Natural Language Processing in aid of FlyBase curators

PubMed Central

Karamanis, Nikiforos; Seal, Ruth; Lewin, Ian; McQuilton, Peter; Vlachos, Andreas; Gasperin, Caroline; Drysdale, Rachel; Briscoe, Ted

2008-01-01

Background Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this technology can facilitate tasks such as database curation remains unclear. Results PaperBrowser is the first NLP-powered interface that was developed under a user-centered approach to improve the way in which FlyBase curators navigate an article. In this paper, we first discuss how observing curators at work informed the design and evaluation of PaperBrowser. Then, we present how we appraise PaperBrowser's navigational functionalities in a user-based study using a text highlighting task and evaluation criteria of Human-Computer Interaction. Our results show that PaperBrowser reduces the amount of interactions between two highlighting events and therefore improves navigational efficiency by about 58% compared to the navigational mechanism that was previously available to the curators. Moreover, PaperBrowser is shown to provide curators with enhanced navigational utility by over 74% irrespective of the different ways in which they highlight text in the article. Conclusion We show that state-of-the-art performance in certain NLP tasks such as Named Entity Recognition and Anaphora Resolution can be combined with the navigational functionalities of PaperBrowser to support curation quite successfully. PMID:18410678

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.

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.

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").

An interactive HTML ocean nowcast GUI based on Perl and JavaScript

NASA Astrophysics Data System (ADS)

Sakalaukus, Peter J.; Fox, Daniel N.; Louise Perkins, A.; Smedstad, Lucy F.

1999-02-01

We describe the use of Hyper Text Markup Language (HTML), JavaScript code, and Perl I/O to create and validate forms in an Internet-based graphical user interface (GUI) for the Naval Research Laboratory (NRL) Ocean models and Assimilation Demonstration System (NOMADS). The resulting nowcast system can be operated from any compatible browser across the Internet, for although the GUI was prepared in a Netscape browser, it used no Netscape extensions. Code available at: http://www.iamg.org/CGEditor/index.htm

Electricity Data Browser

EIA Publications

The Electricity Data Browser shows generation, consumption, fossil fuel receipts, stockpiles, retail sales, and electricity prices. The data appear on an interactive web page and are updated each month. The Electricity Data Browser includes all the datasets collected and published in EIA's Electric Power Monthly and allows users to perform dynamic charting of data sets as well as map the data by state. The data browser includes a series of reports that appear in the Electric Power Monthly and allows readers to drill down to plant level statistics, where available. All images and datasets are available for download. Users can also link to the data series in EIA's Application Programming Interface (API). An API makes our data machine-readable and more accessible to users.

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.

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.

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

NASA Astrophysics Data System (ADS)

Nagino, Norikatsu; Yamada, Seiji

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

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

PubMed

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

2014-01-01

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

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.

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

Web Program for Development of GUIs for Cluster Computers

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

An Online Virtual Laboratory of Electricity

ERIC Educational Resources Information Center

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

2008-01-01

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

CliniSpace: a multiperson 3D online immersive training environment accessible through a browser.

PubMed

Dev, Parvati; Heinrichs, W LeRoy; Youngblood, Patricia

2011-01-01

Immersive online medical environments, with dynamic virtual patients, have been shown to be effective for scenario-based learning (1). However, ease of use and ease of access have been barriers to their use. We used feedback from prior evaluation of these projects to design and develop CliniSpace. To improve usability, we retained the richness of prior virtual environments but modified the user interface. To improve access, we used a Software-as-a-Service (SaaS) approach to present a richly immersive 3D environment within a web browser.

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.

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.

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.

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.

An electronic laboratory notebook based on HTML forms

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

Marstaller, J.E.; Zorn, M.D.

The electronic notebook records information that has traditionally been kept in handwritten laboratory notebooks. It keeps detailed information about the progress of the research , such as the optimization of primers, the screening of the primers and, finally, the mapping of the probes. The notebook provides two areas of services: Data entry, and reviewing of data in all stages. The World wide Web browsers, with HTML based forms provide a fast and easy mechanism to create forms-based user interfaces. The computer scientist can sit down with the biologist and rapidly make changes in response to the user`s comments. Furthermore themore » HTML forms work equally well on a number of different hardware platforms; thus the biologists may continue using their Macintosh computers and find a familiar interface if they have to work on a Unix workstation. The web browser can be run from any machine connected to the Internet: thus the users are free to enter or view information even away from their labs at home or while on travel. Access can be restricted by password and other means to secure the confidentiality of the data. A bonus that is hard to implement otherwise is the facile connection to outside resources. Linking local information to data in public databases is only a hypertext link away with little or no additional programming efforts.« less

Adaptive interface for personalizing information seeking.

PubMed

Narayanan, S; Koppaka, Lavanya; Edala, Narasimha; Loritz, Don; Daley, Raymond

2004-12-01

An adaptive interface autonomously adjusts its display and available actions to current goals and abilities of the user by assessing user status, system task, and the context. Knowledge content adaptability is needed for knowledge acquisition and refinement tasks. In the case of knowledge content adaptability, the requirements of interface design focus on the elicitation of information from the user and the refinement of information based on patterns of interaction. In such cases, the emphasis on adaptability is on facilitating information search and knowledge discovery. In this article, we present research on adaptive interfaces that facilitates personalized information seeking from a large data warehouse. The resulting proof-of-concept system, called source recommendation system (SRS), assists users in locating and navigating data sources in the repository. Based on the initial user query and an analysis of the content of the search results, the SRS system generates a profile of the user tailored to the individual's context during information seeking. The user profiles are refined successively and are used in progressively guiding the user to the appropriate set of sources within the knowledge base. The SRS system is implemented as an Internet browser plug-in to provide a seamless and unobtrusive, personalized experience to the users during the information search process. The rationale behind our approach, system design, empirical evaluation, and implications for research on adaptive interfaces are described in this paper.

A multimedia Anatomy Browser incorporating a knowledge base and 3D images.

PubMed Central

Eno, K.; Sundsten, J. W.; Brinkley, J. F.

1991-01-01

We describe a multimedia program for teaching anatomy. The program, called the Anatomy Browser, displays cross-sectional and topographical images, with outlines around structures and regions of interest. The user may point to these structures and retrieve text descriptions, view symbolic relationships between structures, or view spatial relationships by accessing 3-D graphics animations from videodiscs produced specifically for this program. The software also helps students exercise what they have learned by asking them to identify structures by name and location. The program is implemented in a client-server architecture, with the user interface residing on a Macintosh, while images, data, and a growing symbolic knowledge base of anatomy are stored on a fileserver. This architecture allows us to develop practical tutorial modules that are in current use, while at the same time developing the knowledge base that will lead to more intelligent tutorial systems. PMID:1807699

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

PubMed Central

2015-01-01

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

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

PubMed

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

2014-09-22

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

A component-based, distributed object services architecture for a clinical workstation.

PubMed

Chueh, H C; Raila, W F; Pappas, J J; Ford, M; Zatsman, P; Tu, J; Barnett, G O

1996-01-01

Attention to an architectural framework in the development of clinical applications can promote reusability of both legacy systems as well as newly designed software. We describe one approach to an architecture for a clinical workstation application which is based on a critical middle tier of distributed object-oriented services. This tier of network-based services provides flexibility in the creation of both the user interface and the database tiers. We developed a clinical workstation for ambulatory care using this architecture, defining a number of core services including those for vocabulary, patient index, documents, charting, security, and encounter management. These services can be implemented through proprietary or more standard distributed object interfaces such as CORBA and OLE. Services are accessed over the network by a collection of user interface components which can be mixed and matched to form a variety of interface styles. These services have also been reused with several applications based on World Wide Web browser interfaces.

A component-based, distributed object services architecture for a clinical workstation.

PubMed Central

Chueh, H. C.; Raila, W. F.; Pappas, J. J.; Ford, M.; Zatsman, P.; Tu, J.; Barnett, G. O.

1996-01-01

Attention to an architectural framework in the development of clinical applications can promote reusability of both legacy systems as well as newly designed software. We describe one approach to an architecture for a clinical workstation application which is based on a critical middle tier of distributed object-oriented services. This tier of network-based services provides flexibility in the creation of both the user interface and the database tiers. We developed a clinical workstation for ambulatory care using this architecture, defining a number of core services including those for vocabulary, patient index, documents, charting, security, and encounter management. These services can be implemented through proprietary or more standard distributed object interfaces such as CORBA and OLE. Services are accessed over the network by a collection of user interface components which can be mixed and matched to form a variety of interface styles. These services have also been reused with several applications based on World Wide Web browser interfaces. PMID:8947744

Web 2.0 and You

ERIC Educational Resources Information Center

Baumbach, Donna J.

2009-01-01

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

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

JAX Colony Management System (JCMS): an extensible colony and phenotype data management system.

PubMed

Donnelly, Chuck J; McFarland, Mike; Ames, Abigail; Sundberg, Beth; Springer, Dave; Blauth, Peter; Bult, Carol J

2010-04-01

The Jackson Laboratory Colony Management System (JCMS) is a software application for managing data and information related to research mouse colonies, associated biospecimens, and experimental protocols. JCMS runs directly on computers that run one of the PC Windows operating systems, but can be accessed via web browser interfaces from any computer running a Windows, Macintosh, or Linux operating system. JCMS can be configured for a single user or multiple users in small- to medium-size work groups. The target audience for JCMS includes laboratory technicians, animal colony managers, and principal investigators. The application provides operational support for colony management and experimental workflows, sample and data tracking through transaction-based data entry forms, and date-driven work reports. Flexible query forms allow researchers to retrieve database records based on user-defined criteria. Recent advances in handheld computers with integrated barcode readers, middleware technologies, web browsers, and wireless networks add to the utility of JCMS by allowing real-time access to the database from any networked computer.

The SHIP: A SIP to HTTP Interaction Protocol

NASA Astrophysics Data System (ADS)

Zeiß, Joachim; Gabner, Rene; Bessler, Sandford; Happenhofer, Marco

IMS is capable of providing a wide range of services. As a result, terminal software becomes more and more complex to deliver network intelligence to user applications. Currently mobile terminal software needs to be permanently updated so that the latest network services and functionality can be delivered to the user. In the Internet, browser based user interfaces assure that an interface is made available to the user which offers the latest services in the net immediately. Our approach combines the benefits of the Session Initiation Protocol (SIP) and those of the HTTP protocol to bring the same type of user interfacing to IMS. SIP (IMS) realizes authentication, session management, charging and Quality of Service (QoS), HTTP provides access to Internet services and allows the user interface of an application to run on a mobile terminal while processing and orchestration is done on the server. A SHIP enabled IMS client only needs to handle data transport and session management via SIP, HTTP and RTP and render streaming media, HTML and Javascript. SHIP allows new kinds of applications, which combine audio, video and data within a single multimedia session.

NASA Interactive Forms Type Interface - NIFTI

NASA Technical Reports Server (NTRS)

Jain, Bobby; Morris, Bill

2005-01-01

A flexible database query, update, modify, and delete tool was developed that provides an easy interface to Oracle forms. This tool - the NASA interactive forms type interface, or NIFTI - features on-the- fly forms creation, forms sharing among users, the capability to query the database from user-entered criteria on forms, traversal of query results, an ability to generate tab-delimited reports, viewing and downloading of reports to the user s workstation, and a hypertext-based help system. NIFTI is a very powerful ad hoc query tool that was developed using C++, X-Windows by a Motif application framework. A unique tool, NIFTI s capabilities appear in no other known commercial-off-the- shelf (COTS) tool, because NIFTI, which can be launched from the user s desktop, is a simple yet very powerful tool with a highly intuitive, easy-to-use graphical user interface (GUI) that will expedite the creation of database query/update forms. NIFTI, therefore, can be used in NASA s International Space Station (ISS) as well as within government and industry - indeed by all users of the widely disseminated Oracle base. And it will provide significant cost savings in the areas of user training and scalability while advancing the art over current COTS browsers. No COTS browser performs all the functions NIFTI does, and NIFTI is easier to use. NIFTI s cost savings are very significant considering the very large database with which it is used and the large user community with varying data requirements it will support. Its ease of use means that personnel unfamiliar with databases (e.g., managers, supervisors, clerks, and others) can develop their own personal reports. For NASA, a tool such as NIFTI was needed to query, update, modify, and make deletions within the ISS vehicle master database (VMDB), a repository of engineering data that includes an indentured parts list and associated resource data (power, thermal, volume, weight, and the like). Since the VMDB is used both as a collection point for data and as a common repository for engineering, integration, and operations teams, a tool such as NIFTI had to be designed that could expedite the creation of database query/update forms which could then be shared among users.

Web-based DAQ systems: connecting the user and electronics front-ends

NASA Astrophysics Data System (ADS)

Lenzi, Thomas

2016-12-01

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

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.

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.

THttpServer class in ROOT

NASA Astrophysics Data System (ADS)

Adamczewski-Musch, Joern; Linev, Sergey

2015-12-01

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

Concept Mapping as a Support for Mars Landing-Site Selection

NASA Technical Reports Server (NTRS)

Cabrol, Nathalie A.; Briggs, Geoffrey A.

1999-01-01

The NASA Ames' Center for Mars Exploration (CMEX) serves to coordinate Mars programmatic research at ARC in the sciences, in information technology and in aero-assist and other technologies. Most recently, CMEX has been working with the Institute for Human and Machine Cognition at the University of West Florida to develop a new kind of web browser based on the application of concept maps. These Cmaps, which are demonstrably effective in science teaching, can be used to provide a new kind of information navigation tool that can make web or CD based information more meaningful and more easily navigable. CMEX expects that its 1999 CD-ROM will have this new user interface. CMEX is also engaged with the Mars Surveyor Project Office at JPL in developing an Internet-based source of materials to support the process of selecting landing sites for the next series of Mars landers. This activity -- identifying the most promising sites from which to return samples relevant to the search for evidence of life -- is one that is expected to engage the general public as well as the science community. To make the landing site data easily accessible and meaningful to the public, CMEX is planning to use the IHMC Cmap browser as its user interface.

ABrowse--a customizable next-generation genome browser framework.

PubMed

Kong, Lei; Wang, Jun; Zhao, Shuqi; Gu, Xiaocheng; Luo, Jingchu; Gao, Ge

2012-01-05

With the rapid growth of genome sequencing projects, genome browser is becoming indispensable, not only as a visualization system but also as an interactive platform to support open data access and collaborative work. Thus a customizable genome browser framework with rich functions and flexible configuration is needed to facilitate various genome research projects. Based on next-generation web technologies, we have developed a general-purpose genome browser framework ABrowse which provides interactive browsing experience, open data access and collaborative work support. By supporting Google-map-like smooth navigation, ABrowse offers end users highly interactive browsing experience. To facilitate further data analysis, multiple data access approaches are supported for external platforms to retrieve data from ABrowse. To promote collaborative work, an online user-space is provided for end users to create, store and share comments, annotations and landmarks. For data providers, ABrowse is highly customizable and configurable. The framework provides a set of utilities to import annotation data conveniently. To build ABrowse on existing annotation databases, data providers could specify SQL statements according to database schema. And customized pages for detailed information display of annotation entries could be easily plugged in. For developers, new drawing strategies could be integrated into ABrowse for new types of annotation data. In addition, standard web service is provided for data retrieval remotely, providing underlying machine-oriented programming interface for open data access. ABrowse framework is valuable for end users, data providers and developers by providing rich user functions and flexible customization approaches. The source code is published under GNU Lesser General Public License v3.0 and is accessible at http://www.abrowse.org/. To demonstrate all the features of ABrowse, a live demo for Arabidopsis thaliana genome has been built at http://arabidopsis.cbi.edu.cn/.

Lotus Base: An integrated information portal for the model legume Lotus japonicus

PubMed Central

Mun, Terry; Bachmann, Asger; Gupta, Vikas; Stougaard, Jens; Andersen, Stig U.

2016-01-01

Lotus japonicus is a well-characterized model legume widely used in the study of plant-microbe interactions. However, datasets from various Lotus studies are poorly integrated and lack interoperability. We recognize the need for a comprehensive repository that allows comprehensive and dynamic exploration of Lotus genomic and transcriptomic data. Equally important are user-friendly in-browser tools designed for data visualization and interpretation. Here, we present Lotus Base, which opens to the research community a large, established LORE1 insertion mutant population containing an excess of 120,000 lines, and serves the end-user tightly integrated data from Lotus, such as the reference genome, annotated proteins, and expression profiling data. We report the integration of expression data from the L. japonicus gene expression atlas project, and the development of tools to cluster and export such data, allowing users to construct, visualize, and annotate co-expression gene networks. Lotus Base takes advantage of modern advances in browser technology to deliver powerful data interpretation for biologists. Its modular construction and publicly available application programming interface enable developers to tap into the wealth of integrated Lotus data. Lotus Base is freely accessible at: https://lotus.au.dk. PMID:28008948

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.

Making the PACS workstation a browser of image processing software: a feasibility study using inter-process communication techniques.

PubMed

Wang, Chunliang; Ritter, Felix; Smedby, Orjan

2010-07-01

To enhance the functional expandability of a picture archiving and communication systems (PACS) workstation and to facilitate the integration of third-part image-processing modules, we propose a browser-server style method. In the proposed solution, the PACS workstation shows the front-end user interface defined in an XML file while the image processing software is running in the background as a server. Inter-process communication (IPC) techniques allow an efficient exchange of image data, parameters, and user input between the PACS workstation and stand-alone image-processing software. Using a predefined communication protocol, the PACS workstation developer or image processing software developer does not need detailed information about the other system, but will still be able to achieve seamless integration between the two systems and the IPC procedure is totally transparent to the final user. A browser-server style solution was built between OsiriX (PACS workstation software) and MeVisLab (Image-Processing Software). Ten example image-processing modules were easily added to OsiriX by converting existing MeVisLab image processing networks. Image data transfer using shared memory added <10ms of processing time while the other IPC methods cost 1-5 s in our experiments. The browser-server style communication based on IPC techniques is an appealing method that allows PACS workstation developers and image processing software developers to cooperate while focusing on different interests.

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.

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.

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…

Design and implementation of a P300-based brain-computer interface for controlling an internet browser.

PubMed

Mugler, Emily M; Ruf, Carolin A; Halder, Sebastian; Bensch, Michael; Kubler, Andrea

2010-12-01

An electroencephalographic (EEG) brain-computer interface (BCI) internet browser was designed and evaluated with 10 healthy volunteers and three individuals with advanced amyotrophic lateral sclerosis (ALS), all of whom were given tasks to execute on the internet using the browser. Participants with ALS achieved an average accuracy of 73% and a subsequent information transfer rate (ITR) of 8.6 bits/min and healthy participants with no prior BCI experience over 90% accuracy and an ITR of 14.4 bits/min. We define additional criteria for unrestricted internet access for evaluation of the presented and future internet browsers, and we provide a review of the existing browsers in the literature. The P300-based browser provides unrestricted access and enables free web surfing for individuals with paralysis.

Health Terrain: Visualizing Large Scale Health Data

DTIC Science & Technology

2015-12-01

Text mining ; Data mining . 16. SECURITY  CLASSIFICATION  OF: 17... text   mining  algorithms  to  construct  a  concept  space.  A   browser-­‐based  user  interface  is  developed  to...Public  health  data,  Notifiable  condition  detector,   Text   mining ,  Data   mining   4 of 29 Disease Patient Location Term

SnopViz, an interactive snow profile visualization tool

NASA Astrophysics Data System (ADS)

Fierz, Charles; Egger, Thomas; gerber, Matthias; Bavay, Mathias; Techel, Frank

2016-04-01

SnopViz is a visualization tool for both simulation outputs of the snow-cover model SNOWPACK and observed snow profiles. It has been designed to fulfil the needs of operational services (Swiss Avalanche Warning Service, Avalanche Canada) as well as offer the flexibility required to satisfy the specific needs of researchers. This JavaScript application runs on any modern browser and does not require an active Internet connection. The open source code is available for download from models.slf.ch where examples can also be run. Both the SnopViz library and the SnopViz User Interface will become a full replacement of the current research visualization tool SN_GUI for SNOWPACK. The SnopViz library is a stand-alone application that parses the provided input files, for example, a single snow profile (CAAML file format) or multiple snow profiles as output by SNOWPACK (PRO file format). A plugin architecture allows for handling JSON objects (JavaScript Object Notation) as well and plugins for other file formats may be added easily. The outputs are provided either as vector graphics (SVG) or JSON objects. The SnopViz User Interface (UI) is a browser based stand-alone interface. It runs in every modern browser, including IE, and allows user interaction with the graphs. SVG, the XML based standard for vector graphics, was chosen because of its easy interaction with JS and a good software support (Adobe Illustrator, Inkscape) to manipulate graphs outside SnopViz for publication purposes. SnopViz provides new visualization for SNOWPACK timeline output as well as time series input and output. The actual output format for SNOWPACK timelines was retained while time series are read from SMET files, a file format used in conjunction with the open source data handling code MeteoIO. Finally, SnopViz is able to render single snow profiles, either observed or modelled, that are provided as CAAML-file. This file format (caaml.org/Schemas/V5.0/Profiles/SnowProfileIACS) is an international standard to exchange snow profile data. It is supported by the International Association of Cryospheric Sciences (IACS) and was developed in collaboration with practitioners (Avalanche Canada).

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.

Browsing schematics: Query-filtered graphs with context nodes

NASA Technical Reports Server (NTRS)

Ciccarelli, Eugene C.; Nardi, Bonnie A.

1988-01-01

The early results of a research project to create tools for building interfaces to intelligent systems on the NASA Space Station are reported. One such tool is the Schematic Browser which helps users engaged in engineering problem solving find and select schematics from among a large set. Users query for schematics with certain components, and the Schematic Browser presents a graph whose nodes represent the schematics with those components. The query greatly reduces the number of choices presented to the user, filtering the graph to a manageable size. Users can reformulate and refine the query serially until they locate the schematics of interest. To help users maintain orientation as they navigate a large body of data, the graph also includes nodes that are not matches but provide global and local context for the matching nodes. Context nodes include landmarks, ancestors, siblings, children and previous matches.

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

PubMed

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

2013-12-15

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

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

PubMed Central

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

2018-01-01

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

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.

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

NASA Astrophysics Data System (ADS)

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

2016-03-01

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

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

PubMed

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

2012-09-15

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

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

Real-time shipboard displays for science operation and planning on CGC Healy

NASA Astrophysics Data System (ADS)

Roberts, S.; Chayes, D.; Arko, R.

2007-12-01

To facilitate effective science planning and decision making, we have developed a real-time geospatial browser and other displays widely used by many if not all members of USCGC Healy's science cruises and some officers and crew since 2004. In order to enable a 'zero-configuration' experience to the end user with nearly any modern browser, on any platform, anywhere on the ship with wired (or wireless) network access, we chose a Web-based/server-centric approach that provides a very low barrier to access in an environment where we have many participants constantly coming and going, often with their own computers. The principle interface for planning and operational decision making is a georeferenced, Web-based user interface built on the MapServer Web GIS platform developed at the University of Minnesota (http://mapserver.gis.umn.edu/), using the PostGIS spatial database extensions (http://postgis.refractions.net/) to enable live database connectivity. Data available include current ship position and orientation, historical ship tracks and data, seafloor bathymetry, station locations, RADARSAT, and subbottom profiles among others. In addition to the user interfaces that are part of individual instrumentation (such as the sonars and navigation systems), custom interfaces have been developed to centralize data with high update rates such as sea surface temperature, vessel attitude, position, etc. Underlying data acquisition and storage is provided by the Lamont Data System (LDS) and the NOAA SCS system. All data are stored on RAIDed disk systems and shared across a switched network with a gigabit fiber backbone. The real-time displays access data in a number of ways including real-time UDP datagrams from LDS, accessing files on disk, and querying a PostgreSQL relational backend. This work is supported by grants from the U.S. National Science Foundation, Office of Polar Programs, Arctic Science section.

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

PubMed

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

2018-01-01

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

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

PubMed

Bergsneider, C; Piraino, D; Fuerst, M

2001-06-01

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

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

USGS Publications Warehouse

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

2009-01-01

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

XML-Based Visual Specification of Multidisciplinary Applications

NASA Technical Reports Server (NTRS)

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

2001-01-01

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

Secure Display of Space-Exploration Images

NASA Technical Reports Server (NTRS)

Cheng, Cecilia; Thornhill, Gillian; McAuley, Michael

2006-01-01

Java EDR Display Interface (JEDI) is software for either local display or secure Internet distribution, to authorized clients, of image data acquired from cameras aboard spacecraft engaged in exploration of remote planets. ( EDR signifies experimental data record, which, in effect, signifies image data.) Processed at NASA s Multimission Image Processing Laboratory (MIPL), the data can be from either near-realtime processing streams or stored files. JEDI uses the Java Advanced Imaging application program interface, plus input/output packages that are parts of the Video Image Communication and Retrieval software of the MIPL, to display images. JEDI can be run as either a standalone application program or within a Web browser as a servlet with an applet front end. In either operating mode, JEDI communicates using the HTTP(s) protocol(s). In the Web-browser case, the user must provide a password to gain access. For each user and/or image data type, there is a configuration file, called a "personality file," containing parameters that control the layout of the displays and the information to be included in them. Once JEDI has accepted the user s password, it processes the requested EDR (provided that user is authorized to receive the specific EDR) to create a display according to the user s personality file.

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

PubMed

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

2012-10-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-11-01

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

A Brain-Computer Interface (BCI) system to use arbitrary Windows applications by directly controlling mouse and keyboard.

PubMed

Spuler, Martin

2015-08-01

A Brain-Computer Interface (BCI) allows to control a computer by brain activity only, without the need for muscle control. In this paper, we present an EEG-based BCI system based on code-modulated visual evoked potentials (c-VEPs) that enables the user to work with arbitrary Windows applications. Other BCI systems, like the P300 speller or BCI-based browsers, allow control of one dedicated application designed for use with a BCI. In contrast, the system presented in this paper does not consist of one dedicated application, but enables the user to control mouse cursor and keyboard input on the level of the operating system, thereby making it possible to use arbitrary applications. As the c-VEP BCI method was shown to enable very fast communication speeds (writing more than 20 error-free characters per minute), the presented system is the next step in replacing the traditional mouse and keyboard and enabling complete brain-based control of a computer.

Setting Up the JBrowse Genome Browser

PubMed Central

Skinner, Mitchell E; Holmes, Ian H

2010-01-01

JBrowse is a web-based tool for visualizing genomic data. Unlike most other web-based genome browsers, JBrowse exploits the capabilities of the user's web browser to make scrolling and zooming fast and smooth. It supports the browsers used by almost all internet users, and is relatively simple to install. JBrowse can utilize multiple types of data in a variety of common genomic data formats, including genomic feature data in bioperl databases, GFF files, and BED files, and quantitative data in wiggle files. This unit describes how to obtain the JBrowse software, set it up on a Linux or Mac OS X computer running as a web server and incorporate genome annotation data from multiple sources into JBrowse. After completing the protocols described in this unit, the reader will have a web site that other users can visit to browse the genomic data. PMID:21154710

a Kml-Based Approach for Distributed Collaborative Interpretation of Remote Sensing Images in the Geo-Browser

NASA Astrophysics Data System (ADS)

Huang, L.; Zhu, X.; Guo, W.; Xiang, L.; Chen, X.; Mei, Y.

2012-07-01

Existing implementations of collaborative image interpretation have many limitations for very large satellite imageries, such as inefficient browsing, slow transmission, etc. This article presents a KML-based approach to support distributed, real-time, synchronous collaborative interpretation for remote sensing images in the geo-browser. As an OGC standard, KML (Keyhole Markup Language) has the advantage of organizing various types of geospatial data (including image, annotation, geometry, etc.) in the geo-browser. Existing KML elements can be used to describe simple interpretation results indicated by vector symbols. To enlarge its application, this article expands KML elements to describe some complex image processing operations, including band combination, grey transformation, geometric correction, etc. Improved KML is employed to describe and share interpretation operations and results among interpreters. Further, this article develops some collaboration related services that are collaboration launch service, perceiving service and communication service. The launch service creates a collaborative interpretation task and provides a unified interface for all participants. The perceiving service supports interpreters to share collaboration awareness. Communication service provides interpreters with written words communication. Finally, the GeoGlobe geo-browser (an extensible and flexible geospatial platform developed in LIESMARS) is selected to perform experiments of collaborative image interpretation. The geo-browser, which manage and visualize massive geospatial information, can provide distributed users with quick browsing and transmission. Meanwhile in the geo-browser, GIS data (for example DEM, DTM, thematic map and etc.) can be integrated to assist in improving accuracy of interpretation. Results show that the proposed method is available to support distributed collaborative interpretation of remote sensing image

Using Mobile Devices to Display, Overlay, and Animate Geophysical Data and Imagery

NASA Astrophysics Data System (ADS)

Batzli, S.; Parker, D.

2011-12-01

A major challenge in mobile-device map application development is to offer rich content and features with simple and intuitive controls and fast performance. Our goal is to bring visualization, animation, and notifications of near real-time weather and earth observation information derived from satellite and sensor data to mobile devices. Our robust back-end processing infrastructure can deliver content in the form of images, shapes, standard descriptive formats (eg. KML, JSON) or raw data to a variety of desktop software, browsers, and mobile devices on demand. We have developed custom interfaces for low-bandwidth browsers (including mobile phones) and high-feature browsers (including smartphones), as well as native applications for Android and iOS devices. Mobile devices offer time- and location-awareness and persistent data connections, allowing us to tailor timely notifications and displays to the user's geographic and time context. This presentation includes a live demo of how our mobile apps deliver animation of standard and custom data products in an interactive map interface.

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.

Design and implementation of a cloud based lithography illumination pupil processing application

NASA Astrophysics Data System (ADS)

Zhang, Youbao; Ma, Xinghua; Zhu, Jing; Zhang, Fang; Huang, Huijie

2017-02-01

Pupil parameters are important parameters to evaluate the quality of lithography illumination system. In this paper, a cloud based full-featured pupil processing application is implemented. A web browser is used for the UI (User Interface), the websocket protocol and JSON format are used for the communication between the client and the server, and the computing part is implemented in the server side, where the application integrated a variety of high quality professional libraries, such as image processing libraries libvips and ImageMagic, automatic reporting system latex, etc., to support the program. The cloud based framework takes advantage of server's superior computing power and rich software collections, and the program could run anywhere there is a modern browser due to its web UI design. Compared to the traditional way of software operation model: purchased, licensed, shipped, downloaded, installed, maintained, and upgraded, the new cloud based approach, which is no installation, easy to use and maintenance, opens up a new way. Cloud based application probably is the future of the software development.

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

PubMed Central

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

2013-01-01

Motivation: Easily visualization of complex data features is a necessary step to conduct studies on next-generation sequencing (NGS) data. We developed STAR, an integrated web application that enables online management, visualization and track-based analysis of NGS data. Results: STAR is a multilayer web service system. On the client side, STAR leverages JavaScript, HTML5 Canvas and asynchronous communications to deliver a smoothly scrolling desktop-like graphical user interface with a suite of in-browser analysis tools that range from providing simple track configuration controls to sophisticated feature detection within datasets. On the server side, STAR supports private session state retention via an account management system and provides data management modules that enable collection, visualization and analysis of third-party sequencing data from the public domain with over thousands of tracks hosted to date. Overall, STAR represents a next-generation data exploration solution to match the requirements of NGS data, enabling both intuitive visualization and dynamic analysis of data. Availability and implementation: STAR browser system is freely available on the web at http://wanglab.ucsd.edu/star/browser and https://github.com/angell1117/STAR-genome-browser. Contact: wei-wang@ucsd.edu PMID:24078702

Radar Unix: a complete package for GPR data processing

NASA Astrophysics Data System (ADS)

Grandjean, Gilles; Durand, Herve

1999-03-01

A complete package for ground penetrating radar data interpretation including data processing, forward modeling and a case history database consultation is presented. Running on an Unix operating system, its architecture consists of a graphical user interface generating batch files transmitted to a library of processing routines. This design allows a better software maintenance and the possibility for the user to run processing or modeling batch files by itself and differed in time. A case history data base is available and consists of an hypertext document which can be consulted by using a standard HTML browser. All the software specifications are presented through a realistic example.

A Powerful, Cost Effective, Web Based Engineering Solution Supporting Conjunction Detection and Visual Analysis

NASA Astrophysics Data System (ADS)

Novak, Daniel M.; Biamonti, Davide; Gross, Jeremy; Milnes, Martin

2013-08-01

An innovative and visually appealing tool is presented for efficient all-vs-all conjunction analysis on a large catalogue of objects. The conjunction detection uses a nearest neighbour search algorithm, based on spatial binning and identification of pairs of objects in adjacent bins. This results in the fastest all vs all filtering the authors are aware of. The tool is constructed on a server-client architecture, where the server broadcasts to the client the conjunction data and ephemerides, while the client supports the user interface through a modern browser, without plug-in. In order to make the tool flexible and maintainable, Java software technologies were used on the server side, including Spring, Camel, ActiveMQ and CometD. The user interface and visualisation are based on the latest web technologies: HTML5, WebGL, THREE.js. Importance has been given on the ergonomics and visual appeal of the software. In fact certain design concepts have been borrowed from the gaming industry.

The Philosophy of User Interfaces in HELIO and the Importance of CASSIS

NASA Astrophysics Data System (ADS)

Bonnin, X.; Aboudarham, J.; Renié, C.; Csillaghy, A.; Messerotti, M.; Bentley, R. D.

2012-09-01

HELIO is a European project funded under FP7 (Project No. 238969). One of its goals as a Heliospheric Virtual Observatory is to provide an easy access to many datasets scattered all over the world, in the fields of Solar physics, Heliophysics, and Planetary magnetospheres. The efficiency of such a tool is very much related to the quality of the user interface. HELIO infrastructure is based on a Service Oriented Architecture (SOA), regrouping a network of standalone components, which allows four main types of interfaces: - HELIO Front End (HFE) is a browser-based user interface, which offers a centralized access to the HELIO main functionalities. Especially, it provides the possibility to reach data directly, or to refine selection by determination of observing characteristics, such as which instrument was observing at that time, which instrument was at this location, etc. - Many services/components provide their own standalone graphical user interface. While one can directly access individually each of these interfaces, they can also be connected together. - Most services also provide direct access for any tools through a public interface. A small java library, called Java API, simplifies this access by providing client stubs for services and shields the user from security, discovery and failover issues. - Workflows capabilities are available in HELIO, allowing complex combination of queries over several services. We want the user to be able to navigate easily, at his needs, through the various interfaces, and possibly use a specific one in order to make much-dedicated queries. We will also emphasize the importance of the CASSIS project (Coordination Action for the integration of Solar System Infrastructure and Science) in encouraging the interoperability necessary to undertake scientific studies that span disciplinary boundaries. If related projects follow the guidelines being developed by CASSIS then using external resources with HELIO will be greatly simplified.

Molecular structure input on the web.

PubMed

Ertl, Peter

2010-02-02

A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. This review focuses on a special type of molecule editors, namely those that are used for molecule structure input on the web. Scientific computing is now moving more and more in the direction of web services and cloud computing, with servers scattered all around the Internet. Thus a web browser has become the universal scientific user interface, and a tool to edit molecules directly within the web browser is essential.The review covers a history of web-based structure input, starting with simple text entry boxes and early molecule editors based on clickable maps, before moving to the current situation dominated by Java applets. One typical example - the popular JME Molecule Editor - will be described in more detail. Modern Ajax server-side molecule editors are also presented. And finally, the possible future direction of web-based molecule editing, based on technologies like JavaScript and Flash, is discussed.

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.

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

NASA Astrophysics Data System (ADS)

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

2008-12-01

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

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.

Occam's razor: supporting visual query expression for content-based image queries

NASA Astrophysics Data System (ADS)

Venters, Colin C.; Hartley, Richard J.; Hewitt, William T.

2005-01-01

This paper reports the results of a usability experiment that investigated visual query formulation on three dimensions: effectiveness, efficiency, and user satisfaction. Twenty eight evaluation sessions were conducted in order to assess the extent to which query by visual example supports visual query formulation in a content-based image retrieval environment. In order to provide a context and focus for the investigation, the study was segmented by image type, user group, and use function. The image type consisted of a set of abstract geometric device marks supplied by the UK Trademark Registry. Users were selected from the 14 UK Patent Information Network offices. The use function was limited to the retrieval of images by shape similarity. Two client interfaces were developed for comparison purposes: Trademark Image Browser Engine (TRIBE) and Shape Query Image Retrieval Systems Engine (SQUIRE).

Occam"s razor: supporting visual query expression for content-based image queries

NASA Astrophysics Data System (ADS)

Venters, Colin C.; Hartley, Richard J.; Hewitt, William T.

2004-12-01

This paper reports the results of a usability experiment that investigated visual query formulation on three dimensions: effectiveness, efficiency, and user satisfaction. Twenty eight evaluation sessions were conducted in order to assess the extent to which query by visual example supports visual query formulation in a content-based image retrieval environment. In order to provide a context and focus for the investigation, the study was segmented by image type, user group, and use function. The image type consisted of a set of abstract geometric device marks supplied by the UK Trademark Registry. Users were selected from the 14 UK Patent Information Network offices. The use function was limited to the retrieval of images by shape similarity. Two client interfaces were developed for comparison purposes: Trademark Image Browser Engine (TRIBE) and Shape Query Image Retrieval Systems Engine (SQUIRE).

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.

Route Advising in a Dynamic Environment - A High-Tech Approach

NASA Astrophysics Data System (ADS)

Firdhous, M. F. M.; Basnayake, D. L.; Kodithuwakku, K. H. L.; Hatthalla, N. K.; Charlin, N. W.; Bandara, P. M. R. I. K.

Finding the optimal path between two locations in the Colombo city is not a straight forward task, because of the complex road system and the huge traffic jams etc. This paper presents a system to find the optimal driving direction between two locations within the Colombo city, considering road rules (one way, two ways or fully closed in both directions). The system contains three main modules - core module, web module and mobile module, additionally there are two user interfaces one for normal users and the other for administrative users. Both these interfaces can be accessed using a web browser or a GPRS enabled mobile phone. The system is developed based on the Geographic Information System (GIS) technology. GIS is considered as the best option to integrate hardware, software, and data for capturing, managing, analyzing, and displaying all forms of geographically referenced information. The core of the system is MapServer (MS4W) used along with the other supporting technologies such as PostGIS, PostgreSQL, pgRouting, ASP.NET and C#.

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

PubMed

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

2015-03-01

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

SU-D-BRD-02: A Web-Based Image Processing and Plan Evaluation Platform (WIPPEP) for Future Cloud-Based Radiotherapy

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

Chai, X; Liu, L; Xing, L

Purpose: Visualization and processing of medical images and radiation treatment plan evaluation have traditionally been constrained to local workstations with limited computation power and ability of data sharing and software update. We present a web-based image processing and planning evaluation platform (WIPPEP) for radiotherapy applications with high efficiency, ubiquitous web access, and real-time data sharing. Methods: This software platform consists of three parts: web server, image server and computation server. Each independent server communicates with each other through HTTP requests. The web server is the key component that provides visualizations and user interface through front-end web browsers and relay informationmore » to the backend to process user requests. The image server serves as a PACS system. The computation server performs the actual image processing and dose calculation. The web server backend is developed using Java Servlets and the frontend is developed using HTML5, Javascript, and jQuery. The image server is based on open source DCME4CHEE PACS system. The computation server can be written in any programming language as long as it can send/receive HTTP requests. Our computation server was implemented in Delphi, Python and PHP, which can process data directly or via a C++ program DLL. Results: This software platform is running on a 32-core CPU server virtually hosting the web server, image server, and computation servers separately. Users can visit our internal website with Chrome browser, select a specific patient, visualize image and RT structures belonging to this patient and perform image segmentation running Delphi computation server and Monte Carlo dose calculation on Python or PHP computation server. Conclusion: We have developed a webbased image processing and plan evaluation platform prototype for radiotherapy. This system has clearly demonstrated the feasibility of performing image processing and plan evaluation platform through a web browser and exhibited potential for future cloud based radiotherapy.« less

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.

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

PubMed

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

2014-01-01

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

A Hyperbolic Ontology Visualization Tool for Model Application Programming Interface Documentation

NASA Technical Reports Server (NTRS)

Hyman, Cody

2011-01-01

Spacecraft modeling, a critically important portion in validating planned spacecraft activities, is currently carried out using a time consuming method of mission to mission model implementations and integration. A current project in early development, Integrated Spacecraft Analysis (ISCA), aims to remedy this hindrance by providing reusable architectures and reducing time spent integrating models with planning and sequencing tools. The principle objective of this internship was to develop a user interface for an experimental ontology-based structure visualization of navigation and attitude control system modeling software. To satisfy this, a number of tree and graph visualization tools were researched and a Java based hyperbolic graph viewer was selected for experimental adaptation. Early results show promise in the ability to organize and display large amounts of spacecraft model documentation efficiently and effectively through a web browser. This viewer serves as a conceptual implementation for future development but trials with both ISCA developers and end users should be performed to truly evaluate the effectiveness of continued development of such visualizations.

Cross-Platform User Interface of E-Learning Applications

ERIC Educational Resources Information Center

Stoces, Michal; Masner, Jan; Jarolímek, Jan; Šimek, Pavel; Vanek, Jirí; Ulman, Miloš

2015-01-01

The paper discusses the development of Web educational services for specific groups. A key feature is to allow the display and use of educational materials and training services to the widest possible set of different devices, especially in the browser classic desktop computers, notebooks, tablets, mobile phones and also on different readers for…

myPhyloDB: a local web server for the storage and analysis of metagenomics data

USDA-ARS?s Scientific Manuscript database

myPhyloDB is a user-friendly personal database with a browser-interface designed to facilitate the storage, processing, analysis, and distribution of metagenomics data. MyPhyloDB archives raw sequencing files, and allows for easy selection of project(s)/sample(s) of any combination from all availab...

ASCIIGenome: a command line genome browser for console terminals.

PubMed

Beraldi, Dario

2017-05-15

Current genome browsers are designed to work via graphical user interfaces (GUIs), which, however intuitive, are not amenable to operate within console terminals and therefore are difficult to streamline or integrate in scripts. To circumvent these limitations, ASCIIGenome runs exclusively via command line interface to display genomic data directly in a terminal window. By following the same philosophy of UNIX tools, ASCIIGenome aims to be easily integrated with the command line, including batch processing of data, and therefore enables an effective exploration of the data. ASCIIGenome is written in Java. Consequently, it is a cross-platform tool and requires minimal or no installation. Some of the common genomic data types are supported and data access on remote ftp servers is possible. Speed and memory footprint are comparable to or better than those of common genome browsers. Software and source code (MIT License) are available at https://github.com/dariober/ASCIIGenome with detailed documentation at http://asciigenome.readthedocs.io . Dario.beraldi@cruk.cam.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

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).

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

PubMed Central

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

2007-01-01

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

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.

Savant Genome Browser 2: visualization and analysis for population-scale genomics.

PubMed

Fiume, Marc; Smith, Eric J M; Brook, Andrew; Strbenac, Dario; Turner, Brian; Mezlini, Aziz M; Robinson, Mark D; Wodak, Shoshana J; Brudno, Michael

2012-07-01

High-throughput sequencing (HTS) technologies are providing an unprecedented capacity for data generation, and there is a corresponding need for efficient data exploration and analysis capabilities. Although most existing tools for HTS data analysis are developed for either automated (e.g. genotyping) or visualization (e.g. genome browsing) purposes, such tools are most powerful when combined. For example, integration of visualization and computation allows users to iteratively refine their analyses by updating computational parameters within the visual framework in real-time. Here we introduce the second version of the Savant Genome Browser, a standalone program for visual and computational analysis of HTS data. Savant substantially improves upon its predecessor and existing tools by introducing innovative visualization modes and navigation interfaces for several genomic datatypes, and synergizing visual and automated analyses in a way that is powerful yet easy even for non-expert users. We also present a number of plugins that were developed by the Savant Community, which demonstrate the power of integrating visual and automated analyses using Savant. The Savant Genome Browser is freely available (open source) at www.savantbrowser.com.

Savant Genome Browser 2: visualization and analysis for population-scale genomics

PubMed Central

Smith, Eric J. M.; Brook, Andrew; Strbenac, Dario; Turner, Brian; Mezlini, Aziz M.; Robinson, Mark D.; Wodak, Shoshana J.; Brudno, Michael

2012-01-01

High-throughput sequencing (HTS) technologies are providing an unprecedented capacity for data generation, and there is a corresponding need for efficient data exploration and analysis capabilities. Although most existing tools for HTS data analysis are developed for either automated (e.g. genotyping) or visualization (e.g. genome browsing) purposes, such tools are most powerful when combined. For example, integration of visualization and computation allows users to iteratively refine their analyses by updating computational parameters within the visual framework in real-time. Here we introduce the second version of the Savant Genome Browser, a standalone program for visual and computational analysis of HTS data. Savant substantially improves upon its predecessor and existing tools by introducing innovative visualization modes and navigation interfaces for several genomic datatypes, and synergizing visual and automated analyses in a way that is powerful yet easy even for non-expert users. We also present a number of plugins that were developed by the Savant Community, which demonstrate the power of integrating visual and automated analyses using Savant. The Savant Genome Browser is freely available (open source) at www.savantbrowser.com. PMID:22638571

Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data.

