is having the right tools to gain scientific insight from the data and communicate the understanding to stakeholders. Recent developments in web technologies make it easy to manage, visualize and share large data sets with general public. Novel visualization techniques and dynamic user interfaces allow users to interact with data, and modify the parameters to create custom views of the data to gain insight from simulations and environmental observations. This requires developing new data models and intelligent knowledge discovery techniques to explore and extract information from complex computational simulations or large data repositories. Scientific visualization will be an increasingly important component to build comprehensive environmental information platforms. This presentation provides an overview of the trends and challenges in the field of scientific visualization, and demonstrates information visualization and communication tools in the Iowa Flood Information System (IFIS), developed within the light of these challenges. The IFIS is a web-based platform developed by the Iowa Flood Center (IFC) to provide access to and visualization of flood inundation maps, real-time flood conditions, flood forecasts both short-term and seasonal, and other flood-related data for communities in Iowa. The key element of the system's architecture is the notion of community. Locations of the communities, those near streams and rivers, define basin boundaries. The IFIS provides community-centric watershed and river characteristics, weather (rainfall) conditions, and streamflow data and visualization tools. Interactive interfaces allow access to inundation maps for different stage and return period values, and flooding scenarios with contributions from multiple rivers. Real-time and historical data of water levels, gauge heights, and rainfall conditions are available in the IFIS. 2D and 3D interactive visualizations in the IFIS make the data more understandable to general public. Users are able to filter data sources for their communities and selected rivers. The data and information on IFIS is also accessible through web services and mobile applications. The IFIS is optimized for various browsers and screen sizes to provide access through multiple platforms including tablets and mobile devices. Multiple view modes in the IFIS accommodate different user types from general public to researchers and decision makers by providing different level of tools and details. River view mode allows users to visualize data from multiple IFC bridge sensors and USGS stream gauges to follow flooding condition along a river. The IFIS will help communities make better-informed decisions on the occurrence of floods, and will alert communities in advance to help minimize damage of floods.

Important ingredients for health adaptive information systems.

PubMed

Senathirajah, Yalini; Bakken, Suzanne

2011-01-01

Healthcare information systems frequently do not truly meet clinician needs, due to the complexity, variability, and rapid change in medical contexts. Recently the internet world has been transformed by approaches commonly termed 'Web 2.0'. This paper proposes a Web 2.0 model for a healthcare adaptive architecture. The vision includes creating modular, user-composable systems which aim to make all necessary information from multiple internal and external sources available via a platform, for the user to use, arrange, recombine, author, and share at will, using rich interfaces where advisable. Clinicians can create a set of 'widgets' and 'views' which can transform data, reflect their domain knowledge and cater to their needs, using simple drag and drop interfaces without the intervention of programmers. We have built an example system, MedWISE, embodying the user-facing parts of the model. This approach to HIS is expected to have several advantages, including greater suitability to user needs (reflecting clinician rather than programmer concepts and priorities), incorporation of multiple information sources, agile reconfiguration to meet emerging situations and new treatment deployment, capture of user domain expertise and tacit knowledge, efficiencies due to workflow and human-computer interaction improvements, and greater user acceptance.

Southwest Watershed Research Center Data Access Project

NASA Astrophysics Data System (ADS)

Nichols, M. H.; Anson, E.

2008-05-01

Hydrologic data, including rainfall and runoff data, have been collected on experimental watersheds operated by the U.S. Department of Agriculture Agricultural Research Service (USDA-ARS) in southern Arizona since the 1950s. These data are of national and international importance and make up one of the most comprehensive semiarid watershed data sets in the world. The USDA-ARS Southwest Watershed Research Center has recently developed an electronic data processing system that includes an online interface (http://tucson.ars.ag.gov/dap) to provide public access to the data. The goal of the system is to promote analyses and interpretations of historic and current data by improving data access. Data are collected from sensors in the field and are transmitted to computers in the office. The data are then processed, quality checked, and made available to users via the Internet. The publicly accessible part of the system consists of an interactive Web site, which provides an interface to the data, and a relational database, which is used to process, store, and manage data. The system was released to the public in October 2003, and since that time the online data access Web site has received more than 4500 visitors.

A Grid job monitoring system

NASA Astrophysics Data System (ADS)

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

2010-04-01

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

A multimodal dataset for authoring and editing multimedia content: The MAMEM project.

