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

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.

plas.io: Open Source, Browser-based WebGL Point Cloud Visualization

NASA Astrophysics Data System (ADS)

Butler, H.; Finnegan, D. C.; Gadomski, P. J.; Verma, U. K.

2014-12-01

Point cloud data, in the form of Light Detection and Ranging (LiDAR), RADAR, or semi-global matching (SGM) image processing, are rapidly becoming a foundational data type to quantify and characterize geospatial processes. Visualization of these data, due to overall volume and irregular arrangement, is often difficult. Technological advancement in web browsers, in the form of WebGL and HTML5, have made interactivity and visualization capabilities ubiquitously available which once only existed in desktop software. plas.io is an open source JavaScript application that provides point cloud visualization, exploitation, and compression features in a web-browser platform, reducing the reliance for client-based desktop applications. The wide reach of WebGL and browser-based technologies mean plas.io's capabilities can be delivered to a diverse list of devices -- from phones and tablets to high-end workstations -- with very little custom software development. These properties make plas.io an ideal open platform for researchers and software developers to communicate visualizations of complex and rich point cloud data to devices to which everyone has easy access.

Worldwide Research, Worldwide Participation: Web-Based Test Logger

NASA Technical Reports Server (NTRS)

Clark, David A.

1998-01-01

Thanks to the World Wide Web, a new paradigm has been born. ESCORT (steady state data system) facilities can now be configured to use a Web-based test logger, enabling worldwide participation in tests. NASA Lewis Research Center's new Web-based test logger for ESCORT automatically writes selected test and facility parameters to a browser and allows researchers to insert comments. All data can be viewed in real time via Internet connections, so anyone with a Web browser and the correct URL (universal resource locator, or Web address) can interactively participate. As the test proceeds and ESCORT data are taken, Web browsers connected to the logger are updated automatically. The use of this logger has demonstrated several benefits. First, researchers are free from manual data entry and are able to focus more on the tests. Second, research logs can be printed in report format immediately after (or during) a test. And finally, all test information is readily available to an international public.

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

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-25

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

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.

A browser-based event display for the CMS experiment at the LHC

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

Hategan, M.; McCauley, T.; Nguyen, P.

2012-01-01

The line between native and web applications is becoming increasingly blurred as modern web browsers are becoming powerful platforms on which applications can be run. Such applications are trivial to install and are readily extensible and easy to use. In an educational setting, web applications permit a way to deploy deploy tools in a highly-restrictive computing environment. The I2U2 collaboration has developed a browser-based event display for viewing events in data collected and released to the public by the CMS experiment at the LHC. The application itself reads a JSON event format and uses the JavaScript 3D rendering engine pre3d.more » The only requirement is a modern browser using HTML5 canvas. The event display has been used by thousands of high school students in the context of programs organized by I2U2, QuarkNet, and IPPOG. This browser-based approach to display of events can have broader usage and impact for experts and public alike.« less

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.

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…

Avatar Web-Based Self-Report Survey System Technology for Public Health Research: Technical Outcome Results and Lessons Learned.

PubMed

Savel, Craig; Mierzwa, Stan; Gorbach, Pamina M; Souidi, Samir; Lally, Michelle; Zimet, Gregory; Interventions, Aids

2016-01-01

This paper reports on a specific Web-based self-report data collection system that was developed for a public health research study in the United States. Our focus is on technical outcome results and lessons learned that may be useful to other projects requiring such a solution. The system was accessible from any device that had a browser that supported HTML5. Report findings include: which hardware devices, Web browsers, and operating systems were used; the rate of survey completion; and key considerations for employing Web-based surveys in a clinical trial setting.

jsPsych: a JavaScript library for creating behavioral experiments in a Web browser.

PubMed

de Leeuw, Joshua R

2015-03-01

Online experiments are growing in popularity, and the increasing sophistication of Web technology has made it possible to run complex behavioral experiments online using only a Web browser. Unlike with offline laboratory experiments, however, few tools exist to aid in the development of browser-based experiments. This makes the process of creating an experiment slow and challenging, particularly for researchers who lack a Web development background. This article introduces jsPsych, a JavaScript library for the development of Web-based experiments. jsPsych formalizes a way of describing experiments that is much simpler than writing the entire experiment from scratch. jsPsych then executes these descriptions automatically, handling the flow from one task to another. The jsPsych library is open-source and designed to be expanded by the research community. The project is available online at www.jspsych.org .