PubMed

Robinson, James T; Turner, Douglass; Durand, Neva C; Thorvaldsdóttir, Helga; Mesirov, Jill P; Aiden, Erez Lieberman

2018-02-28

Contact mapping experiments such as Hi-C explore how genomes fold in 3D. Here, we introduce Juicebox.js, a cloud-based web application for exploring the resulting datasets. Like the original Juicebox application, Juicebox.js allows users to zoom in and out of such datasets using an interface similar to Google Earth. Juicebox.js also has many features designed to facilitate data reproducibility and sharing. Furthermore, Juicebox.js encodes the exact state of the browser in a shareable URL. Creating a public browser for a new Hi-C dataset does not require coding and can be accomplished in under a minute. The web app also makes it possible to create interactive figures online that can complement or replace ordinary journal figures. When combined with Juicer, this makes the entire process of data analysis transparent, insofar as every step from raw reads to published figure is publicly available as open source code. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

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.

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.

Emissions & Generation Resource Integrated Database (eGRID), eGRID2002 (with years 1996 - 2000 data)

EPA Pesticide Factsheets

The Emissions & Generation Resource Integrated Database (eGRID) is a comprehensive source of data on the environmental characteristics of almost all electric power generated in the United States. These environmental characteristics include air emissions for nitrogen oxides, sulfur dioxide, carbon dioxide, methane, nitrous oxide, and mercury; emissions rates; net generation; resource mix; and many other attributes. eGRID2002 (years 1996 through 2000 data) contains 16 Excel spreadsheets and the Technical Support Document, as well as the eGRID Data Browser, User's Manual, and Readme file. Archived eGRID data can be viewed as spreadsheets or by using the eGRID Data Browser. The eGRID spreadsheets can be manipulated by data users and enables users to view all the data underlying eGRID. The eGRID Data Browser enables users to view key data using powerful search features. Note that the eGRID Data Browser will not run on a Mac-based machine without Windows emulation.

A browser-based tool for conversion between Fortran NAMELIST and XML/HTML

NASA Astrophysics Data System (ADS)

Naito, O.

A browser-based tool for conversion between Fortran NAMELIST and XML/HTML is presented. It runs on an HTML5 compliant browser and generates reusable XML files to aid interoperability. It also provides a graphical interface for editing and annotating variables in NAMELIST, hence serves as a primitive code documentation environment. Although the tool is not comprehensive, it could be viewed as a test bed for integrating legacy codes into modern systems.

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.

Reliability of SNOMED-CT Coding by Three Physicians using Two Terminology Browsers

PubMed Central

Chiang, Michael F.; Hwang, John C.; Yu, Alexander C.; Casper, Daniel S.; Cimino, James J.; Starren, Justin

2006-01-01

SNOMED-CT has been promoted as a reference terminology for electronic health record (EHR) systems. Many important EHR functions are based on the assumption that medical concepts will be coded consistently by different users. This study is designed to measure agreement among three physicians using two SNOMED-CT terminology browsers to encode 242 concepts from five ophthalmology case presentations in a publicly-available clinical journal. Inter-coder reliability, based on exact coding match by each physician, was 44% using one browser and 53% using the other. Intra-coder reliability testing revealed that a different SNOMED-CT code was obtained up to 55% of the time when the two browsers were used by one user to encode the same concept. These results suggest that the reliability of SNOMED-CT coding is imperfect, and may be a function of browsing methodology. A combination of physician training, terminology refinement, and browser improvement may help increase the reproducibility of SNOMED-CT coding. PMID:17238317

Information-Flow-Based Access Control for Web Browsers

NASA Astrophysics Data System (ADS)

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

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

Online plasma calculator

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

Interactome INSIDER: a structural interactome browser for genomic studies.

PubMed

Meyer, Michael J; Beltrán, Juan Felipe; Liang, Siqi; Fragoza, Robert; Rumack, Aaron; Liang, Jin; Wei, Xiaomu; Yu, Haiyuan

2018-01-01

We present Interactome INSIDER, a tool to link genomic variant information with structural protein-protein interactomes. Underlying this tool is the application of machine learning to predict protein interaction interfaces for 185,957 protein interactions with previously unresolved interfaces in human and seven model organisms, including the entire experimentally determined human binary interactome. Predicted interfaces exhibit functional properties similar to those of known interfaces, including enrichment for disease mutations and recurrent cancer mutations. Through 2,164 de novo mutagenesis experiments, we show that mutations of predicted and known interface residues disrupt interactions at a similar rate and much more frequently than mutations outside of predicted interfaces. To spur functional genomic studies, Interactome INSIDER (http://interactomeinsider.yulab.org) enables users to identify whether variants or disease mutations are enriched in known and predicted interaction interfaces at various resolutions. Users may explore known population variants, disease mutations, and somatic cancer mutations, or they may upload their own set of mutations for this purpose.

PubMedReco: A Real-Time Recommender System for PubMed Citations.

PubMed

Samuel, Hamman W; Zaïane, Osmar R

2017-01-01

We present a recommender system, PubMedReco, for real-time suggestions of medical articles from PubMed, a database of over 23 million medical citations. PubMedReco can recommend medical article citations while users are conversing in a synchronous communication environment such as a chat room. Normally, users would have to leave their chat interface to open a new web browser window, and formulate an appropriate search query to retrieve relevant results. PubMedReco automatically generates the search query and shows relevant citations within the same integrated user interface. PubMedReco analyzes relevant keywords associated with the conversation and uses them to search for relevant citations using the PubMed E-utilities programming interface. Our contributions include improvements to the user experience for searching PubMed from within health forums and chat rooms, and a machine learning model for identifying relevant keywords. We demonstrate the feasibility of PubMedReco using BMJ's Doc2Doc forum discussions.

Fulfillment of HTTP Authentication Based on Alcatel OmniSwitch 9700

NASA Astrophysics Data System (ADS)

Liu, Hefu

This paper provides a way of HTTP authentication On Alcatel OmniSwitch 9700. Authenticated VLANs control user access to network resources based on VLAN assignment and user authentication. The user can be authenticated through the switch via any standard Web browser software. Web browser client displays the username and password prompts. Then a way for HTML forms can be given to pass HTTP authentication data when it's submitted. A radius server will provide a database of user information that the switch checks whenever it tries to authenticate through the switch. Before or after authentication, the client can get an address from a Dhcp server.

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.

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.

Addressing an I/O Bottleneck in a Web-Based CERES QC Tool

NASA Astrophysics Data System (ADS)

Heckert, E.; Sun-Mack, S.; Chen, Y.; Chu, C.; Smith, R. A.

2016-12-01

In this poster, we explore the technologies we have used to overcome the problem of transmitting and analyzing large datasets in our web-based CERES Quality Control tool and consider four technologies to potentially adopt for future performance improvements. The CERES team uses this tool to validate pixel-level data from Terra, Aqua, SNPP, MSG, MTSAT, and many geostationary GOES satellites, as well as to develop cloud retrieval algorithms. The tool includes a histogram feature that allows the user to aggregate data from many different timestamps and different scenes globally or locally selected by the user by drawing bounding boxes. In order to provide a better user experience, the tool passes a large amount of data to the user's browser. The browser then processes the data in order to present it to users in various formats, for example as a histogram. In addition to using multiple servers to subset data and pass a smaller set of data to the browser, the tool also makes use of a compression technology, Gzip, to reduce the size of the data. However, sometimes the application in the browser is still slow when dealing with these large sets of data due to the delay in the browser receiving the server's response. To address this I/O bottleneck, we will investigate four alternatives and present the results in this poster: 1) sending uncompressed data, 2) ESRI's Limited Error Raster Compression (LERC), 3) Gzip, and 4) WebSocket protocol. These approaches are compared to each other and to the uncompressed control to determine the optimal solution.

R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server

PubMed Central

Cannone, Jamie J.; Sweeney, Blake A.; Petrov, Anton I.; Gutell, Robin R.; Zirbel, Craig L.; Leontis, Neocles

2015-01-01

The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa. PMID:26048960

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

ERIC Educational Resources Information Center

Shen, Siu-Tsen

2016-01-01

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

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).

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

PubMed

Zarei, Reza; Kuo, Alex

2017-01-01

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

GrayStarServer: Server-side Spectrum Synthesis with a Browser-based Client-side User Interface

NASA Astrophysics Data System (ADS)

Short, C. Ian

2016-10-01

We present GrayStarServer (GSS), a stellar atmospheric modeling and spectrum synthesis code of pedagogical accuracy that is accessible in any web browser on commonplace computational devices and that runs on a timescale of a few seconds. The addition of spectrum synthesis annotated with line identifications extends the functionality and pedagogical applicability of GSS beyond that of its predecessor, GrayStar3 (GS3). The spectrum synthesis is based on a line list acquired from the NIST atomic spectra database, and the GSS post-processing and user interface client allows the user to inspect the plain text ASCII version of the line list, as well as to apply macroscopic broadening. Unlike GS3, GSS carries out the physical modeling on the server side in Java, and communicates with the JavaScript and HTML client via an asynchronous HTTP request. We also describe other improvements beyond GS3 such as a more physical treatment of background opacity and atmospheric physics, the comparison of key results with those of the Phoenix code, and the use of the HTML < {canvas}> element for higher quality plotting and rendering of results. We also present LineListServer, a Java code for converting custom ASCII line lists in NIST format to the byte data type file format required by GSS so that users can prepare their own custom line lists. We propose a standard for marking up and packaging model atmosphere and spectrum synthesis output for data transmission and storage that will facilitate a web-based approach to stellar atmospheric modeling and spectrum synthesis. We describe some pedagogical demonstrations and exercises enabled by easily accessible, on-demand, responsive spectrum synthesis. GSS may serve as a research support tool by providing quick spectroscopic reconnaissance. GSS may be found at www.ap.smu.ca/~ishort/OpenStars/GrayStarServer/grayStarServer.html, and source tarballs for local installations of both GSS and LineListServer may be found at www.ap.smu.ca/~ishort/OpenStars/.

Generating and Visualizing Climate Indices using Google Earth Engine

NASA Astrophysics Data System (ADS)

Erickson, T. A.; Guentchev, G.; Rood, R. B.

2017-12-01

Climate change is expected to have largest impacts on regional and local scales. Relevant and credible climate information is needed to support the planning and adaptation efforts in our communities. The volume of climate projections of temperature and precipitation is steadily increasing, as datasets are being generated on finer spatial and temporal grids with an increasing number of ensembles to characterize uncertainty. Despite advancements in tools for querying and retrieving subsets of these large, multi-dimensional datasets, ease of access remains a barrier for many existing and potential users who want to derive useful information from these data, particularly for those outside of the climate modelling research community. Climate indices, that can be derived from daily temperature and precipitation data, such as annual number of frost days or growing season length, can provide useful information to practitioners and stakeholders. For this work the NASA Earth Exchange Global Daily Downscaled Projections (NEX-GDDP) dataset was loaded into Google Earth Engine, a cloud-based geospatial processing platform. Algorithms that use the Earth Engine API to generate several climate indices were written. The indices were chosen from the set developed by the joint CCl/CLIVAR/JCOMM Expert Team on Climate Change Detection and Indices (ETCCDI). Simple user interfaces were created that allow users to query, produce maps and graphs of the indices, as well as download results for additional analyses. These browser-based interfaces could allow users in low-bandwidth environments to access climate information. This research shows that calculating climate indices from global downscaled climate projection datasets and sharing them widely using cloud computing technologies is feasible. Further development will focus on exposing the climate indices to existing applications via the Earth Engine API, and building custom user interfaces for presenting climate indices to a diverse set of user groups.

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).

LocusExplorer: a user-friendly tool for integrated visualization of human genetic association data and biological annotations.

PubMed

Dadaev, Tokhir; Leongamornlert, Daniel A; Saunders, Edward J; Eeles, Rosalind; Kote-Jarai, Zsofia

2016-03-15

: In this article, we present LocusExplorer, a data visualization and exploration tool for genetic association data. LocusExplorer is written in R using the Shiny library, providing access to powerful R-based functions through a simple user interface. LocusExplorer allows users to simultaneously display genetic, statistical and biological data for humans in a single image and allows dynamic zooming and customization of the plot features. Publication quality plots may then be produced in a variety of file formats. LocusExplorer is open source and runs through R and a web browser. It is available at www.oncogenetics.icr.ac.uk/LocusExplorer/ or can be installed locally and the source code accessed from https://github.com/oncogenetics/LocusExplorer tokhir.dadaev@icr.ac.uk. © The Author 2015. Published by Oxford University Press.

Multi-user investigation organizer

NASA Technical Reports Server (NTRS)

Panontin, Tina L. (Inventor); Williams, James F. (Inventor); Carvalho, Robert E. (Inventor); Sturken, Ian (Inventor); Wolfe, Shawn R. (Inventor); Gawdiak, Yuri O. (Inventor); Keller, Richard M. (Inventor)

2009-01-01

A system that allows a team of geographically dispersed users to collaboratively analyze a mishap event. The system includes a reconfigurable ontology, including instances that are related to and characterize the mishap, a semantic network that receives, indexes and stores, for retrieval, viewing and editing, the instances and links between the instances, a network browser interface for retrieving and viewing screens that present the instances and links to other instances and that allow editing thereof, and a rule-based inference engine, including a collection of rules associated with establishment of links between the instances. A possible conclusion arising from analysis of the mishap event may be characterized as one or more of: not a credible conclusion; an unlikely conclusion; a credible conclusion; conclusion needs analysis; conclusion needs supporting data; conclusion proposed to be closed; and an un-reviewed conclusion.

Developing Web-based Tools for Collaborative Science and Public Outreach

NASA Astrophysics Data System (ADS)

Friedman, A.; Pizarro, O.; Williams, S. B.

2016-02-01

With the advances in high bandwidth communications and the proliferation of social media tools, education & outreach activities have become commonplace on ocean-bound research cruises. In parallel, advances in underwater robotics & other data collecting platforms, have made it possible to collect copious amounts of oceanographic data. This data then typically undergoes laborious, manual processing to transform it into quantitative information, which normally occurs post cruise resulting in significant lags between collecting data and using it for scientific discovery. This presentation discusses how appropriately designed software systems, can be used to fulfill multiple objectives and attempt to leverage public engagement in order to compliment science goals. We will present two software platforms: the first is a web browser based tool that was developed for real-time tracking of multiple underwater robots and ships. It was designed to allow anyone on board to view or control it on any device with a web browser. It opens up the possibility of remote teleoperation & engagement and was easily adapted to enable live streaming over the internet for public outreach. While the tracking system provided context and engaged people in real-time, it also directed interested participants to Squidle, another online system. Developed for scientists, Squidle supports data management, exploration & analysis and enables direct access to survey data reducing the lag in data processing. It provides a user-friendly streamlined interface that integrates advanced data management & online annotation tools. This system was adapted to provide a simplified user interface, tutorial instructions and a gamified ranking system to encourage "citizen science" participation. These examples show that through a flexible design approach, it is possible to leverage the development effort of creating science tools to facilitate outreach goals, opening up the possibility for acquiring large volumes of crowd-sourced data without compromising science objectives.

Taking advantage of HTML5 browsers to realize the concepts of session state and workflow sharing in web-tool applications

NASA Astrophysics Data System (ADS)

Suftin, I.; Read, J. S.; Walker, J.

2013-12-01

Scientists prefer not having to be tied down to a specific machine or operating system in order to analyze local and remote data sets or publish work. Increasingly, analysis has been migrating to decentralized web services and data sets, using web clients to provide the analysis interface. While simplifying workflow access, analysis, and publishing of data, the move does bring with it its own unique set of issues. Web clients used for analysis typically offer workflows geared towards a single user, with steps and results that are often difficult to recreate and share with others. Furthermore, workflow results often may not be easily used as input for further analysis. Older browsers further complicate things by having no way to maintain larger chunks of information, often offloading the job of storage to the back-end server or trying to squeeze it into a cookie. It has been difficult to provide a concept of "session storage" or "workflow sharing" without a complex orchestration of the back-end for storage depending on either a centralized file system or database. With the advent of HTML5, browsers gained the ability to store more information through the use of the Web Storage API (a browser-cookie holds a maximum of 4 kilobytes). Web Storage gives us the ability to store megabytes of arbitrary data in-browser either with an expiration date or just for a session. This allows scientists to create, update, persist and share their workflow without depending on the backend to store session information, providing the flexibility for new web-based workflows to emerge. In the DSASWeb portal ( http://cida.usgs.gov/DSASweb/ ), using these techniques, the representation of every step in the analyst's workflow is stored as plain-text serialized JSON, which we can generate as a text file and provide to the analyst as an upload. This file may then be shared with others and loaded back into the application, restoring the application to the state it was in when the session file was generated. A user may then view results produced during that session or go back and alter input parameters, creating new results and producing new, unique sessions which they can then again share. This technique not only provides independence for the user to manage their session as they like, but also allows much greater freedom for the application provider to scale out without having to worry about carrying over user information or maintaining it in a central location.

Mercury Shopping Cart Interface

NASA Technical Reports Server (NTRS)

Pfister, Robin; McMahon, Joe

2006-01-01

Mercury Shopping Cart Interface (MSCI) is a reusable component of the Power User Interface 5.0 (PUI) program described in another article. MSCI is a means of encapsulating the logic and information needed to describe an orderable item consistent with Mercury Shopping Cart service protocol. Designed to be used with Web-browser software, MSCI generates Hypertext Markup Language (HTML) pages on which ordering information can be entered. MSCI comprises two types of Practical Extraction and Report Language (PERL) modules: template modules and shopping-cart logic modules. Template modules generate HTML pages for entering the required ordering details and enable submission of the order via a Hypertext Transfer Protocol (HTTP) post. Shopping cart modules encapsulate the logic and data needed to describe an individual orderable item to the Mercury Shopping Cart service. These modules evaluate information entered by the user to determine whether it is sufficient for the Shopping Cart service to process the order. Once an order has been passed from MSCI to a deployed Mercury Shopping Cart server, there is no further interaction with the user.

Using the Browser for Science: A Collaborative Toolkit for Astronomy

NASA Astrophysics Data System (ADS)

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

2011-07-01

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

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

An end-to-end secure patient information access card system.

PubMed

Alkhateeb, A; Singer, H; Yakami, M; Takahashi, T

2000-03-01

The rapid development of the Internet and the increasing interest in Internet-based solutions has promoted the idea of creating Internet-based health information applications. This will force a change in the role of IC cards in healthcare card systems from a data carrier to an access key medium. At the Medical Informatics Department of Kyoto University Hospital we are developing a smart card patient information project where patient databases are accessed via the Internet. Strong end-to-end data encryption is performed via Secure Socket Layers, transparent to transmit patient information. The smart card is playing the crucial role of access key to the database: user authentication is performed internally without ever revealing the actual key. For easy acceptance by healthcare professionals, the user interface is integrated as a plug-in for two familiar Web browsers, Netscape Navigator and MS Internet Explorer.

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.

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

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.

PubMed

Cannone, Jamie J; Sweeney, Blake A; Petrov, Anton I; Gutell, Robin R; Zirbel, Craig L; Leontis, Neocles

2015-07-01

The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

Science Activity Planner for the MER Mission

NASA Technical Reports Server (NTRS)

Norris, Jeffrey S.; Crockett, Thomas M.; Fox, Jason M.; Joswig, Joseph C.; Powell, Mark W.; Shams, Khawaja S.; Torres, Recaredo J.; Wallick, Michael N.; Mittman, David S.

2008-01-01

The Maestro Science Activity Planner is a computer program that assists human users in planning operations of the Mars Explorer Rover (MER) mission and visualizing scientific data returned from the MER rovers. Relative to its predecessors, this program is more powerful and easier to use. This program is built on the Java Eclipse open-source platform around a Web-browser-based user-interface paradigm to provide an intuitive user interface to Mars rovers and landers. This program affords a combination of advanced display and simulation capabilities. For example, a map view of terrain can be generated from images acquired by the High Resolution Imaging Science Explorer instrument aboard the Mars Reconnaissance Orbiter spacecraft and overlaid with images from a navigation camera (more precisely, a stereoscopic pair of cameras) aboard a rover, and an interactive, annotated rover traverse path can be incorporated into the overlay. It is also possible to construct an overhead perspective mosaic image of terrain from navigation-camera images. This program can be adapted to similar use on other outer-space missions and is potentially adaptable to numerous terrestrial applications involving analysis of data, operations of robots, and planning of such operations for acquisition of scientific data.

Where's My Data - WMD

NASA Technical Reports Server (NTRS)

Quach, William L.; Sesplaukis, Tadas; Owen-Mankovich, Kyran J.; Nakamura, Lori L.

2012-01-01

WMD provides a centralized interface to access data stored in the Mission Data Processing and Control System (MPCS) GDS (Ground Data Systems) databases during MSL (Mars Science Laboratory) Testbeds and ATLO (Assembly, Test, and Launch Operations) test sessions. The MSL project organizes its data based on venue (Testbed, ATLO, Ops), with each venue's data stored on a separate database, making it cumbersome for users to access data across the various venues. WMD allows sessions to be retrieved through a Web-based search using several criteria: host name, session start date, or session ID number. Sessions matching the search criteria will be displayed and users can then select a session to obtain and analyze the associated data. The uniqueness of this software comes from its collection of data retrieval and analysis features provided through a single interface. This allows users to obtain their data and perform the necessary analysis without having to worry about where and how to get the data, which may be stored in various locations. Additionally, this software is a Web application that only requires a standard browser without additional plug-ins, providing a cross-platform, lightweight solution for users to retrieve and analyze their data. This software solves the problem of efficiently and easily finding and retrieving data from thousands of MSL Testbed and ATLO sessions. WMD allows the user to retrieve their session in as little as one mouse click, and then to quickly retrieve additional data associated with the session.

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

NASA Astrophysics Data System (ADS)

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

2002-11-01

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

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.

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

ADA and C++ Business Case Analysis

DTIC Science & Technology

1991-07-01

executable mini-specs, to support import of existing code. Automated database population/change propagation. 9. Documentation generation: via FrameMaker ...Backplane. ii. 4GLS H-20 I I IDE/Software through Pictures (StP) 12 June 1991 iii. Interleaf and FrameMaker publishing. 13. Output formats: PostScript... FrameMaker , WordPerfect. 12. User interface: Menu and mouse, windowing, color, on-line help, undo. Database browser via forms/tables component later

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.

Vcs.js - Visualization Control System for the Web

NASA Astrophysics Data System (ADS)

Chaudhary, A.; Lipsa, D.; Doutriaux, C.; Beezley, J. D.; Williams, D. N.; Fries, S.; Harris, M. B.

2016-12-01

VCS is a general purpose visualization library, optimized for climate data, which is part of the UV-CDAT system. It provides a Python API for drawing 2D plots such as lineplots, scatter plots, Taylor diagrams, data colored by scalar values, vector glyphs, isocontours and map projections. VCS is based on the VTK library. Vcs.js is the corresponding JavaScript API, designed to be as close as possible to the original VCS Python API and to provide similar functionality for the Web. Vcs.js includes additional functionality when compared with VCS. This additional API is used to introspect data files available on the server and variables available in a data file. Vcs.js can display plots in the browser window. It always works with a server that reads a data file, extracts variables from the file and subsets the data. From this point, two alternate paths are possible. First the system can render the data on the server using VCS producing an image which is send to the browser to be displayed. This path works for for all plot types and produces a reference image identical with the images produced by VCS. This path uses the VTK-Web library. As an optimization, usable in certain conditions, a second path is possible. Data is packed, and sent to the browser which uses a JavaScript plotting library, such as plotly, to display the data. Plots that work well in the browser are line-plots, scatter-plots for any data and many other plot types for small data and supported grid types. As web technology matures, more plots could be supported for rendering in the browser. Rendering can be done either on the client or on the server and we expect that the best place to render will change depending on the available web technology, data transfer costs, server management costs and value provided to users. We intend to provide a flexible solution that allows for both client and server side rendering and a meaningful way to choose between the two. We provide a web-based user interface called vCdat which uses Vcs.js as its visualization library. Our paper will discuss the principles guiding our design choices for Vcs.js, present our design in detail and show a sample usage of the library.

A Freely-Available Authoring System for Browser-Based CALL with Speech Recognition

ERIC Educational Resources Information Center

O'Brien, Myles

2017-01-01

A system for authoring browser-based CALL material incorporating Google speech recognition has been developed and made freely available for download. The system provides a teacher with a simple way to set up CALL material, including an optional image, sound or video, which will elicit spoken (and/or typed) answers from the user and check them…

Java-based browsing, visualization and processing of heterogeneous medical data from remote repositories.

PubMed

Masseroli, M; Bonacina, S; Pinciroli, F

2004-01-01

The actual development of distributed information technologies and Java programming enables employing them also in the medical arena to support the retrieval, integration and evaluation of heterogeneous data and multimodal images in a web browser environment. With this aim, we used them to implement a client-server architecture based on software agents. The client side is a Java applet running in a web browser and providing a friendly medical user interface to browse and visualize different patient and medical test data, integrating them properly. The server side manages secure connections and queries to heterogeneous remote databases and file systems containing patient personal and clinical data. Based on the Java Advanced Imaging API, processing and analysis tools were developed to support the evaluation of remotely retrieved bioimages through the quantification of their features in different regions of interest. The Java platform-independence allows the centralized management of the implemented prototype and its deployment to each site where an intranet or internet connection is available. Giving healthcare providers effective support for comprehensively browsing, visualizing and evaluating medical images and records located in different remote repositories, the developed prototype can represent an important aid in providing more efficient diagnoses and medical treatments.

Multi-Sector Sustainability Browser (MSSB) User Manual: A ...

EPA Pesticide Factsheets

EPA’s Sustainable and Healthy Communities (SHC) Research Program is developing methodologies, resources, and tools to assist community members and local decision makers in implementing policy choices that facilitate sustainable approaches in managing their resources affecting the built environment, natural environment, and human health. In order to assist communities and decision makers in implementing sustainable practices, EPA is developing computer-based systems including models, databases, web tools, and web browsers to help communities decide upon approaches that support their desired outcomes. Communities need access to resources that will allow them to achieve their sustainability objectives through intelligent decisions in four key sustainability areas: • Land Use • Buildings and Infrastructure • Transportation • Materials Management (i.e., Municipal Solid Waste [MSW] processing and disposal) The Multi-Sector Sustainability Browser (MSSB) is designed to support sustainable decision-making for communities, local and regional planners, and policy and decision makers. Document is an EPA Technical Report, which is the user manual for the Multi-Sector Sustainability Browser (MSSB) tool. The purpose of the document is to provide basic guidance on use of the tool for users

The UCSC genome browser and associated tools

PubMed Central

Haussler, David; Kent, W. James

2013-01-01

The UCSC Genome Browser (http://genome.ucsc.edu) is a graphical viewer for genomic data now in its 13th year. Since the early days of the Human Genome Project, it has presented an integrated view of genomic data of many kinds. Now home to assemblies for 58 organisms, the Browser presents visualization of annotations mapped to genomic coordinates. The ability to juxtapose annotations of many types facilitates inquiry-driven data mining. Gene predictions, mRNA alignments, epigenomic data from the ENCODE project, conservation scores from vertebrate whole-genome alignments and variation data may be viewed at any scale from a single base to an entire chromosome. The Browser also includes many other widely used tools, including BLAT, which is useful for alignments from high-throughput sequencing experiments. Private data uploaded as Custom Tracks and Data Hubs in many formats may be displayed alongside the rich compendium of precomputed data in the UCSC database. The Table Browser is a full-featured graphical interface, which allows querying, filtering and intersection of data tables. The Saved Session feature allows users to store and share customized views, enhancing the utility of the system for organizing multiple trains of thought. Binary Alignment/Map (BAM), Variant Call Format and the Personal Genome Single Nucleotide Polymorphisms (SNPs) data formats are useful for visualizing a large sequencing experiment (whole-genome or whole-exome), where the differences between the data set and the reference assembly may be displayed graphically. Support for high-throughput sequencing extends to compact, indexed data formats, such as BAM, bigBed and bigWig, allowing rapid visualization of large datasets from RNA-seq and ChIP-seq experiments via local hosting. PMID:22908213

The UCSC genome browser and associated tools.

PubMed

Kuhn, Robert M; Haussler, David; Kent, W James

2013-03-01

The UCSC Genome Browser (http://genome.ucsc.edu) is a graphical viewer for genomic data now in its 13th year. Since the early days of the Human Genome Project, it has presented an integrated view of genomic data of many kinds. Now home to assemblies for 58 organisms, the Browser presents visualization of annotations mapped to genomic coordinates. The ability to juxtapose annotations of many types facilitates inquiry-driven data mining. Gene predictions, mRNA alignments, epigenomic data from the ENCODE project, conservation scores from vertebrate whole-genome alignments and variation data may be viewed at any scale from a single base to an entire chromosome. The Browser also includes many other widely used tools, including BLAT, which is useful for alignments from high-throughput sequencing experiments. Private data uploaded as Custom Tracks and Data Hubs in many formats may be displayed alongside the rich compendium of precomputed data in the UCSC database. The Table Browser is a full-featured graphical interface, which allows querying, filtering and intersection of data tables. The Saved Session feature allows users to store and share customized views, enhancing the utility of the system for organizing multiple trains of thought. Binary Alignment/Map (BAM), Variant Call Format and the Personal Genome Single Nucleotide Polymorphisms (SNPs) data formats are useful for visualizing a large sequencing experiment (whole-genome or whole-exome), where the differences between the data set and the reference assembly may be displayed graphically. Support for high-throughput sequencing extends to compact, indexed data formats, such as BAM, bigBed and bigWig, allowing rapid visualization of large datasets from RNA-seq and ChIP-seq experiments via local hosting.

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

PubMed

Dong, Han; Sharma, Diksha; Badano, Aldo

2014-12-01

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

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

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.

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.

The Anatomy of a Grid portal

NASA Astrophysics Data System (ADS)

Licari, Daniele; Calzolari, Federico

2011-12-01

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

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

NASA Astrophysics Data System (ADS)

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

2014-08-01

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

ChRIS--A web-based neuroimaging and informatics system for collecting, organizing, processing, visualizing and sharing of medical data.

PubMed

Pienaar, Rudolph; Rannou, Nicolas; Bernal, Jorge; Hahn, Daniel; Grant, P Ellen

2015-01-01

The utility of web browsers for general purpose computing, long anticipated, is only now coming into fruition. In this paper we present a web-based medical image data and information management software platform called ChRIS ([Boston] Children's Research Integration System). ChRIS' deep functionality allows for easy retrieval of medical image data from resources typically found in hospitals, organizes and presents information in a modern feed-like interface, provides access to a growing library of plugins that process these data - typically on a connected High Performance Compute Cluster, allows for easy data sharing between users and instances of ChRIS and provides powerful 3D visualization and real time collaboration.

jSPyDB, an open source database-independent tool for data management

NASA Astrophysics Data System (ADS)

Pierro, Giuseppe Antonio; Cavallari, Francesca; Di Guida, Salvatore; Innocente, Vincenzo

2011-12-01

Nowadays, the number of commercial tools available for accessing Databases, built on Java or .Net, is increasing. However, many of these applications have several drawbacks: usually they are not open-source, they provide interfaces only with a specific kind of database, they are platform-dependent and very CPU and memory consuming. jSPyDB is a free web-based tool written using Python and Javascript. It relies on jQuery and python libraries, and is intended to provide a simple handler to different database technologies inside a local web browser. Such a tool, exploiting fast access libraries such as SQLAlchemy, is easy to install, and to configure. The design of this tool envisages three layers. The front-end client side in the local web browser communicates with a backend server. Only the server is able to connect to the different databases for the purposes of performing data definition and manipulation. The server makes the data available to the client, so that the user can display and handle them safely. Moreover, thanks to jQuery libraries, this tool supports export of data in different formats, such as XML and JSON. Finally, by using a set of pre-defined functions, users are allowed to create their customized views for a better data visualization. In this way, we optimize the performance of database servers by avoiding short connections and concurrent sessions. In addition, security is enforced since we do not provide users the possibility to directly execute any SQL statement.

Adapting an existing visualization application for browser-based deployment: A case study from the Tropical Rainfall Measuring Mission

NASA Astrophysics Data System (ADS)

Kelley, Owen A.

2013-02-01

THOR, the Tool for High-resolution Observation Review, is a data viewer for the Tropical Rainfall Measuring Mission (TRMM) and the upcoming Global Precipitation Measurement (GPM) mission. THOR began as a desktop application, but now it can be accessed with a web browser, making THOR one of the first online tools for visualizing TRMM satellite data (http://pps.gsfc.nasa.gov/thor). In this effort, the reuse of the existing visualization code was maximized and the complexity of new code was minimized by avoiding unnecessary functionality, frameworks, or libraries. The simplicity of this approach makes it potentially attractive to researchers wishing to adapt their visualization applications for online deployment. To enable THOR to run within a web browser, three new pieces of code are written. First, the graphical user interface (GUI) of the desktop application is translated into HTML, JavaScript, and CSS. Second, a simple communication mechanism is developed over HTTP. Third, a virtual GUI is created on the server that interfaces with the image-generating routines of the existing desktop application so that these routines do not need to be modified for online use. While the basic functionality of THOR is now available online, prototyping is ongoing for enhanced 3D imaging and other aspects of both THOR Desktop and THOR Online. Because TRMM data products are complex and periodically reprocessed with improved algorithms, having a tool such as THOR is important to analysts at the Precipitation Processing System where the algorithms are tested and the products generated, stored, and distributed. Researchers also have found THOR useful for taking a first look at individual files before writing their own software to perform specialized calculations and analyses.

Toward Exposing Timing-Based Probing Attacks in Web Applications.

PubMed

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

2017-02-25

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

Data Archival and Retrieval Enhancement (DARE) Metadata Modeling and Its User Interface

NASA Technical Reports Server (NTRS)

Hyon, Jason J.; Borgen, Rosana B.

1996-01-01

The Defense Nuclear Agency (DNA) has acquired terabytes of valuable data which need to be archived and effectively distributed to the entire nuclear weapons effects community and others...This paper describes the DARE (Data Archival and Retrieval Enhancement) metadata model and explains how it is used as a source for generating HyperText Markup Language (HTML)or Standard Generalized Markup Language (SGML) documents for access through web browsers such as Netscape.

Supercomputer Environments

DTIC Science & Technology

1990-01-09

data structures can easily be presented to the user interface. An emphasis of the Graph Browser was the realization of graph views and graph animation ... animation of the graph. Anima- tion of the graph includes changing node shapes, changing node and arc colors, changing node and arc text, and making...many graphs tend to be tree-like. Animtion of a graph is a useful feature. One of the primary goals of GMB was to support animated graphs. For animation

Choosing a genome browser for a Model Organism Database: surveying the Maize community

PubMed Central

Sen, Taner Z.; Harper, Lisa C.; Schaeffer, Mary L.; Andorf, Carson M.; Seigfried, Trent E.; Campbell, Darwin A.; Lawrence, Carolyn J.

2010-01-01

As the B73 maize genome sequencing project neared completion, MaizeGDB began to integrate a graphical genome browser with its existing web interface and database. To ensure that maize researchers would optimally benefit from the potential addition of a genome browser to the existing MaizeGDB resource, personnel at MaizeGDB surveyed researchers’ needs. Collected data indicate that existing genome browsers for maize were inadequate and suggest implementation of a browser with quick interface and intuitive tools would meet most researchers’ needs. Here, we document the survey’s outcomes, review functionalities of available genome browser software platforms and offer our rationale for choosing the GBrowse software suite for MaizeGDB. Because the genome as represented within the MaizeGDB Genome Browser is tied to detailed phenotypic data, molecular marker information, available stocks, etc., the MaizeGDB Genome Browser represents a novel mechanism by which the researchers can leverage maize sequence information toward crop improvement directly. Database URL: http://gbrowse.maizegdb.org/ PMID:20627860

A general UNIX interface for biocomputing and network information retrieval software.

PubMed

Kiong, B K; Tan, T W

1993-10-01

We describe a UNIX program, HYBROW, which can integrate without modification a wide range of UNIX biocomputing and network information retrieval software. HYBROW works in conjunction with a separate set of ASCII files containing embedded hypertext-like links. The program operates like a hypertext browser featuring five basic links: file link, execute-only link, execute-display link, directory-browse link and field-filling link. Useful features of the interface may be developed using combinations of these links with simple shell scripts and examples of these are briefly described. The system manager who supports biocomputing users should find the program easy to maintain, and useful in assisting new and infrequent users; it is also simple to incorporate new programs. Moreover, the individual user can customize the interface, create dynamic menus, hypertext a document, invoke shell scripts and new programs simply with a basic understanding of the UNIX operating system and any text editor. This program was written in C language and uses the UNIX curses and termcap libraries. It is freely available as a tar compressed file (by anonymous FTP from nuscc.nus.sg).

High school students as a seismic network analysts

NASA Astrophysics Data System (ADS)

Filatov, P.; Fedorenko, Yu.; Beketova, E.; Husebye, E.

2003-04-01

Many research organizations have a large amount of collected seismological data. Some data centers keep data closed from scientists, others have a specific interfaces for access, what is not acceptable for education. For SeisSchool Network in Norway we have developed an universal interface for research and study. The main principles of our interface are: bullet Accessibility - it should provides data access for everybody any where via Internet without restrictions of hardware platform, operational system, Internet browser or bandwidth of connection. bullet Informativity - it should visualize data, have examples of processing routines (filters, envelopes) including phase picking and event location. Also it provides access to various seismology information. bullet Scalability - provide storage for various types of seismic data and a multitude of services for many user levels. This interface (http://pcg1.ifjf.uib.no) helps analysts in basic research and together with information of our Web site we introduces students to theory and practice of seismology. Based on our Web interface group of students won a Norwegian Young Scientists award. In this presentation we demonstrate advantages of our interface, on-line data processing and how to monitoring our network in near real time.

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

PubMed

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

2018-01-01

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

expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform1[OPEN

PubMed Central

2016-01-01

The majority of transcriptome sequencing (RNA-seq) expression studies in plants remain underutilized and inaccessible due to the use of disparate transcriptome references and the lack of skills and resources to analyze and visualize these data. We have developed expVIP, an expression visualization and integration platform, which allows easy analysis of RNA-seq data combined with an intuitive and interactive interface. Users can analyze public and user-specified data sets with minimal bioinformatics knowledge using the expVIP virtual machine. This generates a custom Web browser to visualize, sort, and filter the RNA-seq data and provides outputs for differential gene expression analysis. We demonstrate expVIP’s suitability for polyploid crops and evaluate its performance across a range of biologically relevant scenarios. To exemplify its use in crop research, we developed a flexible wheat (Triticum aestivum) expression browser (www.wheat-expression.com) that can be expanded with user-generated data in a local virtual machine environment. The open-access expVIP platform will facilitate the analysis of gene expression data from a wide variety of species by enabling the easy integration, visualization, and comparison of RNA-seq data across experiments. PMID:26869702

Web-Accessible Scientific Workflow System for Performance Monitoring

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

Roelof Versteeg; Roelof Versteeg; Trevor Rowe

2006-03-01

We describe the design and implementation of a web accessible scientific workflow system for environmental monitoring. This workflow environment integrates distributed, automated data acquisition with server side data management and information visualization through flexible browser based data access tools. Component technologies include a rich browser-based client (using dynamic Javascript and HTML/CSS) for data selection, a back-end server which uses PHP for data processing, user management, and result delivery, and third party applications which are invoked by the back-end using webservices. This environment allows for reproducible, transparent result generation by a diverse user base. It has been implemented for several monitoringmore » systems with different degrees of complexity.« less

Pharmit: interactive exploration of chemical space.

PubMed

Sunseri, Jocelyn; Koes, David Ryan

2016-07-08

Pharmit (http://pharmit.csb.pitt.edu) provides an online, interactive environment for the virtual screening of large compound databases using pharmacophores, molecular shape and energy minimization. Users can import, create and edit virtual screening queries in an interactive browser-based interface. Queries are specified in terms of a pharmacophore, a spatial arrangement of the essential features of an interaction, and molecular shape. Search results can be further ranked and filtered using energy minimization. In addition to a number of pre-built databases of popular compound libraries, users may submit their own compound libraries for screening. Pharmit uses state-of-the-art sub-linear algorithms to provide interactive screening of millions of compounds. Queries typically take a few seconds to a few minutes depending on their complexity. This allows users to iteratively refine their search during a single session. The easy access to large chemical datasets provided by Pharmit simplifies and accelerates structure-based drug design. Pharmit is available under a dual BSD/GPL open-source license. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

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/.

IcyTree: rapid browser-based visualization for phylogenetic trees and networks

PubMed Central

2017-01-01

Abstract Summary: IcyTree is an easy-to-use application which can be used to visualize a wide variety of phylogenetic trees and networks. While numerous phylogenetic tree viewers exist already, IcyTree distinguishes itself by being a purely online tool, having a responsive user interface, supporting phylogenetic networks (ancestral recombination graphs in particular), and efficiently drawing trees that include information such as ancestral locations or trait values. IcyTree also provides intuitive panning and zooming utilities that make exploring large phylogenetic trees of many thousands of taxa feasible. Availability and Implementation: IcyTree is a web application and can be accessed directly at http://tgvaughan.github.com/icytree. Currently supported web browsers include Mozilla Firefox and Google Chrome. IcyTree is written entirely in client-side JavaScript (no plugin required) and, once loaded, does not require network access to run. IcyTree is free software, and the source code is made available at http://github.com/tgvaughan/icytree under version 3 of the GNU General Public License. Contact: tgvaughan@gmail.com PMID:28407035

IcyTree: rapid browser-based visualization for phylogenetic trees and networks.

PubMed

Vaughan, Timothy G

2017-08-01

IcyTree is an easy-to-use application which can be used to visualize a wide variety of phylogenetic trees and networks. While numerous phylogenetic tree viewers exist already, IcyTree distinguishes itself by being a purely online tool, having a responsive user interface, supporting phylogenetic networks (ancestral recombination graphs in particular), and efficiently drawing trees that include information such as ancestral locations or trait values. IcyTree also provides intuitive panning and zooming utilities that make exploring large phylogenetic trees of many thousands of taxa feasible. IcyTree is a web application and can be accessed directly at http://tgvaughan.github.com/icytree . Currently supported web browsers include Mozilla Firefox and Google Chrome. IcyTree is written entirely in client-side JavaScript (no plugin required) and, once loaded, does not require network access to run. IcyTree is free software, and the source code is made available at http://github.com/tgvaughan/icytree under version 3 of the GNU General Public License. tgvaughan@gmail.com. © The Author(s) 2017. Published by Oxford University Press.

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

PubMed Central

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

2012-01-01

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

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

PubMed

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

2012-04-01

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

Argo: an integrative, interactive, text mining-based workbench supporting curation

PubMed Central

Rak, Rafal; Rowley, Andrew; Black, William; Ananiadou, Sophia

2012-01-01

Curation of biomedical literature is often supported by the automatic analysis of textual content that generally involves a sequence of individual processing components. Text mining (TM) has been used to enhance the process of manual biocuration, but has been focused on specific databases and tasks rather than an environment integrating TM tools into the curation pipeline, catering for a variety of tasks, types of information and applications. Processing components usually come from different sources and often lack interoperability. The well established Unstructured Information Management Architecture is a framework that addresses interoperability by defining common data structures and interfaces. However, most of the efforts are targeted towards software developers and are not suitable for curators, or are otherwise inconvenient to use on a higher level of abstraction. To overcome these issues we introduce Argo, an interoperable, integrative, interactive and collaborative system for text analysis with a convenient graphic user interface to ease the development of processing workflows and boost productivity in labour-intensive manual curation. Robust, scalable text analytics follow a modular approach, adopting component modules for distinct levels of text analysis. The user interface is available entirely through a web browser that saves the user from going through often complicated and platform-dependent installation procedures. Argo comes with a predefined set of processing components commonly used in text analysis, while giving the users the ability to deposit their own components. The system accommodates various areas and levels of user expertise, from TM and computational linguistics to ontology-based curation. One of the key functionalities of Argo is its ability to seamlessly incorporate user-interactive components, such as manual annotation editors, into otherwise completely automatic pipelines. As a use case, we demonstrate the functionality of an in-built manual annotation editor that is well suited for in-text corpus annotation tasks. Database URL: http://www.nactem.ac.uk/Argo PMID:22434844

A Web-Based Information System for Field Data Management

NASA Astrophysics Data System (ADS)

Weng, Y. H.; Sun, F. S.