PubMed

Nikolopoulos, Spiros; Petrantonakis, Panagiotis C; Georgiadis, Kostas; Kalaganis, Fotis; Liaros, Georgios; Lazarou, Ioulietta; Adam, Katerina; Papazoglou-Chalikias, Anastasios; Chatzilari, Elisavet; Oikonomou, Vangelis P; Kumar, Chandan; Menges, Raphael; Staab, Steffen; Müller, Daniel; Sengupta, Korok; Bostantjopoulou, Sevasti; Katsarou, Zoe; Zeilig, Gabi; Plotnik, Meir; Gotlieb, Amihai; Kizoni, Racheli; Fountoukidou, Sofia; Ham, Jaap; Athanasiou, Dimitrios; Mariakaki, Agnes; Comanducci, Dario; Sabatini, Edoardo; Nistico, Walter; Plank, Markus; Kompatsiaris, Ioannis

2017-12-01

We present a dataset that combines multimodal biosignals and eye tracking information gathered under a human-computer interaction framework. The dataset was developed in the vein of the MAMEM project that aims to endow people with motor disabilities with the ability to edit and author multimedia content through mental commands and gaze activity. The dataset includes EEG, eye-tracking, and physiological (GSR and Heart rate) signals collected from 34 individuals (18 able-bodied and 16 motor-impaired). Data were collected during the interaction with specifically designed interface for web browsing and multimedia content manipulation and during imaginary movement tasks. The presented dataset will contribute towards the development and evaluation of modern human-computer interaction systems that would foster the integration of people with severe motor impairments back into society.

A Neuroimaging Web Services Interface as a Cyber Physical System for Medical Imaging and Data Management in Brain Research: Design Study

PubMed Central

2018-01-01

Background Structural and functional brain images are essential imaging modalities for medical experts to study brain anatomy. These images are typically visually inspected by experts. To analyze images without any bias, they must be first converted to numeric values. Many software packages are available to process the images, but they are complex and difficult to use. The software packages are also hardware intensive. The results obtained after processing vary depending on the native operating system used and its associated software libraries; data processed in one system cannot typically be combined with data on another system. Objective The aim of this study was to fulfill the neuroimaging community’s need for a common platform to store, process, explore, and visualize their neuroimaging data and results using Neuroimaging Web Services Interface: a series of processing pipelines designed as a cyber physical system for neuroimaging and clinical data in brain research. Methods Neuroimaging Web Services Interface accepts magnetic resonance imaging, positron emission tomography, diffusion tensor imaging, and functional magnetic resonance imaging. These images are processed using existing and custom software packages. The output is then stored as image files, tabulated files, and MySQL tables. The system, made up of a series of interconnected servers, is password-protected and is securely accessible through a Web interface and allows (1) visualization of results and (2) downloading of tabulated data. Results All results were obtained using our processing servers in order to maintain data validity and consistency. The design is responsive and scalable. The processing pipeline started from a FreeSurfer reconstruction of Structural magnetic resonance imaging images. The FreeSurfer and regional standardized uptake value ratio calculations were validated using Alzheimer’s Disease Neuroimaging Initiative input images, and the results were posted at the Laboratory of Neuro Imaging data archive. Notable leading researchers in the field of Alzheimer’s Disease and epilepsy have used the interface to access and process the data and visualize the results. Tabulated results with unique visualization mechanisms help guide more informed diagnosis and expert rating, providing a truly unique multimodal imaging platform that combines magnetic resonance imaging, positron emission tomography, diffusion tensor imaging, and resting state functional magnetic resonance imaging. A quality control component was reinforced through expert visual rating involving at least 2 experts. Conclusions To our knowledge, there is no validated Web-based system offering all the services that Neuroimaging Web Services Interface offers. The intent of Neuroimaging Web Services Interface is to create a tool for clinicians and researchers with keen interest on multimodal neuroimaging. More importantly, Neuroimaging Web Services Interface significantly augments the Alzheimer’s Disease Neuroimaging Initiative data, especially since our data contain a large cohort of Hispanic normal controls and Alzheimer’s Disease patients. The obtained results could be scrutinized visually or through the tabulated forms, informing researchers on subtle changes that characterize the different stages of the disease. PMID:29699962

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

PubMed

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

2015-12-01

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

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

PubMed

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

2000-01-01

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

Internet of People: Opportunities and challenges for engaging stakeholders in watershed planning via the Web

NASA Astrophysics Data System (ADS)

Babbar-Sebens, M.