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

PubMed Central

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

2009-01-01

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

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

PubMed

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

2009-10-01

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

Web Browser Trends and Technologies.

ERIC Educational Resources Information Center

Goodwin-Jones, Bob

2000-01-01

Discusses Web browsers and how their capabilities have been expanded, support for Web browsing on different devices (cell phones, palmtop computers, TV sets), and browser support for the next-generation Web authoring language, XML ("extensible markup language"). (Author/VWL)

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…

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

PubMed

Georgiev, Martin; Jana, Suman; Shmatikov, Vitaly

2014-02-01

Hybrid mobile applications (apps) combine the features of Web applications and "native" mobile apps. Like Web applications, they are implemented in portable, platform-independent languages such as HTML and JavaScript. Like native apps, they have direct access to local device resources-file system, location, camera, contacts, etc. Hybrid apps are typically developed using hybrid application frameworks such as PhoneGap. The purpose of the framework is twofold. First, it provides an embedded Web browser (for example, WebView on Android) that executes the app's Web code. Second, it supplies "bridges" that allow Web code to escape the browser and access local resources on the device. We analyze the software stack created by hybrid frameworks and demonstrate that it does not properly compose the access-control policies governing Web code and local code, respectively. Web code is governed by the same origin policy, whereas local code is governed by the access-control policy of the operating system (for example, user-granted permissions in Android). The bridges added by the framework to the browser have the same local access rights as the entire application, but are not correctly protected by the same origin policy. This opens the door to fracking attacks, which allow foreign-origin Web content included into a hybrid app (e.g., ads confined in iframes) to drill through the layers and directly access device resources. Fracking vulnerabilities are generic: they affect all hybrid frameworks, all embedded Web browsers, all bridge mechanisms, and all platforms on which these frameworks are deployed. We study the prevalence of fracking vulnerabilities in free Android apps based on the PhoneGap framework. Each vulnerability exposes sensitive local resources-the ability to read and write contacts list, local files, etc.-to dozens of potentially malicious Web domains. We also analyze the defenses deployed by hybrid frameworks to prevent resource access by foreign-origin Web content and explain why they are ineffectual. We then present NoFrak, a capability-based defense against fracking attacks. NoFrak is platform-independent, compatible with any framework and embedded browser, requires no changes to the code of the existing hybrid apps, and does not break their advertising-supported business model.

World-Wide Web: Adding Multimedia to Cyberspace.

ERIC Educational Resources Information Center

Descy, Don E.

1994-01-01

Describes the World-Wide Web (WWW), a network information resource based on hypertext. How to access WWW browsers through remote login (telnet) or though free browser software, such as Mosaic, is provided. Eight information sources that can be accessed through the WWW are listed. The address of a listserv reporting on Internet developments is…

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.

Avatar Web-Based Self-Report Survey System Technology for Public Health Research: Technical Outcome Results and Lessons Learned

PubMed Central

Savel, Craig; Mierzwa, Stan; Gorbach, Pamina M.; Souidi, Samir; Lally, Michelle; Zimet, Gregory; Interventions, AIDS

2016-01-01

This paper reports on a specific Web-based self-report data collection system that was developed for a public health research study in the United States. Our focus is on technical outcome results and lessons learned that may be useful to other projects requiring such a solution. The system was accessible from any device that had a browser that supported HTML5. Report findings include: which hardware devices, Web browsers, and operating systems were used; the rate of survey completion; and key considerations for employing Web-based surveys in a clinical trial setting. PMID:28149445

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.

WEBSLIDE: A "Virtual" Slide Projector Based on World Wide Web

NASA Astrophysics Data System (ADS)

Barra, Maria; Ferrandino, Salvatore; Scarano, Vittorio

1999-03-01

We present here the design key concepts of WEBSLIDE, a software project whose objective is to provide a simple, cheap and efficient solution for showing slides during lessons in computer labs. In fact, WEBSLIDE allows the video monitors of several client machines (the "STUDENTS") to be synchronously updated by the actions of a particular client machine, called the "INSTRUCTOR." The system is based on the World Wide Web and the software components of WEBSLIDE mainly consists in a WWW server, browsers and small Cgi-Bill scripts. What makes WEBSLIDE particularly appealing for small educational institutions is that WEBSLIDE is built with "off the shelf" products: it does not involve using a specifically designed program but any Netscape browser, one of the most popular browsers available on the market, is sufficient. Another possible use is to use our system to implement "guided automatic tours" through several pages or Intranets internal news bulletins: the company Web server can broadcast to all employees relevant information on their browser.