2014-12-01

A web-based field data management system has been designed and developed to allow field geologists to store, organize, manage, and share field data online. System requirements were analyzed and clearly defined first regarding what data are to be stored, who the potential users are, and what system functions are needed in order to deliver the right data in the right way to the right user. A 3-tiered architecture was adopted to create this secure, scalable system that consists of a web browser at the front end while a database at the back end and a functional logic server in the middle. Specifically, HTML, CSS, and JavaScript were used to implement the user interface in the front-end tier, the Apache web server runs PHP scripts, and MySQL to server is used for the back-end database. The system accepts various types of field information, including image, audio, video, numeric, and text. It allows users to select data and populate them on either Google Earth or Google Maps for the examination of the spatial relations. It also makes the sharing of field data easy by converting them into XML format that is both human-readable and machine-readable, and thus ready for reuse.

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.

Next generation tools for genomic data generation, distribution, and visualization

PubMed Central

2010-01-01

Background With the rapidly falling cost and availability of high throughput sequencing and microarray technologies, the bottleneck for effectively using genomic analysis in the laboratory and clinic is shifting to one of effectively managing, analyzing, and sharing genomic data. Results Here we present three open-source, platform independent, software tools for generating, analyzing, distributing, and visualizing genomic data. These include a next generation sequencing/microarray LIMS and analysis project center (GNomEx); an application for annotating and programmatically distributing genomic data using the community vetted DAS/2 data exchange protocol (GenoPub); and a standalone Java Swing application (GWrap) that makes cutting edge command line analysis tools available to those who prefer graphical user interfaces. Both GNomEx and GenoPub use the rich client Flex/Flash web browser interface to interact with Java classes and a relational database on a remote server. Both employ a public-private user-group security model enabling controlled distribution of patient and unpublished data alongside public resources. As such, they function as genomic data repositories that can be accessed manually or programmatically through DAS/2-enabled client applications such as the Integrated Genome Browser. Conclusions These tools have gained wide use in our core facilities, research laboratories and clinics and are freely available for non-profit use. See http://sourceforge.net/projects/gnomex/, http://sourceforge.net/projects/genoviz/, and http://sourceforge.net/projects/useq. PMID:20828407

Doing Your Science While You're in Orbit

NASA Astrophysics Data System (ADS)

Green, Mark L.; Miller, Stephen D.; Vazhkudai, Sudharshan S.; Trater, James R.

2010-11-01

Large-scale neutron facilities such as the Spallation Neutron Source (SNS) located at Oak Ridge National Laboratory need easy-to-use access to Department of Energy Leadership Computing Facilities and experiment repository data. The Orbiter thick- and thin-client and its supporting Service Oriented Architecture (SOA) based services (available at https://orbiter.sns.gov) consist of standards-based components that are reusable and extensible for accessing high performance computing, data and computational grid infrastructure, and cluster-based resources easily from a user configurable interface. The primary Orbiter system goals consist of (1) developing infrastructure for the creation and automation of virtual instrumentation experiment optimization, (2) developing user interfaces for thin- and thick-client access, (3) provide a prototype incorporating major instrument simulation packages, and (4) facilitate neutron science community access and collaboration. The secure Orbiter SOA authentication and authorization is achieved through the developed Virtual File System (VFS) services, which use Role-Based Access Control (RBAC) for data repository file access, thin-and thick-client functionality and application access, and computational job workflow management. The VFS Relational Database Management System (RDMS) consists of approximately 45 database tables describing 498 user accounts with 495 groups over 432,000 directories with 904,077 repository files. Over 59 million NeXus file metadata records are associated to the 12,800 unique NeXus file field/class names generated from the 52,824 repository NeXus files. Services that enable (a) summary dashboards of data repository status with Quality of Service (QoS) metrics, (b) data repository NeXus file field/class name full text search capabilities within a Google like interface, (c) fully functional RBAC browser for the read-only data repository and shared areas, (d) user/group defined and shared metadata for data repository files, (e) user, group, repository, and web 2.0 based global positioning with additional service capabilities are currently available. The SNS based Orbiter SOA integration progress with the Distributed Data Analysis for Neutron Scattering Experiments (DANSE) software development project is summarized with an emphasis on DANSE Central Services and the Virtual Neutron Facility (VNF). Additionally, the DANSE utilization of the Orbiter SOA authentication, authorization, and data transfer services best practice implementations are presented.

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.

e-Stars Template Builder

NASA Technical Reports Server (NTRS)

Cox, Brian

2003-01-01

e-Stars Template Builder is a computer program that implements a concept of enabling users to rapidly gain access to information on projects of NASA's Jet Propulsion Laboratory. The information about a given project is not stored in a data base, but rather, in a network that follows the project as it develops. e-Stars Template Builder resides on a server computer, using Practical Extraction and Reporting Language (PERL) scripts to create what are called "e-STARS node templates," which are software constructs that allow for project-specific configurations. The software resides on the server and does not require specific software on the user machine except for an Internet browser. A user's computer need not be equipped with special software (other than an Internet-browser program). e-Stars Template Builder is compatible with Windows, Macintosh, and UNIX operating systems. A user invokes e-Stars Template Builder from a browser window. Operations that can be performed by the user include the creation of child processes and the addition of links and descriptions of documentation to existing pages or nodes. By means of this addition of "child processes" of nodes, a network that reflects the development of a project is generated.

Marky: a tool supporting annotation consistency in multi-user and iterative document annotation projects.

PubMed

Pérez-Pérez, Martín; Glez-Peña, Daniel; Fdez-Riverola, Florentino; Lourenço, Anália

2015-02-01

Document annotation is a key task in the development of Text Mining methods and applications. High quality annotated corpora are invaluable, but their preparation requires a considerable amount of resources and time. Although the existing annotation tools offer good user interaction interfaces to domain experts, project management and quality control abilities are still limited. Therefore, the current work introduces Marky, a new Web-based document annotation tool equipped to manage multi-user and iterative projects, and to evaluate annotation quality throughout the project life cycle. At the core, Marky is a Web application based on the open source CakePHP framework. User interface relies on HTML5 and CSS3 technologies. Rangy library assists in browser-independent implementation of common DOM range and selection tasks, and Ajax and JQuery technologies are used to enhance user-system interaction. Marky grants solid management of inter- and intra-annotator work. Most notably, its annotation tracking system supports systematic and on-demand agreement analysis and annotation amendment. Each annotator may work over documents as usual, but all the annotations made are saved by the tracking system and may be further compared. So, the project administrator is able to evaluate annotation consistency among annotators and across rounds of annotation, while annotators are able to reject or amend subsets of annotations made in previous rounds. As a side effect, the tracking system minimises resource and time consumption. Marky is a novel environment for managing multi-user and iterative document annotation projects. Compared to other tools, Marky offers a similar visually intuitive annotation experience while providing unique means to minimise annotation effort and enforce annotation quality, and therefore corpus consistency. Marky is freely available for non-commercial use at http://sing.ei.uvigo.es/marky. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Browser-Based Online Applications: Something for Everyone!

ERIC Educational Resources Information Center

Descy, Don E.

2007-01-01

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

SoyFN: a knowledge database of soybean functional networks.

PubMed

Xu, Yungang; Guo, Maozu; Liu, Xiaoyan; Wang, Chunyu; Liu, Yang

2014-01-01

Many databases for soybean genomic analysis have been built and made publicly available, but few of them contain knowledge specifically targeting the omics-level gene-gene, gene-microRNA (miRNA) and miRNA-miRNA interactions. Here, we present SoyFN, a knowledge database of soybean functional gene networks and miRNA functional networks. SoyFN provides user-friendly interfaces to retrieve, visualize, analyze and download the functional networks of soybean genes and miRNAs. In addition, it incorporates much information about KEGG pathways, gene ontology annotations and 3'-UTR sequences as well as many useful tools including SoySearch, ID mapping, Genome Browser, eFP Browser and promoter motif scan. SoyFN is a schema-free database that can be accessed as a Web service from any modern programming language using a simple Hypertext Transfer Protocol call. The Web site is implemented in Java, JavaScript, PHP, HTML and Apache, with all major browsers supported. We anticipate that this database will be useful for members of research communities both in soybean experimental science and bioinformatics. Database URL: http://nclab.hit.edu.cn/SoyFN.

Web-Based Environment for Maintaining Legacy Software

NASA Technical Reports Server (NTRS)

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

2007-01-01

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

BrainBrowser: distributed, web-based neurological data visualization.

PubMed

Sherif, Tarek; Kassis, Nicolas; Rousseau, Marc-Étienne; Adalat, Reza; Evans, Alan C

2014-01-01

Recent years have seen massive, distributed datasets become the norm in neuroimaging research, and the methodologies used to analyze them have, in response, become more collaborative and exploratory. Tools and infrastructure are continuously being developed and deployed to facilitate research in this context: grid computation platforms to process the data, distributed data stores to house and share them, high-speed networks to move them around and collaborative, often web-based, platforms to provide access to and sometimes manage the entire system. BrainBrowser is a lightweight, high-performance JavaScript visualization library built to provide easy-to-use, powerful, on-demand visualization of remote datasets in this new research environment. BrainBrowser leverages modern web technologies, such as WebGL, HTML5 and Web Workers, to visualize 3D surface and volumetric neuroimaging data in any modern web browser without requiring any browser plugins. It is thus trivial to integrate BrainBrowser into any web-based platform. BrainBrowser is simple enough to produce a basic web-based visualization in a few lines of code, while at the same time being robust enough to create full-featured visualization applications. BrainBrowser can dynamically load the data required for a given visualization, so no network bandwidth needs to be waisted on data that will not be used. BrainBrowser's integration into the standardized web platform also allows users to consider using 3D data visualization in novel ways, such as for data distribution, data sharing and dynamic online publications. BrainBrowser is already being used in two major online platforms, CBRAIN and LORIS, and has been used to make the 1TB MACACC dataset openly accessible.

BrainBrowser: distributed, web-based neurological data visualization

PubMed Central

Sherif, Tarek; Kassis, Nicolas; Rousseau, Marc-Étienne; Adalat, Reza; Evans, Alan C.

2015-01-01

Recent years have seen massive, distributed datasets become the norm in neuroimaging research, and the methodologies used to analyze them have, in response, become more collaborative and exploratory. Tools and infrastructure are continuously being developed and deployed to facilitate research in this context: grid computation platforms to process the data, distributed data stores to house and share them, high-speed networks to move them around and collaborative, often web-based, platforms to provide access to and sometimes manage the entire system. BrainBrowser is a lightweight, high-performance JavaScript visualization library built to provide easy-to-use, powerful, on-demand visualization of remote datasets in this new research environment. BrainBrowser leverages modern web technologies, such as WebGL, HTML5 and Web Workers, to visualize 3D surface and volumetric neuroimaging data in any modern web browser without requiring any browser plugins. It is thus trivial to integrate BrainBrowser into any web-based platform. BrainBrowser is simple enough to produce a basic web-based visualization in a few lines of code, while at the same time being robust enough to create full-featured visualization applications. BrainBrowser can dynamically load the data required for a given visualization, so no network bandwidth needs to be waisted on data that will not be used. BrainBrowser's integration into the standardized web platform also allows users to consider using 3D data visualization in novel ways, such as for data distribution, data sharing and dynamic online publications. BrainBrowser is already being used in two major online platforms, CBRAIN and LORIS, and has been used to make the 1TB MACACC dataset openly accessible. PMID:25628562

Distributed health care imaging information systems

NASA Astrophysics Data System (ADS)

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

1997-05-01

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

The Jupyter/IPython architecture: a unified view of computational research, from interactive exploration to communication and publication.

NASA Astrophysics Data System (ADS)

Ragan-Kelley, M.; Perez, F.; Granger, B.; Kluyver, T.; Ivanov, P.; Frederic, J.; Bussonnier, M.

2014-12-01

IPython has provided terminal-based tools for interactive computing in Python since 2001. The notebook document format and multi-process architecture introduced in 2011 have expanded the applicable scope of IPython into teaching, presenting, and sharing computational work, in addition to interactive exploration. The new architecture also allows users to work in any language, with implementations in Python, R, Julia, Haskell, and several other languages. The language agnostic parts of IPython have been renamed to Jupyter, to better capture the notion that a cross-language design can encapsulate commonalities present in computational research regardless of the programming language being used. This architecture offers components like the web-based Notebook interface, that supports rich documents that combine code and computational results with text narratives, mathematics, images, video and any media that a modern browser can display. This interface can be used not only in research, but also for publication and education, as notebooks can be converted to a variety of output formats, including HTML and PDF. Recent developments in the Jupyter project include a multi-user environment for hosting notebooks for a class or research group, a live collaboration notebook via Google Docs, and better support for languages other than Python.

New web technologies for astronomy

NASA Astrophysics Data System (ADS)

Sprimont, P.-G.; Ricci, D.; Nicastro, L.

2014-12-01

Thanks to the new HTML5 capabilities and the huge improvements of the JavaScript language, it is now possible to design very complex and interactive web user interfaces. On top of that, the once monolithic and file-server oriented web servers are evolving into easily programmable server applications capable to cope with the complex interactions made possible by the new generation of browsers. We believe that the whole community of amateur and professionals astronomers can benefit from the potential of these new technologies. New web interfaces can be designed to provide the user with a large deal of much more intuitive and interactive tools. Accessing astronomical data archives, schedule, control and monitor observatories, and in particular robotic telescopes, supervising data reduction pipelines, all are capabilities that can now be implemented in a JavaScript web application. In this paper we describe the Sadira package we are implementing exactly to this aim.

WebCN: A web-based computation tool for in situ-produced cosmogenic nuclides

NASA Astrophysics Data System (ADS)

Ma, Xiuzeng; Li, Yingkui; Bourgeois, Mike; Caffee, Marc; Elmore, David; Granger, Darryl; Muzikar, Paul; Smith, Preston

2007-06-01

Cosmogenic nuclide techniques are increasingly being utilized in geoscience research. For this it is critical to establish an effective, easily accessible and well defined tool for cosmogenic nuclide computations. We have been developing a web-based tool (WebCN) to calculate surface exposure ages and erosion rates based on the nuclide concentrations measured by the accelerator mass spectrometry. WebCN for 10Be and 26Al has been finished and published at http://www.physics.purdue.edu/primelab/for_users/rockage.html. WebCN for 36Cl is under construction. WebCN is designed as a three-tier client/server model and uses the open source PostgreSQL for the database management and PHP for the interface design and calculations. On the client side, an internet browser and Microsoft Access are used as application interfaces to access the system. Open Database Connectivity is used to link PostgreSQL and Microsoft Access. WebCN accounts for both spatial and temporal distributions of the cosmic ray flux to calculate the production rates of in situ-produced cosmogenic nuclides at the Earth's surface.

Virtual setting for training in interpreting mammography images

NASA Astrophysics Data System (ADS)

Pezzuol, J. L.; Abreu, F. D. L.; Silva, S. M.; Tendolini, A.; Bissaco, M. A. Se; Rodrigues, S. C. M.

2017-03-01

This work presents a web system for the training of students or residents (users) interested in the detection of breast density in mammography images. The system consists of a breast imaging database with breast density types classified and demarcated by the specialist (tutor) or online database. The planning was based on ISO / IEC 12207. Through the browser (desktop or notebook), the user will visualize the breast images and in them will realize the markings of the density region and even classify them per the BI-RADS protocol. After marking, this will be compared to the gold standard already existing in the image base, and then the system will inform if the area demarcation has been set or not. The shape of this marking is similar to the paint brush. The evaluation was based on ISO / IEC 1926 or 25010: 2011 by 3 software development specialists and 3 in mammary radiology, evaluating usability, configuration, performance and System interface through the Likert scale-based questionnaire. Where they have totally agreed on usability, configuration, performance and partially on the interface. And as a good thing: the system is able to be accessed anywhere and at any time, the hit or error response is in real time, it can be used in the educational area, the limit of the amount of images will depend on the size of the computer memory, At the end the system sends the results achieved by e-mail to the user, reproduction of the system on any type of screen, complementation of the system with other types of breast structures. Negative points are the need for internet.

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

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

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

2014-12-15

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

Tools for Administration of a UNIX-Based Network

NASA Technical Reports Server (NTRS)

LeClaire, Stephen; Farrar, Edward

2004-01-01

Several computer programs have been developed to enable efficient administration of a large, heterogeneous, UNIX-based computing and communication network that includes a variety of computers connected to a variety of subnetworks. One program provides secure software tools for administrators to create, modify, lock, and delete accounts of specific users. This program also provides tools for users to change their UNIX passwords and log-in shells. These tools check for errors. Another program comprises a client and a server component that, together, provide a secure mechanism to create, modify, and query quota levels on a network file system (NFS) mounted by use of the VERITAS File SystemJ software. The client software resides on an internal secure computer with a secure Web interface; one can gain access to the client software from any authorized computer capable of running web-browser software. The server software resides on a UNIX computer configured with the VERITAS software system. Directories where VERITAS quotas are applied are NFS-mounted. Another program is a Web-based, client/server Internet Protocol (IP) address tool that facilitates maintenance lookup of information about IP addresses for a network of computers.

cisPath: an R/Bioconductor package for cloud users for visualization and management of functional protein interaction networks.

PubMed

Wang, Likun; Yang, Luhe; Peng, Zuohan; Lu, Dan; Jin, Yan; McNutt, Michael; Yin, Yuxin

2015-01-01

With the burgeoning development of cloud technology and services, there are an increasing number of users who prefer cloud to run their applications. All software and associated data are hosted on the cloud, allowing users to access them via a web browser from any computer, anywhere. This paper presents cisPath, an R/Bioconductor package deployed on cloud servers for client users to visualize, manage, and share functional protein interaction networks. With this R package, users can easily integrate downloaded protein-protein interaction information from different online databases with private data to construct new and personalized interaction networks. Additional functions allow users to generate specific networks based on private databases. Since the results produced with the use of this package are in the form of web pages, cloud users can easily view and edit the network graphs via the browser, using a mouse or touch screen, without the need to download them to a local computer. This package can also be installed and run on a local desktop computer. Depending on user preference, results can be publicized or shared by uploading to a web server or cloud driver, allowing other users to directly access results via a web browser. This package can be installed and run on a variety of platforms. Since all network views are shown in web pages, such package is particularly useful for cloud users. The easy installation and operation is an attractive quality for R beginners and users with no previous experience with cloud services.

cisPath: an R/Bioconductor package for cloud users for visualization and management of functional protein interaction networks

PubMed Central

2015-01-01

Background With the burgeoning development of cloud technology and services, there are an increasing number of users who prefer cloud to run their applications. All software and associated data are hosted on the cloud, allowing users to access them via a web browser from any computer, anywhere. This paper presents cisPath, an R/Bioconductor package deployed on cloud servers for client users to visualize, manage, and share functional protein interaction networks. Results With this R package, users can easily integrate downloaded protein-protein interaction information from different online databases with private data to construct new and personalized interaction networks. Additional functions allow users to generate specific networks based on private databases. Since the results produced with the use of this package are in the form of web pages, cloud users can easily view and edit the network graphs via the browser, using a mouse or touch screen, without the need to download them to a local computer. This package can also be installed and run on a local desktop computer. Depending on user preference, results can be publicized or shared by uploading to a web server or cloud driver, allowing other users to directly access results via a web browser. Conclusions This package can be installed and run on a variety of platforms. Since all network views are shown in web pages, such package is particularly useful for cloud users. The easy installation and operation is an attractive quality for R beginners and users with no previous experience with cloud services. PMID:25708840

[A web-based biomedical image mosaicing system].

PubMed

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

2006-11-01

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

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

ERIC Educational Resources Information Center

Technology & Learning, 2005

2005-01-01

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

Software architecture and design of the web services facilitating climate model diagnostic analysis

NASA Astrophysics Data System (ADS)

Pan, L.; Lee, S.; Zhang, J.; Tang, B.; Zhai, C.; Jiang, J. H.; Wang, W.; Bao, Q.; Qi, M.; Kubar, T. L.; Teixeira, J.

2015-12-01

Climate model diagnostic analysis is a computationally- and data-intensive task because it involves multiple numerical model outputs and satellite observation data that can both be high resolution. We have built an online tool that facilitates this process. The tool is called Climate Model Diagnostic Analyzer (CMDA). It employs the web service technology and provides a web-based user interface. The benefits of these choices include: (1) No installation of any software other than a browser, hence it is platform compatable; (2) Co-location of computation and big data on the server side, and small results and plots to be downloaded on the client side, hence high data efficiency; (3) multi-threaded implementation to achieve parallel performance on multi-core servers; and (4) cloud deployment so each user has a dedicated virtual machine. In this presentation, we will focus on the computer science aspects of this tool, namely the architectural design, the infrastructure of the web services, the implementation of the web-based user interface, the mechanism of provenance collection, the approach to virtualization, and the Amazon Cloud deployment. As an example, We will describe our methodology to transform an existing science application code into a web service using a Python wrapper interface and Python web service frameworks (i.e., Flask, Gunicorn, and Tornado). Another example is the use of Docker, a light-weight virtualization container, to distribute and deploy CMDA onto an Amazon EC2 instance. Our tool of CMDA has been successfully used in the 2014 Summer School hosted by the JPL Center for Climate Science. Students had positive feedbacks in general and we will report their comments. An enhanced version of CMDA with several new features, some requested by the 2014 students, will be used in the 2015 Summer School soon.

Web-based reactive transport modeling using PFLOTRAN

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

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/

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

PubMed

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

2014-08-15

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

Fast and flexible selection with a single switch.

PubMed

Broderick, Tamara; MacKay, David J C

2009-10-22

Selection methods that require only a single-switch input, such as a button click or blink, are potentially useful for individuals with motor impairments, mobile technology users, and individuals wishing to transmit information securely. We present a single-switch selection method, "Nomon," that is general and efficient. Existing single-switch selection methods require selectable options to be arranged in ways that limit potential applications. By contrast, traditional operating systems, web browsers, and free-form applications (such as drawing) place options at arbitrary points on the screen. Nomon, however, has the flexibility to select any point on a screen. Nomon adapts automatically to an individual's clicking ability; it allows a person who clicks precisely to make a selection quickly and allows a person who clicks imprecisely more time to make a selection without error. Nomon reaps gains in information rate by allowing the specification of beliefs (priors) about option selection probabilities and by avoiding tree-based selection schemes in favor of direct (posterior) inference. We have developed both a Nomon-based writing application and a drawing application. To evaluate Nomon's performance, we compared the writing application with a popular existing method for single-switch writing (row-column scanning). Novice users wrote 35% faster with the Nomon interface than with the scanning interface. An experienced user (author TB, with 10 hours practice) wrote at speeds of 9.3 words per minute with Nomon, using 1.2 clicks per character and making no errors in the final text.

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

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

Baker, M Pauline

2007-06-30

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

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.

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.

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures.

PubMed

Duan, Qiaonan; Flynn, Corey; Niepel, Mario; Hafner, Marc; Muhlich, Jeremy L; Fernandez, Nicolas F; Rouillard, Andrew D; Tan, Christopher M; Chen, Edward Y; Golub, Todd R; Sorger, Peter K; Subramanian, Aravind; Ma'ayan, Avi

2014-07-01

For the Library of Integrated Network-based Cellular Signatures (LINCS) project many gene expression signatures using the L1000 technology have been produced. The L1000 technology is a cost-effective method to profile gene expression in large scale. LINCS Canvas Browser (LCB) is an interactive HTML5 web-based software application that facilitates querying, browsing and interrogating many of the currently available LINCS L1000 data. LCB implements two compacted layered canvases, one to visualize clustered L1000 expression data, and the other to display enrichment analysis results using 30 different gene set libraries. Clicking on an experimental condition highlights gene-sets enriched for the differentially expressed genes from the selected experiment. A search interface allows users to input gene lists and query them against over 100 000 conditions to find the top matching experiments. The tool integrates many resources for an unprecedented potential for new discoveries in systems biology and systems pharmacology. The LCB application is available at http://www.maayanlab.net/LINCS/LCB. Customized versions will be made part of the http://lincscloud.org and http://lincs.hms.harvard.edu websites. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

A Browser-Server-Based Tele-audiology System That Supports Multiple Hearing Test Modalities

PubMed Central

Yao, Daoyuan; Givens, Gregg

2015-01-01

Abstract Introduction: Millions of global citizens suffering from hearing disorders have limited or no access to much needed hearing healthcare. Although tele-audiology presents a solution to alleviate this problem, existing remote hearing diagnosis systems support only pure-tone tests, leaving speech and other test procedures unsolved, due to the lack of software and hardware to enable communication required between audiologists and their remote patients. This article presents a comprehensive remote hearing test system that integrates the two most needed hearing test procedures: a pure-tone audiogram and a speech test. Materials and Methods: This enhanced system is composed of a Web application server, an embedded smart Internet-Bluetooth® (Bluetooth SIG, Kirkland, WA) gateway (or console device), and a Bluetooth-enabled audiometer. Several graphical user interfaces and a relational database are hosted on the application server. The console device has been designed to support the tests and auxiliary communication between the local site and the remote site. Results: The study was conducted at an audiology laboratory. Pure-tone audiogram and speech test results from volunteers tested with this tele-audiology system are comparable with results from the traditional face-to-face approach. Conclusions: This browser-server–based comprehensive tele-audiology offers a flexible platform to expand hearing services to traditionally underserved groups. PMID:25919376

A Browser-Server-Based Tele-audiology System That Supports Multiple Hearing Test Modalities.

PubMed

Yao, Jianchu Jason; Yao, Daoyuan; Givens, Gregg

2015-09-01

Millions of global citizens suffering from hearing disorders have limited or no access to much needed hearing healthcare. Although tele-audiology presents a solution to alleviate this problem, existing remote hearing diagnosis systems support only pure-tone tests, leaving speech and other test procedures unsolved, due to the lack of software and hardware to enable communication required between audiologists and their remote patients. This article presents a comprehensive remote hearing test system that integrates the two most needed hearing test procedures: a pure-tone audiogram and a speech test. This enhanced system is composed of a Web application server, an embedded smart Internet-Bluetooth(®) (Bluetooth SIG, Kirkland, WA) gateway (or console device), and a Bluetooth-enabled audiometer. Several graphical user interfaces and a relational database are hosted on the application server. The console device has been designed to support the tests and auxiliary communication between the local site and the remote site. The study was conducted at an audiology laboratory. Pure-tone audiogram and speech test results from volunteers tested with this tele-audiology system are comparable with results from the traditional face-to-face approach. This browser-server-based comprehensive tele-audiology offers a flexible platform to expand hearing services to traditionally underserved groups.

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

NASA Astrophysics Data System (ADS)

Masseroli, Marco; Pinciroli, Francesco

2000-12-01

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

Smartphone interface to USGS 'Did You Feel It?' - Getting More Citizens Involved in Science

NASA Astrophysics Data System (ADS)

Savran, W. H.; Petersen, R. I.; Wukusick, M.

2013-12-01

Over the last hundred years, we have put forth a concerted effort to install a dense array of seismometers - used to monitor and measure seismic waves propagating through the earth. In addition to expensive instrumentation, citizens provide useful data to the earthquake science community as demonstrated by the USGS 'Did you feel it?' project. Currently, the 'Did You Feel It?' data is acquired, through an internet browser, from a long questionnaire. With the increasing number of smartphone owners, an application interfacing the population with the 'Did you feel it?' project introduces the next logical step in progressing this technology. We are developing an application, which utilizes many features of modern smartphones to provide a better interface from citizen to scientist. Our application will notify users of any earthquake within a predefined distance above a predefined size. At this point, the user has the option to answer the questionnaire and send their experience of the earthquake to the USGS 'Did you feel it?' database or simply decline. Instead of a cumbersome web-form, the user will be prompted for questions in line with the paradigm of current smartphone application development. An easy, interactive interface allows the user to answer the questions rapidly in a fun manner, resulting in more participation. In addition to putting earthquake science into the hands of many more citizens, the application will also allow the user to place an emergency call in case of casualty during the next big one. Future versions of the application will allow users to take, view, and submit photographs of damage caused by the earthquake. Also, users will be able to view intensity maps generated for the event they evaluated. The USGS has already done an incredible job setting up the 'Did you feel it?' framework; having a more accessible user interface to acquire data will greatly expand the possibilities of the 'Did you feel it?' project.

Gesture Interaction Browser-Based 3D Molecular Viewer.

PubMed

Virag, Ioan; Stoicu-Tivadar, Lăcrămioara; Crişan-Vida, Mihaela

2016-01-01

The paper presents an open source system that allows the user to interact with a 3D molecular viewer using associated hand gestures for rotating, scaling and panning the rendered model. The novelty of this approach is that the entire application is browser-based and doesn't require installation of third party plug-ins or additional software components in order to visualize the supported chemical file formats. This kind of solution is suitable for instruction of users in less IT oriented environments, like medicine or chemistry. For rendering various molecular geometries our team used GLmol (a molecular viewer written in JavaScript). The interaction with the 3D models is made with Leap Motion controller that allows real-time tracking of the user's hand gestures. The first results confirmed that the resulting application leads to a better way of understanding various types of translational bioinformatics related problems in both biomedical research and education.

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

PubMed

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

2013-07-09

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

AccessScope project: Accessible light microscope for users with upper limb mobility or visual impairments.

PubMed

Mansoor, Awais; Ahmed, Wamiq M; Samarapungavan, Ala; Cirillo, John; Schwarte, David; Robinson, J Paul; Duerstock, Bradley S

2010-01-01

A web-based application was developed to remotely view slide specimens and control all functions of a research-level light microscopy workstation, called AccessScope. Students and scientists with upper limb mobility and visual impairments are often unable to use a light microscope by themselves and must depend on others in its operation. Users with upper limb mobility impairments and low vision were recruited to assist in the design process of the AccessScope personal computer (PC) user interface. Participants with these disabilities were evaluated in their ability to use AccessScope to perform microscopical tasks. AccessScope usage was compared with inspecting prescanned slide images by grading participants' identification and understanding of histological features and knowledge of microscope operation. With AccessScope subjects were able to independently perform common light microscopy functions through an Internet browser by employing different PC pointing devices or accessibility software according to individual abilities. Subjects answered more histology and microscope usage questions correctly after first participating in an AccessScope test session. AccessScope allowed users with upper limb or visual impairments to successfully perform light microscopy without assistance. This unprecedented capability is crucial for students and scientists with disabilities to perform laboratory coursework or microscope-based research and pursue science, technology, engineering, and mathematics fields.

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

Providing Assistive Technology Applications as a Service Through Cloud Computing.

PubMed

Mulfari, Davide; Celesti, Antonio; Villari, Massimo; Puliafito, Antonio

2015-01-01

Users with disabilities interact with Personal Computers (PCs) using Assistive Technology (AT) software solutions. Such applications run on a PC that a person with a disability commonly uses. However the configuration of AT applications is not trivial at all, especially whenever the user needs to work on a PC that does not allow him/her to rely on his / her AT tools (e.g., at work, at university, in an Internet point). In this paper, we discuss how cloud computing provides a valid technological solution to enhance such a scenario.With the emergence of cloud computing, many applications are executed on top of virtual machines (VMs). Virtualization allows us to achieve a software implementation of a real computer able to execute a standard operating system and any kind of application. In this paper we propose to build personalized VMs running AT programs and settings. By using the remote desktop technology, our solution enables users to control their customized virtual desktop environment by means of an HTML5-based web interface running on any computer equipped with a browser, whenever they are.

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

PubMed

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

1999-01-01

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

Ensemble: a web-based system for psychology survey and experiment management.

PubMed

Tomic, Stefan T; Janata, Petr

2007-08-01

We provide a description of Ensemble, a suite of Web-integrated modules for managing and analyzing data associated with psychology experiments in a small research lab. The system delivers interfaces via a Web browser for creating and presenting simple surveys without the need to author Web pages and with little or no programming effort. The surveys may be extended by selecting and presenting auditory and/or visual stimuli with MATLAB and Flash to enable a wide range of psychophysical and cognitive experiments which do not require the recording of precise reaction times. Additionally, one is provided with the ability to administer and present experiments remotely. The software technologies employed by the various modules of Ensemble are MySQL, PHP, MATLAB, and Flash. The code for Ensemble is open source and available to the public, so that its functions can be readily extended by users. We describe the architecture of the system, the functionality of each module, and provide basic examples of the interfaces.

CTserver: A Computational Thermodynamics Server for the Geoscience Community

NASA Astrophysics Data System (ADS)

Kress, V. C.; Ghiorso, M. S.

2006-12-01

The CTserver platform is an Internet-based computational resource that provides on-demand services in Computational Thermodynamics (CT) to a diverse geoscience user base. This NSF-supported resource can be accessed at ctserver.ofm-research.org. The CTserver infrastructure leverages a high-quality and rigorously tested software library of routines for computing equilibrium phase assemblages and for evaluating internally consistent thermodynamic properties of materials, e.g. mineral solid solutions and a variety of geological fluids, including magmas. Thermodynamic models are currently available for 167 phases. Recent additions include Duan, Møller and Weare's model for supercritical C-O-H-S, extended to include SO2 and S2 species, and an entirely new associated solution model for O-S-Fe-Ni sulfide liquids. This software library is accessed via the CORBA Internet protocol for client-server communication. CORBA provides a standardized, object-oriented, language and platform independent, fast, low-bandwidth interface to phase property modules running on the server cluster. Network transport, language translation and resource allocation are handled by the CORBA interface. Users access server functionality in two principal ways. Clients written as browser- based Java applets may be downloaded which provide specific functionality such as retrieval of thermodynamic properties of phases, computation of phase equilibria for systems of specified composition, or modeling the evolution of these systems along some particular reaction path. This level of user interaction requires minimal programming effort and is ideal for classroom use. A more universal and flexible mode of CTserver access involves making remote procedure calls from user programs directly to the server public interface. The CTserver infrastructure relieves the user of the burden of implementing and testing the often complex thermodynamic models of real liquids and solids. A pilot application of this distributed architecture involves CFD computation of magma convection at Volcan Villarrica with magma properties and phase proportions calculated at each spatial node and at each time step via distributed function calls to MELTS-objects executing on the CTserver. Documentation and programming examples are provided at http://ctserver.ofm- research.org.

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.

Evaluating Web accessibility at different processing phases

NASA Astrophysics Data System (ADS)

Fernandes, N.; Lopes, R.; Carriço, L.

2012-09-01

Modern Web sites use several techniques (e.g. DOM manipulation) that allow for the injection of new content into their Web pages (e.g. AJAX), as well as manipulation of the HTML DOM tree. This has the consequence that the Web pages that are presented to users (i.e. after browser processing) are different from the original structure and content that is transmitted through HTTP communication (i.e. after browser processing). This poses a series of challenges for Web accessibility evaluation, especially on automated evaluation software. This article details an experimental study designed to understand the differences posed by accessibility evaluation after Web browser processing. We implemented a Javascript-based evaluator, QualWeb, that can perform WCAG 2.0 based accessibility evaluations in the two phases of browser processing. Our study shows that, in fact, there are considerable differences between the HTML DOM trees in both phases, which have the consequence of having distinct evaluation results. We discuss the impact of these results in the light of the potential problems that these differences can pose to designers and developers that use accessibility evaluators that function before browser processing.

Efficiently Communicating Rich Heterogeneous Geospatial Data from the FeMO2008 Dive Cruise with FlashMap on EarthRef.org

NASA Astrophysics Data System (ADS)

Minnett, R. C.; Koppers, A. A.; Staudigel, D.; Staudigel, H.

2008-12-01

EarthRef.org is comprehensive and convenient resource for Earth Science reference data and models. It encompasses four main portals: the Geochemical Earth Reference Model (GERM), the Magnetics Information Consortium (MagIC), the Seamount Biogeosciences Network (SBN), and the Enduring Resources for Earth Science Education (ERESE). Their underlying databases are publically available and the scientific community has contributed widely and is urged to continue to do so. However, the net result is a vast and largely heterogeneous warehouse of geospatial data ranging from carefully prepared maps of seamounts to geochemical data/metadata, daily reports from seagoing expeditions, large volumes of raw and processed multibeam data, images of paleomagnetic sampling sites, etc. This presents a considerable obstacle for integrating other rich media content, such as videos, images, data files, cruise tracks, and interoperable database results, without overwhelming the web user. The four EarthRef.org portals clearly lend themselves to a more intuitive user interface and has, therefore, been an invaluable test bed for the design and implementation of FlashMap, a versatile KML-driven geospatial browser written for reliability and speed in Adobe Flash. FlashMap allows layers of content to be loaded and displayed over a streaming high-resolution map which can be zoomed and panned similarly to Google Maps and Google Earth. Many organizations, from National Geographic to the USGS, have begun using Google Earth software to display geospatial content. However, Google Earth, as a desktop application, does not integrate cleanly with existing websites requiring the user to navigate away from the browser and focus on a separate application and Google Maps, written in Java Script, does not scale up reliably to large datasets. FlashMap remedies these problems as a web-based application that allows for seamless integration of the real-time display power of Google Earth and the flexibility of the web without losing scalability and control of the base maps. Our Flash-based application is fully compatible with KML (Keyhole Markup Language) 2.2, the most recent iteration of KML, allowing users with existing Google Earth KML files to effortlessly display their geospatial content embedded in a web page. As a test case for FlashMap, the annual Iron-Oxidizing Microbial Observatory (FeMO) dive cruise to the Loihi Seamount, in conjunction with data available from ongoing and published FeMO laboratory studies, showcases the flexibility of this single web-based application. With a KML 2.2 compatible web-service providing the content, any database can display results in FlashMap. The user can then hide and show multiple layers of content, potentially from several data sources, and rapidly digest a vast quantity of information to narrow the search results. This flexibility gives experienced users the ability to drill down to exactly the record they are looking for (SERC at Carleton College's educational application of FlashMap at http://serc.carleton.edu/sp/erese/activities/22223.html) and allows users familiar with Google Earth the ability to load and view geospatial data content within a browser from any computer with an internet connection.

Bayesian Network Webserver: a comprehensive tool for biological network modeling.

PubMed

Ziebarth, Jesse D; Bhattacharya, Anindya; Cui, Yan

2013-11-01

The Bayesian Network Webserver (BNW) is a platform for comprehensive network modeling of systems genetics and other biological datasets. It allows users to quickly and seamlessly upload a dataset, learn the structure of the network model that best explains the data and use the model to understand relationships between network variables. Many datasets, including those used to create genetic network models, contain both discrete (e.g. genotype) and continuous (e.g. gene expression traits) variables, and BNW allows for modeling hybrid datasets. Users of BNW can incorporate prior knowledge during structure learning through an easy-to-use structural constraint interface. After structure learning, users are immediately presented with an interactive network model, which can be used to make testable hypotheses about network relationships. BNW, including a downloadable structure learning package, is available at http://compbio.uthsc.edu/BNW. (The BNW interface for adding structural constraints uses HTML5 features that are not supported by current version of Internet Explorer. We suggest using other browsers (e.g. Google Chrome or Mozilla Firefox) when accessing BNW). ycui2@uthsc.edu. Supplementary data are available at Bioinformatics online.

Vulnerability Assessment of Open Source Wireshark and Chrome Browser

DTIC Science & Technology

2013-08-01

UNLIMITED 5 We spent much of the initial time learning about the logical model that modern HTML5 web browsers support, including how users interact with...are supposed to protect users of that site against cross-site scripting) and the new powerful an all-encompassing HTML5 standard. This vulnerability

Study of Design Knowledge Capture (DKC) schemes implemented in magnetic bearing applications

NASA Technical Reports Server (NTRS)

1990-01-01

A design knowledge capture (DKC) scheme was implemented using frame-based techniques. The objective of such a system is to capture not only the knowledge which describes a design, but also that which explains how the design decisions were reached. These knowledge types were labelled definitive and explanatory, respectively. Examination of the design process helped determine what knowledge to retain and at what stage that knowledge is used. A discussion of frames resulted in the recognition of their value to knowledge representation and organization. The FORMS frame system was used as a basis for further development, and for examples using magnetic bearing design. The specific contributions made by this research include: determination that frame-based systems provide a useful methodology for management and application of design knowledge; definition of specific user interface requirements, (this consists of a window-based browser); specification of syntax for DKC commands; and demonstration of the feasibility of DKC by applications to existing designs. It was determined that design knowledge capture could become an extremely valuable engineering tool for complicated, long-life systems, but that further work was needed, particularly the development of a graphic, window-based interface.

Reproducible Bioconductor workflows using browser-based interactive notebooks and containers.

PubMed

Almugbel, Reem; Hung, Ling-Hong; Hu, Jiaming; Almutairy, Abeer; Ortogero, Nicole; Tamta, Yashaswi; Yeung, Ka Yee

2018-01-01

Bioinformatics publications typically include complex software workflows that are difficult to describe in a manuscript. We describe and demonstrate the use of interactive software notebooks to document and distribute bioinformatics research. We provide a user-friendly tool, BiocImageBuilder, that allows users to easily distribute their bioinformatics protocols through interactive notebooks uploaded to either a GitHub repository or a private server. We present four different interactive Jupyter notebooks using R and Bioconductor workflows to infer differential gene expression, analyze cross-platform datasets, process RNA-seq data and KinomeScan data. These interactive notebooks are available on GitHub. The analytical results can be viewed in a browser. Most importantly, the software contents can be executed and modified. This is accomplished using Binder, which runs the notebook inside software containers, thus avoiding the need to install any software and ensuring reproducibility. All the notebooks were produced using custom files generated by BiocImageBuilder. BiocImageBuilder facilitates the publication of workflows with a point-and-click user interface. We demonstrate that interactive notebooks can be used to disseminate a wide range of bioinformatics analyses. The use of software containers to mirror the original software environment ensures reproducibility of results. Parameters and code can be dynamically modified, allowing for robust verification of published results and encouraging rapid adoption of new methods. Given the increasing complexity of bioinformatics workflows, we anticipate that these interactive software notebooks will become as necessary for documenting software methods as traditional laboratory notebooks have been for documenting bench protocols, and as ubiquitous. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Remote Patron Validation: Posting a Proxy Server at the Digital Doorway.

ERIC Educational Resources Information Center

Webster, Peter

2002-01-01

Discussion of remote access to library services focuses on proxy servers as a method for remote access, based on experiences at Saint Mary's University (Halifax). Topics include Internet protocol user validation; browser-directed proxies; server software proxies; vendor alternatives for validating remote users; and Internet security issues. (LRW)

Cloud Computing for the Grid: GridControl: A Software Platform to Support the Smart Grid

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

None

GENI Project: Cornell University is creating a new software platform for grid operators called GridControl that will utilize cloud computing to more efficiently control the grid. In a cloud computing system, there are minimal hardware and software demands on users. The user can tap into a network of computers that is housed elsewhere (the cloud) and the network runs computer applications for the user. The user only needs interface software to access all of the cloud’s data resources, which can be as simple as a web browser. Cloud computing can reduce costs, facilitate innovation through sharing, empower users, and improvemore » the overall reliability of a dispersed system. Cornell’s GridControl will focus on 4 elements: delivering the state of the grid to users quickly and reliably; building networked, scalable grid-control software; tailoring services to emerging smart grid uses; and simulating smart grid behavior under various conditions.« less

Polyglot Programming in Applications Used for Genetic Data Analysis

PubMed Central

Nowak, Robert M.

2014-01-01

Applications used for the analysis of genetic data process large volumes of data with complex algorithms. High performance, flexibility, and a user interface with a web browser are required by these solutions, which can be achieved by using multiple programming languages. In this study, I developed a freely available framework for building software to analyze genetic data, which uses C++, Python, JavaScript, and several libraries. This system was used to build a number of genetic data processing applications and it reduced the time and costs of development. PMID:25197633

Polyglot programming in applications used for genetic data analysis.

PubMed

Nowak, Robert M

2014-01-01

Applications used for the analysis of genetic data process large volumes of data with complex algorithms. High performance, flexibility, and a user interface with a web browser are required by these solutions, which can be achieved by using multiple programming languages. In this study, I developed a freely available framework for building software to analyze genetic data, which uses C++, Python, JavaScript, and several libraries. This system was used to build a number of genetic data processing applications and it reduced the time and costs of development.

Data display and analysis with μView

NASA Astrophysics Data System (ADS)

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

2006-03-01

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

CAPER 3.0: A Scalable Cloud-Based System for Data-Intensive Analysis of Chromosome-Centric Human Proteome Project Data Sets.