2016-12-01

Social computing technologies are transforming the way our society interacts and generates content on the Web via collective intelligence. Previously unimagined possibilities have arisen for using these technologies to engage stakeholders and involve them in policy making and planning efforts. While the Internet has been used in the past to support education and communication endeavors, we have developed a novel, web-based, interactive planning tool that engages the community in using science-based methods for the design of potential conservation practices on their landscape, and thereby, reducing undesirable impacts of extreme hydroclimatic events. The tool, Watershed REstoration using Spatio-Temporal Optimization of Resources (WRESTORE), uses a democratic voting process coupled with visualization interfaces, computational simulation and optimization models, and user modeling techniques to support a human-centered design approach. This human-centered design approach, which is reinforced by use of Web 2.0 technologies, has the potential to enable policy makers to connect to a larger community of stakeholders and directly engage them in environmental stewardship efforts. Additionally, the design framework can be used by watershed groups to plug-in their own hydrologic models, climate observations and forecasts, and various other simulation models unique to their watersheds. In this presentation, we will demonstrate the effectiveness of WRESTORE for designing alternatives of conservation practices in a HUC-11 Midwestern watershed, results of various experiments with a diverse set of test users and stakeholders, and discuss potential for future developments.

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

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

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

2008-05-04

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

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

NASA Astrophysics Data System (ADS)

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

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

A Web Interface for Eco System Modeling

NASA Astrophysics Data System (ADS)

McHenry, K.; Kooper, R.; Serbin, S. P.; LeBauer, D. S.; Desai, A. R.; Dietze, M. C.

2012-12-01

We have developed the Predictive Ecosystem Analyzer (PEcAn) as an open-source scientific workflow system and ecoinformatics toolbox that manages the flow of information in and out of regional-scale terrestrial biosphere models, facilitates heterogeneous data assimilation, tracks data provenance, and enables more effective feedback between models and field research. The over-arching goal of PEcAn is to make otherwise complex analyses transparent, repeatable, and accessible to a diverse array of researchers, allowing both novice and expert users to focus on using the models to examine complex ecosystems rather than having to deal with complex computer system setup and configuration questions in order to run the models. Through the developed web interface we hide much of the data and model details and allow the user to simply select locations, ecosystem models, and desired data sources as inputs to the model. Novice users are guided by the web interface through setting up a model execution and plotting the results. At the same time expert users are given enough freedom to modify specific parameters before the model gets executed. This will become more important as more and more models are added to the PEcAn workflow as well as more and more data that will become available as NEON comes online. On the backend we support the execution of potentially computationally expensive models on different High Performance Computers (HPC) and/or clusters. The system can be configured with a single XML file that gives it the flexibility needed for configuring and running the different models on different systems using a combination of information stored in a database as well as pointers to files on the hard disk. While the web interface usually creates this configuration file, expert users can still directly edit it to fine tune the configuration.. Once a workflow is finished the web interface will allow for the easy creation of plots over result data while also allowing the user to download the results for further processing. The current workflow in the web interface is a simple linear workflow, but will be expanded to allow for more complex workflows. We are working with Kepler and Cyberintegrator to allow for these more complex workflows as well as collecting provenance of the workflow being executed. This provenance regarding model executions is stored in a database along with the derived results. All of this information is then accessible using the BETY database web frontend. The PEcAn interface.

A Web Tool for Generating High Quality Machine-readable Biological Pathways.

PubMed

Ramirez-Gaona, Miguel; Marcu, Ana; Pon, Allison; Grant, Jason; Wu, Anthony; Wishart, David S

2017-02-08

PathWhiz is a web server built to facilitate the creation of colorful, interactive, visually pleasing pathway diagrams that are rich in biological information. The pathways generated by this online application are machine-readable and fully compatible with essentially all web-browsers and computer operating systems. It uses a specially developed, web-enabled pathway drawing interface that permits the selection and placement of different combinations of pre-drawn biological or biochemical entities to depict reactions, interactions, transport processes and binding events. This palette of entities consists of chemical compounds, proteins, nucleic acids, cellular membranes, subcellular structures, tissues, and organs. All of the visual elements in it can be interactively adjusted and customized. Furthermore, because this tool is a web server, all pathways and pathway elements are publicly accessible. This kind of pathway "crowd sourcing" means that PathWhiz already contains a large and rapidly growing collection of previously drawn pathways and pathway elements. Here we describe a protocol for the quick and easy creation of new pathways and the alteration of existing pathways. To further facilitate pathway editing and creation, the tool contains replication and propagation functions. The replication function allows existing pathways to be used as templates to create or edit new pathways. The propagation function allows one to take an existing pathway and automatically propagate it across different species. Pathways created with this tool can be "re-styled" into different formats (KEGG-like or text-book like), colored with different backgrounds, exported to BioPAX, SBGN-ML, SBML, or PWML data exchange formats, and downloaded as PNG or SVG images. The pathways can easily be incorporated into online databases, integrated into presentations, posters or publications, or used exclusively for online visualization and exploration. This protocol has been successfully applied to generate over 2,000 pathway diagrams, which are now found in many online databases including HMDB, DrugBank, SMPDB, and ECMDB.