WebCSD: the online portal to the Cambridge Structural Database

PubMed Central

Thomas, Ian R.; Bruno, Ian J.; Cole, Jason C.; Macrae, Clare F.; Pidcock, Elna; Wood, Peter A.

2010-01-01

WebCSD, a new web-based application developed by the Cambridge Crystallographic Data Centre, offers fast searching of the Cambridge Structural Database using only a standard internet browser. Search facilities include two-dimensional substructure, molecular similarity, text/numeric and reduced cell searching. Text, chemical diagrams and three-dimensional structural information can all be studied in the results browser using the efficient entry summaries and embedded three-dimensional viewer. PMID:22477776

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.

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.

Brain-controlled applications using dynamic P300 speller matrices.

PubMed

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

2015-01-01

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

Development of a Web-Based Periscope Simulator for Submarine Officer Training

DTIC Science & Technology

2014-09-01

31 2. The Evolution of Web-Based technology .........................................32...DEVELOPMENT ............................................................................65 A. TECHNOLOGY ...the possibility to deliver 3D simulations using the web browsers and web technology . The objective is to create an effective and efficient WBLE that

YADBrowser: A Browser for Web-Based Educational Applications

ERIC Educational Resources Information Center

Zaldivar, Vicente Arturo Romero; Arandia, Jon Ander Elorriaga; Brito, Mateo Lezcano

2005-01-01

In this article, the main characteristics of the educational browser YADBrowser are described. One of the main objectives of this project is to define new languages and object models which facilitate the creation of educational applications for the Internet. The fundamental characteristics of the object model of the browser are also described.…

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

PubMed Central

Georgiev, Martin; Jana, Suman; Shmatikov, Vitaly

2014-01-01

Hybrid mobile applications (apps) combine the features of Web applications and “native” mobile apps. Like Web applications, they are implemented in portable, platform-independent languages such as HTML and JavaScript. Like native apps, they have direct access to local device resources—file system, location, camera, contacts, etc. Hybrid apps are typically developed using hybrid application frameworks such as PhoneGap. The purpose of the framework is twofold. First, it provides an embedded Web browser (for example, WebView on Android) that executes the app's Web code. Second, it supplies “bridges” that allow Web code to escape the browser and access local resources on the device. We analyze the software stack created by hybrid frameworks and demonstrate that it does not properly compose the access-control policies governing Web code and local code, respectively. Web code is governed by the same origin policy, whereas local code is governed by the access-control policy of the operating system (for example, user-granted permissions in Android). The bridges added by the framework to the browser have the same local access rights as the entire application, but are not correctly protected by the same origin policy. This opens the door to fracking attacks, which allow foreign-origin Web content included into a hybrid app (e.g., ads confined in iframes) to drill through the layers and directly access device resources. Fracking vulnerabilities are generic: they affect all hybrid frameworks, all embedded Web browsers, all bridge mechanisms, and all platforms on which these frameworks are deployed. We study the prevalence of fracking vulnerabilities in free Android apps based on the PhoneGap framework. Each vulnerability exposes sensitive local resources—the ability to read and write contacts list, local files, etc.—to dozens of potentially malicious Web domains. We also analyze the defenses deployed by hybrid frameworks to prevent resource access by foreign-origin Web content and explain why they are ineffectual. We then present NoFrak, a capability-based defense against fracking attacks. NoFrak is platform-independent, compatible with any framework and embedded browser, requires no changes to the code of the existing hybrid apps, and does not break their advertising-supported business model. PMID:25485311

[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.

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.

Concept Mapping Your Web Searches: A Design Rationale and Web-Enabled Application

ERIC Educational Resources Information Center

Lee, Y.-J.