PubMed

Yang, Shuai; Zhang, Xinlei; Diao, Lihong; Guo, Feifei; Wang, Dan; Liu, Zhongyang; Li, Honglei; Zheng, Junjie; Pan, Jingshan; Nice, Edouard C; Li, Dong; He, Fuchu

2015-09-04

The Chromosome-centric Human Proteome Project (C-HPP) aims to catalog genome-encoded proteins using a chromosome-by-chromosome strategy. As the C-HPP proceeds, the increasing requirement for data-intensive analysis of the MS/MS data poses a challenge to the proteomic community, especially small laboratories lacking computational infrastructure. To address this challenge, we have updated the previous CAPER browser into a higher version, CAPER 3.0, which is a scalable cloud-based system for data-intensive analysis of C-HPP data sets. CAPER 3.0 uses cloud computing technology to facilitate MS/MS-based peptide identification. In particular, it can use both public and private cloud, facilitating the analysis of C-HPP data sets. CAPER 3.0 provides a graphical user interface (GUI) to help users transfer data, configure jobs, track progress, and visualize the results comprehensively. These features enable users without programming expertise to easily conduct data-intensive analysis using CAPER 3.0. Here, we illustrate the usage of CAPER 3.0 with four specific mass spectral data-intensive problems: detecting novel peptides, identifying single amino acid variants (SAVs) derived from known missense mutations, identifying sample-specific SAVs, and identifying exon-skipping events. CAPER 3.0 is available at http://prodigy.bprc.ac.cn/caper3.

Sealife: a semantic grid browser for the life sciences applied to the study of infectious diseases.

PubMed

Schroeder, Michael; Burger, Albert; Kostkova, Patty; Stevens, Robert; Habermann, Bianca; Dieng-Kuntz, Rose

2006-01-01

The objective of Sealife is the conception and realisation of a semantic Grid browser for the life sciences, which will link the existing Web to the currently emerging eScience infrastructure. The SeaLife Browser will allow users to automatically link a host of Web servers and Web/Grid services to the Web content he/she is visiting. This will be accomplished using eScience's growing number of Web/Grid Services and its XML-based standards and ontologies. The browser will identify terms in the pages being browsed through the background knowledge held in ontologies. Through the use of Semantic Hyperlinks, which link identified ontology terms to servers and services, the SeaLife Browser will offer a new dimension of context-based information integration. In this paper, we give an overview over the different components of the browser and their interplay. This SeaLife Browser will be demonstrated within three application scenarios in evidence-based medicine, literature & patent mining, and molecular biology, all relating to the study of infectious diseases. The three applications vertically integrate the molecule/cell, the tissue/organ and the patient/population level by covering the analysis of high-throughput screening data for endocytosis (the molecular entry pathway into the cell), the expression of proteins in the spatial context of tissue and organs, and a high-level library on infectious diseases designed for clinicians and their patients. For more information see http://www.biote.ctu-dresden.de/sealife.

Arachne—A web-based event viewer for MINERνA

NASA Astrophysics Data System (ADS)

Tagg, N.; Brangham, J.; Chvojka, J.; Clairemont, M.; Day, M.; Eberly, B.; Felix, J.; Fields, L.; Gago, A. M.; Gran, R.; Harris, D. A.; Kordosky, M.; Lee, H.; Maggi, G.; Maher, E.; Mann, W. A.; Marshall, C. M.; McFarland, K. S.; McGowan, A. M.; Mislivec, A.; Mousseau, J.; Osmanov, B.; Osta, J.; Paolone, V.; Perdue, G.; Ransome, R. D.; Ray, H.; Schellman, H.; Schmitz, D. W.; Simon, C.; Solano Salinas, C. J.; Tice, B. G.; Walding, J.; Walton, T.; Wolcott, J.; Zhang, D.; Ziemer, B. P.; MinerνA Collaboration

2012-06-01

Neutrino interaction events in the MINERνA detector are visually represented with a web-based tool called Arachne. Data are retrieved from a central server via AJAX, and client-side JavaScript draws images into the user's browser window using the draft HTML 5 standard. These technologies allow neutrino interactions to be viewed by anyone with a web browser, allowing for easy hand-scanning of particle interactions. Arachne has been used in MINERνA to evaluate neutrino data in a prototype detector, to tune reconstruction algorithms, and for public outreach and education.

Arachne - A web-based event viewer for MINERvA

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

Tagg, N.; /Otterbein Coll.; Brangham, J.

2011-11-01

Neutrino interaction events in the MINERvA detector are visually represented with a web-based tool called Arachne. Data are retrieved from a central server via AJAX, and client-side JavaScript draws images into the user's browser window using the draft HTML 5 standard. These technologies allow neutrino interactions to be viewed by anyone with a web browser, allowing for easy hand-scanning of particle interactions. Arachne has been used in MINERvA to evaluate neutrino data in a prototype detector, to tune reconstruction algorithms, and for public outreach and education.

TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks.

PubMed

Lepoivre, Cyrille; Bergon, Aurélie; Lopez, Fabrice; Perumal, Narayanan B; Nguyen, Catherine; Imbert, Jean; Puthier, Denis

2012-01-31

Deciphering gene regulatory networks by in silico approaches is a crucial step in the study of the molecular perturbations that occur in diseases. The development of regulatory maps is a tedious process requiring the comprehensive integration of various evidences scattered over biological databases. Thus, the research community would greatly benefit from having a unified database storing known and predicted molecular interactions. Furthermore, given the intrinsic complexity of the data, the development of new tools offering integrated and meaningful visualizations of molecular interactions is necessary to help users drawing new hypotheses without being overwhelmed by the density of the subsequent graph. We extend the previously developed TranscriptomeBrowser database with a set of tables containing 1,594,978 human and mouse molecular interactions. The database includes: (i) predicted regulatory interactions (computed by scanning vertebrate alignments with a set of 1,213 position weight matrices), (ii) potential regulatory interactions inferred from systematic analysis of ChIP-seq experiments, (iii) regulatory interactions curated from the literature, (iv) predicted post-transcriptional regulation by micro-RNA, (v) protein kinase-substrate interactions and (vi) physical protein-protein interactions. In order to easily retrieve and efficiently analyze these interactions, we developed In-teractomeBrowser, a graph-based knowledge browser that comes as a plug-in for Transcriptome-Browser. The first objective of InteractomeBrowser is to provide a user-friendly tool to get new insight into any gene list by providing a context-specific display of putative regulatory and physical interactions. To achieve this, InteractomeBrowser relies on a "cell compartments-based layout" that makes use of a subset of the Gene Ontology to map gene products onto relevant cell compartments. This layout is particularly powerful for visual integration of heterogeneous biological information and is a productive avenue in generating new hypotheses. The second objective of InteractomeBrowser is to fill the gap between interaction databases and dynamic modeling. It is thus compatible with the network analysis software Cytoscape and with the Gene Interaction Network simulation software (GINsim). We provide examples underlying the benefits of this visualization tool for large gene set analysis related to thymocyte differentiation. The InteractomeBrowser plugin is a powerful tool to get quick access to a knowledge database that includes both predicted and validated molecular interactions. InteractomeBrowser is available through the TranscriptomeBrowser framework and can be found at: http://tagc.univ-mrs.fr/tbrowser/. Our database is updated on a regular basis.

Just-in-time Database-Driven Web Applications

PubMed Central

2003-01-01

"Just-in-time" database-driven Web applications are inexpensive, quickly-developed software that can be put to many uses within a health care organization. Database-driven Web applications garnered 73873 hits on our system-wide intranet in 2002. They enabled collaboration and communication via user-friendly Web browser-based interfaces for both mission-critical and patient-care-critical functions. Nineteen database-driven Web applications were developed. The application categories that comprised 80% of the hits were results reporting (27%), graduate medical education (26%), research (20%), and bed availability (8%). The mean number of hits per application was 3888 (SD = 5598; range, 14-19879). A model is described for just-in-time database-driven Web application development and an example given with a popular HTML editor and database program. PMID:14517109

Development of water environment information management and water pollution accident response system

NASA Astrophysics Data System (ADS)

Zhang, J.; Ruan, H.

2009-12-01

In recent years, many water pollution accidents occurred with the rapid economical development. In this study, water environment information management and water pollution accident response system are developed based on geographic information system (GIS) techniques. The system integrated spatial database, attribute database, hydraulic model, and water quality model under a user-friendly interface in a GIS environment. System ran in both Client/Server (C/S) and Browser/Server (B/S) platform which focused on model and inquiry respectively. System provided spatial and attribute data inquiry, water quality evaluation, statics, water pollution accident response case management (opening reservoir etc) and 2D and 3D visualization function, and gave assistant information to make decision on water pollution accident response. Polluted plume in Huaihe River were selected to simulate the transport of pollutes.

CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline.

PubMed

Agrawal, Sonia; Arze, Cesar; Adkins, Ricky S; Crabtree, Jonathan; Riley, David; Vangala, Mahesh; Galens, Kevin; Fraser, Claire M; Tettelin, Hervé; White, Owen; Angiuoli, Samuel V; Mahurkar, Anup; Fricke, W Florian

2017-04-27

The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuitive, automated, and cloud-enabled analysis pipeline for comparative microbial genomics. CloVR-Comparative runs on annotated complete or draft genome sequences that are uploaded by the user or selected via a taxonomic tree-based user interface and downloaded from NCBI. CloVR-Comparative runs reference-free multiple whole-genome alignments to determine unique, shared and core coding sequences (CDSs) and single nucleotide polymorphisms (SNPs). Output includes short summary reports and detailed text-based results files, graphical visualizations (phylogenetic trees, circular figures), and a database file linked to the Sybil comparative genome browser. Data up- and download, pipeline configuration and monitoring, and access to Sybil are managed through CloVR-Comparative web interface. CloVR-Comparative and Sybil are distributed as part of the CloVR virtual appliance, which runs on local computers or the Amazon EC2 cloud. Representative datasets (e.g. 40 draft and complete Escherichia coli genomes) are processed in <36 h on a local desktop or at a cost of <$20 on EC2. CloVR-Comparative allows anybody with Internet access to run comparative genomics projects, while eliminating the need for on-site computational resources and expertise.

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.

CAI System with Multi-Media Text Through Web Browser for NC Lathe Programming

NASA Astrophysics Data System (ADS)

Mizugaki, Yoshio; Kikkawa, Koichi; Mizui, Masahiko; Kamijo, Keisuke

A new Computer Aided Instruction (CAI) system for NC lathe programming has been developed with use of multi-media texts including movies, animations, pictures, sound and texts through Web browser. Although many CAI systems developed previously for NC programming consist of text-based instructions, it is difficult for beginners to learn NC programming with use of them. In the developed CAI system, multi-media texts are adopted for the help of users' understanding, and it is available through Web browser anytime and anywhere. Also the error log is automatically recorded for the future references. According to the NC programming coded by a user, the movement of the NC lathe is animated and shown in the monitor screen in front of the user. If its movement causes the collision between a cutting tool and the lathe, some sound and the caution remark are generated. If the user makes mistakes some times at a certain stage in learning NC, the corresponding suggestion is shown in the form of movies, animations, and so forth. By using the multimedia texts, users' attention is kept concentrated during a training course. In this paper, the configuration of the CAI system is explained and the actual procedures for users to learn the NC programming are also explained too. Some beginners tested this CAI system and their results are illustrated and discussed from the viewpoint of the efficiency and usefulness of this CAI system. A brief conclusion is also mentioned.

Web-based segmentation and display of three-dimensional radiologic image data.

PubMed

Silverstein, J; Rubenstein, J; Millman, A; Panko, W

1998-01-01

In many clinical circumstances, viewing sequential radiological image data as three-dimensional models is proving beneficial. However, designing customized computer-generated radiological models is beyond the scope of most physicians, due to specialized hardware and software requirements. We have created a simple method for Internet users to remotely construct and locally display three-dimensional radiological models using only a standard web browser. Rapid model construction is achieved by distributing the hardware intensive steps to a remote server. Once created, the model is automatically displayed on the requesting browser and is accessible to multiple geographically distributed users. Implementation of our server software on large scale systems could be of great service to the worldwide medical community.

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.

Quantifying the web browser ecosystem

PubMed Central

Ferdman, Sela; Minkov, Einat; Gefen, David

2017-01-01

Contrary to the assumption that web browsers are designed to support the user, an examination of a 900,000 distinct PCs shows that web browsers comprise a complex ecosystem with millions of addons collaborating and competing with each other. It is possible for addons to “sneak in” through third party installations or to get “kicked out” by their competitors without user involvement. This study examines that ecosystem quantitatively by constructing a large-scale graph with nodes corresponding to users, addons, and words (terms) that describe addon functionality. Analyzing addon interactions at user level using the Personalized PageRank (PPR) random walk measure shows that the graph demonstrates ecological resilience. Adapting the PPR model to analyzing the browser ecosystem at the level of addon manufacturer, the study shows that some addon companies are in symbiosis and others clash with each other as shown by analyzing the behavior of 18 prominent addon manufacturers. Results may herald insight on how other evolving internet ecosystems may behave, and suggest a methodology for measuring this behavior. Specifically, applying such a methodology could transform the addon market. PMID:28644833

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.

EDGE3: A web-based solution for management and analysis of Agilent two color microarray experiments

PubMed Central

Vollrath, Aaron L; Smith, Adam A; Craven, Mark; Bradfield, Christopher A

2009-01-01

Background The ability to generate transcriptional data on the scale of entire genomes has been a boon both in the improvement of biological understanding and in the amount of data generated. The latter, the amount of data generated, has implications when it comes to effective storage, analysis and sharing of these data. A number of software tools have been developed to store, analyze, and share microarray data. However, a majority of these tools do not offer all of these features nor do they specifically target the commonly used two color Agilent DNA microarray platform. Thus, the motivating factor for the development of EDGE3 was to incorporate the storage, analysis and sharing of microarray data in a manner that would provide a means for research groups to collaborate on Agilent-based microarray experiments without a large investment in software-related expenditures or extensive training of end-users. Results EDGE3 has been developed with two major functions in mind. The first function is to provide a workflow process for the generation of microarray data by a research laboratory or a microarray facility. The second is to store, analyze, and share microarray data in a manner that doesn't require complicated software. To satisfy the first function, EDGE3 has been developed as a means to establish a well defined experimental workflow and information system for microarray generation. To satisfy the second function, the software application utilized as the user interface of EDGE3 is a web browser. Within the web browser, a user is able to access the entire functionality, including, but not limited to, the ability to perform a number of bioinformatics based analyses, collaborate between research groups through a user-based security model, and access to the raw data files and quality control files generated by the software used to extract the signals from an array image. Conclusion Here, we present EDGE3, an open-source, web-based application that allows for the storage, analysis, and controlled sharing of transcription-based microarray data generated on the Agilent DNA platform. In addition, EDGE3 provides a means for managing RNA samples and arrays during the hybridization process. EDGE3 is freely available for download at . PMID:19732451

EDGE(3): a web-based solution for management and analysis of Agilent two color microarray experiments.

PubMed

Vollrath, Aaron L; Smith, Adam A; Craven, Mark; Bradfield, Christopher A

2009-09-04

The ability to generate transcriptional data on the scale of entire genomes has been a boon both in the improvement of biological understanding and in the amount of data generated. The latter, the amount of data generated, has implications when it comes to effective storage, analysis and sharing of these data. A number of software tools have been developed to store, analyze, and share microarray data. However, a majority of these tools do not offer all of these features nor do they specifically target the commonly used two color Agilent DNA microarray platform. Thus, the motivating factor for the development of EDGE(3) was to incorporate the storage, analysis and sharing of microarray data in a manner that would provide a means for research groups to collaborate on Agilent-based microarray experiments without a large investment in software-related expenditures or extensive training of end-users. EDGE(3) has been developed with two major functions in mind. The first function is to provide a workflow process for the generation of microarray data by a research laboratory or a microarray facility. The second is to store, analyze, and share microarray data in a manner that doesn't require complicated software. To satisfy the first function, EDGE3 has been developed as a means to establish a well defined experimental workflow and information system for microarray generation. To satisfy the second function, the software application utilized as the user interface of EDGE(3) is a web browser. Within the web browser, a user is able to access the entire functionality, including, but not limited to, the ability to perform a number of bioinformatics based analyses, collaborate between research groups through a user-based security model, and access to the raw data files and quality control files generated by the software used to extract the signals from an array image. Here, we present EDGE(3), an open-source, web-based application that allows for the storage, analysis, and controlled sharing of transcription-based microarray data generated on the Agilent DNA platform. In addition, EDGE(3) provides a means for managing RNA samples and arrays during the hybridization process. EDGE(3) is freely available for download at http://edge.oncology.wisc.edu/.

The Ensembl Web Site: Mechanics of a Genome Browser

PubMed Central

Stalker, James; Gibbins, Brian; Meidl, Patrick; Smith, James; Spooner, William; Hotz, Hans-Rudolf; Cox, Antony V.

2004-01-01

The Ensembl Web site (http://www.ensembl.org/) is the principal user interface to the data of the Ensembl project, and currently serves >500,000 pages (∼2.5 million hits) per week, providing access to >80 GB (gigabyte) of data to users in more than 80 countries. Built atop an open-source platform comprising Apache/mod_perl and the MySQL relational database management system, it is modular, extensible, and freely available. It is being actively reused and extended in several different projects, and has been downloaded and installed in companies and academic institutions worldwide. Here, we describe some of the technical features of the site, with particular reference to its dynamic configuration that enables it to handle disparate data from multiple species. PMID:15123591

The Ensembl Web site: mechanics of a genome browser.

PubMed

Stalker, James; Gibbins, Brian; Meidl, Patrick; Smith, James; Spooner, William; Hotz, Hans-Rudolf; Cox, Antony V

2004-05-01

The Ensembl Web site (http://www.ensembl.org/) is the principal user interface to the data of the Ensembl project, and currently serves >500,000 pages (approximately 2.5 million hits) per week, providing access to >80 GB (gigabyte) of data to users in more than 80 countries. Built atop an open-source platform comprising Apache/mod_perl and the MySQL relational database management system, it is modular, extensible, and freely available. It is being actively reused and extended in several different projects, and has been downloaded and installed in companies and academic institutions worldwide. Here, we describe some of the technical features of the site, with particular reference to its dynamic configuration that enables it to handle disparate data from multiple species.

Medical high-resolution image sharing and electronic whiteboard system: A pure-web-based system for accessing and discussing lossless original images in telemedicine.

PubMed

Qiao, Liang; Li, Ying; Chen, Xin; Yang, Sheng; Gao, Peng; Liu, Hongjun; Feng, Zhengquan; Nian, Yongjian; Qiu, Mingguo

2015-09-01

There are various medical image sharing and electronic whiteboard systems available for diagnosis and discussion purposes. However, most of these systems ask clients to install special software tools or web plug-ins to support whiteboard discussion, special medical image format, and customized decoding algorithm of data transmission of HRIs (high-resolution images). This limits the accessibility of the software running on different devices and operating systems. In this paper, we propose a solution based on pure web pages for medical HRIs lossless sharing and e-whiteboard discussion, and have set up a medical HRI sharing and e-whiteboard system, which has four-layered design: (1) HRIs access layer: we improved an tile-pyramid model named unbalanced ratio pyramid structure (URPS), to rapidly share lossless HRIs and to adapt to the reading habits of users; (2) format conversion layer: we designed a format conversion engine (FCE) on server side to real time convert and cache DICOM tiles which clients requesting with window-level parameters, to make browsers compatible and keep response efficiency to server-client; (3) business logic layer: we built a XML behavior relationship storage structure to store and share users' behavior, to keep real time co-browsing and discussion between clients; (4) web-user-interface layer: AJAX technology and Raphael toolkit were used to combine HTML and JavaScript to build client RIA (rich Internet application), to meet clients' desktop-like interaction on any pure webpage. This system can be used to quickly browse lossless HRIs, and support discussing and co-browsing smoothly on any web browser in a diversified network environment. The proposal methods can provide a way to share HRIs safely, and may be used in the field of regional health, telemedicine and remote education at a low cost. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Design and development of an IoT-based web application for an intelligent remote SCADA system

NASA Astrophysics Data System (ADS)

Kao, Kuang-Chi; Chieng, Wei-Hua; Jeng, Shyr-Long

2018-03-01

This paper presents a design of an intelligent remote electrical power supervisory control and data acquisition (SCADA) system based on the Internet of Things (IoT), with Internet Information Services (IIS) for setting up web servers, an ASP.NET model-view- controller (MVC) for establishing a remote electrical power monitoring and control system by using responsive web design (RWD), and a Microsoft SQL Server as the database. With the web browser connected to the Internet, the sensing data is sent to the client by using the TCP/IP protocol, which supports mobile devices with different screen sizes. The users can provide instructions immediately without being present to check the conditions, which considerably reduces labor and time costs. The developed system incorporates a remote measuring function by using a wireless sensor network and utilizes a visual interface to make the human-machine interface (HMI) more instinctive. Moreover, it contains an analog input/output and a basic digital input/output that can be applied to a motor driver and an inverter for integration with a remote SCADA system based on IoT, and thus achieve efficient power management.

Southern California Earthquake Center Geologic Vertical Motion Database

NASA Astrophysics Data System (ADS)

Niemi, Nathan A.; Oskin, Michael; Rockwell, Thomas K.

2008-07-01

The Southern California Earthquake Center Geologic Vertical Motion Database (VMDB) integrates disparate sources of geologic uplift and subsidence data at 104- to 106-year time scales into a single resource for investigations of crustal deformation in southern California. Over 1800 vertical deformation rate data points in southern California and northern Baja California populate the database. Four mature data sets are now represented: marine terraces, incised river terraces, thermochronologic ages, and stratigraphic surfaces. An innovative architecture and interface of the VMDB exposes distinct data sets and reference frames, permitting user exploration of this complex data set and allowing user control over the assumptions applied to convert geologic and geochronologic information into absolute uplift rates. Online exploration and download tools are available through all common web browsers, allowing the distribution of vertical motion results as HTML tables, tab-delimited GIS-compatible text files, or via a map interface through the Google Maps™ web service. The VMDB represents a mature product for research of fault activity and elastic deformation of southern California.

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

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

PubMed Central

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

2014-01-01

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

Analysis of Sea Level Rise in Action

NASA Astrophysics Data System (ADS)

Gill, K. M.; Huang, T.; Quach, N. T.; Boening, C.

2016-12-01

NASA's Sea Level Change Portal provides scientists and the general public with "one-stop" source for current sea level change information and data. Sea Level Rise research is a multidisciplinary research and in order to understand its causes, scientists must be able to access different measurements and to be able to compare them. The portal includes an interactive tool, called the Data Analysis Tool (DAT), for accessing, visualizing, and analyzing observations and models relevant to the study of Sea Level Rise. Using NEXUS, an open source, big data analytic technology developed at the Jet Propulsion Laboratory, the DAT is able provide user on-the-fly data analysis on all relevant parameters. DAT is composed of three major components: A dedicated instance of OnEarth (a WMTS service), NEXUS deep data analytic platform, and the JPL Common Mapping Client (CMC) for web browser based user interface (UI). Utilizing the global imagery, a user is capable of browsing the data in a visual manner and isolate areas of interest for further study. The interfaces "Analysis" tool provides tools for area or point selection, single and/or comparative dataset selection, and a range of options, algorithms, and plotting. This analysis component utilizes the Nexus cloud computing platform to provide on-demand processing of the data within the user-selected parameters and immediate display of the results. A RESTful web API is exposed for users comfortable with other interfaces and who may want to take advantage of the cloud computing capabilities. This talk discuss how DAT enables on-the-fly sea level research. The talk will introduce the DAT with an end-to-end tour of the tool with exploration and animating of available imagery, a demonstration of comparative analysis and plotting, and how to share and export data along with images for use in publications/presentations. The session will cover what kind of data is available, what kind of analysis is possible, and what are the outputs.

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.

Enabling a systems biology knowledgebase with gaggle and firegoose

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

Baliga, Nitin S.

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

Retrieving high-resolution images over the Internet from an anatomical image database

NASA Astrophysics Data System (ADS)

Strupp-Adams, Annette; Henderson, Earl

1999-12-01

The Visible Human Data set is an important contribution to the national collection of anatomical images. To enhance the availability of these images, the National Library of Medicine has supported the design and development of a prototype object-oriented image database which imports, stores, and distributes high resolution anatomical images in both pixel and voxel formats. One of the key database modules is its client-server Internet interface. This Web interface provides a query engine with retrieval access to high-resolution anatomical images that range in size from 100KB for browser viewable rendered images, to 1GB for anatomical structures in voxel file formats. The Web query and retrieval client-server system is composed of applet GUIs, servlets, and RMI application modules which communicate with each other to allow users to query for specific anatomical structures, and retrieve image data as well as associated anatomical images from the database. Selected images can be downloaded individually as single files via HTTP or downloaded in batch-mode over the Internet to the user's machine through an applet that uses Netscape's Object Signing mechanism. The image database uses ObjectDesign's object-oriented DBMS, ObjectStore that has a Java interface. The query and retrieval systems has been tested with a Java-CDE window system, and on the x86 architecture using Windows NT 4.0. This paper describes the Java applet client search engine that queries the database; the Java client module that enables users to view anatomical images online; the Java application server interface to the database which organizes data returned to the user, and its distribution engine that allow users to download image files individually and/or in batch-mode.

Sequence alignment visualization in HTML5 without Java.

PubMed

Gille, Christoph; Birgit, Weyand; Gille, Andreas

2014-01-01

Java has been extensively used for the visualization of biological data in the web. However, the Java runtime environment is an additional layer of software with an own set of technical problems and security risks. HTML in its new version 5 provides features that for some tasks may render Java unnecessary. Alignment-To-HTML is the first HTML-based interactive visualization for annotated multiple sequence alignments. The server side script interpreter can perform all tasks like (i) sequence retrieval, (ii) alignment computation, (iii) rendering, (iv) identification of a homologous structural models and (v) communication with BioDAS-servers. The rendered alignment can be included in web pages and is displayed in all browsers on all platforms including touch screen tablets. The functionality of the user interface is similar to legacy Java applets and includes color schemes, highlighting of conserved and variable alignment positions, row reordering by drag and drop, interlinked 3D visualization and sequence groups. Novel features are (i) support for multiple overlapping residue annotations, such as chemical modifications, single nucleotide polymorphisms and mutations, (ii) mechanisms to quickly hide residue annotations, (iii) export to MS-Word and (iv) sequence icons. Alignment-To-HTML, the first interactive alignment visualization that runs in web browsers without additional software, confirms that to some extend HTML5 is already sufficient to display complex biological data. The low speed at which programs are executed in browsers is still the main obstacle. Nevertheless, we envision an increased use of HTML and JavaScript for interactive biological software. Under GPL at: http://www.bioinformatics.org/strap/toHTML/.

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

High-performance web viewer for cardiac images

NASA Astrophysics Data System (ADS)

dos Santos, Marcelo; Furuie, Sergio S.

2004-04-01

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

Trajectory Browser: An Online Tool for Interplanetary Trajectory Analysis and Visualization

NASA Technical Reports Server (NTRS)

Foster, Cyrus James

2013-01-01

The trajectory browser is a web-based tool developed at the NASA Ames Research Center for finding preliminary trajectories to planetary bodies and for providing relevant launch date, time-of-flight and (Delta)V requirements. The site hosts a database of transfer trajectories from Earth to planets and small-bodies for various types of missions such as rendezvous, sample return or flybys. A search engine allows the user to find trajectories meeting desired constraints on the launch window, mission duration and (Delta)V capability, while a trajectory viewer tool allows the visualization of the heliocentric trajectory and the detailed mission itinerary. The anticipated user base of this tool consists primarily of scientists and engineers designing interplanetary missions in the context of pre-phase A studies, particularly for performing accessibility surveys to large populations of small-bodies.

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

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

Rosen, C; Ramsay, B; Konerth, S

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

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

PubMed

Guigas, Bruno

2017-09-01

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

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

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

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

2012-01-17

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

Smartphone-based secure authenticated session sharing in Internet of Personal Things

NASA Astrophysics Data System (ADS)

Krishnan, Ram; Ninglekhu, Jiwan

2015-03-01

In the context of password-based authentication, a user can only memorize limited number of usernames and passwords. They are generally referred to as user-credentials. Longer character length of passwords further adds complication in mastering them. The expansion of the Internet and our growing dependency on it, has made it almost impossible for us to handle the big pool of user-credentials. Using simple, same or similar passwords is considered a poor practice, as it can easily be compromised by password cracking tools and social engineering attacks. Therefore, a robust and painless technique to manage personal credentials for websites is desirable. In this paper, a novel technique for user-credentials management via a smart mobile device such as a smartphone in a local network is proposed. We present a secure user-credential management scheme in which user's account login (username) and password associated with websites domain name is saved into the mobile device's database using a mobile application. We develop a custom browser extension application for client and use it to import user's credentials linked with the corresponding website from the mobile device via the local Wi-Fi network connection. The browser extension imports and identifies the authentication credentials and pushes them into the target TextBox locations in the webpage, ready for the user to execute. This scheme is suitably demonstrated between two personal devices in a local network.

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.

Rice-Map: a new-generation rice genome browser.

PubMed

Wang, Jun; Kong, Lei; Zhao, Shuqi; Zhang, He; Tang, Liang; Li, Zhe; Gu, Xiaocheng; Luo, Jingchu; Gao, Ge

2011-03-30

The concurrent release of rice genome sequences for two subspecies (Oryza sativa L. ssp. japonica and Oryza sativa L. ssp. indica) facilitates rice studies at the whole genome level. Since the advent of high-throughput analysis, huge amounts of functional genomics data have been delivered rapidly, making an integrated online genome browser indispensable for scientists to visualize and analyze these data. Based on next-generation web technologies and high-throughput experimental data, we have developed Rice-Map, a novel genome browser for researchers to navigate, analyze and annotate rice genome interactively. More than one hundred annotation tracks (81 for japonica and 82 for indica) have been compiled and loaded into Rice-Map. These pre-computed annotations cover gene models, transcript evidences, expression profiling, epigenetic modifications, inter-species and intra-species homologies, genetic markers and other genomic features. In addition to these pre-computed tracks, registered users can interactively add comments and research notes to Rice-Map as User-Defined Annotation entries. By smoothly scrolling, dragging and zooming, users can browse various genomic features simultaneously at multiple scales. On-the-fly analysis for selected entries could be performed through dedicated bioinformatic analysis platforms such as WebLab and Galaxy. Furthermore, a BioMart-powered data warehouse "Rice Mart" is offered for advanced users to fetch bulk datasets based on complex criteria. Rice-Map delivers abundant up-to-date japonica and indica annotations, providing a valuable resource for both computational and bench biologists. Rice-Map is publicly accessible at http://www.ricemap.org/, with all data available for free downloading.

Autonomous Cryogenics Loading Operations Simulation Software: Knowledgebase Autonomous Test Engineer

NASA Technical Reports Server (NTRS)

Wehner, Walter S., Jr.

2013-01-01

Working on the ACLO (Autonomous Cryogenics Loading Operations) project I have had the opportunity to add functionality to the physics simulation software known as KATE (Knowledgebase Autonomous Test Engineer), create a new application allowing WYSIWYG (what-you-see-is-what-you-get) creation of KATE schematic files and begin a preliminary design and implementation of a new subsystem that will provide vision services on the IHM (Integrated Health Management) bus. The functionality I added to KATE over the past few months includes a dynamic visual representation of the fluid height in a pipe based on number of gallons of fluid in the pipe and implementing the IHM bus connection within KATE. I also fixed a broken feature in the system called the Browser Display, implemented many bug fixes and made changes to the GUI (Graphical User Interface).

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.

Concertina browsers: a formative evaluation of user preference.

PubMed

Harper, Simon; Christophorou, Nicola

2008-09-01

Evidence suggests that concertina browsers - browsers with the facility to expand and contract sections of information - are important in providing the reader with an enhanced cognition of small to medium amounts of information. These systems have been shown to be useful for visually disabled users surfing the World Wide Web (Web), and with the development of the Mobile Web, there has been renewed interest in their use. This is due to the similarities of reduced or constrained vision found to exist between visually impaired users and the users of mobile devices. The cognition of information fragments is key to the user experience and the reduction of 'information overload'; as such we are concerned with assisting designers of concertina browsers in providing an enhanced user experience by ascertaining user preference through a formative evaluation of concertina summaries. This aspect of browsing is important because in all concertina systems there is a distinct cognition speed/depth trade-off. Here we investigate a number of these concertina summarization techniques against each other. We describe a formative evaluation which concludes that users prefer concertina summarization of Web documents starting from 6.25% slices of both the top and bottom and expanding from the top in 2% steps to a target maximum of 18.50% (being 12.25% from the top and 6.25% from the bottom). These preferences were found to be representative of documents of less than 600 words of content, and included the preference to not fragment an individual sentence even if that meant slightly increasing the target: Starting, maximum, and step percentage slices.

Plugin free remote visualization in the browser

NASA Astrophysics Data System (ADS)

Tamm, Georg; Slusallek, Philipp

2015-01-01

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

StreamStats in North Carolina: a water-resources Web application

USGS Publications Warehouse

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

2012-01-01

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

Web Services and Other Enhancements at the Northern California Earthquake Data Center

NASA Astrophysics Data System (ADS)

Neuhauser, D. S.; Zuzlewski, S.; Allen, R. M.

2012-12-01

The Northern California Earthquake Data Center (NCEDC) provides data archive and distribution services for seismological and geophysical data sets that encompass northern California. The NCEDC is enhancing its ability to deliver rapid information through Web Services. NCEDC Web Services use well-established web server and client protocols and REST software architecture to allow users to easily make queries using web browsers or simple program interfaces and to receive the requested data in real-time rather than through batch or email-based requests. Data are returned to the user in the appropriate format such as XML, RESP, or MiniSEED depending on the service, and are compatible with the equivalent IRIS DMC web services. The NCEDC is currently providing the following Web Services: (1) Station inventory and channel response information delivered in StationXML format, (2) Channel response information delivered in RESP format, (3) Time series availability delivered in text and XML formats, (4) Single channel and bulk data request delivered in MiniSEED format. The NCEDC is also developing a rich Earthquake Catalog Web Service to allow users to query earthquake catalogs based on selection parameters such as time, location or geographic region, magnitude, depth, azimuthal gap, and rms. It will return (in QuakeML format) user-specified results that can include simple earthquake parameters, as well as observations such as phase arrivals, codas, amplitudes, and computed parameters such as first motion mechanisms, moment tensors, and rupture length. The NCEDC will work with both IRIS and the International Federation of Digital Seismograph Networks (FDSN) to define a uniform set of web service specifications that can be implemented by multiple data centers to provide users with a common data interface across data centers. The NCEDC now hosts earthquake catalogs and waveforms from the US Department of Energy (DOE) Enhanced Geothermal Systems (EGS) monitoring networks. These data can be accessed through the above web services and through special NCEDC web pages.

Multimedia data repository for the World Wide Web

NASA Astrophysics Data System (ADS)

Chen, Ken; Lu, Dajin; Xu, Duanyi

1998-08-01

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

Unlocking data: federated identity with LSDMA and dCache

NASA Astrophysics Data System (ADS)

Millar, AP; Behrmann, G.; Bernardt, C.; Fuhrmann, P.; Hardt, M.; Hayrapetyan, A.; Litvintsev, D.; Mkrtchyan, T.; Rossi, A.; Schwank, K.

2015-12-01

X.509, the dominant identity system from grid computing, has proved unpopular for many user communities. More popular alternatives generally assume the user is interacting via their web-browser. Such alternatives allow a user to authenticate with many services with the same credentials (user-name and password). They also allow users from different organisations form collaborations quickly and simply. Scientists generally require that their custom analysis software has direct access to the data. Such direct access is not currently supported by alternatives to X.509, as they require the use of a web-browser. Various approaches to solve this issue are being investigated as part of the Large Scale Data Management and Analysis (LSDMA) project, a German funded national R&D project. These involve dynamic credential translation (creating an X.509 credential) to allow backwards compatibility in addition to direct SAML- and OpenID Connect-based authentication. We present a summary of the current state of art and the current status of the federated identity work funded by the LSDMA project along with the future road map.

The GIS portal based on JSR168 portlet technology and WSRP

NASA Astrophysics Data System (ADS)

Wu, Defu; Chen, Nengcheng; Zhu, Xinyan; Gong, Jianya

2005-10-01

A portal is a powerful Web site that gives users a single point of access to applications and information in a unified interface. A portal lets users view each application or web page in its own window, called a portlet, and a single browser window can contain multiple portlets. The portlet based on JSP168&WSRP is a new technology for interactive, user-facing web services that plug and play with portals. Thanks to the development of Portal&Web GIS, the GIS Poratl is focused on more and more by the researcheres. This paper studies the GIS Portal defined by ESRI and analyzes the development's status, compares with the commercial Portal and points out the great shortage of the ESRI GIS Portal: lack in Personal content and UI. Therefor this paper goes into depth on the discussion of design and implementation scheme of real GIS Portal, and proposes the new idea of developing customized, plug and play GIS Portal Module based on JSP168 Portlet technology and WSRP standard. This way can resolve the difficult problem of the GIS Portal on lacking of content and customization function. According to this idea, this paper plans to use the JaveBeans provided by GeoSurf to develop visual portlet which have basic operating fuction of GIS. Finally deploys the GIS Portal uing the WebLogic Portal.

A Bookmarking Service for Organizing and Sharing URLs

NASA Technical Reports Server (NTRS)

Keller, Richard M.; Wolfe, Shawn R.; Chen, James R.; Mathe, Nathalie; Rabinowitz, Joshua L.

1997-01-01

Web browser bookmarking facilities predominate as the method of choice for managing URLs. In this paper, we describe some deficiencies of current bookmarking schemes, and examine an alternative to current approaches. We present WebTagger(TM), an implemented prototype of a personal bookmarking service that provides both individuals and groups with a customizable means of organizing and accessing Web-based information resources. In addition, the service enables users to supply feedback on the utility of these resources relative to their information needs, and provides dynamically-updated ranking of resources based on incremental user feedback. Individuals may access the service from anywhere on the Internet, and require no special software. This service greatly simplifies the process of sharing URLs within groups, in comparison with manual methods involving email. The underlying bookmark organization scheme is more natural and flexible than current hierarchical schemes supported by the major Web browsers, and enables rapid access to stored bookmarks.

Exploring the enjoyment of playing browser games.

PubMed

Klimmt, Christoph; Schmid, Hannah; Orthmann, Julia

2009-04-01

Browser games--mostly persistent game worlds that can be used without client software and monetary cost with a Web browser--belong to the understudied digital game types, although they attract large player communities and motivate sustained play. The present work reports findings from an online survey of 8,203 players of a German strategy browser game ("Travian"). Results suggest that multiplayer browser games are enjoyed primarily because of the social relationships involved in game play and the specific time and flexibility characteristics ("easy-in, easy-out"). Competition, in contrast, seems to be less important for browser gamers than for users of other game types. Findings are discussed in terms of video game enjoyment and game addiction.

Arrowland v1.0

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

BIRKEL, GARRETT; GARCIA MARTIN, HECTOR; MORRELL, WILLIAM

"Arrowland" is a web-based software application primarily for mapping, integrating and visualizing a variety of metabolism data of living organisms, including but not limited to metabolomics, proteomics, transcriptomics and fluxomics. This software application makes multi-omics data analysis intuitive and interactive. It improves data sharing and communication by enabling users to visualize their omics data using a web browser (on a PC or mobile device). It increases user's productivity by simplifying multi-omics data analysis using well developed maps as a guide. Users using this tool can gain insights into their data sets that would be difficult or even impossible to teasemore » out by looking at raw number, or using their currently existing toolchains to generate static single-use maps. Arrowland helps users save time by visualizing relative changes in different conditions or over time, and helps users to produce more significant insights faster. Preexisting maps decrease the learning curve for beginners in the omics field. Sets of multi-omics data are presented in the browser, as a two-dimensional flowchart resembling a map, with varying levels of detail information, based on the scaling of the map. Users can pan and zoom to explore different maps, compare maps, upload their own research data sets onto desired maps, alter map appearance in ways that facilitate interpretation, visualization and analysis of the given data, and export data, reports and actionable items to help the user initiative.« less

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

Software for Sharing and Management of Information

NASA Technical Reports Server (NTRS)

Chen, James R.; Wolfe, Shawn R.; Wragg, Stephen D.

2003-01-01

DIAMS is a set of computer programs that implements a system of collaborative agents that serve multiple, geographically distributed users communicating via the Internet. DIAMS provides a user interface as a Java applet that runs on each user s computer and that works within the context of the user s Internet-browser software. DIAMS helps all its users to manage, gain access to, share, and exchange information in databases that they maintain on their computers. One of the DIAMS agents is a personal agent that helps its owner find information most relevant to current needs. It provides software tools and utilities for users to manage their information repositories with dynamic organization and virtual views. Capabilities for generating flexible hierarchical displays are integrated with capabilities for indexed- query searching to support effective access to information. Automatic indexing methods are employed to support users queries and communication between agents. The catalog of a repository is kept in object-oriented storage to facilitate sharing of information. Collaboration between users is aided by matchmaker agents and by automated exchange of information. The matchmaker agents are designed to establish connections between users who have similar interests and expertise.

[A Terahertz Spectral Database Based on Browser/Server Technique].

PubMed

Zhang, Zhuo-yong; Song, Yue

2015-09-01

With the solution of key scientific and technical problems and development of instrumentation, the application of terahertz technology in various fields has been paid more and more attention. Owing to the unique characteristic advantages, terahertz technology has been showing a broad future in the fields of fast, non-damaging detections, as well as many other fields. Terahertz technology combined with other complementary methods can be used to cope with many difficult practical problems which could not be solved before. One of the critical points for further development of practical terahertz detection methods depends on a good and reliable terahertz spectral database. We developed a BS (browser/server) -based terahertz spectral database recently. We designed the main structure and main functions to fulfill practical requirements. The terahertz spectral database now includes more than 240 items, and the spectral information was collected based on three sources: (1) collection and citation from some other abroad terahertz spectral databases; (2) collected from published literatures; and (3) spectral data measured in our laboratory. The present paper introduced the basic structure and fundament functions of the terahertz spectral database developed in our laboratory. One of the key functions of this THz database is calculation of optical parameters. Some optical parameters including absorption coefficient, refractive index, etc. can be calculated based on the input THz time domain spectra. The other main functions and searching methods of the browser/server-based terahertz spectral database have been discussed. The database search system can provide users convenient functions including user registration, inquiry, displaying spectral figures and molecular structures, spectral matching, etc. The THz database system provides an on-line searching function for registered users. Registered users can compare the input THz spectrum with the spectra of database, according to the obtained correlation coefficient one can perform the searching task very fast and conveniently. Our terahertz spectral database can be accessed at http://www.teralibrary.com. The proposed terahertz spectral database is based on spectral information so far, and will be improved in the future. We hope this terahertz spectral database can provide users powerful, convenient, and high efficient functions, and could promote the broader applications of terahertz technology.

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2014-01-01

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

Web Searching: A Process-Oriented Experimental Study of Three Interactive Search Paradigms.

ERIC Educational Resources Information Center

Dennis, Simon; Bruza, Peter; McArthur, Robert

2002-01-01

Compares search effectiveness when using query-based Internet search via the Google search engine, directory-based search via Yahoo, and phrase-based query reformulation-assisted search via the Hyperindex browser by means of a controlled, user-based experimental study of undergraduates at the University of Queensland. Discusses cognitive load,…

GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes.

PubMed

Hallin, Peter F; Stærfeldt, Hans-Henrik; Rotenberg, Eva; Binnewies, Tim T; Benham, Craig J; Ussery, David W

2009-09-25

We present an interactive web application for visualizing genomic data of prokaryotic chromosomes. The tool (GeneWiz browser) allows users to carry out various analyses such as mapping alignments of homologous genes to other genomes, mapping of short sequencing reads to a reference chromosome, and calculating DNA properties such as curvature or stacking energy along the chromosome. The GeneWiz browser produces an interactive graphic that enables zooming from a global scale down to single nucleotides, without changing the size of the plot. Its ability to disproportionally zoom provides optimal readability and increased functionality compared to other browsers. The tool allows the user to select the display of various genomic features, color setting and data ranges. Custom numerical data can be added to the plot allowing, for example, visualization of gene expression and regulation data. Further, standard atlases are pre-generated for all prokaryotic genomes available in GenBank, providing a fast overview of all available genomes, including recently deposited genome sequences. The tool is available online from http://www.cbs.dtu.dk/services/gwBrowser. Supplemental material including interactive atlases is available online at http://www.cbs.dtu.dk/services/gwBrowser/suppl/.

Interactive Educational Tool for Turbofan and Afterburning Turbojet Engines

NASA Technical Reports Server (NTRS)

Benson, Thomas J.