visPIG--a web tool for producing multi-region, multi-track, multi-scale plots of genetic data.

PubMed

Scales, Matthew; Jäger, Roland; Migliorini, Gabriele; Houlston, Richard S; Henrion, Marc Y R

2014-01-01

We present VISual Plotting Interface for Genetics (visPIG; http://vispig.icr.ac.uk), a web application to produce multi-track, multi-scale, multi-region plots of genetic data. visPIG has been designed to allow users not well versed with mathematical software packages and/or programming languages such as R, Matlab®, Python, etc., to integrate data from multiple sources for interpretation and to easily create publication-ready figures. While web tools such as the UCSC Genome Browser or the WashU Epigenome Browser allow custom data uploads, such tools are primarily designed for data exploration. This is also true for the desktop-run Integrative Genomics Viewer (IGV). Other locally run data visualisation software such as Circos require significant computer skills of the user. The visPIG web application is a menu-based interface that allows users to upload custom data tracks and set track-specific parameters. Figures can be downloaded as PDF or PNG files. For sensitive data, the underlying R code can also be downloaded and run locally. visPIG is multi-track: it can display many different data types (e.g association, functional annotation, intensity, interaction, heat map data,…). It also allows annotation of genes and other custom features in the plotted region(s). Data tracks can be plotted individually or on a single figure. visPIG is multi-region: it supports plotting multiple regions, be they kilo- or megabases apart or even on different chromosomes. Finally, visPIG is multi-scale: a sub-region of particular interest can be 'zoomed' in. We describe the various features of visPIG and illustrate its utility with examples. visPIG is freely available through http://vispig.icr.ac.uk under a GNU General Public License (GPLv3).

QuakeSim: a Web Service Environment for Productive Investigations with Earth Surface Sensor Data

NASA Astrophysics Data System (ADS)

Parker, J. W.; Donnellan, A.; Granat, R. A.; Lyzenga, G. A.; Glasscoe, M. T.; McLeod, D.; Al-Ghanmi, R.; Pierce, M.; Fox, G.; Grant Ludwig, L.; Rundle, J. B.

2011-12-01

The QuakeSim science gateway environment includes a visually rich portal interface, web service access to data and data processing operations, and the QuakeTables ontology-based database of fault models and sensor data. The integrated tools and services are designed to assist investigators by covering the entire earthquake cycle of strain accumulation and release. The Web interface now includes Drupal-based access to diverse and changing content, with new ability to access data and data processing directly from the public page, as well as the traditional project management areas that require password access. The system is designed to make initial browsing of fault models and deformation data particularly engaging for new users. Popular data and data processing include GPS time series with data mining techniques to find anomalies in time and space, experimental forecasting methods based on catalogue seismicity, faulted deformation models (both half-space and finite element), and model-based inversion of sensor data. The fault models include the CGS and UCERF 2.0 faults of California and are easily augmented with self-consistent fault models from other regions. The QuakeTables deformation data include the comprehensive set of UAVSAR interferograms as well as a growing collection of satellite InSAR data.. Fault interaction simulations are also being incorporated in the web environment based on Virtual California. A sample usage scenario is presented which follows an investigation of UAVSAR data from viewing as an overlay in Google Maps, to selection of an area of interest via a polygon tool, to fast extraction of the relevant correlation and phase information from large data files, to a model inversion of fault slip followed by calculation and display of a synthetic model interferogram.

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

NASA Astrophysics Data System (ADS)

Nelson, J.; Swain, N. R.