2004-01-01

Although it has become very common to use World Wide Web-based information in many educational settings, there has been little research on how to better search and organize Web-based information. This paper discusses the shortcomings of Web search engines and Web browsers as learning environments and describes an alternative Web search environment…

Ajax Architecture Implementation Techniques

NASA Astrophysics Data System (ADS)

Hussaini, Syed Asadullah; Tabassum, S. Nasira; Baig, Tabassum, M. Khader

2012-03-01

Today's rich Web applications use a mix of Java Script and asynchronous communication with the application server. This mechanism is also known as Ajax: Asynchronous JavaScript and XML. The intent of Ajax is to exchange small pieces of data between the browser and the application server, and in doing so, use partial page refresh instead of reloading the entire Web page. AJAX (Asynchronous JavaScript and XML) is a powerful Web development model for browser-based Web applications. Technologies that form the AJAX model, such as XML, JavaScript, HTTP, and XHTML, are individually widely used and well known. However, AJAX combines these technologies to let Web pages retrieve small amounts of data from the server without having to reload the entire page. This capability makes Web pages more interactive and lets them behave like local applications. Web 2.0 enabled by the Ajax architecture has given rise to a new level of user interactivity through web browsers. Many new and extremely popular Web applications have been introduced such as Google Maps, Google Docs, Flickr, and so on. Ajax Toolkits such as Dojo allow web developers to build Web 2.0 applications quickly and with little effort.

Web-Based Testing: Exploring the Relationship between Hardware Usability and Test Performance

ERIC Educational Resources Information Center

Huff, Kyle; Cline, Melinda; Guynes, Carl S.

2012-01-01

Web-based testing has recently become common in both academic and professional settings. A web-based test is administered through a web browser. Individuals may complete a web-based test at nearly any time and at any place. In addition, almost any computer lab can become a testing center. It is important to understand the environmental issues that…

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.

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.

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).

The Evolution of Web Searching.

ERIC Educational Resources Information Center

Green, David

2000-01-01

Explores the interrelation between Web publishing and information retrieval technologies and lists new approaches to Web indexing and searching. Highlights include Web directories; search engines; portalisation; Internet service providers; browser providers; meta search engines; popularity based analysis; natural language searching; links-based…

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.

Thin client (web browser)-based collaboration for medical imaging and web-enabled data.

PubMed

Le, Tuong Huu; Malhi, Nadeem

2002-01-01

Utilizing thin client software and open source server technology, a collaborative architecture was implemented allowing for sharing of Digital Imaging and Communications in Medicine (DICOM) and non-DICOM images with real-time markup. Using the Web browser as a thin client integrated with standards-based components, such as DHTML (dynamic hypertext markup language), JavaScript, and Java, collaboration was achieved through a Web server/proxy server combination utilizing Java Servlets and Java Server Pages. A typical collaborative session involved the driver, who directed the navigation of the other collaborators, the passengers, and provided collaborative markups of medical and nonmedical images. The majority of processing was performed on the server side, allowing for the client to remain thin and more accessible.

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...

The PubChem chemical structure sketcher

PubMed Central

2009-01-01

PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects. PMID:20298522

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.

Optimizing real-time Web-based user interfaces for observatories

NASA Astrophysics Data System (ADS)

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

2008-08-01

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

Development of a Global Marine Environmental Library

DTIC Science & Technology

2010-06-01

Gulf. Marine Geology , 129, 237- 269. [4] Lerner, S., & Maffei, A. (2001). 4DGeoBrowser: A Web-based data browser and server for accessing and...Digital Library as a Catalyst for Collaboration: Voyages across Disciplinary and Institutional Boundaries with SIO Explorer; Digital Scholarship

Lamprey: tracking users on the World Wide Web.

PubMed

Felciano, R M; Altman, R B

1996-01-01

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

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.

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.

Use of Web Technology to Access and Update College Plans

ERIC Educational Resources Information Center

Valeau, Edward J.; Luan, Jing

2007-01-01

In this study, the process and outcome of a web-based planning application, called Ports of Call, are discussed. The application allows college management to create, edit, and report out activities relating to college plans, all through a web browser. Its design was based on best practices in modern web technology and the application can be easily…

WebGL for Rosetta Science Planning

NASA Astrophysics Data System (ADS)