1997-01-01

A workstation-based, interactive educational computer program has been developed at the NASA Lewis Research Center to aid in the teaching and understanding of turbine engine design and analysis. This tool has recently been extended to model the performance of two-spool turbofans and afterburning turbojets. The program solves for the flow conditions through the engine by using classical one-dimensional thermodynamic analysis found in various propulsion textbooks. Either an approximately thermally perfect or calorically perfect gas can be used in the thermodynamic analysis. Students can vary the design conditions through a graphical user interface; engine performance is calculated immediately. A variety of graphical formats are used to present results, including numerical results, moving bar charts, and student-generated temperature versus entropy (Ts), pressure versus specific volume (pv), and engine performance plots. The package includes user-controlled printed output, restart capability, online help screens, and a browser that displays teacher-prepared lessons in turbomachinery. The program runs on a variety of workstations or a personal computer using the UNIX operating system and X-based graphics. It is being tested at several universities in the midwestern United States; the source and executables are available free from the author.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Toward Exposing Timing-Based Probing Attacks in Web Applications †

PubMed Central

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

2017-01-01

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

mod_bio: Apache modules for Next-Generation sequencing data.

PubMed

Lindenbaum, Pierre; Redon, Richard

2015-01-01

We describe mod_bio, a set of modules for the Apache HTTP server that allows the users to access and query fastq, tabix, fasta and bam files through a Web browser. Those data are made available in plain text, HTML, XML, JSON and JSON-P. A javascript-based genome browser using the JSON-P communication technique is provided as an example of cross-domain Web service. https://github.com/lindenb/mod_bio. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Simulation Platform: a cloud-based online simulation environment.

PubMed

Yamazaki, Tadashi; Ikeno, Hidetoshi; Okumura, Yoshihiro; Satoh, Shunji; Kamiyama, Yoshimi; Hirata, Yutaka; Inagaki, Keiichiro; Ishihara, Akito; Kannon, Takayuki; Usui, Shiro

2011-09-01

For multi-scale and multi-modal neural modeling, it is needed to handle multiple neural models described at different levels seamlessly. Database technology will become more important for these studies, specifically for downloading and handling the neural models seamlessly and effortlessly. To date, conventional neuroinformatics databases have solely been designed to archive model files, but the databases should provide a chance for users to validate the models before downloading them. In this paper, we report our on-going project to develop a cloud-based web service for online simulation called "Simulation Platform". Simulation Platform is a cloud of virtual machines running GNU/Linux. On a virtual machine, various software including developer tools such as compilers and libraries, popular neural simulators such as GENESIS, NEURON and NEST, and scientific software such as Gnuplot, R and Octave, are pre-installed. When a user posts a request, a virtual machine is assigned to the user, and the simulation starts on that machine. The user remotely accesses to the machine through a web browser and carries out the simulation, without the need to install any software but a web browser on the user's own computer. Therefore, Simulation Platform is expected to eliminate impediments to handle multiple neural models that require multiple software. Copyright © 2011 Elsevier Ltd. All rights reserved.

Reprint of: Simulation Platform: a cloud-based online simulation environment.

PubMed

Yamazaki, Tadashi; Ikeno, Hidetoshi; Okumura, Yoshihiro; Satoh, Shunji; Kamiyama, Yoshimi; Hirata, Yutaka; Inagaki, Keiichiro; Ishihara, Akito; Kannon, Takayuki; Usui, Shiro

2011-11-01

For multi-scale and multi-modal neural modeling, it is needed to handle multiple neural models described at different levels seamlessly. Database technology will become more important for these studies, specifically for downloading and handling the neural models seamlessly and effortlessly. To date, conventional neuroinformatics databases have solely been designed to archive model files, but the databases should provide a chance for users to validate the models before downloading them. In this paper, we report our on-going project to develop a cloud-based web service for online simulation called "Simulation Platform". Simulation Platform is a cloud of virtual machines running GNU/Linux. On a virtual machine, various software including developer tools such as compilers and libraries, popular neural simulators such as GENESIS, NEURON and NEST, and scientific software such as Gnuplot, R and Octave, are pre-installed. When a user posts a request, a virtual machine is assigned to the user, and the simulation starts on that machine. The user remotely accesses to the machine through a web browser and carries out the simulation, without the need to install any software but a web browser on the user's own computer. Therefore, Simulation Platform is expected to eliminate impediments to handle multiple neural models that require multiple software. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

π Scope: python based scientific workbench with visualization tool for MDSplus data

NASA Astrophysics Data System (ADS)

Shiraiwa, S.

2014-10-01

π Scope is a python based scientific data analysis and visualization tool constructed on wxPython and Matplotlib. Although it is designed to be a generic tool, the primary motivation for developing the new software is 1) to provide an updated tool to browse MDSplus data, with functionalities beyond dwscope and jScope, and 2) to provide a universal foundation to construct interface tools to perform computer simulation and modeling for Alcator C-Mod. It provides many features to visualize MDSplus data during tokamak experiments including overplotting different signals and discharges, various plot types (line, contour, image, etc.), in-panel data analysis using python scripts, and publication quality graphics generation. Additionally, the logic to produce multi-panel plots is designed to be backward compatible with dwscope, enabling smooth migration for dwscope users. πScope uses multi-threading to reduce data transfer latency, and its object-oriented design makes it easy to modify and expand while the open source nature allows portability. A built-in tree data browser allows a user to approach the data structure both from a GUI and a script, enabling relatively complex data analysis workflow to be built quickly. As an example, an IDL-based interface to perform GENRAY/CQL3D simulations was ported on πScope, thus allowing LHCD simulation to be run between-shot using C-Mod experimental profiles. This workflow is being used to generate a large database to develop a LHCD actuator model for the plasma control system. Supported by USDoE Award DE-FC02-99ER54512.

Using Galaxy to Perform Large-Scale Interactive Data Analyses

PubMed Central

Hillman-Jackson, Jennifer; Clements, Dave; Blankenberg, Daniel; Taylor, James; Nekrutenko, Anton

2012-01-01

Innovations in biomedical research technologies continue to provide experimental biologists with novel and increasingly large genomic and high-throughput data resources to be analyzed. As creating and obtaining data has become easier, the key decision faced by many researchers is a practical one: where and how should an analysis be performed? Datasets are large and analysis tool set-up and use is riddled with complexities outside of the scope of core research activities. The authors believe that Galaxy (galaxyproject.org) provides a powerful solution that simplifies data acquisition and analysis in an intuitive web-application, granting all researchers access to key informatics tools previously only available to computational specialists working in Unix-based environments. We will demonstrate through a series of biomedically relevant protocols how Galaxy specifically brings together 1) data retrieval from public and private sources, for example, UCSC’s Eukaryote and Microbial Genome Browsers (genome.ucsc.edu), 2) custom tools (wrapped Unix functions, format standardization/conversions, interval operations) and 3rd party analysis tools, for example, Bowtie/Tuxedo Suite (bowtie-bio.sourceforge.net), Lastz (www.bx.psu.edu/~rsharris/lastz/), SAMTools (samtools.sourceforge.net), FASTX-toolkit (hannonlab.cshl.edu/fastx_toolkit), and MACS (liulab.dfci.harvard.edu/MACS), and creates results formatted for visualization in tools such as the Galaxy Track Browser (GTB, galaxyproject.org/wiki/Learn/Visualization), UCSC Genome Browser (genome.ucsc.edu), Ensembl (www.ensembl.org), and GeneTrack (genetrack.bx.psu.edu). Galaxy rapidly has become the most popular choice for integrated next generation sequencing (NGS) analytics and collaboration, where users can perform, document, and share complex analysis within a single interface in an unprecedented number of ways. PMID:18428782

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

PubMed

Veidenberg, Andres; Medlar, Alan; Löytynoja, Ari

2016-04-01

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

MediLink: a wearable telemedicine system for emergency and mobile applications.

PubMed

Koval, T; Dudziak, M

1999-01-01

The practical needs of the medical professional faced with critical care or emergency situations differ from those working in many environments where telemedicine and mobile computing have been introduced and tested. One constructive criticism of the telemedicine initiative has been to question what positive benefits are gained from videoconferencing, paperless transactions, and online access to patient record. With a goal of producing a positive answer to such questions an architecture for multipurpose mobile telemedicine applications has been developed. The core technology is based upon a wearable personal computer with a smart-card interface coupled with speech, pen, video input and wireless intranet connectivity. The TransPAC system with the MedLink software system is designed to provide an integrated solution for a broad range of health care functions where mobile and hands-free or limited-access systems are preferred or necessary and where the capabilities of other mobile devices are insufficient or inappropriate. Structured and noise-resistant speech-to-text interfacing plus the use of a web browser-like display, accessible through either a flatpanel, standard, or headset monitor, gives the beltpack TransPAC computer the functions of a complete desktop including PCMCIA card interfaces for internet connectivity and a secure smartcard with 16-bit microprocessor and upwards of 64K memory. The card acts to provide user access control for security, user custom configuration of applications and display and vocabulary, and memory to diminish the need for PC-server communications while in an active session. TransPAC is being implemented for EMT and ER staff usage.

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

77 FR 47867 - Agency Information Collection Activities: Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-10

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

Storage and distribution of pathology digital images using integrated web-based viewing systems.

PubMed

Marchevsky, Alberto M; Dulbandzhyan, Ronda; Seely, Kevin; Carey, Steve; Duncan, Raymond G

2002-05-01

Health care providers have expressed increasing interest in incorporating digital images of gross pathology specimens and photomicrographs in routine pathology reports. To describe the multiple technical and logistical challenges involved in the integration of the various components needed for the development of a system for integrated Web-based viewing, storage, and distribution of digital images in a large health system. An Oracle version 8.1.6 database was developed to store, index, and deploy pathology digital photographs via our Intranet. The database allows for retrieval of images by patient demographics or by SNOMED code information. The Intranet of a large health system accessible from multiple computers located within the medical center and at distant private physician offices. The images can be viewed using any of the workstations of the health system that have authorized access to our Intranet, using a standard browser or a browser configured with an external viewer or inexpensive plug-in software, such as Prizm 2.0. The images can be printed on paper or transferred to film using a digital film recorder. Digital images can also be displayed at pathology conferences by using wireless local area network (LAN) and secure remote technologies. The standardization of technologies and the adoption of a Web interface for all our computer systems allows us to distribute digital images from a pathology database to a potentially large group of users distributed in multiple locations throughout a large medical center.

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.

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

ERIC Educational Resources Information Center

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

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

Coal Data Browser

EIA Publications

The Coal Data Browser gives users easy access to coal information from EIA's electricity and coal surveys as well as data from the Mine Safety and Health Administration and trade information from the U.S. Census Bureau. Users can also see the shipment data from individual mines that deliver coal to the U.S. electric power fleet, have the ability to track supplies delivered to a given power plant, and to see which mines serve each particular plant.

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.

A TCP/IP framework for ethernet-based measurement, control and experiment data distribution

NASA Astrophysics Data System (ADS)

Ocaya, R. O.; Minny, J.

2010-11-01

A complete modular but scalable TCP/IP based scientific instrument control and data distribution system has been designed and realized. The system features an IEEE 802.3 compliant 10 Mbps Medium Access Controller (MAC) and Physical Layer Device that is suitable for the full-duplex monitoring and control of various physically widespread measurement transducers in the presence of a local network infrastructure. The cumbersomeness of exchanging and synchronizing data between the various transducer units using physical storage media led to the choice of TCP/IP as a logical alternative. The system and methods developed are scalable for broader usage over the Internet. The system comprises a PIC18f2620 and ENC28j60 based hardware and a software component written in C, Java/Javascript and Visual Basic.NET programming languages for event-level monitoring and browser user-interfaces respectively. The system exchanges data with the host network through IPv4 packets requested and received on a HTTP page. It also responds to ICMP echo, UDP and ARP requests through a user selectable integrated DHCP and static IPv4 address allocation scheme. The round-trip time, throughput and polling frequency are estimated and reported. A typical application to temperature monitoring and logging is also presented.

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

NASA Astrophysics Data System (ADS)

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

2014-07-01

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

A 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.

CDAPubMed: a browser extension to retrieve EHR-based biomedical literature.

PubMed

Perez-Rey, David; Jimenez-Castellanos, Ana; Garcia-Remesal, Miguel; Crespo, Jose; Maojo, Victor

2012-04-05

Over the last few decades, the ever-increasing output of scientific publications has led to new challenges to keep up to date with the literature. In the biomedical area, this growth has introduced new requirements for professionals, e.g., physicians, who have to locate the exact papers that they need for their clinical and research work amongst a huge number of publications. Against this backdrop, novel information retrieval methods are even more necessary. While web search engines are widespread in many areas, facilitating access to all kinds of information, additional tools are required to automatically link information retrieved from these engines to specific biomedical applications. In the case of clinical environments, this also means considering aspects such as patient data security and confidentiality or structured contents, e.g., electronic health records (EHRs). In this scenario, we have developed a new tool to facilitate query building to retrieve scientific literature related to EHRs. We have developed CDAPubMed, an open-source web browser extension to integrate EHR features in biomedical literature retrieval approaches. Clinical users can use CDAPubMed to: (i) load patient clinical documents, i.e., EHRs based on the Health Level 7-Clinical Document Architecture Standard (HL7-CDA), (ii) identify relevant terms for scientific literature search in these documents, i.e., Medical Subject Headings (MeSH), automatically driven by the CDAPubMed configuration, which advanced users can optimize to adapt to each specific situation, and (iii) generate and launch literature search queries to a major search engine, i.e., PubMed, to retrieve citations related to the EHR under examination. CDAPubMed is a platform-independent tool designed to facilitate literature searching using keywords contained in specific EHRs. CDAPubMed is visually integrated, as an extension of a widespread web browser, within the standard PubMed interface. It has been tested on a public dataset of HL7-CDA documents, returning significantly fewer citations since queries are focused on characteristics identified within the EHR. For instance, compared with more than 200,000 citations retrieved by breast neoplasm, fewer than ten citations were retrieved when ten patient features were added using CDAPubMed. This is an open source tool that can be freely used for non-profit purposes and integrated with other existing systems.

CDAPubMed: a browser extension to retrieve EHR-based biomedical literature

PubMed Central

2012-01-01

Background Over the last few decades, the ever-increasing output of scientific publications has led to new challenges to keep up to date with the literature. In the biomedical area, this growth has introduced new requirements for professionals, e.g., physicians, who have to locate the exact papers that they need for their clinical and research work amongst a huge number of publications. Against this backdrop, novel information retrieval methods are even more necessary. While web search engines are widespread in many areas, facilitating access to all kinds of information, additional tools are required to automatically link information retrieved from these engines to specific biomedical applications. In the case of clinical environments, this also means considering aspects such as patient data security and confidentiality or structured contents, e.g., electronic health records (EHRs). In this scenario, we have developed a new tool to facilitate query building to retrieve scientific literature related to EHRs. Results We have developed CDAPubMed, an open-source web browser extension to integrate EHR features in biomedical literature retrieval approaches. Clinical users can use CDAPubMed to: (i) load patient clinical documents, i.e., EHRs based on the Health Level 7-Clinical Document Architecture Standard (HL7-CDA), (ii) identify relevant terms for scientific literature search in these documents, i.e., Medical Subject Headings (MeSH), automatically driven by the CDAPubMed configuration, which advanced users can optimize to adapt to each specific situation, and (iii) generate and launch literature search queries to a major search engine, i.e., PubMed, to retrieve citations related to the EHR under examination. Conclusions CDAPubMed is a platform-independent tool designed to facilitate literature searching using keywords contained in specific EHRs. CDAPubMed is visually integrated, as an extension of a widespread web browser, within the standard PubMed interface. It has been tested on a public dataset of HL7-CDA documents, returning significantly fewer citations since queries are focused on characteristics identified within the EHR. For instance, compared with more than 200,000 citations retrieved by breast neoplasm, fewer than ten citations were retrieved when ten patient features were added using CDAPubMed. This is an open source tool that can be freely used for non-profit purposes and integrated with other existing systems. PMID:22480327

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

PubMed Central

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

2016-01-01

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

Earth Science Data Archive and Access at the NASA/Goddard Space Flight Center Distributed Active Archive Center (DAAC)

NASA Technical Reports Server (NTRS)

Leptoukh, Gregory

1999-01-01

The Goddard Distributed Active Archive Center (DAAC), as an integral part of the Earth Observing System Data and Information System (EOSDIS), is the official source of data for several important earth remote sensing missions. These include the Sea-viewing Wide-Field-of-view Sensor (SeaWiFS) launched in August 1997, the Tropical Rainfall Measuring Mission (TRMM) launched in November 1997, and the Moderate Resolution Imaging Spectroradiometer (MODIS) scheduled for launch in mid 1999 as part of the EOS AM-1 instrumentation package. The data generated from these missions supports a host of users in the hydrological, land biosphere and oceanographic research and applications communities. The volume and nature of the data present unique challenges to an Earth science data archive and distribution system such as the DAAC. The DAAC system receives, archives and distributes a large number of standard data products on a daily basis, including data files that have been reprocessed with updated calibration data or improved analytical algorithms. A World Wide Web interface is provided allowing interactive data selection and automatic data subscriptions as distribution options. The DAAC also creates customized and value-added data products, which allow additional user flexibility and reduced data volume. Another significant part of our overall mission is to provide ancillary data support services and archive support for worldwide field campaigns designed to validate the results from the various satellite-derived measurements. In addition to direct data services, accompanying documentation, WWW links to related resources, support for EOSDIS data formats, and informed response to inquiries are routinely provided to users. The current GDAAC WWW search and order system is being restructured to provide users with a simplified, hierarchical access to data. Data Browsers have been developed for several data sets to aid users in ordering data. These Browsers allow users to specify spatial, temporal, and other parameter criteria in searching for and previewing data.

ITOHealth: a multimodal middleware-oriented integrated architecture for discovering medical entities.

PubMed

Alor-Hernández, Giner; Sánchez-Cervantes, José Luis; Juárez-Martínez, Ulises; Posada-Gómez, Rubén; Cortes-Robles, Guillermo; Aguilar-Laserre, Alberto

2012-03-01

Emergency healthcare is one of the emerging application domains for information services, which requires highly multimodal information services. The time of consuming pre-hospital emergency process is critical. Therefore, the minimization of required time for providing primary care and consultation to patients is one of the crucial factors when trying to improve the healthcare delivery in emergency situations. In this sense, dynamic location of medical entities is a complex process that needs time and it can be critical when a person requires medical attention. This work presents a multimodal location-based system for locating and assigning medical entities called ITOHealth. ITOHealth provides a multimodal middleware-oriented integrated architecture using a service-oriented architecture in order to provide information of medical entities in mobile devices and web browsers with enriched interfaces providing multimodality support. ITOHealth's multimodality is based on the use of Microsoft Agent Characters, the integration of natural language voice to the characters, and multi-language and multi-characters support providing an advantage for users with visual impairments.

Science Plan Visualisation for Rosetta

NASA Astrophysics Data System (ADS)

Schmidt, A.; Grieger, B.; Völk, S.

2013-12-01

Rosetta is a mission of the European Space Agency (ESA) to rendez-vous with comet Churyumov-Gerasimenko in mid-2014. The trajectories and their corresponding operations are flexible and particularly complex. To make informed decisions among the many free parameters novel ways to communicate operations to the community have been explored. To support science planning by communicating operational ideas and disseminating operational scenarios, the science ground segment makes use of Web-based visualisation technologies. To keep the threshold to analysing operations proposals as low as possible, various implementation techniques have been investigated. An important goal was to use the Web to make the content as accessible as possible. By adopting the recent standard WebGL and generating static pages of time-dependent three-dimensional views of the spacecraft as well as the corresponding field-of-views of instruments, directly from the operational and for-study files, users are given the opportunity to explore interactively in their Web browsers what is being proposed in addition to using the traditional file products and analysing them in detail. The scenes and animations can be viewed in any modern Web browser and be combined with other analyses. This is to facilitate verification and cross-validation of complex products, often done by comparing different independent analyses and studies. By providing different timesteps in animations, it is possible to focus on long-term planning or short-term planning without distracting the user from the essentials. This is particularly important since the information that can be displayed in a Web browser is somewhat related to data volume that can be transferred across the wire. In Web browsers, it is more challenging to do numerical calculations on demand. Since requests for additional data have to be passed through a Web server, they are more complex and also require a more complex infrastructure. The volume of data that can be kept in a browser environment is limited and might have to be transferred over often slow network links. Thus, careful design and reduction of data is required. Regarding user interaction, Web browsers are often limited to a mouse and keyboards. In terms of benefits, the threshold and turn-around times for discussing operational ideas by using the visualisation techniques described here are lowered. An additional benefit of the approach was the cooperative use of products by distributed users which resulted in higher-quality software and data by incorporating more feedback than what would usually have been available.

Communication of Science Plans in the Rosetta Mission

NASA Astrophysics Data System (ADS)

Schmidt, Albrecht; Grieger, Björn; Völk, Stefan

2014-05-01

Rosetta is a mission of the European Space Agency (ESA) to rendez-vous with comet Churyumov-Gerasimenko in mid-2014. The trajectories and their corresponding operations are both flexible and particularly complex. To make informed decisions among the many free parameters, novel ways to communicate operations to the community have been explored. To support science planning by communicating operational ideas and disseminating operational scenarios, the science ground segment makes use of Web-based visualisation technologies. To keep the threshold to analysing operations proposals as low as possible, various implementation techniques have been investigated. An important goal was to use the Web to make the content as accessible as possible. By adopting the recent standard WebGL and generating static pages of time-dependent three-dimensional views of the spacecraft as well as the corresponding field-of-views of instruments, directly from the operational and for-study files, users are given the opportunity to explore interactively in their Web browsers what is being proposed in addition to using the traditional file products and analysing them in detail. The scenes and animations can be viewed in any modern Web browser and be combined with other analyses. This is to facilitate verification and cross-validation of complex products, often done by comparing different independent analyses and studies. By providing different timesteps in animations, it is possible to focus on long-term planning or short-term planning without distracting the user from the essentials. This is particularly important since the information that can be displayed in a Web browser is somewhat related to data volume that can be transferred across the wire. In Web browsers, it is more challenging to do numerical calculations on demand. Since requests for additional data have to be passed through a Web server, they are more complex and also require a more complex infrastructure. The volume of data that can be kept in a browser environment is limited and might have to be transferred over often slow network links. Thus, careful design and reduction of data is required. Regarding user interaction, Web browsers are often limited to a mouse and keyboards. In terms of benefits, the threshold and turn-around times for discussing operational ideas by using the visualisation techniques described here are lowered. An additional benefit of the approach was the cooperative use of products by distributed users which resulted in higher-quality software and data by incorporating more feedback than what would usually have been available.

Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.

PubMed

Sakai, Hiroaki; Lee, Sung Shin; Tanaka, Tsuyoshi; Numa, Hisataka; Kim, Jungsok; Kawahara, Yoshihiro; Wakimoto, Hironobu; Yang, Ching-chia; Iwamoto, Masao; Abe, Takashi; Yamada, Yuko; Muto, Akira; Inokuchi, Hachiro; Ikemura, Toshimichi; Matsumoto, Takashi; Sasaki, Takuji; Itoh, Takeshi

2013-02-01

The Rice Annotation Project Database (RAP-DB, http://rapdb.dna.affrc.go.jp/) has been providing a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare. Since the first release in 2005, RAP-DB has been updated several times along with the genome assembly updates. Here, we present our newest RAP-DB based on the latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP-1.0), which was released in 2011. We detected 37,869 loci by mapping transcript and protein sequences of 150 monocot species. To provide plant researchers with highly reliable and up to date rice gene annotations, we have been incorporating literature-based manually curated data, and 1,626 loci currently incorporate literature-based annotation data, including commonly used gene names or gene symbols. Transcriptional activities are shown at the nucleotide level by mapping RNA-Seq reads derived from 27 samples. We also mapped the Illumina reads of a Japanese leading japonica cultivar, Koshihikari, and a Chinese indica cultivar, Guangluai-4, to the genome and show alignments together with the single nucleotide polymorphisms (SNPs) and gene functional annotations through a newly developed browser, Short-Read Assembly Browser (S-RAB). We have developed two satellite databases, Plant Gene Family Database (PGFD) and Integrative Database of Cereal Gene Phylogeny (IDCGP), which display gene family and homologous gene relationships among diverse plant species. RAP-DB and the satellite databases offer simple and user-friendly web interfaces, enabling plant and genome researchers to access the data easily and facilitating a broad range of plant research topics.

PhenoTips: patient phenotyping software for clinical and research use.

PubMed

Girdea, Marta; Dumitriu, Sergiu; Fiume, Marc; Bowdin, Sarah; Boycott, Kym M; Chénier, Sébastien; Chitayat, David; Faghfoury, Hanna; Meyn, M Stephen; Ray, Peter N; So, Joyce; Stavropoulos, Dimitri J; Brudno, Michael

2013-08-01

We have developed PhenoTips: open source software for collecting and analyzing phenotypic information for patients with genetic disorders. Our software combines an easy-to-use interface, compatible with any device that runs a Web browser, with a standardized database back end. The PhenoTips' user interface closely mirrors clinician workflows so as to facilitate the recording of observations made during the patient encounter. Collected data include demographics, medical history, family history, physical and laboratory measurements, physical findings, and additional notes. Phenotypic information is represented using the Human Phenotype Ontology; however, the complexity of the ontology is hidden behind a user interface, which combines simple selection of common phenotypes with error-tolerant, predictive search of the entire ontology. PhenoTips supports accurate diagnosis by analyzing the entered data, then suggesting additional clinical investigations and providing Online Mendelian Inheritance in Man (OMIM) links to likely disorders. By collecting, classifying, and analyzing phenotypic information during the patient encounter, PhenoTips allows for streamlining of clinic workflow, efficient data entry, improved diagnosis, standardization of collected patient phenotypes, and sharing of anonymized patient phenotype data for the study of rare disorders. Our source code and a demo version of PhenoTips are available at http://phenotips.org. © 2013 WILEY PERIODICALS, INC.

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

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-27

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

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.

New NED XML/VOtable Services and Client Interface Applications

NASA Astrophysics Data System (ADS)

Pevunova, O.; Good, J.; Mazzarella, J.; Berriman, G. B.; Madore, B.

2005-12-01

The NASA/IPAC Extragalactic Database (NED) provides data and cross-identifications for over 7 million extragalactic objects fused from thousands of survey catalogs and journal articles. The data cover all frequencies from radio through gamma rays and include positions, redshifts, photometry and spectral energy distributions (SEDs), sizes, and images. NED services have traditionally supplied data in HTML format for connections from Web browsers, and a custom ASCII data structure for connections by remote computer programs written in the C programming language. We describe new services that provide responses from NED queries in XML documents compliant with the international virtual observatory VOtable protocol. The XML/VOtable services support cone searches, all-sky searches based on object attributes (survey names, cross-IDs, redshifts, flux densities), and requests for detailed object data. Initial services have been inserted into the NVO registry, and others will follow soon. The first client application is a Style Sheet specification for rendering NED VOtable query results in Web browsers that support XML. The second prototype application is a Java applet that allows users to compare multiple SEDs. The new XML/VOtable output mode will also simplify the integration of data from NED into visualization and analysis packages, software agents, and other virtual observatory applications. We show an example SED from NED plotted using VOPlot. The NED website is: http://nedwww.ipac.caltech.edu.

The Physiology Constant Database of Teen-Agers in Beijing

PubMed Central

Wei-Qi, Wei; Guang-Jin, Zhu; Cheng-Li, Xu; Shao-Mei, Han; Bao-Shen, Qi; Li, Chen; Shu-Yu, Zu; Xiao-Mei, Zhou; Wen-Feng, Hu; Zheng-Guo, Zhang

2004-01-01

Physiology constants of adolescents are important to understand growing living systems and are a useful reference in clinical and epidemiological research. Until recently, physiology constants were not available in China and therefore most physiologists, physicians, and nutritionists had to use data from abroad for reference. However, the very difference between the Eastern and Western races casts doubt on the usefulness of overseas data. We have therefore created a database system to provide a repository for the storage of physiology constants of teen-agers in Beijing. The several thousands of pieces of data are now divided into hematological biochemistry, lung function, and cardiac function with all data manually checked before being transferred into the database. The database was accomplished through the development of a web interface, scripts, and a relational database. The physiology data were integrated into the relational database system to provide flexible facilities by using combinations of various terms and parameters. A web browser interface was designed for the users to facilitate their searching. The database is available on the web. The statistical table, scatter diagram, and histogram of the data are available for both anonym and user according to queries, while only the user can achieve detail, including download data and advanced search. PMID:15258669

HEP Computing

Science.gov Websites

Argonne National Laboratory High Energy Physics Division Windows Desktops Problem Report Service Request Password Help New Users Back to HEP Computing Email on ANL Exchange: See Windows Clients section (Outlook or Thunderbird recommended) Web Browsers: Web Browsers for Windows Desktops Software: Available

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

PubMed

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

2017-06-01

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

Design and implementation of the NPOI database and website

NASA Astrophysics Data System (ADS)

Newman, K.; Jorgensen, A. M.; Landavazo, M.; Sun, B.; Hutter, D. J.; Armstrong, J. T.; Mozurkewich, David; Elias, N.; van Belle, G. T.; Schmitt, H. R.; Baines, E. K.

2014-07-01

The Navy Precision Optical Interferometer (NPOI) has been recording astronomical observations for nearly two decades, at this point with hundreds of thousands of individual observations recorded to date for a total data volume of many terabytes. To make maximum use of the NPOI data it is necessary to organize them in an easily searchable manner and be able to extract essential diagnostic information from the data to allow users to quickly gauge data quality and suitability for a specific science investigation. This sets the motivation for creating a comprehensive database of observation metadata as well as, at least, reduced data products. The NPOI database is implemented in MySQL using standard database tools and interfaces. The use of standard database tools allows us to focus on top-level database and interface implementation and take advantage of standard features such as backup, remote access, mirroring, and complex queries which would otherwise be time-consuming to implement. A website was created in order to give scientists a user friendly interface for searching the database. It allows the user to select various metadata to search for and also allows them to decide how and what results are displayed. This streamlines the searches, making it easier and quicker for scientists to find the information they are looking for. The website has multiple browser and device support. In this paper we present the design of the NPOI database and website, and give examples of its use.

The ATLAS PanDA Monitoring System and its Evolution

NASA Astrophysics Data System (ADS)

Klimentov, A.; Nevski, P.; Potekhin, M.; Wenaus, T.

2011-12-01

The PanDA (Production and Distributed Analysis) Workload Management System is used for ATLAS distributed production and analysis worldwide. The needs of ATLAS global computing imposed challenging requirements on the design of PanDA in areas such as scalability, robustness, automation, diagnostics, and usability for both production shifters and analysis users. Through a system-wide job database, the PanDA monitor provides a comprehensive and coherent view of the system and job execution, from high level summaries to detailed drill-down job diagnostics. It is (like the rest of PanDA) an Apache-based Python application backed by Oracle. The presentation layer is HTML code generated on the fly in the Python application which is also responsible for managing database queries. However, this approach is lacking in user interface flexibility, simplicity of communication with external systems, and ease of maintenance. A decision was therefore made to migrate the PanDA monitor server to Django Web Application Framework and apply JSON/AJAX technology in the browser front end. This allows us to greatly reduce the amount of application code, separate data preparation from presentation, leverage open source for tools such as authentication and authorization mechanisms, and provide a richer and more dynamic user experience. We describe our approach, design and initial experience with the migration process.

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.

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.

Web3DMol: interactive protein structure visualization based on WebGL.

PubMed

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

2017-07-03

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

Web-based hydrodynamics computing

NASA Astrophysics Data System (ADS)

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

2005-01-01

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

Web-based hydrodynamics computing

NASA Astrophysics Data System (ADS)

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

2004-12-01

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

Development of a Google-based search engine for data mining radiology reports.

PubMed

Erinjeri, Joseph P; Picus, Daniel; Prior, Fred W; Rubin, David A; Koppel, Paul

2009-08-01

The aim of this study is to develop a secure, Google-based data-mining tool for radiology reports using free and open source technologies and to explore its use within an academic radiology department. A Health Insurance Portability and Accountability Act (HIPAA)-compliant data repository, search engine and user interface were created to facilitate treatment, operations, and reviews preparatory to research. The Institutional Review Board waived review of the project, and informed consent was not required. Comprising 7.9 GB of disk space, 2.9 million text reports were downloaded from our radiology information system to a fileserver. Extensible markup language (XML) representations of the reports were indexed using Google Desktop Enterprise search engine software. A hypertext markup language (HTML) form allowed users to submit queries to Google Desktop, and Google's XML response was interpreted by a practical extraction and report language (PERL) script, presenting ranked results in a web browser window. The query, reason for search, results, and documents visited were logged to maintain HIPAA compliance. Indexing averaged approximately 25,000 reports per hour. Keyword search of a common term like "pneumothorax" yielded the first ten most relevant results of 705,550 total results in 1.36 s. Keyword search of a rare term like "hemangioendothelioma" yielded the first ten most relevant results of 167 total results in 0.23 s; retrieval of all 167 results took 0.26 s. Data mining tools for radiology reports will improve the productivity of academic radiologists in clinical, educational, research, and administrative tasks. By leveraging existing knowledge of Google's interface, radiologists can quickly perform useful searches.

A browser-based 3D Visualization Tool designed for comparing CERES/CALIOP/CloudSAT level-2 data sets.

NASA Astrophysics Data System (ADS)

Chu, C.; Sun-Mack, S.; Chen, Y.; Heckert, E.; Doelling, D. R.

2017-12-01

In Langley NASA, Clouds and the Earth's Radiant Energy System (CERES) and Moderate Resolution Imaging Spectroradiometer (MODIS) are merged with Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) on the Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) and CloudSat Cloud Profiling Radar (CPR). The CERES merged product (C3M) matches up to three CALIPSO footprints with each MODIS pixel along its ground track. It then assigns the nearest CloudSat footprint to each of those MODIS pixels. The cloud properties from MODIS, retrieved using the CERES algorithms, are included in C3M with the matched CALIPSO and CloudSat products along with radiances from 18 MODIS channels. The dataset is used to validate the CERES retrieved MODIS cloud properties and the computed TOA and surface flux difference using MODIS or CALIOP/CloudSAT retrieved clouds. This information is then used to tune the computed fluxes to match the CERES observed TOA flux. A visualization tool will be invaluable to determine the cause of these large cloud and flux differences in order to improve the methodology. This effort is part of larger effort to allow users to order the CERES C3M product sub-setted by time and parameter as well as the previously mentioned visualization capabilities. This presentation will show a new graphical 3D-interface, 3D-CERESVis, that allows users to view both passive remote sensing satellites (MODIS and CERES) and active satellites (CALIPSO and CloudSat), such that the detailed vertical structures of cloud properties from CALIPSO and CloudSat are displayed side by side with horizontally retrieved cloud properties from MODIS and CERES. Similarly, the CERES computed profile fluxes whether using MODIS or CALIPSO and CloudSat clouds can also be compared. 3D-CERESVis is a browser-based visualization tool that makes uses of techniques such as multiple synchronized cursors, COLLADA format data and Cesium.

Gramene 2016: comparative plant genomics and pathway resources

PubMed Central

Tello-Ruiz, Marcela K.; Stein, Joshua; Wei, Sharon; Preece, Justin; Olson, Andrew; Naithani, Sushma; Amarasinghe, Vindhya; Dharmawardhana, Palitha; Jiao, Yinping; Mulvaney, Joseph; Kumari, Sunita; Chougule, Kapeel; Elser, Justin; Wang, Bo; Thomason, James; Bolser, Daniel M.; Kerhornou, Arnaud; Walts, Brandon; Fonseca, Nuno A.; Huerta, Laura; Keays, Maria; Tang, Y. Amy; Parkinson, Helen; Fabregat, Antonio; McKay, Sheldon; Weiser, Joel; D'Eustachio, Peter; Stein, Lincoln; Petryszak, Robert; Kersey, Paul J.; Jaiswal, Pankaj; Ware, Doreen

2016-01-01

Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The genomes section features 39 fully assembled reference genomes that are integrated using ontology-based annotation and comparative analyses, and accessed through both visual and programmatic interfaces. Additional community data, such as genetic variation, expression and methylation, are also mapped for a subset of genomes. The Plant Reactome pathway portal (http://plantreactome.gramene.org) provides a reference resource for analyzing plant metabolic and regulatory pathways. In addition to ∼200 curated rice reference pathways, the portal hosts gene homology-based pathway projections for 33 plant species. Both the genome and pathway browsers interface with the EMBL-EBI's Expression Atlas to enable the projection of baseline and differential expression data from curated expression studies in plants. Gramene's archive website (http://archive.gramene.org) continues to provide previously reported resources on comparative maps, markers and QTL. To further aid our users, we have also introduced a live monthly educational webinar series and a Gramene YouTube channel carrying video tutorials. PMID:26553803

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.

Provenance for Runtime Workflow Steering and Validation in Computational Seismology

NASA Astrophysics Data System (ADS)

Spinuso, A.; Krischer, L.; Krause, A.; Filgueira, R.; Magnoni, F.; Muraleedharan, V.; David, M.

2014-12-01

Provenance systems may be offered by modern workflow engines to collect metadata about the data transformations at runtime. If combined with effective visualisation and monitoring interfaces, these provenance recordings can speed up the validation process of an experiment, suggesting interactive or automated interventions with immediate effects on the lifecycle of a workflow run. For instance, in the field of computational seismology, if we consider research applications performing long lasting cross correlation analysis and high resolution simulations, the immediate notification of logical errors and the rapid access to intermediate results, can produce reactions which foster a more efficient progress of the research. These applications are often executed in secured and sophisticated HPC and HTC infrastructures, highlighting the need for a comprehensive framework that facilitates the extraction of fine grained provenance and the development of provenance aware components, leveraging the scalability characteristics of the adopted workflow engines, whose enactment can be mapped to different technologies (MPI, Storm clusters, etc). This work looks at the adoption of W3C-PROV concepts and data model within a user driven processing and validation framework for seismic data, supporting also computational and data management steering. Validation needs to balance automation with user intervention, considering the scientist as part of the archiving process. Therefore, the provenance data is enriched with community-specific metadata vocabularies and control messages, making an experiment reproducible and its description consistent with the community understandings. Moreover, it can contain user defined terms and annotations. The current implementation of the system is supported by the EU-Funded VERCE (http://verce.eu). It provides, as well as the provenance generation mechanisms, a prototypal browser-based user interface and a web API built on top of a NoSQL storage technology, experimenting ways to ensure a rapid and flexible access to the lineage traces. It supports the users with the visualisation of graphical products and offers combined operations to access and download the data which may be selectively stored at runtime, into dedicated data archives.

Design and implementation of a unified certification management system based on seismic business

NASA Astrophysics Data System (ADS)

Tang, Hongliang

2018-04-01

Many business software for seismic systems are based on web pages, users can simply open a browser and enter their IP address. However, how to achieve unified management and security management of many IP addresses, this paper introduces the design concept based on seismic business and builds a unified authentication management system using ASP technology.

EarthServer - 3D Visualization on the Web

NASA Astrophysics Data System (ADS)

Wagner, Sebastian; Herzig, Pasquale; Bockholt, Ulrich; Jung, Yvonne; Behr, Johannes

2013-04-01

EarthServer (www.earthserver.eu), funded by the European Commission under its Seventh Framework Program, is a project to enable the management, access and exploration of massive, multi-dimensional datasets using Open GeoSpatial Consortium (OGC) query and processing language standards like WCS 2.0 and WCPS. To this end, a server/client architecture designed to handle Petabyte/Exabyte volumes of multi-dimensional data is being developed and deployed. As an important part of the EarthServer project, six Lighthouse Applications, major scientific data exploitation initiatives, are being established to make cross-domain, Earth Sciences related data repositories available in an open and unified manner, as service endpoints based on solutions and infrastructure developed within the project. Clients technology developed and deployed in EarthServer ranges from mobile and web clients to immersive virtual reality systems, all designed to interact with a physically and logically distributed server infrastructure using exclusively OGC standards. In this contribution, we would like to present our work on a web-based 3D visualization and interaction client for Earth Sciences data using only technology found in standard web browsers without requiring the user to install plugins or addons. Additionally, we are able to run the earth data visualization client on a wide range of different platforms with very different soft- and hardware requirements such as smart phones (e.g. iOS, Android), different desktop systems etc. High-quality, hardware-accelerated visualization of 3D and 4D content in standard web browsers can be realized now and we believe it will become more and more common to use this fast, lightweight and ubiquitous platform to provide insights into big datasets without requiring the user to set up a specialized client first. With that in mind, we will also point out some of the limitations we encountered using current web technologies. Underlying the EarthServer web client and on top of HTML5, WebGL and JavaScript we have developed the X3DOM framework (www.x3dom.org), which makes possible to embed declarative X3D scenegraphs, an ISO standard XML-based file format for representing 3D computer graphics, directly within HTML, thus enabling developers to rapidly design 3D content that blends seamlessly into HTML interfaces using Javascript. This approach (commonly referred to as a polyfill layer) is used to mimic native web browser support for declarative 3D content and is an important component in our web client architecture.

Creating context for the experiment record. User-defined metadata: investigations into metadata usage in the LabTrove ELN.

PubMed

Willoughby, Cerys; Bird, Colin L; Coles, Simon J; Frey, Jeremy G

2014-12-22

The drive toward more transparency in research, the growing willingness to make data openly available, and the reuse of data to maximize the return on research investment all increase the importance of being able to find information and make links to the underlying data. The use of metadata in Electronic Laboratory Notebooks (ELNs) to curate experiment data is an essential ingredient for facilitating discovery. The University of Southampton has developed a Web browser-based ELN that enables users to add their own metadata to notebook entries. A survey of these notebooks was completed to assess user behavior and patterns of metadata usage within ELNs, while user perceptions and expectations were gathered through interviews and user-testing activities within the community. The findings indicate that while some groups are comfortable with metadata and are able to design a metadata structure that works effectively, many users are making little attempts to use it, thereby endangering their ability to recover data in the future. A survey of patterns of metadata use in these notebooks, together with feedback from the user community, indicated that while a few groups are comfortable with metadata and are able to design a metadata structure that works effectively, many users adopt a "minimum required" approach to metadata. To investigate whether the patterns of metadata use in LabTrove were unusual, a series of surveys were undertaken to investigate metadata usage in a variety of platforms supporting user-defined metadata. These surveys also provided the opportunity to investigate whether interface designs in these other environments might inform strategies for encouraging metadata creation and more effective use of metadata in LabTrove.

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

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

NATIONAL LANDSCAPE METRICS BROWSER (V1.0)

EPA Science Inventory

This metric browser website describes and displays wall-to-wall landscape metrics that have been calculated for the entire conterminous U.S. The intent is to provide the user with an overview of the nature and utility of this landscape metric data set. The land cover and pattern ...

International Portal

EIA Publications

The International Energy Portal includes a powerful data browser that provides country-level energy data; many countries have at least 30 years of historical data. The data browser provides users the ability to view and download complete datasets for consumption, production, trade, reserves, and carbon dioxide emissions for different fuels and energy sources.

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

PubMed

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

2014-09-15

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

Panorama: A Targeted Proteomics Knowledge Base

PubMed Central

2015-01-01

Panorama is a web application for storing, sharing, analyzing, and reusing targeted assays created and refined with Skyline,1 an increasingly popular Windows client software tool for targeted proteomics experiments. Panorama allows laboratories to store and organize curated results contained in Skyline documents with fine-grained permissions, which facilitates distributed collaboration and secure sharing of published and unpublished data via a web-browser interface. It is fully integrated with the Skyline workflow and supports publishing a document directly to a Panorama server from the Skyline user interface. Panorama captures the complete Skyline document information content in a relational database schema. Curated results published to Panorama can be aggregated and exported as chromatogram libraries. These libraries can be used in Skyline to pick optimal targets in new experiments and to validate peak identification of target peptides. Panorama is open-source and freely available. It is distributed as part of LabKey Server,2 an open source biomedical research data management system. Laboratories and organizations can set up Panorama locally by downloading and installing the software on their own servers. They can also request freely hosted projects on https://panoramaweb.org, a Panorama server maintained by the Department of Genome Sciences at the University of Washington. PMID:25102069

Diamond Eye: a distributed architecture for image data mining

NASA Astrophysics Data System (ADS)

Burl, Michael C.; Fowlkes, Charless; Roden, Joe; Stechert, Andre; Mukhtar, Saleem

1999-02-01

Diamond Eye is a distributed software architecture, which enables users (scientists) to analyze large image collections by interacting with one or more custom data mining servers via a Java applet interface. Each server is coupled with an object-oriented database and a computational engine, such as a network of high-performance workstations. The database provides persistent storage and supports querying of the 'mined' information. The computational engine provides parallel execution of expensive image processing, object recognition, and query-by-content operations. Key benefits of the Diamond Eye architecture are: (1) the design promotes trial evaluation of advanced data mining and machine learning techniques by potential new users (all that is required is to point a web browser to the appropriate URL), (2) software infrastructure that is common across a range of science mining applications is factored out and reused, and (3) the system facilitates closer collaborations between algorithm developers and domain experts.