2015-12-01

The interactive nature of web applications or "web apps" makes it an excellent medium for conveying complex scientific concepts to lay audiences and creating decision support tools that harness cutting edge modeling techniques. However, the technical expertise required to develop web apps represents a barrier for would-be developers. This barrier can be characterized by the following hurdles that developers must overcome: (1) identify, select, and install software that meet the spatial and computational capabilities commonly required for water resources modeling; (2) orchestrate the use of multiple free and open source (FOSS) projects and navigate their differing application programming interfaces; (3) learn the multi-language programming skills required for modern web development; and (4) develop a web-secure and fully featured web portal to host the app. Tethys Platform has been developed to lower the technical barrier and minimize the initial development investment that prohibits many scientists and engineers from making use of the web app medium. It includes (1) a suite of FOSS that address the unique data and computational needs common to water resources web app development, (2) a Python software development kit that streamlines development, and (3) a customizable web portal that is used to deploy the completed web apps. Tethys synthesizes several software projects including PostGIS, 52°North WPS, GeoServer, Google Maps™, OpenLayers, and Highcharts. It has been used to develop a broad array of web apps for water resources modeling and decision support for several projects including CI-WATER, HydroShare, and the National Flood Interoperability Experiment. The presentation will include live demos of some of the apps that have been developed using Tethys to demonstrate its capabilities.

Tapir: A web interface for transit/eclipse observability

NASA Astrophysics Data System (ADS)

Jensen, Eric

2013-06-01

Tapir is a set of tools, written in Perl, that provides a web interface for showing the observability of periodic astronomical events, such as exoplanet transits or eclipsing binaries. The package provides tools for creating finding charts for each target and airmass plots for each event. The code can access target lists that are stored on-line in a Google spreadsheet or in a local text file.

A Cross-Cultural Comparison of Kuwaiti and British Citizens' Views of E-Government Interface Quality

ERIC Educational Resources Information Center

Aladwani, Adel M.

2013-01-01

It is difficult to conceive how Web users from different cultures can be encouraged to reap the benefits of an e-government initiative when its portal is suffering from culture-indifferent interface quality. Thus far, the e-government literature not only has paid scanty attention to web evaluation issues but also has been slow to embarking on…

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

PubMed

Jeliazkova, Nina; Jeliazkov, Vedrin

2011-05-16

The AMBIT web services package is one of the several existing independent implementations of the OpenTox Application Programming Interface and is built according to the principles of the Representational State Transfer (REST) architecture. The Open Source Predictive Toxicology Framework, developed by the partners in the EC FP7 OpenTox project, aims at providing a unified access to toxicity data and predictive models, as well as validation procedures. This is achieved by i) an information model, based on a common OWL-DL ontology ii) links to related ontologies; iii) data and algorithms, available through a standardized REST web services interface, where every compound, data set or predictive method has a unique web address, used to retrieve its Resource Description Framework (RDF) representation, or initiate the associated calculations.The AMBIT web services package has been developed as an extension of AMBIT modules, adding the ability to create (Quantitative) Structure-Activity Relationship (QSAR) models and providing an OpenTox API compliant interface. The representation of data and processing resources in W3C Resource Description Framework facilitates integrating the resources as Linked Data. By uploading datasets with chemical structures and arbitrary set of properties, they become automatically available online in several formats. The services provide unified interfaces to several descriptor calculation, machine learning and similarity searching algorithms, as well as to applicability domain and toxicity prediction models. All Toxtree modules for predicting the toxicological hazard of chemical compounds are also integrated within this package. The complexity and diversity of the processing is reduced to the simple paradigm "read data from a web address, perform processing, write to a web address". The online service allows to easily run predictions, without installing any software, as well to share online datasets and models. The downloadable web application allows researchers to setup an arbitrary number of service instances for specific purposes and at suitable locations. These services could be used as a distributed framework for processing of resource-intensive tasks and data sharing or in a fully independent way, according to the specific needs. The advantage of exposing the functionality via the OpenTox API is seamless interoperability, not only within a single web application, but also in a network of distributed services. Last, but not least, the services provide a basis for building web mashups, end user applications with friendly GUIs, as well as embedding the functionalities in existing workflow systems.