Schmidt, Albrecht; Völk, Stefan; Grieger, Björn

2013-04-01

Rosetta is a mission of the European Space Agency (ESA) to rendez-vous with comet Churyumov-Gerasimenko in 2014. The trajectory and operations of the mission are particularly complex, have many free parameters and are novel to the community. To support science planning, communicate operational ideas and disseminate operational scenarios to the scientific community, the science ground segment makes use of Web-based visualisation technologies. Using the recent standard WebGL, static pages of time-dependent three-dimensional views of the spacecraft and the field-of-views of the instruments are generated, directly from the operational files. These can then be viewed in modern Web browsers for understanding or verification, be analysed and correlated with other studies. Variable timesteps make it possible to provide both overviews and detailed animated scenes. The technical challenges that are particular to Web-based environments include: (1) In traditional OpenGL, is much easier to compute needed data on demand since the visualisation runs natively on a usually quite powerful computer. In WebGL application, since requests for additional data have to be passed through a Web server, they are more complex and also require a more complex infrastructure. (2) The volume of data that can be kept in a browser environment is limited and has to be transferred over often slow network links. Thus, careful design and reduction of data is required. (3) Although browser support for WebGL has improved since the authors started using it, it is often not well supported on mobile and small devices. (4) Web browsers often only support limited end user interactions with a mouse or keyboards. While some of the challenges can be expected to become less important as technological progress continues, others seem to be more inherent to the approach. On the positive side, the authors' experiences include: (1) low threshold in the community to using the visualisations, (2), thus, cooperative use of the products, and (3) good and still improving tool and library support.

The ABCs of PDFs.

ERIC Educational Resources Information Center

Adler, Steve

2000-01-01

Explains the use of Adobe Acrobat's Portable Document Format (PDF) for school Web sites and Intranets. Explains the PDF workflow; components for Web-based PDF delivery, including the Web server, preparing content of the PDF files, and the browser; incorporating PDFs into the Web site; incorporating multimedia; and software. (LRW)

Modelling Safe Interface Interactions in Web Applications

NASA Astrophysics Data System (ADS)

Brambilla, Marco; Cabot, Jordi; Grossniklaus, Michael

Current Web applications embed sophisticated user interfaces and business logic. The original interaction paradigm of the Web based on static content pages that are browsed by hyperlinks is, therefore, not valid anymore. In this paper, we advocate a paradigm shift for browsers and Web applications, that improves the management of user interaction and browsing history. Pages are replaced by States as basic navigation nodes, and Back/Forward navigation along the browsing history is replaced by a full-fledged interactive application paradigm, supporting transactions at the interface level and featuring Undo/Redo capabilities. This new paradigm offers a safer and more precise interaction model, protecting the user from unexpected behaviours of the applications and the browser.

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.

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...

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

pWeb: A High-Performance, Parallel-Computing Framework for Web-Browser-Based Medical Simulation.

PubMed

Halic, Tansel; Ahn, Woojin; De, Suvranu

2014-01-01

This work presents a pWeb - a new language and compiler for parallelization of client-side compute intensive web applications such as surgical simulations. The recently introduced HTML5 standard has enabled creating unprecedented applications on the web. Low performance of the web browser, however, remains the bottleneck of computationally intensive applications including visualization of complex scenes, real time physical simulations and image processing compared to native ones. The new proposed language is built upon web workers for multithreaded programming in HTML5. The language provides fundamental functionalities of parallel programming languages as well as the fork/join parallel model which is not supported by web workers. The language compiler automatically generates an equivalent parallel script that complies with the HTML5 standard. A case study on realistic rendering for surgical simulations demonstrates enhanced performance with a compact set of instructions.

Implementing a distributed intranet-based information system.

PubMed

O'Kane, K C; McColligan, E E; Davis, G A

1996-11-01

The article discusses Internet and intranet technologies and describes how to install an intranet-based information system using the Merle language facility and other readily available components. Merle is a script language designed to support decentralized medical record information retrieval applications on the World Wide Web. The goal of this work is to provide a script language tool to facilitate construction of efficient, fully functional, multipoint medical record information systems that can be accessed anywhere by low-cost Web browsers to search, retrieve, and analyze patient information. The language allows legacy MUMPS applications to function in a Web environment and to make use of the Web graphical, sound, and video presentation services. It also permits downloading of script applets for execution on client browsers, and it can be used in standalone mode with the Unix, Windows 95, Windows NT, and OS/2 operating systems.

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.

Baby Steps: Starting Out on the World Wide Web.

ERIC Educational Resources Information Center

Simpson, Carol; McElmeel, Sharron L.

1997-01-01

While the Internet is the physical medium used to transport data, the World Wide Web is the collection of protocols and standards used to access the information. This article provides a basic explanation of what the Web is and describes common browser commands. Discusses graphic Web browsers; universal resource locators (URLs); file, message,…

Genome Maps, a new generation genome browser.

PubMed

Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

2013-07-01

Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

Genome Maps, a new generation genome browser

PubMed Central

Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

2013-01-01

Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

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.

A Java viewer to publish Digital Imaging and Communications in Medicine (DICOM) radiologic images on the World Wide Web.