Secure web-based access to radiology: forms and databases for fast queries

NASA Astrophysics Data System (ADS)

McColl, Roderick W.; Lane, Thomas J.

2002-05-01

Currently, Web-based access to mini-PACS or similar databases commonly utilizes either JavaScript, Java applets or ActiveX controls. Many sites do not permit applets or controls or other binary objects for fear of viruses or worms sent by malicious users. In addition, the typical CGI query mechanism requires several parameters to be sent with the http GET/POST request, which may identify the patient in some way; this in unacceptable for privacy protection. Also unacceptable are pages produced by server-side scripts which can be cached by the browser, since these may also contain sensitive information. We propose a simple mechanism for access to patient information, including images, which guarantees security of information, makes it impossible to bookmark the page, or to return to the page after some defined length of time. In addition, this mechanism is simple, therefore permitting rapid access without the need to initially download an interface such as an applet or control. In addition to image display, the design of the site allows the user to view and save movies of multi-phasic data, or to construct multi-frame datasets from entire series. These capabilities make the site attractive for research purposes such as teaching file preparation.

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

PubMed Central

Chen, Jung-Wei; Zhang, Jiajie

2007-01-01

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

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

PubMed

Chen, Jung-Wei; Zhang, Jiajie

2007-10-11

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

Genomes as geography: using GIS technology to build interactive genome feature maps

PubMed Central

Dolan, Mary E; Holden, Constance C; Beard, M Kate; Bult, Carol J

2006-01-01

Background Many commonly used genome browsers display sequence annotations and related attributes as horizontal data tracks that can be toggled on and off according to user preferences. Most genome browsers use only simple keyword searches and limit the display of detailed annotations to one chromosomal region of the genome at a time. We have employed concepts, methodologies, and tools that were developed for the display of geographic data to develop a Genome Spatial Information System (GenoSIS) for displaying genomes spatially, and interacting with genome annotations and related attribute data. In contrast to the paradigm of horizontally stacked data tracks used by most genome browsers, GenoSIS uses the concept of registered spatial layers composed of spatial objects for integrated display of diverse data. In addition to basic keyword searches, GenoSIS supports complex queries, including spatial queries, and dynamically generates genome maps. Our adaptation of the geographic information system (GIS) model in a genome context supports spatial representation of genome features at multiple scales with a versatile and expressive query capability beyond that supported by existing genome browsers. Results We implemented an interactive genome sequence feature map for the mouse genome in GenoSIS, an application that uses ArcGIS, a commercially available GIS software system. The genome features and their attributes are represented as spatial objects and data layers that can be toggled on and off according to user preferences or displayed selectively in response to user queries. GenoSIS supports the generation of custom genome maps in response to complex queries about genome features based on both their attributes and locations. Our example application of GenoSIS to the mouse genome demonstrates the powerful visualization and query capability of mature GIS technology applied in a novel domain. Conclusion Mapping tools developed specifically for geographic data can be exploited to display, explore and interact with genome data. The approach we describe here is organism independent and is equally useful for linear and circular chromosomes. One of the unique capabilities of GenoSIS compared to existing genome browsers is the capacity to generate genome feature maps dynamically in response to complex attribute and spatial queries. PMID:16984652

Internet Medline providers.

PubMed

Vine, D L; Coady, T R

1998-01-01

Each database in this review has features that will appeal to some users. Each provides a credible interface to information available within the Medline database. The major differences are pricing and interface design. In this context, features that cost more and might seem trivial to the occasional searcher may actually save time and money when used by the professional. Internet Grateful Med is free, but Ms. Coady and I agree the availability of only three ANDable search fields is a major functional limitation. PubMed is also free but much more powerful. The command line interface that permits very sophisticated searches requires a commitment that casual users will find intimidating. Ms. Coady did not believe the feedback currently provided during a search was sufficient for sustained professional use. Paper Chase and Knowledge Finder are mature, modestly priced Medline search services. Paper Chase provides a menu-driven interface that is very easy to use, yet permits the user to search virtually all of Medline's data fields. Knowledge Finder emphasizes the use of natural language queries but fully supports more traditional search strategies. The impact of the tradeoff between fuzzy and Boolean strategies offered by Knowledge Finder is unclear and beyond the scope of this review. Additional software must be downloaded to use all of Knowledge Finders' features. Other providers required no software beyond the basic Internet browser, and this requirement prevented Ms. Coady from evaluating Knowledge Finder. Ovid and Silver Platter offer well-designed interfaces that simplify the construction of complex queries. These are clearly services designed for professional users. While pricing eliminates these for casual use, it should be emphasized that Medline citation access is only a portion of the service provided by these high-end vendors. Finally, we should comment that each of the vendors and government-sponsored services provided prompt and useful feedback to e-mail questions about usage. In conclusion, we would suggest you try the various services, determine which interface suits your style and budget, then perform simple searches until you learn the strengths and weaknesses of the service you select.

An Integrated Approach for Accessing Multiple Datasets through LANCE

NASA Astrophysics Data System (ADS)

Murphy, K. J.; Teague, M.; Conover, H.; Regner, K.; Beaumont, B.; Masuoka, E.; Vollmer, B.; Theobald, M.; Durbin, P.; Michael, K.; Boller, R. A.; Schmaltz, J. E.; Davies, D.; Horricks, K.; Ilavajhala, S.; Thompson, C. K.; Bingham, A.

2011-12-01

The NASA/GSFC Land Atmospheres Near-real time Capability for EOS (LANCE) provides imagery for approximately 40 data products from MODIS, AIRS, AMSR-E and OMI to support the applications community in the study of a variety of phenomena. Thirty-six of these products are available within 2.5 hours of observation at the spacecraft. The data set includes the population density data provided by the EOSDIS Socio-Economic Data and Applications Center (SEDAC). The purpose of this paper is to describe the variety of tools that have been developed by LANCE to support user access to the imagery. The long-standing Rapid Response system has been integrated into LANCE and is a major vehicle for the distribution of the imagery to end users. There are presently approximately 10,000 anonymous users per month accessing these imagery. The products are grouped into 14 applications categories such as Smoke Plumes, Pollution, Fires, Agriculture and the selection of any category will make relevant subsets of the 40 products available as possible overlays in an interactive Web Client utilizing Web Mapping Service (WMS) to support user investigations (http://lance2.modaps.eosdis.nasa.gov/wms/). For example, selecting Severe Storms will include 6 products for MODIS, OMI, AIRS, and AMSR-E plus the SEDAC population density data. The client and WMS were developed using open-source technologies such as OpenLayers and MapServer and provides a uniform, browser-based access to data products. All overlays are downloadable in PNG, JPEG, or GeoTiff form up to 200MB per request. The WMS was beta-tested with the user community and substantial performance improvements were made through the use of such techniques as tile-caching. LANCE established a partnership with Physical Oceanography Distributed Active Archive Center (PO DAAC) to develop an alternative presentation for the 40 data products known as the State of the Earth (SOTE). This provides a Google Earth-based interface to the products grouped in the same fashion as the WMS. The SOTE servers stream imagery and data in the OGC KML format and these feeds can be visualized through the Google Earth browser plug-in. SOTE provides visualization through a virtual globe environment by allowing users to interact with the globe via zooming, rotating, and tilting. In addition, SOTE also allows adding custom KML feeds. LANCE also provides datacasting feeds to facilitate user access to imagery for the 40 products and the related HDF-EOS products (available in a variety of formats). These XML-based data feeds contain data attribute and geolocation information, and metadata including an identification of the related application category. Users can subscribe to any feeds through the LANCE web site and use the PO DAAC Feed Reader to filter and view the content. The WMS, SOTE, and datacasting tools can be accessed through http://lance.nasa.gov.

Visual Links in the World-Wide Web: The Uses and Limitations of Image Maps.

ERIC Educational Resources Information Center

Cochenour, John J.; And Others

As information delivery systems on the Internet increasingly evolve into World Wide Web browsers, understanding key graphical elements of the browser interface is critical to the design of effective information display and access tools. Image maps are one such element, and this document describes a pilot study that collected, reviewed, and…

NASA SensorWeb and OGC Standards for Disaster Management

NASA Technical Reports Server (NTRS)

Mandl, Dan

2010-01-01

I. Goal: Enable user to cost-effectively find and create customized data products to help manage disasters; a) On-demand; b) Low cost and non-specialized tools such as Google Earth and browsers; c) Access via open network but with sufficient security. II. Use standards to interface various sensors and resultant data: a) Wrap sensors in Open Geospatial Consortium (OGC) standards; b) Wrap data processing algorithms and servers with OGC standards c) Use standardized workflows to orchestrate and script the creation of these data; products. III. Target Web 2.0 mass market: a) Make it simple and easy to use; b) Leverage new capabilities and tools that are emerging; c) Improve speed and responsiveness.

D-peaks: a visual tool to display ChIP-seq peaks along the genome.

PubMed

Brohée, Sylvain; Bontempi, Gianluca

2012-01-01

ChIP-sequencing is a method of choice to localize the positions of protein binding sites on DNA on a whole genomic scale. The deciphering of the sequencing data produced by this novel technique is challenging and it is achieved by their rigorous interpretation using dedicated tools and adapted visualization programs. Here, we present a bioinformatics tool (D-peaks) that adds several possibilities (including, user-friendliness, high-quality, relative position with respect to the genomic features) to the well-known visualization browsers or databases already existing. D-peaks is directly available through its web interface http://rsat.ulb.ac.be/dpeaks/ as well as a command line tool.

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.

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

NASA Astrophysics Data System (ADS)

Husar, R. B.; Hoijarvi, K.

2017-12-01

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

NCBI Epigenomics: what's new for 2013.

PubMed

Fingerman, Ian M; Zhang, Xuan; Ratzat, Walter; Husain, Nora; Cohen, Robert F; Schuler, Gregory D

2013-01-01

The Epigenomics resource at the National Center for Biotechnology Information (NCBI) has been created to serve as a comprehensive public repository for whole-genome epigenetic data sets (www.ncbi.nlm.nih.gov/epigenomics). We have constructed this resource by selecting the subset of epigenetics-specific data from the Gene Expression Omnibus (GEO) database and then subjecting them to further review and annotation. Associated data tracks can be viewed using popular genome browsers or downloaded for local analysis. We have performed extensive user testing throughout the development of this resource, and new features and improvements are continuously being implemented based on the results. We have made substantial usability improvements to user interfaces, enhanced functionality, made identification of data tracks of interest easier and created new tools for preliminary data analyses. Additionally, we have made efforts to enhance the integration between the Epigenomics resource and other NCBI databases, including the Gene database and PubMed. Data holdings have also increased dramatically since the initial publication describing the NCBI Epigenomics resource and currently consist of >3700 viewable and downloadable data tracks from 955 biological sources encompassing five well-studied species. This updated manuscript highlights these changes and improvements.

NCBI Epigenomics: What’s new for 2013

PubMed Central

Fingerman, Ian M.; Zhang, Xuan; Ratzat, Walter; Husain, Nora; Cohen, Robert F.; Schuler, Gregory D.

2013-01-01

The Epigenomics resource at the National Center for Biotechnology Information (NCBI) has been created to serve as a comprehensive public repository for whole-genome epigenetic data sets (www.ncbi.nlm.nih.gov/epigenomics). We have constructed this resource by selecting the subset of epigenetics-specific data from the Gene Expression Omnibus (GEO) database and then subjecting them to further review and annotation. Associated data tracks can be viewed using popular genome browsers or downloaded for local analysis. We have performed extensive user testing throughout the development of this resource, and new features and improvements are continuously being implemented based on the results. We have made substantial usability improvements to user interfaces, enhanced functionality, made identification of data tracks of interest easier and created new tools for preliminary data analyses. Additionally, we have made efforts to enhance the integration between the Epigenomics resource and other NCBI databases, including the Gene database and PubMed. Data holdings have also increased dramatically since the initial publication describing the NCBI Epigenomics resource and currently consist of >3700 viewable and downloadable data tracks from 955 biological sources encompassing five well-studied species. This updated manuscript highlights these changes and improvements. PMID:23193265

phpMs: A PHP-Based Mass Spectrometry Utilities Library.

PubMed

Collins, Andrew; Jones, Andrew R

2018-03-02

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

Estimation of toxicity using a Java based software tool

EPA Science Inventory

A software tool has been developed that will allow a user to estimate the toxicity for a variety of endpoints (such as acute aquatic toxicity). The software tool is coded in Java and can be accessed using a web browser (or alternatively downloaded and ran as a stand alone applic...

WEB-BASED MODELING OF A FERTILIZER SOLUTION SPILL IN THE OHIO RIVER

EPA Science Inventory

Environmental computer models are usually desktop models. Some web-enabled models are beginning to appear where the user can use a browser to run the models on a central web server. Several issues arise when a desktop model is transferred to a web architecture. This paper discuss...

Knowledge-base browsing: an application of hybrid distributed/local connectionist networks

NASA Astrophysics Data System (ADS)

Samad, Tariq; Israel, Peggy

1990-08-01

We describe a knowledge base browser based on a connectionist (or neural network) architecture that employs both distributed and local representations. The distributed representations are used for input and output thereby enabling associative noise-tolerant interaction with the environment. Internally all representations are fully local. This simplifies weight assignment and facilitates network configuration for specific applications. In our browser concepts and relations in a knowledge base are represented using " microfeatures. " The microfeatures can encode semantic attributes structural features contextual information etc. Desired portions of the knowledge base can then be associatively retrieved based on a structured cue. An ordered list of partial matches is presented to the user for selection. Microfeatures can also be used as " bookmarks" they can be placed dynamically at appropriate points in the knowledge base and subsequently used as retrieval cues. A proof-of-concept system has been implemented for an internally developed Honeywell-proprietary knowledge acquisition tool. 1.

An autonomous observation and control system based on EPICS and RTS2 for Antarctic telescopes

NASA Astrophysics Data System (ADS)

Zhang, Guang-yu; Wang, Jian; Tang, Peng-yi; Jia, Ming-hao; Chen, Jie; Dong, Shu-cheng; Jiang, Fengxin; Wu, Wen-qing; Liu, Jia-jing; Zhang, Hong-fei

2016-01-01

For unattended telescopes in Antarctic, the remote operation, autonomous observation and control are essential. An EPICS-(Experimental Physics and Industrial Control System) and RTS2-(Remote Telescope System, 2nd Version) based autonomous observation and control system with remoted operation is introduced in this paper. EPICS is a set of open source software tools, libraries and applications developed collaboratively and used worldwide to create distributed soft real-time control systems for scientific instruments while RTS2 is an open source environment for control of a fully autonomous observatory. Using the advantage of EPICS and RTS2, respectively, a combined integrated software framework for autonomous observation and control is established that use RTS2 to fulfil the function of astronomical observation and use EPICS to fulfil the device control of telescope. A command and status interface for EPICS and RTS2 is designed to make the EPICS IOC (Input/Output Controller) components integrate to RTS2 directly. For the specification and requirement of control system of telescope in Antarctic, core components named Executor and Auto-focus for autonomous observation is designed and implemented with remote operation user interface based on browser-server mode. The whole system including the telescope is tested in Lijiang Observatory in Yunnan Province for practical observation to complete the autonomous observation and control, including telescope control, camera control, dome control, weather information acquisition with the local and remote operation.

Bridging the Gap - Networking Educators using Real-Time Seismic Data

NASA Astrophysics Data System (ADS)

Ortiz, A. M.; Renwald, M. D.; Baldwin, T. K.; Hall, M. K.

2004-12-01

After nearly a decade, the seismology community has made critical advances in identifying what is effective and what is needed for success in incorporating real-time seismic data in the classroom. Today's K-16 classroom teachers have many options and opportunities for incorporating short- and long-term inquiry activities for monitoring earthquakes and analyzing seismic data in their daily instruction. Through the SpiNet program, we are providing web-based tools that support educators working with real-time seismic data (http://www.scieds.com/spinet/). Our site includes a Recent Seismicity section, which allows users to share seismic data in real-time, and provides near real-time information about global seismicity. Our Activities section provides data and lessons to assist educators who wish to integrate seismology into their classroom. The Research section, currently under development, will allow educators to share general information about how they teach seismology in their classroom through a discussion board and by posting lesson plans. In addition, we are developing a user-friendly tool for students to post results of their research projects. Designing a website which targets a range of users requires a working knowledge of both user needs and website programming and design. User needs include providing a logical navigational structure and accounting for differences in browser functionality, internet access, and users' abilities. Using website development tools, such as PHP, MySQL, RDF feeds, and specialized geoscience applications, we are automating site maintenance; incorporating databases for information storage and retrieval; and providing accessibility for users with a range of skills and physical limitations. By incorporating these features, we have built a dynamic interface for a broad range of users interested in educational seismology.

Toward a workbench for rodent brain image data: systems architecture and design.

PubMed

Moene, Ivar A; Subramaniam, Shankar; Darin, Dmitri; Leergaard, Trygve B; Bjaalie, Jan G

2007-01-01

We present a novel system for storing and manipulating microscopic images from sections through the brain and higher-level data extracted from such images. The system is designed and built on a three-tier paradigm and provides the research community with a web-based interface for facile use in neuroscience research. The Oracle relational database management system provides the ability to store a variety of objects relevant to the images and provides the framework for complex querying of data stored in the system. Further, the suite of applications intimately tied into the infrastructure in the application layer provide the user the ability not only to query and visualize the data, but also to perform analysis operations based on the tools embedded into the system. The presentation layer uses extant protocols of the modern web browser and this provides ease of use of the system. The present release, named Functional Anatomy of the Cerebro-Cerebellar System (FACCS), available through The Rodent Brain Workbench (http:// rbwb.org/), is targeted at the functional anatomy of the cerebro-cerebellar system in rats, and holds axonal tracing data from these projections. The system is extensible to other circuits and projections and to other categories of image data and provides a unique environment for analysis of rodent brain maps in the context of anatomical data. The FACCS application assumes standard animal brain atlas models and can be extended to future models. The system is available both for interactive use from a remote web-browser client as well as for download to a local server machine.

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

NASA Astrophysics Data System (ADS)

McCauley, T.

2017-10-01

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

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.

Ubiquitous remote operation collaborative interface for MRI scanners

NASA Astrophysics Data System (ADS)

Morris, H. Douglas

2001-05-01

We have developed a remote control interface for research class magnetic resonance imaging (MRI) spectrometers. The goal of the interface is to provide a better collaborative environment for geographically dispersed researchers and a tool that can teach students of medical imaging in a network-based laboratory using state-of-the-art MR instrumentation that would not otherwise be available. The interface for the remote operator(s) is now ubiquitous web browser, which was chosen for the ease of controlling the operator interface, the display of both image and text information, and the wide availability on many computer platforms. The remote operator is presented with an active display in which they may select and control most of the parameters in the MRI experiment. The MR parameters are relayed via web browser to a CGI program running in a standard web server, which passes said parameters to the MRI manufacturers control software. The data returned to the operator(s) consists of the parameters used in acquiring that image, a flat 8-bit grayscale GIF representation of the image, and a 16-bit grayscale image that can be viewed by an appropriate application. It is obvious that the utility of this interface would be helpful for researchers of regional and national facilities to more closely collaborate with colleagues across their region, the nation, or the world. And medical imaging students can put much of their classroom discussions into practice on machinery that would not normally be available to them.

An optimized web-based approach for collaborative stereoscopic medical visualization

PubMed Central

Kaspar, Mathias; Parsad, Nigel M; Silverstein, Jonathan C

2013-01-01

Objective Medical visualization tools have traditionally been constrained to tethered imaging workstations or proprietary client viewers, typically part of hospital radiology systems. To improve accessibility to real-time, remote, interactive, stereoscopic visualization and to enable collaboration among multiple viewing locations, we developed an open source approach requiring only a standard web browser with no added client-side software. Materials and Methods Our collaborative, web-based, stereoscopic, visualization system, CoWebViz, has been used successfully for the past 2 years at the University of Chicago to teach immersive virtual anatomy classes. It is a server application that streams server-side visualization applications to client front-ends, comprised solely of a standard web browser with no added software. Results We describe optimization considerations, usability, and performance results, which make CoWebViz practical for broad clinical use. We clarify technical advances including: enhanced threaded architecture, optimized visualization distribution algorithms, a wide range of supported stereoscopic presentation technologies, and the salient theoretical and empirical network parameters that affect our web-based visualization approach. Discussion The implementations demonstrate usability and performance benefits of a simple web-based approach for complex clinical visualization scenarios. Using this approach overcomes technical challenges that require third-party web browser plug-ins, resulting in the most lightweight client. Conclusions Compared to special software and hardware deployments, unmodified web browsers enhance remote user accessibility to interactive medical visualization. Whereas local hardware and software deployments may provide better interactivity than remote applications, our implementation demonstrates that a simplified, stable, client approach using standard web browsers is sufficient for high quality three-dimensional, stereoscopic, collaborative and interactive visualization. PMID:23048008

Web-based visualization of gridded dataset usings OceanBrowser

NASA Astrophysics Data System (ADS)

Barth, Alexander; Watelet, Sylvain; Troupin, Charles; Beckers, Jean-Marie

2015-04-01

OceanBrowser is a web-based visualization tool for gridded oceanographic data sets. Those data sets are typically four-dimensional (longitude, latitude, depth and time). OceanBrowser allows one to visualize horizontal sections at a given depth and time to examine the horizontal distribution of a given variable. It also offers the possibility to display the results on an arbitrary vertical section. To study the evolution of the variable in time, the horizontal and vertical sections can also be animated. Vertical section can be generated by using a fixed distance from coast or fixed ocean depth. The user can customize the plot by changing the color-map, the range of the color-bar, the type of the plot (linearly interpolated color, simple contours, filled contours) and download the current view as a simple image or as Keyhole Markup Language (KML) file for visualization in applications such as Google Earth. The data products can also be accessed as NetCDF files and through OPeNDAP. Third-party layers from a web map service can also be integrated. OceanBrowser is used in the frame of the SeaDataNet project (http://gher-diva.phys.ulg.ac.be/web-vis/) and EMODNET Chemistry (http://oceanbrowser.net/emodnet/) to distribute gridded data sets interpolated from in situ observation using DIVA (Data-Interpolating Variational Analysis).

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.

The MycoBrowser portal: a comprehensive and manually annotated resource for mycobacterial genomes.

PubMed

Kapopoulou, Adamandia; Lew, Jocelyne M; Cole, Stewart T

2011-01-01

In this paper, we present the MycoBrowser portal (http://mycobrowser.epfl.ch/), a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. A central component of MycoBrowser is TubercuList (http://tuberculist.epfl.ch), which has recently benefited from a new data management system and web interface. These improvements were extended to all MycoBrowser databases. We provide an overview of the functionalities available and the different ways of interrogating the data then discuss how both the new information and the latest features are helping the mycobacterial research communities. Copyright © 2010 Elsevier Ltd. All rights reserved.

Network Computing Infrastructure to Share Tools and Data in Global Nuclear Energy Partnership

NASA Astrophysics Data System (ADS)

Kim, Guehee; Suzuki, Yoshio; Teshima, Naoya

CCSE/JAEA (Center for Computational Science and e-Systems/Japan Atomic Energy Agency) integrated a prototype system of a network computing infrastructure for sharing tools and data to support the U.S. and Japan collaboration in GNEP (Global Nuclear Energy Partnership). We focused on three technical issues to apply our information process infrastructure, which are accessibility, security, and usability. In designing the prototype system, we integrated and improved both network and Web technologies. For the accessibility issue, we adopted SSL-VPN (Security Socket Layer-Virtual Private Network) technology for the access beyond firewalls. For the security issue, we developed an authentication gateway based on the PKI (Public Key Infrastructure) authentication mechanism to strengthen the security. Also, we set fine access control policy to shared tools and data and used shared key based encryption method to protect tools and data against leakage to third parties. For the usability issue, we chose Web browsers as user interface and developed Web application to provide functions to support sharing tools and data. By using WebDAV (Web-based Distributed Authoring and Versioning) function, users can manipulate shared tools and data through the Windows-like folder environment. We implemented the prototype system in Grid infrastructure for atomic energy research: AEGIS (Atomic Energy Grid Infrastructure) developed by CCSE/JAEA. The prototype system was applied for the trial use in the first period of GNEP.

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

USGS Publications Warehouse

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

2011-01-01

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

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

ERIC Educational Resources Information Center

Li, Liang-Yi; Chen, Gwo-Dong

2010-01-01

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

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.

Developing an educational curriculum for EnviroAtlas ...

EPA Pesticide Factsheets

EnviroAtlas is a web-based tool developed by the EPA and its partners, which provides interactive tools and resources for users to explore the benefits that people receive from nature, often referred to as ecosystem goods and services.Ecosystem goods and services are important to human health and well-being. Using EnviroAtlas, users can access, view, and analyze diverse information to better understand the potential impacts of decisions. EnviroAtlas provides two primary tools, the Interactive Map and the Eco-Health Relationship Browser. EnviroAtlas integrates geospatial data from a variety of sources so that users can visualize the impacts of decision-making on ecosystems. The Interactive Map allows users to investigate various ecosystem elements (i.e. land cover, pollution, and community development) and compare them across localities in the United States. The best part of the Interactive Map is that it does not require specialized software for map application; rather, it requires only a computer and an internet connection. As such, it can be used as a powerful educational tool. The Eco-Health Relationship Browser is also a web-based, highly interactive tool that uses existing scientific literature to visually demonstrate the connections between the environment and human health.As an ASPPH/EPA Fellow with a background in environmental science and secondary science education, I am currently developing an educational curriculum to support the EnviroAtlas to

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.

A Cloud-Computing Service for Environmental Geophysics and Seismic Data Processing

NASA Astrophysics Data System (ADS)

Heilmann, B. Z.; Maggi, P.; Piras, A.; Satta, G.; Deidda, G. P.; Bonomi, E.

2012-04-01

Cloud computing is establishing worldwide as a new high performance computing paradigm that offers formidable possibilities to industry and science. The presented cloud-computing portal, part of the Grida3 project, provides an innovative approach to seismic data processing by combining open-source state-of-the-art processing software and cloud-computing technology, making possible the effective use of distributed computation and data management with administratively distant resources. We substituted the user-side demanding hardware and software requirements by remote access to high-performance grid-computing facilities. As a result, data processing can be done quasi in real-time being ubiquitously controlled via Internet by a user-friendly web-browser interface. Besides the obvious advantages over locally installed seismic-processing packages, the presented cloud-computing solution creates completely new possibilities for scientific education, collaboration, and presentation of reproducible results. The web-browser interface of our portal is based on the commercially supported grid portal EnginFrame, an open framework based on Java, XML, and Web Services. We selected the hosted applications with the objective to allow the construction of typical 2D time-domain seismic-imaging workflows as used for environmental studies and, originally, for hydrocarbon exploration. For data visualization and pre-processing, we chose the free software package Seismic Un*x. We ported tools for trace balancing, amplitude gaining, muting, frequency filtering, dip filtering, deconvolution and rendering, with a customized choice of options as services onto the cloud-computing portal. For structural imaging and velocity-model building, we developed a grid version of the Common-Reflection-Surface stack, a data-driven imaging method that requires no user interaction at run time such as manual picking in prestack volumes or velocity spectra. Due to its high level of automation, CRS stacking can benefit largely from the hardware parallelism provided by the cloud deployment. The resulting output, post-stack section, coherence, and NMO-velocity panels are used to generate a smooth migration-velocity model. Residual static corrections are calculated as a by-product of the stack and can be applied iteratively. As a final step, a time migrated subsurface image is obtained by a parallelized Kirchhoff time migration scheme. Processing can be done step-by-step or using a graphical workflow editor that can launch a series of pipelined tasks. The status of the submitted jobs is monitored by a dedicated service. All results are stored in project directories, where they can be downloaded of viewed directly in the browser. Currently, the portal has access to three research clusters having a total number of 70 nodes with 4 cores each. They are shared with four other cloud-computing applications bundled within the GRIDA3 project. To demonstrate the functionality of our "seismic cloud lab", we will present results obtained for three different types of data, all taken from hydrogeophysical studies: (1) a seismic reflection data set, made of compressional waves from explosive sources, recorded in Muravera, Sardinia; (2) a shear-wave data set from, Sardinia; (3) a multi-offset Ground-Penetrating-Radar data set from Larreule, France. The presented work was funded by the government of the Autonomous Region of Sardinia and by the Italian Ministry of Research and Education.

Recommendation Systems for Geoscience Data Portals Built by Analyzing Usage Patterns

NASA Astrophysics Data System (ADS)

Crosby, C.; Nandigam, V.; Baru, C.

2009-04-01

Since its launch five years ago, the National Science Foundation-funded GEON Project (www.geongrid.org) has been providing access to a variety of geoscience data sets such as geologic maps and other geographic information system (GIS)-oriented data, paleontologic databases, gravity and magnetics data and LiDAR topography via its online portal interface. In addition to data, the GEON Portal also provides web-based tools and other resources that enable users to process and interact with data. Examples of these tools include functions to dynamically map and integrate GIS data, compute synthetic seismograms, and to produce custom digital elevation models (DEMs) with user defined parameters such as resolution. The GEON portal built on the Gridsphere-portal framework allows us to capture user interaction with the system. In addition to the site access statistics captured by tools like Google Analystics which capture hits per unit time, search key words, operating systems, browsers, and referring sites, we also record additional statistics such as which data sets are being downloaded and in what formats, processing parameters, and navigation pathways through the portal. With over four years of data now available from the GEON Portal, this record of usage is a rich resource for exploring how earth scientists discover and utilize online data sets. Furthermore, we propose that this data could ultimately be harnessed to optimize the way users interact with the data portal, design intelligent processing and data management systems, and to make recommendations on algorithm settings and other available relevant data. The paradigm of integrating popular and commonly used patterns to make recommendations to a user is well established in the world of e-commerce where users receive suggestions on books, music and other products that they may find interesting based on their website browsing and purchasing history, as well as the patterns of fellow users who have made similar selections. However, this paradigm has not yet been explored for geoscience data portals. In this presentation we will present an initial analysis of user interaction and access statistics for the GEON OpenTopography LiDAR data distribution and processing system to illustrate what they reveal about user's spatial and temporal data access patterns, data processing parameter selections, and pathways through the data portal. We also demonstrate what these usage statistics can illustrate about aspects of the data sets that are of greatest interest. Finally, we explore how these usage statistics could be used to improve the user's experience in the data portal and to optimize how data access interfaces and tools are designed and implemented.

An online analytical processing multi-dimensional data warehouse for malaria data

PubMed Central

Madey, Gregory R; Vyushkov, Alexander; Raybaud, Benoit; Burkot, Thomas R; Collins, Frank H

2017-01-01

Abstract Malaria is a vector-borne disease that contributes substantially to the global burden of morbidity and mortality. The management of malaria-related data from heterogeneous, autonomous, and distributed data sources poses unique challenges and requirements. Although online data storage systems exist that address specific malaria-related issues, a globally integrated online resource to address different aspects of the disease does not exist. In this article, we describe the design, implementation, and applications of a multi-dimensional, online analytical processing data warehouse, named the VecNet Data Warehouse (VecNet-DW). It is the first online, globally-integrated platform that provides efficient search, retrieval and visualization of historical, predictive, and static malaria-related data, organized in data marts. Historical and static data are modelled using star schemas, while predictive data are modelled using a snowflake schema. The major goals, characteristics, and components of the DW are described along with its data taxonomy and ontology, the external data storage systems and the logical modelling and physical design phases. Results are presented as screenshots of a Dimensional Data browser, a Lookup Tables browser, and a Results Viewer interface. The power of the DW emerges from integrated querying of the different data marts and structuring those queries to the desired dimensions, enabling users to search, view, analyse, and store large volumes of aggregated data, and responding better to the increasing demands of users. Database URL https://dw.vecnet.org/datawarehouse/ PMID:29220463

Beam Dynamics Simulation Platform and Studies of Beam Breakup in Dielectric Wakefield Structures

NASA Astrophysics Data System (ADS)

Schoessow, P.; Kanareykin, A.; Jing, C.; Kustov, A.; Altmark, A.; Gai, W.

2010-11-01

A particle-Green's function beam dynamics code (BBU-3000) to study beam breakup effects is incorporated into a parallel computing framework based on the Boinc software environment, and supports both task farming on a heterogeneous cluster and local grid computing. User access to the platform is through a web browser.

Browser-Based Accessibility Evaluation Tools for Beginners

ERIC Educational Resources Information Center

McHale, Nina

2011-01-01

There are hundreds of Web accessibility software options out in the world that serve many different functions. Not surprisingly, many of them are designed for users with a wide range of abilities, with the intent of making the use of computers and the Internet easier for both work and entertainment. There are, however, numerous products available…

Managing Personal and Group Collections of Information

NASA Technical Reports Server (NTRS)

Wolfe, Shawn R.; Wragg, Stephen D.; Chen, James R.; Koga, Dennis (Technical Monitor)

1999-01-01

The internet revolution has dramatically increased the amount of information available to users. Various tools such as search engines have been developed to help users find the information they need from this vast repository. Users often also need tools to help manipulate the growing amount of useful information they have discovered. Current tools available for this purpose are typically local components of web browsers designed to manage URL bookmarks. They provide limited functionalities to handle high information complexities. To tackle this have created DIAMS, an agent-based tool to help users or groups manage their information collections and share their collections with other. the main features of DIAMS are described here.

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

Multiple sequence alignment in HTML: colored, possibly hyperlinked, compact representations.

PubMed

Campagne, F; Maigret, B

1998-02-01

Protein sequence alignments are widely used in protein structure prediction, protein engineering, modeling of proteins, etc. This type of representation is useful at different stages of scientific activity: looking at previous results, working on a research project, and presenting the results. There is a need to make it available through a network (intranet or WWW), in a way that allows biologists, chemists, and noncomputer specialists to look at the data and carry on research--possibly in a collaborative research. Previous methods (text-based, Java-based) are reported and their advantages are discussed. We have developed two novel approaches to represent the alignments as colored, hyper-linked HTML pages. The first method creates an HTML page that uses efficiently the image cache mechanism of a WWW browser, thereby allowing the user to browse different alignments without waiting for the images to be loaded through the network, but only for the first viewed alignment. The generated pages can be browsed with any HTML2.0-compliant browser. The second method that we propose uses W3C-CSS1-style sheets to render alignments. This new method generates pages that require recent browsers to be viewed. We implemented these methods in the Viseur program and made a WWW service available that allows a user to convert an MSF alignment file in HTML for WWW publishing. The latter service is available at http:@www.lctn.u-nancy.fr/viseur/services.htm l.

A web access script language to support clinical application development.

PubMed

O'Kane, K C; McColligan, E E

1998-02-01

This paper describes the development of a script language to support the implementation of decentralized, clinical information applications on the World Wide Web (Web). The goal of this work is to facilitate construction of low overhead, fully functional clinical information systems that can be accessed anywhere by low cost Web browsers to search, retrieve and analyze stored patient data. The Web provides a model of network access to data bases on a global scale. Although it was originally conceived as a means to exchange scientific documents, Web browsers and servers currently support access to a wide variety of audio, video, graphical and text based data to a rapidly growing community. Access to these services is via inexpensive client software browsers that connect to servers by means of the open architecture of the Internet. In this paper, the design and implementation of a script language that supports the development of low cost, Web-based, distributed clinical information systems for both Inter- and Intra-Net use is presented. The language is based on the Mumps language and, consequently, supports many legacy applications with few modifications. Several enhancements, however, have been made to support modern programming practices and the Web interface. The interpreter for the language also supports standalone program execution on Unix, MS-Windows, OS/2 and other operating systems.

Design and deployment of a large brain-image database for clinical and nonclinical research

NASA Astrophysics Data System (ADS)

Yang, Guo Liang; Lim, Choie Cheio Tchoyoson; Banukumar, Narayanaswami; Aziz, Aamer; Hui, Francis; Nowinski, Wieslaw L.

2004-04-01

An efficient database is an essential component of organizing diverse information on image metadata and patient information for research in medical imaging. This paper describes the design, development and deployment of a large database system serving as a brain image repository that can be used across different platforms in various medical researches. It forms the infrastructure that links hospitals and institutions together and shares data among them. The database contains patient-, pathology-, image-, research- and management-specific data. The functionalities of the database system include image uploading, storage, indexing, downloading and sharing as well as database querying and management with security and data anonymization concerns well taken care of. The structure of database is multi-tier client-server architecture with Relational Database Management System, Security Layer, Application Layer and User Interface. Image source adapter has been developed to handle most of the popular image formats. The database has a user interface based on web browsers and is easy to handle. We have used Java programming language for its platform independency and vast function libraries. The brain image database can sort data according to clinically relevant information. This can be effectively used in research from the clinicians" points of view. The database is suitable for validation of algorithms on large population of cases. Medical images for processing could be identified and organized based on information in image metadata. Clinical research in various pathologies can thus be performed with greater efficiency and large image repositories can be managed more effectively. The prototype of the system has been installed in a few hospitals and is working to the satisfaction of the clinicians.

The Cadmio XML healthcare record.

PubMed

Barbera, Francesco; Ferri, Fernando; Ricci, Fabrizio L; Sottile, Pier Angelo

2002-01-01

The management of clinical data is a complex task. Patient related information reported in patient folders is a set of heterogeneous and structured data accessed by different users having different goals (in local or geographical networks). XML language provides a mechanism for describing, manipulating, and visualising structured data in web-based applications. XML ensures that the structured data is managed in a uniform and transparent manner independently from the applications and their providers guaranteeing some interoperability. Extracting data from the healthcare record and structuring them according to XML makes the data available through browsers. The MIC/MIE model (Medical Information Category/Medical Information Elements), which allows the definition and management of healthcare records and used in CADMIO, a HISA based project, is described in this paper, using XML for allowing the data to be visualised through web browsers.

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

NASA Technical Reports Server (NTRS)

Bauman, William H., III

2007-01-01

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

Model My Watershed: A high-performance cloud application for public engagement, watershed modeling and conservation decision support

NASA Astrophysics Data System (ADS)

Aufdenkampe, A. K.; Tarboton, D. G.; Horsburgh, J. S.; Mayorga, E.; McFarland, M.; Robbins, A.; Haag, S.; Shokoufandeh, A.; Evans, B. M.; Arscott, D. B.

2017-12-01

The Model My Watershed Web app (https://app.wikiwatershed.org/) and the BiG-CZ Data Portal (http://portal.bigcz.org/) and are web applications that share a common codebase and a common goal to deliver high-performance discovery, visualization and analysis of geospatial data in an intuitive user interface in web browser. Model My Watershed (MMW) was designed as a decision support system for watershed conservation implementation. BiG CZ Data Portal was designed to provide context and background data for research sites. Users begin by creating an Area of Interest, via an automated watershed delineation tool, a free draw tool, selection of a predefined area such as a county or USGS Hydrological Unit (HUC), or uploading a custom polygon. Both Web apps visualize and provide summary statistics of land use, soil groups, streams, climate and other geospatial information. MMW then allows users to run a watershed model to simulate different scenarios of human impacts on stormwater runoff and water-quality. BiG CZ Data Portal allows users to search for scientific and monitoring data within the Area of Interest, which also serves as a prototype for the upcoming Monitor My Watershed web app. Both systems integrate with CUAHSI cyberinfrastructure, including visualizing observational data from CUAHSI Water Data Center and storing user data via CUAHSI HydroShare. Both systems also integrate with the new EnviroDIY Water Quality Data Portal (http://data.envirodiy.org/), a system for crowd-sourcing environmental monitoring data using open-source sensor stations (http://envirodiy.org/mayfly/) and based on the Observations Data Model v2.

USDA Plant Hardiness Zone Map

Science.gov Websites

those with slower Internet access. Users may also simply type in a ZIP Code and find the hardiness zone : Find Javascript is not enabled in this Internet Browser For a better experience throughout this web site, please enable Javascript in your Internet Browser What is a Captcha and why am I seeing one (on

Integration and visualization of systems biology data in context of the genome

PubMed Central

2010-01-01

Background High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment. Results The Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing high-throughput data in the context of the genome. Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework. Users may bookmark locations on the genome with descriptive annotations and share these bookmarks with other users. The program handles large sets of user-generated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data. A key aspect of the Gaggle Genome Browser is interoperability. By connecting to the Gaggle framework, the genome browser joins a suite of interconnected bioinformatics tools for analysis and visualization with connectivity to major public repositories of sequences, interactions and pathways. To this flexible environment for exploring and combining data, the Gaggle Genome Browser adds the ability to visualize diverse types of data in relation to its coordinates on the genome. Conclusions Genomic coordinates function as a common key by which disparate biological data types can be related to one another. In the Gaggle Genome Browser, heterogeneous data are joined by their location on the genome to create information-rich visualizations yielding insight into genome organization, transcription and its regulation and, ultimately, a better understanding of the mechanisms that enable the cell to dynamically respond to its environment. PMID:20642854

Human interface to large multimedia databases

NASA Astrophysics Data System (ADS)

Davis, Ben; Marks, Linn; Collins, Dave; Mack, Robert; Malkin, Peter; Nguyen, Tam

1994-04-01

The emergence of high-speed networking for multimedia will have the effect of turning the computer screen into a window on a very large information space. As this information space increases in size and complexity, providing users with easy and intuitive means of accessing information will become increasingly important. Providing access to large amounts of text has been the focus of work for hundreds of years and has resulted in the evolution of a set of standards, from the Dewey Decimal System for libraries to the recently proposed ANSI standards for representing information on-line: KIF, Knowledge Interchange Format, and CG's, Conceptual Graphs. Certain problems remain unsolved by these efforts, though: how to let users know the contents of the information space, so that they know whether or not they want to search it in the first place, how to facilitate browsing, and, more specifically, how to facilitate visual browsing. These issues are particularly important for users in educational contexts and have been the focus of much of our recent work. In this paper we discuss some of the solutions we have prototypes: specifically, visual means, visual browsers, and visual definitional sequences.

User's Manual for the Object User Interface (OUI): An Environmental Resource Modeling Framework

USGS Publications Warehouse

Markstrom, Steven L.; Koczot, Kathryn M.

2008-01-01

The Object User Interface is a computer application that provides a framework for coupling environmental-resource models and for managing associated temporal and spatial data. The Object User Interface is designed to be easily extensible to incorporate models and data interfaces defined by the user. Additionally, the Object User Interface is highly configurable through the use of a user-modifiable, text-based control file that is written in the eXtensible Markup Language. The Object User Interface user's manual provides (1) installation instructions, (2) an overview of the graphical user interface, (3) a description of the software tools, (4) a project example, and (5) specifications for user configuration and extension.

Prototyping Tool for Web-Based Multiuser Online Role-Playing Game

NASA Astrophysics Data System (ADS)

Okamoto, Shusuke; Kamada, Masaru; Yonekura, Tatsuhiro

This letter proposes a prototyping tool for Web-based Multiuser Online Role-Playing Game (MORPG). The design goal is to make this tool simple and powerful. The tool is comprised of a GUI editor, a translator and a runtime environment. The GUI editor is used to edit state-transition diagrams, each of which defines the behavior of the fictional characters. The state-transition diagrams are translated into C program codes, which plays the role of a game engine in RPG system. The runtime environment includes PHP, JavaScript with Ajax and HTML. So the prototype system can be played on the usual Web browser, such as Fire-fox, Safari and IE. On a click or key press by a player, the Web browser sends it to the Web server to reflect its consequence on the screens which other players are looking at. Prospected users of this tool include programming novices and schoolchildren. The knowledge or skill of any specific programming languages is not required to create state-transition diagrams. Its structure is not only suitable for the definition of a character behavior but also intuitive to help novices understand. Therefore, the users can easily create Web-based MORPG system with the tool.

SPICE Supports Planetary Science Observation Geometry

NASA Astrophysics Data System (ADS)

Hall Acton, Charles; Bachman, Nathaniel J.; Semenov, Boris V.; Wright, Edward D.

2015-11-01

"SPICE" is an information system, comprising both data and software, providing scientists with the observation geometry needed to plan observations from instruments aboard robotic spacecraft, and to subsequently help in analyzing the data returned from those observations. The SPICE system has been used on the majority of worldwide planetary exploration missions since the time of NASA's Galileo mission to Jupiter. Along with its "free" price tag, portability and the absence of licensing and export restrictions, its stable, enduring qualities help make it a popular choice. But stability does not imply rigidity-improvements and new capabilities are regularly added. This poster highlights recent additions that could be of interest to planetary scientists.Geometry Finder allows one to find all the times or time intervals when a particular geometric condition exists (e.g. occultation) or when a particular geometric parameter is within a given range or has reached a maximum or minimum.Digital Shape Kernel (DSK) provides means to compute observation geometry using accurately modeled target bodies: a tessellated plate model for irregular bodies and a digital elevation model for large, regular bodies.WebGeocalc (WGC) provides a graphical user interface (GUI) to a SPICE "geometry engine" installed at a mission operations facility, such as the one operated by NAIF. A WGC user need have only a computer with a web browser to access this geometry engine. Using traditional GUI widgets-drop-down menus, check boxes, radio buttons and fill-in boxes-the user inputs the data to be used, the kind of calculation wanted, and the details of that calculation. The WGC server makes the specified calculations and returns results to the user's browser.Cosmographia is a mission visualization program. This tool provides 3D visualization of solar system (target) bodies, spacecraft trajectory and orientation, instrument field-of-view "cones" and footprints, and more.The research described in this publication was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration.