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

PubMed Central

2011-01-01

The AMBIT web services package is one of the several existing independent implementations of the OpenTox Application Programming Interface and is built according to the principles of the Representational State Transfer (REST) architecture. The Open Source Predictive Toxicology Framework, developed by the partners in the EC FP7 OpenTox project, aims at providing a unified access to toxicity data and predictive models, as well as validation procedures. This is achieved by i) an information model, based on a common OWL-DL ontology ii) links to related ontologies; iii) data and algorithms, available through a standardized REST web services interface, where every compound, data set or predictive method has a unique web address, used to retrieve its Resource Description Framework (RDF) representation, or initiate the associated calculations. The AMBIT web services package has been developed as an extension of AMBIT modules, adding the ability to create (Quantitative) Structure-Activity Relationship (QSAR) models and providing an OpenTox API compliant interface. The representation of data and processing resources in W3C Resource Description Framework facilitates integrating the resources as Linked Data. By uploading datasets with chemical structures and arbitrary set of properties, they become automatically available online in several formats. The services provide unified interfaces to several descriptor calculation, machine learning and similarity searching algorithms, as well as to applicability domain and toxicity prediction models. All Toxtree modules for predicting the toxicological hazard of chemical compounds are also integrated within this package. The complexity and diversity of the processing is reduced to the simple paradigm "read data from a web address, perform processing, write to a web address". The online service allows to easily run predictions, without installing any software, as well to share online datasets and models. The downloadable web application allows researchers to setup an arbitrary number of service instances for specific purposes and at suitable locations. These services could be used as a distributed framework for processing of resource-intensive tasks and data sharing or in a fully independent way, according to the specific needs. The advantage of exposing the functionality via the OpenTox API is seamless interoperability, not only within a single web application, but also in a network of distributed services. Last, but not least, the services provide a basis for building web mashups, end user applications with friendly GUIs, as well as embedding the functionalities in existing workflow systems. PMID:21575202

Web GIS in practice III: creating a simple interactive map of England's Strategic Health Authorities using Google Maps API, Google Earth KML, and MSN Virtual Earth Map Control

PubMed Central

Boulos, Maged N Kamel

2005-01-01

This eye-opener article aims at introducing the health GIS community to the emerging online consumer geoinformatics services from Google and Microsoft (MSN), and their potential utility in creating custom online interactive health maps. Using the programmable interfaces provided by Google and MSN, we created three interactive demonstrator maps of England's Strategic Health Authorities. These can be browsed online at – Google Maps API (Application Programming Interface) version, – Google Earth KML (Keyhole Markup Language) version, and – MSN Virtual Earth Map Control version. Google and MSN's worldwide distribution of "free" geospatial tools, imagery, and maps is to be commended as a significant step towards the ultimate "wikification" of maps and GIS. A discussion is provided of these emerging online mapping trends, their expected future implications and development directions, and associated individual privacy, national security and copyrights issues. Although ESRI have announced their planned response to Google (and MSN), it remains to be seen how their envisaged plans will materialize and compare to the offerings from Google and MSN, and also how Google and MSN mapping tools will further evolve in the near future. PMID:16176577

Accessing Solar Irradiance Data Products From the LASP Interactive Solar IRradiance Datacenter (LISIRD)

NASA Astrophysics Data System (ADS)

Ware Dewolfe, A.; Wilson, A.; Lindholm, D. M.; Pankratz, C. K.; Snow, M.; Woods, T. N.

2009-12-01

The Laboratory for Atmospheric and Space Physics (LASP) is enhancing the LASP Interactive Solar IRradiance Datacenter (LISIRD) to provide access to a comprehensive set of solar spectral irradiance measurements. LISIRD has recently been updated to serve many new datasets and models, including sunspot index, photometric sunspot index, Lyman-alpha, and magnesium-II core-to-wing ratio. A new user interface emphasizes web-based interactive visualizations, allowing users to explore and compare this data before downloading it for analysis. The data provided covers a wavelength range from soft X-ray (XUV) at 0.1 nm up to the near infrared (NIR) at 2400 nm, as well as wavelength-independent Total Solar Irradiance (TSI). Combined data from the SORCE, TIMED-SEE, UARS-SOLSTICE, and SME instruments provide almost continuous coverage from 1981 to the present, while Hydrogen Lyman-alpha (121.6 nm) measurements / models date from 1947 to the present. This poster provides an overview of the LISIRD system, summarizes the data sets currently available, describes future plans and capabilities, and provides details on how to access solar irradiance data through LISIRD interfaces at http://lasp.colorado.edu/lisird/.

Solar Irradiance Data Products at the LASP Interactive Solar IRradiance Datacenter (LISIRD)

NASA Astrophysics Data System (ADS)

Ware Dewolfe, A.; Wilson, A.; Lindholm, D. M.; Pankratz, C. K.; Snow, M. A.; Woods, T. N.