PubMed

Setti, E; Musumeci, R

2001-06-01

The world wide web is an exciting service that allows one to publish electronic documents made of text and images on the internet. Client software called a web browser can access these documents, and display and print them. The most popular browsers are currently Microsoft Internet Explorer (Microsoft, Redmond, WA) and Netscape Communicator (Netscape Communications, Mountain View, CA). These browsers can display text in hypertext markup language (HTML) format and images in Joint Photographic Expert Group (JPEG) and Graphic Interchange Format (GIF). Currently, neither browser can display radiologic images in native Digital Imaging and Communications in Medicine (DICOM) format. With the aim to publish radiologic images on the internet, we wrote a dedicated Java applet. Our software can display radiologic and histologic images in DICOM, JPEG, and GIF formats, and provides a a number of functions like windowing and magnification lens. The applet is compatible with some web browsers, even the older versions. The software is free and available from the author.

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…

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

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.

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

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.

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.

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.

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

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.

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.

Accountable Information Flow for Java-Based Web Applications

DTIC Science & Technology

2010-01-01

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

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…

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.

JavaScript Access to DICOM Network and Objects in Web Browser.

PubMed

Drnasin, Ivan; Grgić, Mislav; Gogić, Goran

2017-10-01

Digital imaging and communications in medicine (DICOM) 3.0 standard provides the baseline for the picture archiving and communication systems (PACS). The development of Internet and various communication media initiated demand for non-DICOM access to PACS systems. Ever-increasing utilization of the web browsers, laptops and handheld devices, as opposed to desktop applications and static organizational computers, lead to development of different web technologies. The DICOM standard officials accepted those subsequently as tools of alternative access. This paper provides an overview of the current state of development of the web access technology to the DICOM repositories. It presents a different approach of using HTML5 features of the web browsers through the JavaScript language and the WebSocket protocol by enabling real-time communication with DICOM repositories. JavaScript DICOM network library, DICOM to WebSocket proxy and a proof-of-concept web application that qualifies as a DICOM 3.0 device were developed.

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.

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

On the Nets. Comparing Web Browsers: Mosaic, Cello, Netscape, WinWeb and InternetWorks Life.

ERIC Educational Resources Information Center

Notess, Greg R.

1995-01-01

World Wide Web browsers are compared by speed, setup, hypertext transport protocol (HTTP) handling, management of file transfer protocol (FTP), telnet, gopher, and wide area information server (WAIS); bookmark options; and communication functions. Netscape has the most features, the fastest retrieval, sophisticated bookmark capabilities. (JMV)

Visits, Hits, Caching and Counting on the World Wide Web: Old Wine in New Bottles?

ERIC Educational Resources Information Center

Berthon, Pierre; Pitt, Leyland; Prendergast, Gerard

1997-01-01

Although web browser caching speeds up retrieval, reduces network traffic, and decreases the load on servers and browser's computers, an unintended consequence for marketing research is that Web servers undercount hits. This article explores counting problems, caching, proxy servers, trawler software and presents a series of correction factors…

Decoding Technology: Web Browsers

ERIC Educational Resources Information Center

Walker, Tim; Donohue, Chip

2007-01-01

More than ever, early childhood administrators are relying on the Internet for information. A key to becoming an exceptional Web "surfer" is getting to know the ins and outs of the Web browser being used. There are several options available, and almost all can be downloaded for free. However, many of the functions and features they offer are very…

IBM techexplorer and MathML: Interactive Multimodal Scientific Documents

NASA Astrophysics Data System (ADS)

Diaz, Angel

2001-06-01

The World Wide Web provides a standard publishing platform for disseminating scientific and technical articles, books, journals, courseware, or even homework on the internet; however, the transition from paper to web-based interactive content has brought new opportunities for creating interactive content. Students, scientists, and engineers are now faced with the task of rendering the 2D presentational structure of mathematics, harnessing the wealth of scientific and technical software, and creating truly accessible scientific portals across international boundaries and markets. The recent emergence of World Wide Web Consortium (W3C) standards such as the Mathematical Markup Language (MathML), Language (XSL), and Aural CSS (ACSS) provide a foundation whereby mathematics can be displayed, enlivened, computed, and audio formatted. With interoperability ensured by standards, software applications can be easily brought together to create extensible and interactive scientific content. In this presentation we will provide an overview of the IBM techexplorer Hypermedia Browser, a web browser plug-in and ActiveX control aimed at bringing interactive mathematics to the masses across platforms and applications. We will demonstrate "live" mathematics where documents that contain MathML expressions can be edited and computed right inside your favorite web browser. This demonstration will be generalized as we show how MathML can be used to enliven even PowerPoint presentations. Finally, we will close the loop by demonstrating a novel approach to spoken mathematics based on MathML, DOM, XSL, ACSS, techexplorer, and IBM ViaVoice. By making use of techexplorer as the glue that binds the rendered content to the web browser, the back-end computation software, the Java applets that augment the exposition, and voice-rendering systems such as ViaVoice, authors can indeed create truly extensible and interactive scientific content. For more information see: [http://www.software.ibm.com/techexplorer] [http://www.alphaworks.ibm.com] [http://www.w3.org