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

NASA Astrophysics Data System (ADS)

Djalalian, Amir; Mukhtar, Rami; Zukerman, Moshe

2002-09-01

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

iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website

PubMed Central

Good, Benjamin M; Kawas, Edward A; Kuo, Byron Yu-Lin; Wilkinson, Mark D

2006-01-01

Background User-scripts are programs stored in Web browsers that can manipulate the content of websites prior to display in the browser. They provide a novel mechanism by which users can conveniently gain increased control over the content and the display of the information presented to them on the Web. As the Web is the primary medium by which scientists retrieve biological information, any improvements in the mechanisms that govern the utility or accessibility of this information may have profound effects. GreaseMonkey is a Mozilla Firefox extension that facilitates the development and deployment of user-scripts for the Firefox web-browser. We utilize this to enhance the content and the presentation of the iHOP (information Hyperlinked Over Proteins) website. Results The iHOPerator is a GreaseMonkey user-script that augments the gene-centred pages on iHOP by providing a compact, configurable visualization of the defining information for each gene and by enabling additional data, such as biochemical pathway diagrams, to be collected automatically from third party resources and displayed in the same browsing context. Conclusion This open-source script provides an extension to the iHOP website, demonstrating how user-scripts can personalize and enhance the Web browsing experience in a relevant biological setting. The novel, user-driven controls over the content and the display of Web resources made possible by user-scripts, such as the iHOPerator, herald the beginning of a transition from a resource-centric to a user-centric Web experience. We believe that this transition is a necessary step in the development of Web technology that will eventually result in profound improvements in the way life scientists interact with information. PMID:17173692

Q.U.E.S.T. An Interactive Earth Science Study Tool: Connecting Real Students to Digital Libraries

NASA Astrophysics Data System (ADS)

Moore, A.; Danowski, D.; Brindisi, C.; Sandvol, C.; Seber, D.

2001-05-01

Quick Use Earth Study Tool (QUEST) is an experimental educational interface to the Cornell University's Geoscience Information System (http://atlas.geo.cornell.edu). The information system currently includes more than 100 geographic, geologic, and geophysical data sets along with World Wide Web based interactive mapping tools for data display and analysis. The system is GIS based and accessible via any web browser that support Java applets. QUEST is the companion module that has been developed to assist educators who wish to use these data to their fullest potential, providing tutorials, sample exercises, and suggested projects. Clearly, students learn best when they engage in the practice of science. One means to accomplish this is to have students access primary scientific data. Our experience suggests that a structured exploration of original data sets enhances student learning. For this reason we have selected a subset of Cornell's available geoscience data, and have designed a series of activities that allow students to explore dynamic Earth processes. Currently, these data include the ISC seismicity catalog, volcanism data from the Smithsonian Institution, and digital topography from the USGS and NOAA. The QUEST interface allows students to query the data sets based on a variety of criteria (e.g., earthquakes can be sorted by date, magnitude, depth, and location), or perform computations on data (e.g., sea level can be interactively mapped at any elevation on the DEM). Because the system is GIS-based, multiple data sets can be displayed simultaneously in order for users to examine the spatial relationships between geological features. Users can zoom in to regions of interest, and a map history window keeps track of student work so that comparisons are easily made. QUEST is accompanied by a Teacher's Manual to assist teachers in extracting the most information from the available data and tools. Through these efforts we hope to provide teachers and students with access to a wide variety of data applicable to problems in Earth science, along with the ability to easily display and analyze multiple data types--thus providing all users with access to state-of-the-art information.

CIP Training Manual: Collaborative Information Portal Advance Training Information for Field Test Participants

NASA Technical Reports Server (NTRS)

Schreiner, John; Clancy, Daniel (Technical Monitor)

2002-01-01

The Collaborative Information Portal (CIP) is a web-based information management and retrieval system. Its purpose is to provide users at MER (Mars Exploration Rover) mission operations with easy access to a broad range of mission data and products and contextual information such as the current operations schedule. The CIP web-server provides this content in a user customizable web-portal environment. Since CIP is still under development, only a subset of the full feature set will be available for the EDO field test. The CIP web-portal will be accessed through a standard web browser. CIP is intended to be intuitive and simple to use, however, at the training session, users will receive a one to two page reference guide, which should aid them in using CIP. Users must provide their own computers for accessing CIP during the field test. These computers should be configured with Java 1.3 and a Java 2 enabled browser. Macintosh computers should be running OS 10.1.3 or later. Classic Mac OS (OS 9) is not supported. For more information please read section 7.3 in the FIASCO Rover Science Operations Test Mission Plan. Several screen shots of the Beta Release of CIP are shown on the following pages.

Teaching People and Machines to Enhance Images

NASA Astrophysics Data System (ADS)

Berthouzoz, Floraine Sara Martianne

Procedural tasks such as following a recipe or editing an image are very common. They require a person to execute a sequence of operations (e.g. chop onions, or sharpen the image) in order to achieve the goal of the task. People commonly use step-by-step tutorials to learn these tasks. We focus on software tutorials, more specifically photo manipulation tutorials, and present a set of tools and techniques to help people learn, compare and automate photo manipulation procedures. We describe three different systems that are each designed to help with a different stage in acquiring procedural knowledge. Today, people primarily rely on hand-crafted tutorials in books and on websites to learn photo manipulation procedures. However, putting together a high quality step-by-step tutorial is a time-consuming process. As a consequence, many online tutorials are poorly designed which can lead to confusion and slow down the learning process. We present a demonstration-based system for automatically generating succinct step-by-step visual tutorials of photo manipulations. An author first demonstrates the manipulation using an instrumented version of GIMP (GNU Image Manipulation Program) that records all changes in interface and application state. From the example recording, our system automatically generates tutorials that illustrate the manipulation using images, text, and annotations. It leverages automated image labeling (recognition of facial features and outdoor scene structures in our implementation) to generate more precise text descriptions of many of the steps in the tutorials. A user study finds that our tutorials are effective for learning the steps of a procedure; users are 20-44% faster and make 60-95% fewer errors when using our tutorials than when using screencapture video tutorials or hand-designed tutorials. We also demonstrate a new interface that allows learners to navigate, explore and compare large collections (i.e. thousands) of photo manipulation tutorials based on their command-level structure. Sites such as tutorialized.com or good-tutorials.com collect tens of thousands of photo manipulation tutorials. These collections typically contain many different tutorials for the same task. For example, there are many different tutorials that describe how to recolor the hair of a person in an image. Learners often want to compare these tutorials to understand the different ways a task can be done. They may also want to identify common strategies that are used across tutorials for a variety of tasks. However, the large number of tutorials in these collections and their inconsistent formats can make it difficult for users to systematically explore and compare them. Current tutorial collections do not exploit the underlying command-level structure of tutorials, and to explore the collection users have to either page through long lists of tutorial titles or perform keyword searches on the natural language tutorial text. We present a new browsing interface to help learners navigate, explore and compare collections of photo manipulation tutorials based on their command-level structure. Our browser indexes tutorials by their commands, identifies common strategies within the tutorial collection, and highlights the similarities and differences between sets of tutorials that execute the same task. User feedback suggests that our interface is easy to understand and use, and that users find command-level browsing to be useful for exploring large tutorial collections. They strongly preferred to explore tutorial collections with our browser over keyword search. Finally, we present a framework for generating content-adaptive macros (programs) that can transfer complex photo manipulation procedures to new target images. After learners master a photo manipulation procedure, they often repeatedly apply it to multiple images. For example, they might routinely apply the same vignetting effect to all their photographs. This process can be very tedious especially for procedures that involve many steps. While image manipulation programs provide basic macro authoring tools that allow users to record and then replay a sequence of operations, these macros are very brittle and cannot adapt to new images. We present a more comprehensive approach for generating content-adaptive macros that can automatically transfer operations to new target images. To create these macro, we make use of multiple training demonstrations. Specifically, we use automated image labeling and machine learning techniques to to adapt the parameters of each operation to the new image content. We show that our framework is able to learn a large class of the most commonly-used manipulations using as few as 20 training demonstrations. Our content-adaptive macros allow users to transfer photo manipulation procedures with a single button click and thereby significantly simplify repetitive procedures.

'Fly Like This': Natural Language Interface for UAV Mission Planning

NASA Technical Reports Server (NTRS)

Chandarana, Meghan; Meszaros, Erica L.; Trujillo, Anna; Allen, B. Danette

2017-01-01

With the increasing presence of unmanned aerial vehicles (UAVs) in everyday environments, the user base of these powerful and potentially intelligent machines is expanding beyond exclusively highly trained vehicle operators to include non-expert system users. Scientists seeking to augment costly and often inflexible methods of data collection historically used are turning towards lower cost and reconfigurable UAVs. These new users require more intuitive and natural methods for UAV mission planning. This paper explores two natural language interfaces - gesture and speech - for UAV flight path generation through individual user studies. Subjects who participated in the user studies also used a mouse-based interface for a baseline comparison. Each interface allowed the user to build flight paths from a library of twelve individual trajectory segments. Individual user studies evaluated performance, efficacy, and ease-of-use of each interface using background surveys, subjective questionnaires, and observations on time and correctness. Analysis indicates that natural language interfaces are promising alternatives to traditional interfaces. The user study data collected on the efficacy and potential of each interface will be used to inform future intuitive UAV interface design for non-expert users.

Dynamic Distribution and Layouting of Model-Based User Interfaces in Smart Environments

NASA Astrophysics Data System (ADS)

Roscher, Dirk; Lehmann, Grzegorz; Schwartze, Veit; Blumendorf, Marco; Albayrak, Sahin

The developments in computer technology in the last decade change the ways of computer utilization. The emerging smart environments make it possible to build ubiquitous applications that assist users during their everyday life, at any time, in any context. But the variety of contexts-of-use (user, platform and environment) makes the development of such ubiquitous applications for smart environments and especially its user interfaces a challenging and time-consuming task. We propose a model-based approach, which allows adapting the user interface at runtime to numerous (also unknown) contexts-of-use. Based on a user interface modelling language, defining the fundamentals and constraints of the user interface, a runtime architecture exploits the description to adapt the user interface to the current context-of-use. The architecture provides automatic distribution and layout algorithms for adapting the applications also to contexts unforeseen at design time. Designers do not specify predefined adaptations for each specific situation, but adaptation constraints and guidelines. Furthermore, users are provided with a meta user interface to influence the adaptations according to their needs. A smart home energy management system serves as running example to illustrate the approach.

A new forecast presentation tool for offshore contractors

NASA Astrophysics Data System (ADS)

Jørgensen, M.

2009-09-01

Contractors working off shore are often very sensitive to both sea and weather conditions, and it's essential that they have easy access to reliable information on coming conditions to enable planning of when to start or shut down offshore operations to avoid loss of life and materials. Danish Meteorological Institute, DMI, recently, in cooperation with business partners in the field, developed a new application to accommodate that need. The "Marine Forecast Service” is a browser based forecast presentation tool. It provides an interface for the user to enable easy and quick access to all relevant meteorological and oceanographic forecasts and observations for a given area of interest. Each customer gains access to the application via a standard login/password procedure. Once logged in, the user can inspect animated forecast maps of parameters like wind, gust, wave height, swell and current among others. Supplementing the general maps, the user can choose to look at forecast graphs for each of the locations where the user is running operations. These forecast graphs can also be overlaid with the user's own in situ observations, if such exist. Furthermore, the data from the graphs can be exported as data files that the customer can use in his own applications as he desires. As part of the application, a forecaster's view on the current and near future weather situation is presented to the user as well, adding further value to the information presented through maps and graphs. Among other features of the product, animated radar and satellite images could be mentioned. And finally the application provides the possibility of a "second opinion” through traditional weather charts from another recognized provider of weather forecasts. The presentation will provide more detailed insights into the contents of the applications as well as some of the experiences with the product.

User interface support

NASA Technical Reports Server (NTRS)

Lewis, Clayton; Wilde, Nick

1989-01-01

Space construction will require heavy investment in the development of a wide variety of user interfaces for the computer-based tools that will be involved at every stage of construction operations. Using today's technology, user interface development is very expensive for two reasons: (1) specialized and scarce programming skills are required to implement the necessary graphical representations and complex control regimes for high-quality interfaces; (2) iteration on prototypes is required to meet user and task requirements, since these are difficult to anticipate with current (and foreseeable) design knowledge. We are attacking this problem by building a user interface development tool based on extensions to the spreadsheet model of computation. The tool provides high-level support for graphical user interfaces and permits dynamic modification of interfaces, without requiring conventional programming concepts and skills.

SVGMap: configurable image browser for experimental data.

PubMed

Rafael-Palou, Xavier; Schroeder, Michael P; Lopez-Bigas, Nuria

2012-01-01

Spatial data visualization is very useful to represent biological data and quickly interpret the results. For instance, to show the expression pattern of a gene in different tissues of a fly, an intuitive approach is to draw the fly with the corresponding tissues and color the expression of the gene in each of them. However, the creation of these visual representations may be a burdensome task. Here we present SVGMap, a java application that automatizes the generation of high-quality graphics for singular data items (e.g. genes) and biological conditions. SVGMap contains a browser that allows the user to navigate the different images created and can be used as a web-based results publishing tool. SVGMap is freely available as precompiled java package as well as source code at http://bg.upf.edu/svgmap. It requires Java 6 and any recent web browser with JavaScript enabled. The software can be run on Linux, Mac OS X and Windows systems. nuria.lopez@upf.edu

Composing only by thought: Novel application of the P300 brain-computer interface.

PubMed

Pinegger, Andreas; Hiebel, Hannah; Wriessnegger, Selina C; Müller-Putz, Gernot R

2017-01-01

The P300 event-related potential is a well-known pattern in the electroencephalogram (EEG). This kind of brain signal is used for many different brain-computer interface (BCI) applications, e.g., spellers, environmental controllers, web browsers, or for painting. In recent times, BCI systems are mature enough to leave the laboratories to be used by the end-users, namely severely disabled people. Therefore, new challenges arise and the systems should be implemented and evaluated according to user-centered design (USD) guidelines. We developed and implemented a new system that utilizes the P300 pattern to compose music. Our Brain Composing system consists of three parts: the EEG acquisition device, the P300-based BCI, and the music composing software. Seventeen musical participants and one professional composer performed a copy-spelling, a copy-composing, and a free-composing task with the system. According to the USD guidelines, we investigated the efficiency, the effectiveness and subjective criteria in terms of satisfaction, enjoyment, frustration, and attractiveness. The musical participants group achieved high average accuracies: 88.24% (copy-spelling), 88.58% (copy-composing), and 76.51% (free-composing). The professional composer achieved also high accuracies: 100% (copy-spelling), 93.62% (copy-composing), and 98.20% (free-composing). General results regarding the subjective criteria evaluation were that the participants enjoyed the usage of the Brain Composing system and were highly satisfied with the system. Showing very positive results with healthy people in this study, this was the first step towards a music composing system for severely disabled people.

Composing only by thought: Novel application of the P300 brain-computer interface

PubMed Central

Hiebel, Hannah; Wriessnegger, Selina C.; Müller-Putz, Gernot R.

2017-01-01

The P300 event-related potential is a well-known pattern in the electroencephalogram (EEG). This kind of brain signal is used for many different brain-computer interface (BCI) applications, e.g., spellers, environmental controllers, web browsers, or for painting. In recent times, BCI systems are mature enough to leave the laboratories to be used by the end-users, namely severely disabled people. Therefore, new challenges arise and the systems should be implemented and evaluated according to user-centered design (USD) guidelines. We developed and implemented a new system that utilizes the P300 pattern to compose music. Our Brain Composing system consists of three parts: the EEG acquisition device, the P300-based BCI, and the music composing software. Seventeen musical participants and one professional composer performed a copy-spelling, a copy-composing, and a free-composing task with the system. According to the USD guidelines, we investigated the efficiency, the effectiveness and subjective criteria in terms of satisfaction, enjoyment, frustration, and attractiveness. The musical participants group achieved high average accuracies: 88.24% (copy-spelling), 88.58% (copy-composing), and 76.51% (free-composing). The professional composer achieved also high accuracies: 100% (copy-spelling), 93.62% (copy-composing), and 98.20% (free-composing). General results regarding the subjective criteria evaluation were that the participants enjoyed the usage of the Brain Composing system and were highly satisfied with the system. Showing very positive results with healthy people in this study, this was the first step towards a music composing system for severely disabled people. PMID:28877175

Computer-Based Tools for Evaluating Graphical User Interfaces

NASA Technical Reports Server (NTRS)

Moore, Loretta A.

1997-01-01

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

Internet-based support for the production of holographic stereograms

NASA Astrophysics Data System (ADS)

Gustafsson, Jonny

1998-03-01

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

Web-Based Geographic Information System Tool for Accessing Hanford Site Environmental Data

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

Triplett, Mark B.; Seiple, Timothy E.; Watson, David J.

Data volume, complexity, and access issues pose severe challenges for analysts, regulators and stakeholders attempting to efficiently use legacy data to support decision making at the U.S. Department of Energy’s (DOE) Hanford Site. DOE has partnered with the Pacific Northwest National Laboratory (PNNL) on the PHOENIX (PNNL-Hanford Online Environmental Information System) project, which seeks to address data access, transparency, and integration challenges at Hanford to provide effective decision support. PHOENIX is a family of spatially-enabled web applications providing quick access to decades of valuable scientific data and insight through intuitive query, visualization, and analysis tools. PHOENIX realizes broad, public accessibilitymore » by relying only on ubiquitous web-browsers, eliminating the need for specialized software. It accommodates a wide range of users with intuitive user interfaces that require little or no training to quickly obtain and visualize data. Currently, PHOENIX is actively hosting three applications focused on groundwater monitoring, groundwater clean-up performance reporting, and in-tank monitoring. PHOENIX-based applications are being used to streamline investigative and analytical processes at Hanford, saving time and money. But more importantly, by integrating previously isolated datasets and developing relevant visualization and analysis tools, PHOENIX applications are enabling DOE to discover new correlations hidden in legacy data, allowing them to more effectively address complex issues at Hanford.« less

UCSC genome browser: deep support for molecular biomedical research.

PubMed

Mangan, Mary E; Williams, Jennifer M; Lathe, Scott M; Karolchik, Donna; Lathe, Warren C

2008-01-01

The volume and complexity of genomic sequence data, and the additional experimental data required for annotation of the genomic context, pose a major challenge for display and access for biomedical researchers. Genome browsers organize this data and make it available in various ways to extract useful information to advance research projects. The UCSC Genome Browser is one of these resources. The official sequence data for a given species forms the framework to display many other types of data such as expression, variation, cross-species comparisons, and more. Visual representations of the data are available for exploration. Data can be queried with sequences. Complex database queries are also easily achieved with the Table Browser interface. Associated tools permit additional query types or access to additional data sources such as images of in situ localizations. Support for solving researcher's issues is provided with active discussion mailing lists and by providing updated training materials. The UCSC Genome Browser provides a source of deep support for a wide range of biomedical molecular research (http://genome.ucsc.edu).

Controlling EPICS from a web browser.

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

Evans, K., Jr.

1999-04-13

An alternative to using a large graphical display manager like MEDM [1,2] to interface to a control system, is to use individual control objects, such as text boxes, meters, etc., running in a browser. This paper presents three implementations of this concept, one using ActiveX controls, one with Java applets, and another with Microsoft Agent. The ActiveX controls have performance nearing that of MEDM, but they only work on Windows platforms. The Java applets require a server to get around Web security restrictions and are not as fast, but they have the advantage of working on most platforms and withmore » both of the leading Web browsers. The agent works on Windows platforms with and without a browser and allows voice recognition and speech synthesis, making it somewhat more innovative than MEDM.« less

JHelioviewer: Open-Source Software for Discovery and Image Access in the Petabyte Age

NASA Astrophysics Data System (ADS)

Mueller, D.; Dimitoglou, G.; Garcia Ortiz, J.; Langenberg, M.; Nuhn, M.; Dau, A.; Pagel, S.; Schmidt, L.; Hughitt, V. K.; Ireland, J.; Fleck, B.

2011-12-01

The unprecedented torrent of data returned by the Solar Dynamics Observatory is both a blessing and a barrier: a blessing for making available data with significantly higher spatial and temporal resolution, but a barrier for scientists to access, browse and analyze them. With such staggering data volume, the data is accessible only from a few repositories and users have to deal with data sets effectively immobile and practically difficult to download. From a scientist's perspective this poses three challenges: accessing, browsing and finding interesting data while avoiding the proverbial search for a needle in a haystack. To address these challenges, we have developed JHelioviewer, an open-source visualization software that lets users browse large data volumes both as still images and movies. We did so by deploying an efficient image encoding, storage, and dissemination solution using the JPEG 2000 standard. This solution enables users to access remote images at different resolution levels as a single data stream. Users can view, manipulate, pan, zoom, and overlay JPEG 2000 compressed data quickly, without severe network bandwidth penalties. Besides viewing data, the browser provides third-party metadata and event catalog integration to quickly locate data of interest, as well as an interface to the Virtual Solar Observatory to download science-quality data. As part of the ESA/NASA Helioviewer Project, JHelioviewer offers intuitive ways to browse large amounts of heterogeneous data remotely and provides an extensible and customizable open-source platform for the scientific community. In addition, the easy-to-use graphical user interface enables the general public and educators to access, enjoy and reuse data from space missions without barriers.

Access Control of Web- and Java-Based Applications

NASA Technical Reports Server (NTRS)

Tso, Kam S.; Pajevski, Michael J.

2013-01-01

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

COPRED: prediction of fold, GO molecular function and functional residues at the domain level.

PubMed

López, Daniel; Pazos, Florencio

2013-07-15

Only recently the first resources devoted to the functional annotation of proteins at the domain level started to appear. The next step is to develop specific methodologies for predicting function at the domain level based on these resources, and to implement them in web servers to be used by the community. In this work, we present COPRED, a web server for the concomitant prediction of fold, molecular function and functional sites at the domain level, based on a methodology for domain molecular function prediction and a resource of domain functional annotations previously developed and benchmarked. COPRED can be freely accessed at http://csbg.cnb.csic.es/copred. The interface works in all standard web browsers. WebGL (natively supported by most browsers) is required for the in-line preview and manipulation of protein 3D structures. The website includes a detailed help section and usage examples. pazos@cnb.csic.es.

Intelligent Context-Aware and Adaptive Interface for Mobile LBS

PubMed Central

Liu, Yanhong

2015-01-01

Context-aware user interface plays an important role in many human-computer Interaction tasks of location based services. Although spatial models for context-aware systems have been studied extensively, how to locate specific spatial information for users is still not well resolved, which is important in the mobile environment where location based services users are impeded by device limitations. Better context-aware human-computer interaction models of mobile location based services are needed not just to predict performance outcomes, such as whether people will be able to find the information needed to complete a human-computer interaction task, but to understand human processes that interact in spatial query, which will in turn inform the detailed design of better user interfaces in mobile location based services. In this study, a context-aware adaptive model for mobile location based services interface is proposed, which contains three major sections: purpose, adjustment, and adaptation. Based on this model we try to describe the process of user operation and interface adaptation clearly through the dynamic interaction between users and the interface. Then we show how the model applies users' demands in a complicated environment and suggested the feasibility by the experimental results. PMID:26457077

Bayesian accrual prediction for interim review of clinical studies: open source R package and smartphone application.

PubMed

Jiang, Yu; Guarino, Peter; Ma, Shuangge; Simon, Steve; Mayo, Matthew S; Raghavan, Rama; Gajewski, Byron J

2016-07-22

Subject recruitment for medical research is challenging. Slow patient accrual leads to increased costs and delays in treatment advances. Researchers need reliable tools to manage and predict the accrual rate. The previously developed Bayesian method integrates researchers' experience on former trials and data from an ongoing study, providing a reliable prediction of accrual rate for clinical studies. In this paper, we present a user-friendly graphical user interface program developed in R. A closed-form solution for the total subjects that can be recruited within a fixed time is derived. We also present a built-in Android system using Java for web browsers and mobile devices. Using the accrual software, we re-evaluated the Veteran Affairs Cooperative Studies Program 558- ROBOTICS study. The application of the software in monitoring and management of recruitment is illustrated for different stages of the trial. This developed accrual software provides a more convenient platform for estimation and prediction of the accrual process.

TissueWikiMobile: an Integrative Protein Expression Image Browser for Pathological Knowledge Sharing and Annotation on a Mobile Device

PubMed Central

Cheng, Chihwen; Stokes, Todd H.; Hang, Sovandy; Wang, May D.

2016-01-01

Doctors need fast and convenient access to medical data. This motivates the use of mobile devices for knowledge retrieval and sharing. We have developed TissueWikiMobile on the Apple iPhone and iPad to seamlessly access TissueWiki, an enormous repository of medical histology images. TissueWiki is a three terabyte database of antibody information and histology images from the Human Protein Atlas (HPA). Using TissueWikiMobile, users are capable of extracting knowledge from protein expression, adding annotations to highlight regions of interest on images, and sharing their professional insight. By providing an intuitive human computer interface, users can efficiently operate TissueWikiMobile to access important biomedical data without losing mobility. TissueWikiMobile furnishes the health community a ubiquitous way to collaborate and share their expert opinions not only on the performance of various antibodies stains but also on histology image annotation. PMID:27532057

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.

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration

PubMed Central

Ong, Edison; Xiang, Zuoshuang; Zhao, Bin; Liu, Yue; Lin, Yu; Zheng, Jie; Mungall, Chris; Courtot, Mélanie; Ruttenberg, Alan; He, Yongqun

2017-01-01

Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies. PMID:27733503

The Qatar National Historic Environment Record: a Platform for the Development of a Fully-Integrated Cultural Heritage Management Application

NASA Astrophysics Data System (ADS)

Cuttler, R. T. H.; Tonner, T. W. W.; Al-Naimi, F. A.; Dingwall, L. M.; Al-Hemaidi, N.

2013-07-01

The development of the Qatar National Historic Environment Record (QNHER) by the Qatar Museums Authority and the University of Birmingham in 2008 was based on a customised, bilingual Access database and ArcGIS. While both platforms are stable and well supported, neither was designed for the documentation and retrieval of cultural heritage data. As a result it was decided to develop a custom application using Open Source code. The core module of this application is now completed and is orientated towards the storage and retrieval of geospatial heritage data for the curation of heritage assets. Based on MIDAS Heritage data standards and regionally relevant thesauri, it is a truly bilingual system. Significant attention has been paid to the user interface, which is userfriendly and intuitive. Based on a suite of web services and accessed through a web browser, the system makes full use of internet resources such as Google Maps and Bing Maps. The application avoids long term vendor ''tie-ins'' and as a fully integrated data management system, is now an important tool for both cultural resource managers and heritage researchers in Qatar.

Sensor node for remote monitoring of waterborne disease-causing bacteria.

PubMed

Kim, Kyukwang; Myung, Hyun

2015-05-05

A sensor node for sampling water and checking for the presence of harmful bacteria such as E. coli in water sources was developed in this research. A chromogenic enzyme substrate assay method was used to easily detect coliform bacteria by monitoring the color change of the sampled water mixed with a reagent. Live webcam image streaming to the web browser of the end user with a Wi-Fi connected sensor node shows the water color changes in real time. The liquid can be manipulated on the web-based user interface, and also can be observed by webcam feeds. Image streaming and web console servers run on an embedded processor with an expansion board. The UART channel of the expansion board is connected to an external Arduino board and a motor driver to control self-priming water pumps to sample the water, mix the reagent, and remove the water sample after the test is completed. The sensor node can repeat water testing until the test reagent is depleted. The authors anticipate that the use of the sensor node developed in this research can decrease the cost and required labor for testing samples in a factory environment and checking the water quality of local water sources in developing countries.

Disaster relief through composite signatures

NASA Astrophysics Data System (ADS)

Hawley, Chadwick T.; Hyde, Brian; Carpenter, Tom; Nichols, Steve

2012-06-01

A composite signature is a group of signatures that are related in such a way to more completely or further define a target or operational endeavor at a higher fidelity. This paper builds on previous work developing innovative composite signatures associated with civil disasters, including physical, chemical and pattern/behavioral. For the composite signature approach to be successful it requires effective data fusion and visualization. This plays a key role in both preparedness and the response and recovery which are critical to saving lives. Visualization tools enhance the overall understanding of the crisis by pulling together and analyzing the data, and providing a clear and complete analysis of the information to the organizations/agencies dependant on it for a successful operation. An example of this, Freedom Web, is an easy-to-use data visualization and collaboration solution for use in homeland security, emergency preparedness, situational awareness, and event management. The solution provides a nationwide common operating picture for all levels of government through a web based, map interface. The tool was designed to be utilized by non-geospatial experts and is easily tailored to the specific needs of the users. Consisting of standard COTS and open source databases and a web server, users can view, edit, share, and highlight information easily and quickly through a standard internet browser.

Observing proposals on the Web at the National Optical Astronomy Observatories

NASA Astrophysics Data System (ADS)

Pilachowski, Catherine A.; Barnes, Jeannette; Bell, David J.

1998-07-01

Proposals for telescope time at facilities available through the National Optical Astronomy Observatories can now be prepared and submitted via the WWW. Investigators submit proposal information through a series of HTML forms to the NOAO server, where the information is processed by Perl CGI scripts. PostScript figures and ASCII files may be attached by investigators for inclusion in their proposals using their browser's upload feature. Proposal information is saved on the server so that investigators can return in later sessions to continue work on a proposal and so that collaborators can participate in writing the proposal if they have access to the proposal account name and password. The system provides on-line verification of LATEX syntax and a spellchecker, and confirms that all sections of the proposal are filled out. Users can request a LATEX or PostScript copy of their proposal by e-mail, or view the proposal on line. The advantages of the Web-based process for our users are convenience, access to on-line documentation, and the simple interface which avoids direct confrontation with LATEX. From the NOAO point of view, the advantage is the use of standardized formats and syntax, particularly as we begin to receive proposals for the Gemini telescopes and some independent observatories.

Providing Access to a Diverse Set of Global Reanalysis Dataset Collections

NASA Astrophysics Data System (ADS)

Schuster, D.; Worley, S. J.

2015-12-01

The National Center for Atmospheric Research (NCAR) Research Data Archive (RDA, http://rda.ucar.edu) provides open access to a variety of global reanalysis dataset collections to support atmospheric and related sciences research worldwide. These include products from the European Centre for Medium-Range Weather Forecasts (ECMWF), Japan Meteorological Agency (JMA), National Centers for Environmental Prediction (NCEP), National Oceanic and Atmospheric Administration (NOAA), and NCAR.All RDA hosted reanalysis collections are freely accessible to registered users through a variety of methods. Standard access methods include traditional browser and scripted HTTP file download. Enhanced downloads are available through the Globus GridFTP "fire and forget" data transfer service, which provides an efficient, reliable, and preferred alternative to traditional HTTP-based methods. For those that favor interoperable access using compatible tools, the Unidata THREDDS Data server provides remote access to complete reanalysis collections by virtual dataset aggregation "files". Finally, users can request data subsets and format conversions to be prepared for them through web interface form requests or web service API batch requests. This approach uses NCAR HPC and central file systems to effectively prepare products from the high-resolution and very large reanalyses archives. The presentation will include a detailed inventory of all RDA reanalysis dataset collection holdings, and highlight access capabilities to these collections through use case examples.

Visualization of data in radiotherapy using web services for optimization of workflow.

PubMed

Kirrmann, Stefan; Gainey, Mark; Röhner, Fred; Hall, Markus; Bruggmoser, Gregor; Schmucker, Marianne; Heinemann, Felix E

2015-01-20

Every day a large amount of data is produced within a radiotherapy department. Although this data is available in one form or other within the centralised systems, it is often not in the form which is of interest to the departmental staff. This work presents a flexible browser based reporting and visualization system for clinical and scientific use, not currently found in commercially available software such as MOSAIQ(TM) or ARIA(TM). Moreover, the majority of user merely wish to retrieve data and not record and/or modify data. Thus the idea was conceived, to present the user with all relevant information in a simple and effective manner in the form of web-services. Due to the widespread availability of the internet, most people can master the use of a web-browser. Ultimately the aim is to optimize clinical procedures, enhance transparency and improve revenue. Our working group (BAS) examined many internal procedures, to find out whether relevant information suitable for our purposes lay therein. After the results were collated, it was necessary to select an effective software platform. After a more detailed analysis of all data, it became clear that the implementation of web-services was appropriate. In our institute several such web-based information services had already been developed over the last few years, with which we gained invaluable experience. Moreover, we strived for high acceptance amongst staff members. By employing web-services, we attained high effectiveness, transparency and efficient information processing for the user. Furthermore, we achieved an almost maintenance-free and low support system. The aim of the project, making web-based information available to the user from the departmental system MOSAIQ, physician letter system MEDATEC(R) and the central finding server MiraPlus (laboratory, pathology and radiology) were implemented without restrictions. Due to widespread use of web-based technology the training effort was effectively nil, since practically every member of staff can master the use of a web-browser. Moreover, we have achieved high acceptance amongst staff members and have improved our effectiveness resulting in a considerable time saving. The many MOSAIQ-specific parts of the system can be readily used by departments which use MOSAIQ as the departmental system.

The Invasive Species Forecasting System (ISFS): An iRODS-Based, Cloud-Enabled Decision Support System for Invasive Species Habitat Suitability Modeling

NASA Technical Reports Server (NTRS)

Gill, Roger; Schnase, John L.

2012-01-01

The Invasive Species Forecasting System (ISFS) is an online decision support system that allows users to load point occurrence field sample data for a plant species of interest and quickly generate habitat suitability maps for geographic regions of interest, such as a national park, monument, forest, or refuge. Target customers for ISFS are natural resource managers and decision makers who have a need for scientifically valid, model- based predictions of the habitat suitability of plant species of management concern. In a joint project involving NASA and the Maryland Department of Natural Resources, ISFS has been used to model the potential distribution of Wavyleaf Basketgrass in Maryland's Chesapeake Bay Watershed. Maximum entropy techniques are used to generate predictive maps using predictor datasets derived from remotely sensed data and climate simulation outputs. The workflow to run a model is implemented in an iRODS microservice using a custom ISFS file driver that clips and re-projects data to geographic regions of interest, then shells out to perform MaxEnt processing on the input data. When the model completes, all output files and maps from the model run are registered in iRODS and made accessible to the user. The ISFS user interface is a web browser that uses the iRODS PHP client to interact with the ISFS/iRODS- server. ISFS is designed to reside in a VMware virtual machine running SLES 11 and iRODS 3.0. The ISFS virtual machine is hosted in a VMware vSphere private cloud infrastructure to deliver the online service.

Automatic optimisation of gamma dose rate sensor networks: The DETECT Optimisation Tool

NASA Astrophysics Data System (ADS)

Helle, K. B.; Müller, T. O.; Astrup, P.; Dyve, J. E.

2014-05-01

Fast delivery of comprehensive information on the radiological situation is essential for decision-making in nuclear emergencies. Most national radiological agencies in Europe employ gamma dose rate sensor networks to monitor radioactive pollution of the atmosphere. Sensor locations were often chosen using regular grids or according to administrative constraints. Nowadays, however, the choice can be based on more realistic risk assessment, as it is possible to simulate potential radioactive plumes. To support sensor planning, we developed the DETECT Optimisation Tool (DOT) within the scope of the EU FP 7 project DETECT. It evaluates the gamma dose rates that a proposed set of sensors might measure in an emergency and uses this information to optimise the sensor locations. The gamma dose rates are taken from a comprehensive library of simulations of atmospheric radioactive plumes from 64 source locations. These simulations cover the whole European Union, so the DOT allows evaluation and optimisation of sensor networks for all EU countries, as well as evaluation of fencing sensors around possible sources. Users can choose from seven cost functions to evaluate the capability of a given monitoring network for early detection of radioactive plumes or for the creation of dose maps. The DOT is implemented as a stand-alone easy-to-use JAVA-based application with a graphical user interface and an R backend. Users can run evaluations and optimisations, and display, store and download the results. The DOT runs on a server and can be accessed via common web browsers; it can also be installed locally.

WAZA-ARI: computational dosimetry system for X-ray CT examinations II: development of web-based system.

PubMed

Ban, Nobuhiko; Takahashi, Fumiaki; Ono, Koji; Hasegawa, Takayuki; Yoshitake, Takayasu; Katsunuma, Yasushi; Sato, Kaoru; Endo, Akira; Kai, Michiaki

2011-07-01

A web-based dose computation system, WAZA-ARI, is being developed for patients undergoing X-ray CT examinations. The system is implemented in Java on a Linux server running Apache Tomcat. Users choose scanning options and input parameters via a web browser over the Internet. Dose coefficients, which were calculated in a Japanese adult male phantom (JM phantom) are called upon user request and are summed over the scan range specified by the user to estimate a normalised dose. Tissue doses are finally computed based on the radiographic exposure (mA s) and the pitch factor. While dose coefficients are currently available only for limited CT scanner models, the system has achieved a high degree of flexibility and scalability without the use of commercial software.

Use of scientific social networking to improve the research strategies of PubMed readers.

PubMed

Evdokimov, Pavel; Kudryavtsev, Alexey; Ilgisonis, Ekaterina; Ponomarenko, Elena; Lisitsa, Andrey

2016-02-18

Keeping up with journal articles on a daily basis is an important activity of scientists engaged in biomedical research. Usually, journal articles and papers in the field of biomedicine are accessed through the Medline/PubMed electronic library. In the process of navigating PubMed, researchers unknowingly generate user-specific reading profiles that can be shared within a social networking environment. This paper examines the structure of the social networking environment generated by PubMed users. A web browser plugin was developed to map [in Medical Subject Headings (MeSH) terms] the reading patterns of individual PubMed users. We developed a scientific social network based on the personal research profiles of readers of biomedical articles. A browser plugin is used to record the digital object identifier or PubMed ID of web pages. Recorded items are posted on the activity feed and automatically mapped to PubMed abstract. Within the activity feed a user can trace back previously browsed articles and insert comments. By calculating the frequency with which specific MeSH occur, the research interests of PubMed users can be visually represented with a tag cloud. Finally, research profiles can be searched for matches between network users. A social networking environment was created using MeSH terms to map articles accessed through the Medline/PubMed online library system. In-network social communication is supported by the recommendation of articles and by matching users with similar scientific interests. The system is available at http://bioknol.org/en/.

iSyTE 2.0: a database for expression-based gene discovery in the eye

PubMed Central

Kakrana, Atul; Yang, Andrian; Anand, Deepti; Djordjevic, Djordje; Ramachandruni, Deepti; Singh, Abhyudai; Huang, Hongzhan

2018-01-01

Abstract Although successful in identifying new cataract-linked genes, the previous version of the database iSyTE (integrated Systems Tool for Eye gene discovery) was based on expression information on just three mouse lens stages and was functionally limited to visualization by only UCSC-Genome Browser tracks. To increase its efficacy, here we provide an enhanced iSyTE version 2.0 (URL: http://research.bioinformatics.udel.edu/iSyTE) based on well-curated, comprehensive genome-level lens expression data as a one-stop portal for the effective visualization and analysis of candidate genes in lens development and disease. iSyTE 2.0 includes all publicly available lens Affymetrix and Illumina microarray datasets representing a broad range of embryonic and postnatal stages from wild-type and specific gene-perturbation mouse mutants with eye defects. Further, we developed a new user-friendly web interface for direct access and cogent visualization of the curated expression data, which supports convenient searches and a range of downstream analyses. The utility of these new iSyTE 2.0 features is illustrated through examples of established genes associated with lens development and pathobiology, which serve as tutorials for its application by the end-user. iSyTE 2.0 will facilitate the prioritization of eye development and disease-linked candidate genes in studies involving transcriptomics or next-generation sequencing data, linkage analysis and GWAS approaches. PMID:29036527

Methods for Improving the User-Computer Interface. Technical Report.

ERIC Educational Resources Information Center

McCann, Patrick H.

This summary of methods for improving the user-computer interface is based on a review of the pertinent literature. Requirements of the personal computer user are identified and contrasted with computer designer perspectives towards the user. The user's psychological needs are described, so that the design of the user-computer interface may be…

Interface Metaphors for Interactive Machine Learning

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

Jasper, Robert J.; Blaha, Leslie M.

To promote more interactive and dynamic machine learn- ing, we revisit the notion of user-interface metaphors. User-interface metaphors provide intuitive constructs for supporting user needs through interface design elements. A user-interface metaphor provides a visual or action pattern that leverages a user’s knowledge of another domain. Metaphors suggest both the visual representations that should be used in a display as well as the interactions that should be afforded to the user. We argue that user-interface metaphors can also offer a method of extracting interaction-based user feedback for use in machine learning. Metaphors offer indirect, context-based information that can be usedmore » in addition to explicit user inputs, such as user-provided labels. Implicit information from user interactions with metaphors can augment explicit user input for active learning paradigms. Or it might be leveraged in systems where explicit user inputs are more challenging to obtain. Each interaction with the metaphor provides an opportunity to gather data and learn. We argue this approach is especially important in streaming applications, where we desire machine learning systems that can adapt to dynamic, changing data.« less

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

PubMed

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

2005-11-03

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

Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context

PubMed Central

Faith, Jeremiah J; Olson, Andrew J; Gardner, Timothy S; Sachidanandam, Ravi

2007-01-01

Background Lightweight genome viewer (lwgv) is a web-based tool for visualization of sequence annotations in their chromosomal context. It performs most of the functions of larger genome browsers, while relying on standard flat-file formats and bypassing the database needs of most visualization tools. Visualization as an aide to discovery requires display of novel data in conjunction with static annotations in their chromosomal context. With database-based systems, displaying dynamic results requires temporary tables that need to be tracked for removal. Results lwgv simplifies the visualization of user-generated results on a local computer. The dynamic results of these analyses are written to transient files, which can import static content from a more permanent file. lwgv is currently used in many different applications, from whole genome browsers to single-gene RNAi design visualization, demonstrating its applicability in a large variety of contexts and scales. Conclusion lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses in their chromosomal context. It is particularly suited for applications ranging from short sequences to medium-sized genomes when the creation and maintenance of a large software and database infrastructure is not necessary or desired. PMID:17877794

Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.

PubMed

Faith, Jeremiah J; Olson, Andrew J; Gardner, Timothy S; Sachidanandam, Ravi

2007-09-18

Lightweight genome viewer (lwgv) is a web-based tool for visualization of sequence annotations in their chromosomal context. It performs most of the functions of larger genome browsers, while relying on standard flat-file formats and bypassing the database needs of most visualization tools. Visualization as an aide to discovery requires display of novel data in conjunction with static annotations in their chromosomal context. With database-based systems, displaying dynamic results requires temporary tables that need to be tracked for removal. lwgv simplifies the visualization of user-generated results on a local computer. The dynamic results of these analyses are written to transient files, which can import static content from a more permanent file. lwgv is currently used in many different applications, from whole genome browsers to single-gene RNAi design visualization, demonstrating its applicability in a large variety of contexts and scales. lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses in their chromosomal context. It is particularly suited for applications ranging from short sequences to medium-sized genomes when the creation and maintenance of a large software and database infrastructure is not necessary or desired.

GAIA virtual observatory - development and practices

NASA Astrophysics Data System (ADS)

Syrjäsuo, Mikko; Marple, Steve

2010-05-01

The Global Auroral Imaging Access, or GAIA, is a virtual observatory providing quick access to summary data from satellite and ground-based instruments that remote sense auroral precipitation (http://gaia-vxo.org). This web-based service facilitates locating data relevant to particular events by simultaneously displaying summary images from various data sets around the world. At the moment, there are GAIA server nodes in Canada, Finland, Norway and the UK. The development is an international effort and the software and metadata are freely available. The GAIA system is based on a relational database which is queried by a dedicated software suite that also creates the graphical end-user interface if such is needed. Most commonly, the virtual observatory is used interactively by using a web browser: the user provides the date and the type of data of interest. As the summary data from multiple instruments are displayed simultaneously, the user can conveniently explore the recorded data. The virtual observatory provides essentially instant access to the images originating from all major auroral instrument networks including THEMIS, NORSTAR, GLORIA and MIRACLE. The scientific, educational and outreach use is limited by creativity rather than access. The first version of the GAIA was developed at the University of Calgary (Alberta, Canada) in 2004-2005. This proof-of-concept included mainly THEMIS and MIRACLE data, which comprised of millions of summary plots and thumbnail images. However, it was soon realised that a complete re-design was necessary to increase flexibility. In the presentation, we will discuss the early history and motivation of GAIA as well as how the development continued towards the current version. The emphasis will be on practical problems and their solutions. Relevant design choices will also be highlighted.