2010-12-01

The Laboratory for Atmospheric and Space Physics (LASP) has developed the LASP Interactive Solar IRradiance Datacenter (LISIRD) to provide access to a comprehensive set of solar irradiance measurements. LISIRD has recently been updated to serve many new datasets and models, including data from SORCE, UARS-SOLSTICE, SME, and TIMED-SEE, and model data from the Flare Irradiance Spectral Model (FISM). The user interface emphasizes web-based interactive visualizations, allowing users to explore and compare this data before downloading it for analysis. The data provided covers a wavelength range from soft X-ray (XUV) at 0.1 nm up to the near infrared (NIR) at 2400 nm, as well as wavelength-independent Total Solar Irradiance (TSI). Combined data from the SORCE, TIMED-SEE, UARS-SOLSTICE, and SME instruments provide continuous coverage from 1981 to the present, while Lyman-alpha measurements, FISM daily data, and TSI models date from the 1940s to the present. LISIRD will also host Glory TSI data as part of the SORCE data system. This poster provides an overview of the LISIRD system, summarizes the data sets currently available, describes future plans and capabilities, and provides details on how to access solar irradiance data through LISIRD’s interfaces.

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

PubMed Central

2013-01-01

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

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

PubMed

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

2013-10-07

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

Checking an integrated model of web accessibility and usability evaluation for disabled people.

PubMed

Federici, Stefano; Micangeli, Andrea; Ruspantini, Irene; Borgianni, Stefano; Corradi, Fabrizio; Pasqualotto, Emanuele; Olivetti Belardinelli, Marta

2005-07-08

A combined objective-oriented and subjective-oriented method for evaluating accessibility and usability of web pages for students with disability was tested. The objective-oriented approach is devoted to verifying the conformity of interfaces to standard rules stated by national and international organizations responsible for web technology standardization, such as W3C. Conversely, the subjective-oriented approach allows assessing how the final users interact with the artificial system, accessing levels of user satisfaction based on personal factors and environmental barriers. Five kinds of measurements were applied as objective-oriented and subjective-oriented tests. Objective-oriented evaluations were performed on the Help Desk web page for students with disability, included in the website of a large Italian state university. Subjective-oriented tests were administered to 19 students labeled as disabled on the basis of their own declaration at the University enrolment: 13 students were tested by means of the SUMI test and six students by means of the 'Cooperative evaluation'. Objective-oriented and subjective-oriented methods highlighted different and sometimes conflicting results. Both methods have pointed out much more consistency regarding levels of accessibility than of usability. Since usability is largely affected by individual differences in user's own (dis)abilities, subjective-oriented measures underscored the fact that blind students encountered much more web surfing difficulties.

3DNOW: Image-Based 3d Reconstruction and Modeling via Web

NASA Astrophysics Data System (ADS)

Tefera, Y.; Poiesi, F.; Morabito, D.; Remondino, F.; Nocerino, E.; Chippendale, P.

2018-05-01

This paper presents a web-based 3D imaging pipeline, namely 3Dnow, that can be used by anyone without the need of installing additional software other than a browser. By uploading a set of images through the web interface, 3Dnow can generate sparse and dense point clouds as well as mesh models. 3D reconstructed models can be downloaded with standard formats or previewed directly on the web browser through an embedded visualisation interface. In addition to reconstructing objects, 3Dnow offers the possibility to evaluate and georeference point clouds. Reconstruction statistics, such as minimum, maximum and average intersection angles, point redundancy and density can also be accessed. The paper describes all features available in the web service and provides an analysis of the computational performance using servers with different GPU configurations.

A Web Based Collaborative Design Environment for Spacecraft

NASA Technical Reports Server (NTRS)

Dunphy, Julia

1998-01-01

In this era of shrinking federal budgets in the USA we need to dramatically improve our efficiency in the spacecraft engineering design process. We have come up with a method which captures much of the experts' expertise in a dataflow design graph: Seamlessly connectable set of local and remote design tools; Seamlessly connectable web based design tools; and Web browser interface to the developing spacecraft design. We have recently completed our first web browser interface and demonstrated its utility in the design of an aeroshell using design tools located at web sites at three NASA facilities. Multiple design engineers and managers are now able to interrogate the design engine simultaneously and find out what the design looks like at any point in the design cycle, what its parameters are, and how it reacts to adverse space environments.

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.