Research on phone contacts online status based on mobile cloud computing

NASA Astrophysics Data System (ADS)

Wang, Wen-jinga; Ge, Weib

2013-03-01

Because the limited ability of storage space, CPU processing on mobile phone, it is difficult to realize complex applications on mobile phones, but along with the development of cloud computing, we can place the computing and storage in the clouds, provide users with rich cloud services, helping users complete various function through the browser has become the trend for future mobile communication. This article is taking the mobile phone contacts online status as an example to analysis the development and application of mobile cloud computing.

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

PubMed Central

2012-01-01

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

Starting Over: Current Issues in Online Catalog User Interface Design.

ERIC Educational Resources Information Center

Crawford, Walt

1992-01-01

Discussion of online catalogs focuses on issues in interface design. Issues addressed include understanding the user base; common user access (CUA) with personal computers; common command language (CCL); hyperlinks; screen design issues; differences from card catalogs; indexes; graphic user interfaces (GUIs); color; online help; and remote users.…

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

ERIC Educational Resources Information Center

Zorn, Margaret; Marshall, Lucy

1995-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

STEREO In-situ Data Analysis

NASA Astrophysics Data System (ADS)

Schroeder, P. C.; Luhmann, J. G.; Davis, A. J.; Russell, C. T.

2007-05-01

STEREO's IMPACT (In-situ Measurements of Particles and CME Transients) investigation provides the first opportunity for long duration, detailed observations of 1 AU magnetic field structures, plasma and suprathermal electrons, and energetic particles at points bracketing Earth's heliospheric location. The PLASTIC instrument takes plasma ion composition measurements completing STEREO's comprehensive in-situ perspective. Stereoscopic/3D information from the STEREO SECCHI imagers and SWAVES radio experiment make it possible to use both multipoint and quadrature studies to connect interplanetary Coronal Mass Ejections (ICME) and solar wind structures to CMEs and coronal holes observed at the Sun. The uniqueness of the STEREO mission requires novel data analysis tools and techniques to take advantage of the mission's full scientific potential. An interactive browser with the ability to create publication-quality plots has been developed which integrates STEREO's in-situ data with data from a variety of other missions including WIND and ACE. Static summary plots and a key-parameter type data set with a related online browser provide alternative data access. Finally, an application program interface (API) is provided allowing users to create custom software that ties directly into STEREO's data set. The API allows for more advanced forms of data mining than currently available through most web-based data services. A variety of data access techniques and the development of cross- spacecraft data analysis tools allow the larger scientific community to combine STEREO's unique in-situ data with those of other missions, particularly the L1 missions, and, therefore, to maximize STEREO's scientific potential in gaining a greater understanding of the heliosphere.

CruiseViewer: SIOExplorer Graphical Interface to Metadata and Archives.

NASA Astrophysics Data System (ADS)

Sutton, D. W.; Helly, J. J.; Miller, S. P.; Chase, A.; Clark, D.

2002-12-01

We are introducing "CruiseViewer" as a prototype graphical interface for the SIOExplorer digital library project, part of the overall NSF National Science Digital Library (NSDL) effort. When complete, CruiseViewer will provide access to nearly 800 cruises, as well as 100 years of documents and images from the archives of the Scripps Institution of Oceanography (SIO). The project emphasizes data object accessibility, a rich metadata format, efficient uploading methods and interoperability with other digital libraries. The primary function of CruiseViewer is to provide a human interface to the metadata database and to storage systems filled with archival data. The system schema is based on the concept of an "arbitrary digital object" (ADO). Arbitrary in that if the object can be stored on a computer system then SIOExplore can manage it. Common examples are a multibeam swath bathymetry file, a .pdf cruise report, or a tar file containing all the processing scripts used on a cruise. We require a metadata file for every ADO in an ascii "metadata interchange format" (MIF), which has proven to be highly useful for operability and extensibility. Bulk ADO storage is managed using the Storage Resource Broker, SRB, data handling middleware developed at the San Diego Supercomputer Center that centralizes management and access to distributed storage devices. MIF metadata are harvested from several sources and housed in a relational (Oracle) database. For CruiseViewer, cgi scripts resident on an Apache server are the primary communication and service request handling tools. Along with the CruiseViewer java application, users can query, access and download objects via a separate method that operates through standard web browsers, http://sioexplorer.ucsd.edu. Both provide the functionability to query and view object metadata, and select and download ADOs. For the CruiseViewer application Java 2D is used to add a geo-referencing feature that allows users to select basemap images and have vector shapes representing query results mapped over the basemap in the image panel. The two methods together address a wide range of user access needs and will allow for widespread use of SIOExplorer.

Trajectory Browser Website

NASA Technical Reports Server (NTRS)

Foster, Cyrus; Jaroux, Belgacem A.

2012-01-01

The Trajectory Browser is a web-based tool developed at the NASA Ames Research Center to be used for the preliminary assessment of trajectories to small-bodies and planets and for providing relevant launch date, time-of-flight and V requirements. The site hosts a database of transfer trajectories from Earth to asteroids and planets for various types of missions such as rendezvous, sample return or flybys. A search engine allows the user to find trajectories meeting desired constraints on the launch window, mission duration and delta V capability, while a trajectory viewer tool allows the visualization of the heliocentric trajectory and the detailed mission itinerary. The anticipated user base of this tool consists primarily of scientists and engineers designing interplanetary missions in the context of pre-phase A studies, particularly for performing accessibility surveys to large populations of small-bodies. The educational potential of the website is also recognized for academia and the public with regards to trajectory design, a field that has generally been poorly understood by the public. The website is currently hosted on NASA-internal URL http://trajbrowser.arc.nasa.gov/ with plans for a public release as soon as development is complete.

On-demand server-side image processing for web-based DICOM image display

NASA Astrophysics Data System (ADS)

Sakusabe, Takaya; Kimura, Michio; Onogi, Yuzo

2000-04-01

Low cost image delivery is needed in modern networked hospitals. If a hospital has hundreds of clients, cost of client systems is a big problem. Naturally, a Web-based system is the most effective solution. But a Web browser could not display medical images with certain image processing such as a lookup table transformation. We developed a Web-based medical image display system using Web browser and on-demand server-side image processing. All images displayed on a Web page are generated from DICOM files on a server, delivered on-demand. User interaction on the Web page is handled by a client-side scripting technology such as JavaScript. This combination makes a look-and-feel of an imaging workstation not only for its functionality but also for its speed. Real time update of images with tracing mouse motion is achieved on Web browser without any client-side image processing which may be done by client-side plug-in technology such as Java Applets or ActiveX. We tested performance of the system in three cases. Single client, small number of clients in a fast speed network, and large number of clients in a normal speed network. The result shows that there are very slight overhead for communication and very scalable in number of clients.

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

PubMed

Rademacher, Jens D M; Lippke, Sonia

2007-08-01

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

A radiology department intranet: development and applications.

PubMed

Willing, S J; Berland, L L

1999-01-01

An intranet is a "private Internet" that uses the protocols of the World Wide Web to share information resources within a company or with the company's business partners and clients. The hardware requirements for an intranet begin with a dedicated Web server permanently connected to the departmental network. The heart of a Web server is the hypertext transfer protocol (HTTP) service, which receives a page request from a client's browser and transmits the page back to the client. Although knowledge of hypertext markup language (HTML) is not essential for authoring a Web page, a working familiarity with HTML is useful, as is knowledge of programming and database management. Security can be ensured by using scripts to write information in hidden fields or by means of "cookies." Interfacing databases and database management systems with the Web server and conforming the user interface to HTML syntax can be achieved by means of the common gateway interface (CGI), Active Server Pages (ASP), or other methods. An intranet in a radiology department could include the following types of content: on-call schedules, work schedules and a calendar, a personnel directory, resident resources, memorandums and discussion groups, software for a radiology information system, and databases.

Reefgenomics.Org - a repository for marine genomics data.

PubMed

Liew, Yi Jin; Aranda, Manuel; Voolstra, Christian R

2016-01-01

Over the last decade, technological advancements have substantially decreased the cost and time of obtaining large amounts of sequencing data. Paired with the exponentially increased computing power, individual labs are now able to sequence genomes or transcriptomes to investigate biological questions of interest. This has led to a significant increase in available sequence data. Although the bulk of data published in articles are stored in public sequence databases, very often, only raw sequencing data are available; miscellaneous data such as assembled transcriptomes, genome annotations etc. are not easily obtainable through the same means. Here, we introduce our website (http://reefgenomics.org) that aims to centralize genomic and transcriptomic data from marine organisms. Besides providing convenient means to download sequences, we provide (where applicable) a genome browser to explore available genomic features, and a BLAST interface to search through the hosted sequences. Through the interface, multiple datasets can be queried simultaneously, allowing for the retrieval of matching sequences from organisms of interest. The minimalistic, no-frills interface reduces visual clutter, making it convenient for end-users to search and explore processed sequence data. DATABASE URL: http://reefgenomics.org. © The Author(s) 2016. Published by Oxford University Press.

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.

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

A web-based solution for 3D medical image visualization

NASA Astrophysics Data System (ADS)

Hou, Xiaoshuai; Sun, Jianyong; Zhang, Jianguo

2015-03-01

In this presentation, we present a web-based 3D medical image visualization solution which enables interactive large medical image data processing and visualization over the web platform. To improve the efficiency of our solution, we adopt GPU accelerated techniques to process images on the server side while rapidly transferring images to the HTML5 supported web browser on the client side. Compared to traditional local visualization solution, our solution doesn't require the users to install extra software or download the whole volume dataset from PACS server. By designing this web-based solution, it is feasible for users to access the 3D medical image visualization service wherever the internet is available.

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2014-01-01

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

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

PubMed

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

2015-01-01

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

Application of interactive motion charts for displaying liver transplantation data in public websites.

PubMed

Santori, G

2014-09-01

In the past several years a vast amount of digital information has become available in every field of science, and ideas to apply improved strategies for obtaining a more in-depth knowledge of the data are considered in many areas. Although several American and European organizations show regularly in their public websites the aggregated results of organ donation and transplantation, no tools are provided to engage with the final users and to enable them to handle these data. In this study, a new model of Web-based interactive motion charts was applied to aggregated liver transplantation data obtained from a consecutive 28-year series of liver transplantation performed in a single Italian center. The interactive charts were obtained by combining the Google visualization application programming interface and the googleVis package within the open source statistical environment R. The interactive charts may be embedded into online/offline Web pages and rendered in each common browser. The users may interact with the charts by selecting chart type (bubble, bar, or line chart), x- and y-axis scales (linear or logarithmic), variables, bubble size, color, and even changing opacity of unselected items. Moreover, the charts may dynamically display the trend over time of each continuous/categoric variable, allowing users both to trace how the lines changes over time and to control the animation speed. The interactive motion charts should be used in the public websites that manage aggregated data concerning organ donation and transplantation. Copyright © 2014 Elsevier Inc. All rights reserved.

Developing A Web-based User Interface for Semantic Information Retrieval

NASA Technical Reports Server (NTRS)

Berrios, Daniel C.; Keller, Richard M.

2003-01-01

While there are now a number of languages and frameworks that enable computer-based systems to search stored data semantically, the optimal design for effective user interfaces for such systems is still uncle ar. Such interfaces should mask unnecessary query detail from users, yet still allow them to build queries of arbitrary complexity without significant restrictions. We developed a user interface supporting s emantic query generation for Semanticorganizer, a tool used by scient ists and engineers at NASA to construct networks of knowledge and dat a. Through this interface users can select node types, node attribute s and node links to build ad-hoc semantic queries for searching the S emanticOrganizer network.

SNPversity: a web-based tool for visualizing diversity

PubMed Central

Schott, David A; Vinnakota, Abhinav G; Portwood, John L; Andorf, Carson M

2018-01-01

Abstract Many stand-alone desktop software suites exist to visualize single nucleotide polymorphism (SNP) diversity, but web-based software that can be easily implemented and used for biological databases is absent. SNPversity was created to answer this need by building an open-source visualization tool that can be implemented on a Unix-like machine and served through a web browser that can be accessible worldwide. SNPversity consists of a HDF5 database back-end for SNPs, a data exchange layer powered by TASSEL libraries that represent data in JSON format, and an interface layer using PHP to visualize SNP information. SNPversity displays data in real-time through a web browser in grids that are color-coded according to a given SNP’s allelic status and mutational state. SNPversity is currently available at MaizeGDB, the maize community’s database, and will be soon available at GrainGenes, the clade-oriented database for Triticeae and Avena species, including wheat, barley, rye, and oat. The code and documentation are uploaded onto github, and they are freely available to the public. We expect that the tool will be highly useful for other biological databases with a similar need to display SNP diversity through their web interfaces. Database URL: https://www.maizegdb.org/snpversity PMID:29688387

Optimization of knowledge sharing through multi-forum using cloud computing architecture

NASA Astrophysics Data System (ADS)

Madapusi Vasudevan, Sriram; Sankaran, Srivatsan; Muthuswamy, Shanmugasundaram; Ram, N. Sankar

2011-12-01

Knowledge sharing is done through various knowledge sharing forums which requires multiple logins through multiple browser instances. Here a single Multi-Forum knowledge sharing concept is introduced which requires only one login session which makes user to connect multiple forums and display the data in a single browser window. Also few optimization techniques are introduced here to speed up the access time using cloud computing architecture.

The new Planetary Science Archive: A tool for exploration and discovery of scientific datasets from ESA's planetary missions

NASA Astrophysics Data System (ADS)

Heather, David

2016-07-01

Introduction: The Planetary Science Archive (PSA) is the European Space Agency's (ESA) repository of science data from all planetary science and exploration missions. The PSA provides access to scientific datasets through various interfaces (e.g. FTP browser, Map based, Advanced search, and Machine interface): http://archives.esac.esa.int/psa All datasets are scientifically peer-reviewed by independent scientists, and are compliant with the Planetary Data System (PDS) standards. Updating the PSA: The PSA is currently implementing a number of significant changes, both to its web-based interface to the scientific community, and to its database structure. The new PSA will be up-to-date with versions 3 and 4 of the PDS standards, as PDS4 will be used for ESA's upcoming ExoMars and BepiColombo missions. The newly designed PSA homepage will provide direct access to scientific datasets via a text search for targets or missions. This will significantly reduce the complexity for users to find their data and will promote one-click access to the datasets. Additionally, the homepage will provide direct access to advanced views and searches of the datasets. Users will have direct access to documentation, information and tools that are relevant to the scientific use of the dataset, including ancillary datasets, Software Interface Specification (SIS) documents, and any tools/help that the PSA team can provide. A login mechanism will provide additional functionalities to the users to aid / ease their searches (e.g. saving queries, managing default views). Queries to the PSA database will be possible either via the homepage (for simple searches of missions or targets), or through a filter menu for more tailored queries. The filter menu will offer multiple options to search for a particular dataset or product, and will manage queries for both in-situ and remote sensing instruments. Parameters such as start-time, phase angle, and heliocentric distance will be emphasized. A further advanced search function will allow users to query all the metadata present in the PSA database. Results will be displayed in 3 different ways: 1) A table listing all the corresponding data matching the criteria in the filter menu, 2) a projection of the products onto the surface of the object when applicable (i.e. planets, small bodies), and 3) a list of images for the relevant instruments to enjoy the beauty of our Solar System. These different ways of viewing the datasets will ensure that scientists and non-professionals alike will have access to the specific data they are looking for, regardless of their background. Conclusions: The new PSA will maintain the various interfaces and services it had in the past, and will include significant improvements designed to allow easier and more effective access to the scientific data and supporting materials. The new PSA is expected to be released by mid-2016. It will support the past, present and future missions, ancillary datasets, and will enhance the scientific output of ESA's missions. As such, the PSA will become a unique archive ensuring the long-term preservation and usage of scientific datasets together with user-friendly access.

The new Planetary Science Archive: A tool for exploration and discovery of scientific datasets from ESA's planetary missions.

NASA Astrophysics Data System (ADS)

Heather, David; Besse, Sebastien; Barbarisi, Isa; Arviset, Christophe; de Marchi, Guido; Barthelemy, Maud; Docasal, Ruben; Fraga, Diego; Grotheer, Emmanuel; Lim, Tanya; Macfarlane, Alan; Martinez, Santa; Rios, Carlos

2016-04-01

Introduction: The Planetary Science Archive (PSA) is the European Space Agency's (ESA) repository of science data from all planetary science and exploration missions. The PSA provides access to scientific datasets through various interfaces (e.g. FTP browser, Map based, Advanced search, and Machine interface): http://archives.esac.esa.int/psa All datasets are scientifically peer-reviewed by independent scientists, and are compliant with the Planetary Data System (PDS) standards. Updating the PSA: The PSA is currently implementing a number of significant changes, both to its web-based interface to the scientific community, and to its database structure. The new PSA will be up-to-date with versions 3 and 4 of the PDS standards, as PDS4 will be used for ESA's upcoming ExoMars and BepiColombo missions. The newly designed PSA homepage will provide direct access to scientific datasets via a text search for targets or missions. This will significantly reduce the complexity for users to find their data and will promote one-click access to the datasets. Additionally, the homepage will provide direct access to advanced views and searches of the datasets. Users will have direct access to documentation, information and tools that are relevant to the scientific use of the dataset, including ancillary datasets, Software Interface Specification (SIS) documents, and any tools/help that the PSA team can provide. A login mechanism will provide additional functionalities to the users to aid / ease their searches (e.g. saving queries, managing default views). Queries to the PSA database will be possible either via the homepage (for simple searches of missions or targets), or through a filter menu for more tailored queries. The filter menu will offer multiple options to search for a particular dataset or product, and will manage queries for both in-situ and remote sensing instruments. Parameters such as start-time, phase angle, and heliocentric distance will be emphasized. A further advanced search function will allow users to query all the metadata present in the PSA database. Results will be displayed in 3 different ways: 1) A table listing all the corresponding data matching the criteria in the filter menu, 2) a projection of the products onto the surface of the object when applicable (i.e. planets, small bodies), and 3) a list of images for the relevant instruments to enjoy the beauty of our Solar System. These different ways of viewing the datasets will ensure that scientists and non-professionals alike will have access to the specific data they are looking for, regardless of their background. Conclusions: The new PSA will maintain the various interfaces and services it had in the past, and will include significant improvements designed to allow easier and more effective access to the scientific data and supporting materials. The new PSA is expected to be released by mid-2016. It will support the past, present and future missions, ancillary datasets, and will enhance the scientific output of ESA's missions. As such, the PSA will become a unique archive ensuring the long-term preservation and usage of scientific datasets together with user-friendly access.

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.

Developing a distributed HTML5-based search engine for geospatial resource discovery

NASA Astrophysics Data System (ADS)

ZHOU, N.; XIA, J.; Nebert, D.; Yang, C.; Gui, Z.; Liu, K.

2013-12-01

With explosive growth of data, Geospatial Cyberinfrastructure(GCI) components are developed to manage geospatial resources, such as data discovery and data publishing. However, the efficiency of geospatial resources discovery is still challenging in that: (1) existing GCIs are usually developed for users of specific domains. Users may have to visit a number of GCIs to find appropriate resources; (2) The complexity of decentralized network environment usually results in slow response and pool user experience; (3) Users who use different browsers and devices may have very different user experiences because of the diversity of front-end platforms (e.g. Silverlight, Flash or HTML). To address these issues, we developed a distributed and HTML5-based search engine. Specifically, (1)the search engine adopts a brokering approach to retrieve geospatial metadata from various and distributed GCIs; (2) the asynchronous record retrieval mode enhances the search performance and user interactivity; (3) the search engine based on HTML5 is able to provide unified access capabilities for users with different devices (e.g. tablet and smartphone).

Application of open source standards and technologies in the http://climate4impact.eu/ portal

NASA Astrophysics Data System (ADS)

Plieger, Maarten; Som de Cerff, Wim; Pagé, Christian; Tatarinova, Natalia

2015-04-01

This presentation will demonstrate how to calculate and visualize the climate indice SU (number of summer days) on the climate4impact portal. The following topics will be covered during the demonstration: - Security: Login using OpenID for access to the Earth System Grid Fedeation (ESGF) data nodes. The ESGF works in conjunction with several external websites and systems. The climate4impact portal uses X509 based short lived credentials, generated on behalf of the user with a MyProxy service. Single Sign-on (SSO) is used to make these websites and systems work together. - Discovery: Facetted search based on e.g. variable name, model and institute using the ESGF search services. A catalog browser allows for browsing through CMIP5 and any other climate model data catalogues (e.g. ESSENCE, EOBS, UNIDATA). - Processing using Web Processing Services (WPS): Transform data, subset, export into other formats, and perform climate indices calculations using Web Processing Services implemented by PyWPS, based on NCAR NCPP OpenClimateGIS and IS-ENES2 ICCLIM. - Visualization using Web Map Services (WMS): Visualize data from ESGF data nodes using ADAGUC Web Map Services. The aim of climate4impact is to enhance the use of Climate Research Data and to enhance the interaction with climate effect/impact communities. The portal is based on 21 impact use cases from 5 different European countries, and is evaluated by a user panel consisting of use case owners. It has been developed within the European projects IS-ENES and IS-ENES2 for more than 5 years, and its development currently continues within IS-ENES2 and CLIPC. As the climate impact community is very broad, the focus is mainly on the scientific impact community. This work has resulted in the ENES portal interface for climate impact communities and can be visited at http://climate4impact.eu/ The current main objectives for climate4impact can be summarized in two objectives. The first one is to work on a web interface which automatically generates a graphical user interface on WPS endpoints. The WPS calculates climate indices and subset data using OpenClimateGIS/ICCLIM on data stored in ESGF data nodes. Data is then transmitted from ESGF nodes over secured OpenDAP and becomes available in a new, per user, secured OpenDAP server. The results can then be visualized again using ADAGUC WMS. Dedicated wizards for processing of climate indices will be developed in close collaboration with users. The second one is to expose climate4impact services, so as to offer standardized services which can be used by other portals. This has the advantage to add interoperability between several portals, as well as to enable the design of specific portals aimed at different impact communities, either thematic or national, for example.

Standards for the user interface - Developing a user consensus. [for Space Station Information System

NASA Technical Reports Server (NTRS)

Moe, Karen L.; Perkins, Dorothy C.; Szczur, Martha R.

1987-01-01

The user support environment (USE) which is a set of software tools for a flexible standard interactive user interface to the Space Station systems, platforms, and payloads is described in detail. Included in the USE concept are a user interface language, a run time environment and user interface management system, support tools, and standards for human interaction methods. The goals and challenges of the USE are discussed as well as a methodology based on prototype demonstrations for involving users in the process of validating the USE concepts. By prototyping the key concepts and salient features of the proposed user interface standards, the user's ability to respond is greatly enhanced.

VRML and Collaborative Environments: New Tools for Networked Visualization

NASA Astrophysics Data System (ADS)

Crutcher, R. M.; Plante, R. L.; Rajlich, P.

We present two new applications that engage the network as a tool for astronomical research and/or education. The first is a VRML server which allows users over the Web to interactively create three-dimensional visualizations of FITS images contained in the NCSA Astronomy Digital Image Library (ADIL). The server's Web interface allows users to select images from the ADIL, fill in processing parameters, and create renderings featuring isosurfaces, slices, contours, and annotations; the often extensive computations are carried out on an NCSA SGI supercomputer server without the user having an individual account on the system. The user can then download the 3D visualizations as VRML files, which may be rotated and manipulated locally on virtually any class of computer. The second application is the ADILBrowser, a part of the NCSA Horizon Image Data Browser Java package. ADILBrowser allows a group of participants to browse images from the ADIL within a collaborative session. The collaborative environment is provided by the NCSA Habanero package which includes text and audio chat tools and a white board. The ADILBrowser is just an example of a collaborative tool that can be built with the Horizon and Habanero packages. The classes provided by these packages can be assembled to create custom collaborative applications that visualize data either from local disk or from anywhere on the network.

PrimerMapper: high throughput primer design and graphical assembly for PCR and SNP detection

PubMed Central

O’Halloran, Damien M.

2016-01-01

Primer design represents a widely employed gambit in diverse molecular applications including PCR, sequencing, and probe hybridization. Variations of PCR, including primer walking, allele-specific PCR, and nested PCR provide specialized validation and detection protocols for molecular analyses that often require screening large numbers of DNA fragments. In these cases, automated sequence retrieval and processing become important features, and furthermore, a graphic that provides the user with a visual guide to the distribution of designed primers across targets is most helpful in quickly ascertaining primer coverage. To this end, I describe here, PrimerMapper, which provides a comprehensive graphical user interface that designs robust primers from any number of inputted sequences while providing the user with both, graphical maps of primer distribution for each inputted sequence, and also a global assembled map of all inputted sequences with designed primers. PrimerMapper also enables the visualization of graphical maps within a browser and allows the user to draw new primers directly onto the webpage. Other features of PrimerMapper include allele-specific design features for SNP genotyping, a remote BLAST window to NCBI databases, and remote sequence retrieval from GenBank and dbSNP. PrimerMapper is hosted at GitHub and freely available without restriction. PMID:26853558

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

Vang, Leng; Prescott, Steven R; Smith, Curtis

In collaborating scientific research arena it is important to have an environment where analysts have access to a shared of information documents, software tools and be able to accurately maintain and track historical changes in models. A new cloud-based environment would be accessible remotely from anywhere regardless of computing platforms given that the platform has available of Internet access and proper browser capabilities. Information stored at this environment would be restricted based on user assigned credentials. This report reviews development of a Cloud-based Architecture Capabilities (CAC) as a web portal for PRA tools.

Engineering Analysis Using a Web-based Protocol

NASA Technical Reports Server (NTRS)

Schoeffler, James D.; Claus, Russell W.

2002-01-01

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

A method of designing smartphone interface based on the extended user's mental model

NASA Astrophysics Data System (ADS)

Zhao, Wei; Li, Fengmin; Bian, Jiali; Pan, Juchen; Song, Song

2017-01-01

The user's mental model is the core guiding theory of product design, especially practical products. The essence of practical product is a tool which is used by users to meet their needs. Then, the most important feature of a tool is usability. The design method based on the user's mental model provides a series of practical and feasible theoretical guidance for improving the usability of the product according to the user's awareness of things. In this paper, we propose a method of designing smartphone interface based on the extended user's mental model according to further research on user groups. This approach achieves personalized customization of smartphone application interface and enhance application using efficiency.

World Wide Web Metaphors for Search Mission Data

NASA Technical Reports Server (NTRS)

Norris, Jeffrey S.; Wallick, Michael N.; Joswig, Joseph C.; Powell, Mark W.; Torres, Recaredo J.; Mittman, David S.; Abramyan, Lucy; Crockett, Thomas M.; Shams, Khawaja S.; Fox, Jason M.;

KMeyeDB: a graphical database of mutations in genes that cause eye diseases.

PubMed

Kawamura, Takashi; Ohtsubo, Masafumi; Mitsuyama, Susumu; Ohno-Nakamura, Saho; Shimizu, Nobuyoshi; Minoshima, Shinsei

2010-06-01

KMeyeDB (http://mutview.dmb.med.keio.ac.jp/) is a database of human gene mutations that cause eye diseases. We have substantially enriched the amount of data in the database, which now contains information about the mutations of 167 human genes causing eye-related diseases including retinitis pigmentosa, cone-rod dystrophy, night blindness, Oguchi disease, Stargardt disease, macular degeneration, Leber congenital amaurosis, corneal dystrophy, cataract, glaucoma, retinoblastoma, Bardet-Biedl syndrome, and Usher syndrome. KMeyeDB is operated using the database software MutationView, which deals with various characters of mutations, gene structure, protein functional domains, and polymerase chain reaction (PCR) primers, as well as clinical data for each case. Users can access the database using an ordinary Internet browser with smooth user-interface, without user registration. The results are displayed on the graphical windows together with statistical calculations. All mutations and associated data have been collected from published articles. Careful data analysis with KMeyeDB revealed many interesting features regarding the mutations in 167 genes that cause 326 different types of eye diseases. Some genes are involved in multiple types of eye diseases, whereas several eye diseases are caused by different mutations in one gene.

Gramene 2016: comparative plant genomics and pathway resources.

PubMed

Tello-Ruiz, Marcela K; Stein, Joshua; Wei, Sharon; Preece, Justin; Olson, Andrew; Naithani, Sushma; Amarasinghe, Vindhya; Dharmawardhana, Palitha; Jiao, Yinping; Mulvaney, Joseph; Kumari, Sunita; Chougule, Kapeel; Elser, Justin; Wang, Bo; Thomason, James; Bolser, Daniel M; Kerhornou, Arnaud; Walts, Brandon; Fonseca, Nuno A; Huerta, Laura; Keays, Maria; Tang, Y Amy; Parkinson, Helen; Fabregat, Antonio; McKay, Sheldon; Weiser, Joel; D'Eustachio, Peter; Stein, Lincoln; Petryszak, Robert; Kersey, Paul J; Jaiswal, Pankaj; Ware, Doreen

2016-01-04

Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The genomes section features 39 fully assembled reference genomes that are integrated using ontology-based annotation and comparative analyses, and accessed through both visual and programmatic interfaces. Additional community data, such as genetic variation, expression and methylation, are also mapped for a subset of genomes. The Plant Reactome pathway portal (http://plantreactome.gramene.org) provides a reference resource for analyzing plant metabolic and regulatory pathways. In addition to ∼ 200 curated rice reference pathways, the portal hosts gene homology-based pathway projections for 33 plant species. Both the genome and pathway browsers interface with the EMBL-EBI's Expression Atlas to enable the projection of baseline and differential expression data from curated expression studies in plants. Gramene's archive website (http://archive.gramene.org) continues to provide previously reported resources on comparative maps, markers and QTL. To further aid our users, we have also introduced a live monthly educational webinar series and a Gramene YouTube channel carrying video tutorials. Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Securing a web-based teleradiology platform according to German law and "best practices".

PubMed

Spitzer, Michael; Ullrich, Tobias; Ueckert, Frank

2009-01-01

The Medical Data and Picture Exchange platform (MDPE), as a teleradiology system, facilitates the exchange of digital medical imaging data among authorized users. It features extensive support of the DICOM standard including networking functions. Since MDPE is designed as a web service, security and confidentiality of data and communication pose an outstanding challenge. To comply with demands of German laws and authorities, a generic data security concept considered as "best practice" in German health telematics was adapted to the specific demands of MDPE. The concept features strict logical and physical separation of diagnostic and identity data and thus an all-encompassing pseudonymization throughout the system. Hence, data may only be merged at authorized clients. MDPE's solution of merging data from separate sources within a web browser avoids technically questionable techniques such as deliberate cross-site scripting. Instead, data is merged dynamically by JavaScriptlets running in the user's browser. These scriptlets are provided by one server, while content and method calls are generated by another server. Additionally, MDPE uses encrypted temporary IDs for communication and merging of data.

Interactive Radiology teaching file system: the development of a MIRC-compliant and user-centered e-learning resource.

PubMed

dos-Santos, M; Fujino, A

2012-01-01

Radiology teaching usually employs a systematic and comprehensive set of medical images and related information. Databases with representative radiological images and documents are highly desirable and widely used in Radiology teaching programs. Currently, computer-based teaching file systems are widely used in Medicine and Radiology teaching as an educational resource. This work addresses a user-centered radiology electronic teaching file system as an instance of MIRC compliant medical image database. Such as a digital library, the clinical cases are available to access by using a web browser. The system has offered great opportunities to some Radiology residents interact with experts. This has been done by applying user-centered techniques and creating usage context-based tools in order to make available an interactive system.

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

PubMed

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

2016-12-01

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

A Visual Editor in Java for View

NASA Technical Reports Server (NTRS)

Stansifer, Ryan

2000-01-01

In this project we continued the development of a visual editor in the Java programming language to create screens on which to display real-time data. The data comes from the numerous systems monitoring the operation of the space shuttle while on the ground and in space, and from the many tests of subsystems. The data can be displayed on any computer platform running a Java-enabled World Wide Web (WWW) browser and connected to the Internet. Previously a special-purpose program bad been written to display data on emulations of character-based display screens used for many years at NASA. The goal now is to display bit-mapped screens created by a visual editor. We report here on the visual editor that creates the display screens. This project continues the work we bad done previously. Previously we had followed the design of the 'beanbox,' a prototype visual editor created by Sun Microsystems. We abandoned this approach and implemented a prototype using a more direct approach. In addition, our prototype is based on newly released Java 2 graphical user interface (GUI) libraries. The result has been a visually more appealing appearance and a more robust application.

Developing cloud applications using the e-Science Central platform.

PubMed

Hiden, Hugo; Woodman, Simon; Watson, Paul; Cala, Jacek

2013-01-28

This paper describes the e-Science Central (e-SC) cloud data processing system and its application to a number of e-Science projects. e-SC provides both software as a service (SaaS) and platform as a service for scientific data management, analysis and collaboration. It is a portable system and can be deployed on both private (e.g. Eucalyptus) and public clouds (Amazon AWS and Microsoft Windows Azure). The SaaS application allows scientists to upload data, edit and run workflows and share results in the cloud, using only a Web browser. It is underpinned by a scalable cloud platform consisting of a set of components designed to support the needs of scientists. The platform is exposed to developers so that they can easily upload their own analysis services into the system and make these available to other users. A representational state transfer-based application programming interface (API) is also provided so that external applications can leverage the platform's functionality, making it easier to build scalable, secure cloud-based applications. This paper describes the design of e-SC, its API and its use in three different case studies: spectral data visualization, medical data capture and analysis, and chemical property prediction.

Developing cloud applications using the e-Science Central platform

PubMed Central

Hiden, Hugo; Woodman, Simon; Watson, Paul; Cala, Jacek

2013-01-01

This paper describes the e-Science Central (e-SC) cloud data processing system and its application to a number of e-Science projects. e-SC provides both software as a service (SaaS) and platform as a service for scientific data management, analysis and collaboration. It is a portable system and can be deployed on both private (e.g. Eucalyptus) and public clouds (Amazon AWS and Microsoft Windows Azure). The SaaS application allows scientists to upload data, edit and run workflows and share results in the cloud, using only a Web browser. It is underpinned by a scalable cloud platform consisting of a set of components designed to support the needs of scientists. The platform is exposed to developers so that they can easily upload their own analysis services into the system and make these available to other users. A representational state transfer-based application programming interface (API) is also provided so that external applications can leverage the platform's functionality, making it easier to build scalable, secure cloud-based applications. This paper describes the design of e-SC, its API and its use in three different case studies: spectral data visualization, medical data capture and analysis, and chemical property prediction. PMID:23230161

The IS-ENES climate4impact portal: bridging the CMIP5 and CORDEX data to impact users

NASA Astrophysics Data System (ADS)

Som de Cerff, Wim; Plieger, Maarten; Page, Christian; Tatarinova, Natalia; Hutjes, Ronald; de Jong, Fokke; Bärring, Lars; Sjökvist, Elin; Vega Saldarriaga, Manuel; Santiago Cofiño Gonzalez, Antonio

2015-04-01

The aim of climate4impact (climate4impact.eu) is to enhance the use of Climate Research Data and to enhance the interaction with climate effect/impact communities. The portal is based on 17 impact use cases from 5 different European countries, and is evaluated by a user panel consisting of use case owners. It has been developed within the IS-ENES European project and is currently operated and further developed in the IS ENES2 project. As the climate impact community is very broad, the focus is mainly on the scientific impact community. Climate4impact is connected to the Earth System Grid Federation (ESGF) nodes containing global climate model data (GCM data) from the fifth phase of the Coupled Model Intercomparison Project (CMIP5) and regional climate model data (RCM) data from the Coordinated Regional Climate Downscaling Experiment (CORDEX). This global network of climate model data centers offers services for data description, discovery and download. The climate4impact portal connects to these services using OpenID, and offers a user interface for searching, visualizing and downloading global climate model data and more. A challenging task is to describe the available model data and how it can be used. The portal informs users about possible caveats when using climate model data. All impact use cases are described in the documentation section, using highlighted keywords pointing to detailed information in the glossary. Climate4impact currently has two main objectives. The first one is to work on a web interface which automatically generates a graphical user interface on WPS endpoints. The WPS calculates climate indices and subset data using OpenClimateGIS/icclim on data stored in ESGF data nodes. Data is then transmitted from ESGF nodes over secured OpenDAP and becomes available in a new, per user, secured OpenDAP server. The results can then be visualized again using ADAGUC WMS. Dedicated wizards for processing of climate indices will be developed in close collaboration with users. The second one is to expose climate4impact services, so as to offer standardized services which can be used by other portals (like the future Copernicus platform, developed in the EU FP7 CLIPC project). This has the advantage to add interoperability between several portals, as well as to enable the design of specific portals aimed at different impact communities, either thematic or national. In the presentation the following subjects will be detailed: - Lessons learned developing climate4impact.eu - Download: Directly from ESGF nodes and other THREDDS catalogs - Connection with the downscaling portal of the university of Cantabria - Experiences on the question and answer site via Askbot - Visualization: Visualize data from ESGF data nodes using ADAGUC Web Map Services. - Processing: Transform data, subset, export into other formats, and perform climate indices calculations using Web Processing Services implemented by PyWPS, based on NCAR NCPP OpenClimateGIS and IS-ENES2 icclim. - Security: Login using OpenID for access to the ESGF data nodes. The ESGF works in conjunction with several external websites and systems. The climate4impact portal uses X509 based short lived credentials, generated on behalf of the user with a MyProxy service. Single Sign-on (SSO) is used to make these websites and systems work together. - Discovery: Facetted search based on e.g. variable name, model and institute using the ESGF search services. A catalog browser allows for browsing through CMIP5 and any other climate model data catalogues (e.g. ESSENCE, EOBS, UNIDATA).

GeoMapApp, Virtual Ocean, and other Free Data Resources for the 21st Century Classroom

NASA Astrophysics Data System (ADS)

Goodwillie, A. M.; Ryan, W.; Carbotte, S.; Melkonian, A.; Coplan, J.; Arko, R.; Ferrini, V.; O'Hara, S.; Leung, A.; Bonckzowski, J.

2008-12-01

With funding from the U.S. National Science Foundation, the Marine Geoscience Data System (MGDS) (http://www.marine-geo.org/) is developing GeoMapApp (http://www.geomapapp.org) - a computer application that provides wide-ranging map-based visualization and manipulation options for interdisciplinary geosciences research and education. The novelty comes from the use of this visual tool to discover and explore data, with seamless links to further discovery using traditional text-based approaches. Users can generate custom maps and grids and import their own data sets. Built-in functionality allows users to readily explore a broad suite of interactive data sets and interfaces. Examples include multi-resolution global digital models of topography, gravity, sediment thickness, and crustal ages; rock, fluid, biology and sediment sample information; research cruise underway geophysical and multibeam data; earthquake events; submersible dive photos of hydrothermal vents; geochemical analyses; DSDP/ODP core logs; seismic reflection profiles; contouring, shading, profiling of grids; and many more. On-line audio-visual tutorials lead users step-by-step through GeoMapApp functionality (http://www.geomapapp.org/tutorials/). Virtual Ocean (http://www.virtualocean.org/) integrates GeoMapApp with a 3-D earth browser based upon NASA WorldWind, providing yet more powerful capabilities. The searchable MGDS Media Bank (http://media.marine-geo.org/) supports viewing of remarkable images and video from the NSF Ridge 2000 and MARGINS programs. For users familiar with Google Earth (tm), KML files are available for viewing several MGDS data sets (http://www.marine-geo.org/education/kmls.php). Examples of accessing and manipulating a range of geoscience data sets from various NSF-funded programs will be shown. GeoMapApp, Virtual Ocean, the MGDS Media Bank and KML files are free MGDS data resources and work on any type of computer. They are currently used by educators, researchers, school teachers and the general public.

Managing multiple image stacks from confocal laser scanning microscopy

NASA Astrophysics Data System (ADS)

Zerbe, Joerg; Goetze, Christian H.; Zuschratter, Werner

1999-05-01

A major goal in neuroanatomy is to obtain precise information about the functional organization of neuronal assemblies and their interconnections. Therefore, the analysis of histological sections frequently requires high resolution images in combination with an overview about the structure. To overcome this conflict we have previously introduced a software for the automatic acquisition of multiple image stacks (3D-MISA) in confocal laser scanning microscopy. Here, we describe a Windows NT based software for fast and easy navigation through the multiple images stacks (MIS-browser), the visualization of individual channels and layers and the selection of user defined subregions. In addition, the MIS browser provides useful tools for the visualization and evaluation of the datavolume, as for instance brightness and contrast corrections of individual layers and channels. Moreover, it includes a maximum intensity projection, panning and zoom in/out functions within selected channels or focal planes (x/y) and tracking along the z-axis. The import module accepts any tiff-format and reconstructs the original image arrangement after the user has defined the sequence of images in x/y and z and the number of channels. The implemented export module allows storage of user defined subregions (new single image stacks) for further 3D-reconstruction and evaluation.

Intelligent retrieval of medical images from the Internet

NASA Astrophysics Data System (ADS)

Tang, Yau-Kuo; Chiang, Ted T.

1996-05-01

The object of this study is using Internet resources to provide a cost-effective, user-friendly method to access the medical image archive system and to provide an easy method for the user to identify the images required. This paper describes the prototype system architecture, the implementation, and results. In the study, we prototype the Intelligent Medical Image Retrieval (IMIR) system as a Hypertext Transport Prototype server and provide Hypertext Markup Language forms for user, as an Internet client, using browser to enter image retrieval criteria for review. We are developing the intelligent retrieval engine, with the capability to map the free text search criteria to the standard terminology used for medical image identification. We evaluate retrieved records based on the number of the free text entries matched and their relevance level to the standard terminology. We are in the integration and testing phase. We have collected only a few different types of images for testing and have trained a few phrases to map the free text to the standard medical terminology. Nevertheless, we are able to demonstrate the IMIR's ability to search, retrieve, and review medical images from the archives using general Internet browser. The prototype also uncovered potential problems in performance, security, and accuracy. Additional studies and enhancements will make the system clinically operational.

The annotation-enriched non-redundant patent sequence databases.

PubMed

Li, Weizhong; Kondratowicz, Bartosz; McWilliam, Hamish; Nauche, Stephane; Lopez, Rodrigo

2013-01-01

The EMBL-European Bioinformatics Institute (EMBL-EBI) offers public access to patent sequence data, providing a valuable service to the intellectual property and scientific communities. The non-redundant (NR) patent sequence databases comprise two-level nucleotide and protein sequence clusters (NRNL1, NRNL2, NRPL1 and NRPL2) based on sequence identity (level-1) and patent family (level-2). Annotation from the source entries in these databases is merged and enhanced with additional information from the patent literature and biological context. Corrections in patent publication numbers, kind-codes and patent equivalents significantly improve the data quality. Data are available through various user interfaces including web browser, downloads via FTP, SRS, Dbfetch and EBI-Search. Sequence similarity/homology searches against the databases are available using BLAST, FASTA and PSI-Search. In this article, we describe the data collection and annotation and also outline major changes and improvements introduced since 2009. Apart from data growth, these changes include additional annotation for singleton clusters, the identifier versioning for tracking entry change and the entry mappings between the two-level databases. Database URL: http://www.ebi.ac.uk/patentdata/nr/

The Annotation-enriched non-redundant patent sequence databases

PubMed Central

Li, Weizhong; Kondratowicz, Bartosz; McWilliam, Hamish; Nauche, Stephane; Lopez, Rodrigo

2013-01-01

The EMBL-European Bioinformatics Institute (EMBL-EBI) offers public access to patent sequence data, providing a valuable service to the intellectual property and scientific communities. The non-redundant (NR) patent sequence databases comprise two-level nucleotide and protein sequence clusters (NRNL1, NRNL2, NRPL1 and NRPL2) based on sequence identity (level-1) and patent family (level-2). Annotation from the source entries in these databases is merged and enhanced with additional information from the patent literature and biological context. Corrections in patent publication numbers, kind-codes and patent equivalents significantly improve the data quality. Data are available through various user interfaces including web browser, downloads via FTP, SRS, Dbfetch and EBI-Search. Sequence similarity/homology searches against the databases are available using BLAST, FASTA and PSI-Search. In this article, we describe the data collection and annotation and also outline major changes and improvements introduced since 2009. Apart from data growth, these changes include additional annotation for singleton clusters, the identifier versioning for tracking entry change and the entry mappings between the two-level databases. Database URL: http://www.ebi.ac.uk/patentdata/nr/ PMID:23396323