Perspectives for Electronic Books in the World Wide Web Age.

ERIC Educational Resources Information Center

Bry, Francois; Kraus, Michael

2002-01-01

Discusses the rapid growth of the World Wide Web and the lack of use of electronic books and suggests that specialized contents and device independence can make Web-based books compete with print. Topics include enhancing the hypertext model of XML; client-side adaptation, including browsers and navigation; and semantic modeling. (Author/LRW)

A web-based approach for electrocardiogram monitoring in the home.

PubMed

Magrabi, F; Lovell, N H; Celler, B G

1999-05-01

A Web-based electrocardiogram (ECG) monitoring service in which a longitudinal clinical record is used for management of patients, is described. The Web application is used to collect clinical data from the patient's home. A database on the server acts as a central repository where this clinical information is stored. A Web browser provides access to the patient's records and ECG data. We discuss the technologies used to automate the retrieval and storage of clinical data from a patient database, and the recording and reviewing of clinical measurement data. On the client's Web browser, ActiveX controls embedded in the Web pages provide a link between the various components including the Web server, Web page, the specialised client side ECG review and acquisition software, and the local file system. The ActiveX controls also implement FTP functions to retrieve and submit clinical data to and from the server. An intelligent software agent on the server is activated whenever new ECG data is sent from the home. The agent compares historical data with newly acquired data. Using this method, an optimum patient care strategy can be evaluated, a summarised report along with reminders and suggestions for action is sent to the doctor and patient by email.

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.

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.

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

PubMed Central

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

2012-01-01

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

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

PubMed

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

2012-01-01

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

Using Web Speech Technology with Language Learning Applications

ERIC Educational Resources Information Center

Daniels, Paul

2015-01-01

In this article, the author presents the history of human-to-computer interaction based upon the design of sophisticated computerized speech recognition algorithms. Advancements such as the arrival of cloud-based computing and software like Google's Web Speech API allows anyone with an Internet connection and Chrome browser to take advantage of…

Exploratory Visual Analytics of a Dynamically Built Network of Nodes in a WebGL-Enabled Browser

DTIC Science & Technology

2014-01-01

dimensionality reduction, feature extraction, high-dimensional data, t-distributed stochastic neighbor embedding, neighbor retrieval visualizer, visual...WebGL-enabled rendering is supported natively by browsers such as the latest Mozilla Firefox , Google Chrome, and Microsoft Internet Explorer 11. At the...appropriate names. The resultant 26-node network is displayed in a Mozilla Firefox browser in figure 2 (also see appendix B). 3 Figure 1. The

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.

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

Density-based parallel skin lesion border detection with webCL

PubMed Central

2015-01-01

Background Dermoscopy is a highly effective and noninvasive imaging technique used in diagnosis of melanoma and other pigmented skin lesions. Many aspects of the lesion under consideration are defined in relation to the lesion border. This makes border detection one of the most important steps in dermoscopic image analysis. In current practice, dermatologists often delineate borders through a hand drawn representation based upon visual inspection. Due to the subjective nature of this technique, intra- and inter-observer variations are common. Because of this, the automated assessment of lesion borders in dermoscopic images has become an important area of study. Methods Fast density based skin lesion border detection method has been implemented in parallel with a new parallel technology called WebCL. WebCL utilizes client side computing capabilities to use available hardware resources such as multi cores and GPUs. Developed WebCL-parallel density based skin lesion border detection method runs efficiently from internet browsers. Results Previous research indicates that one of the highest accuracy rates can be achieved using density based clustering techniques for skin lesion border detection. While these algorithms do have unfavorable time complexities, this effect could be mitigated when implemented in parallel. In this study, density based clustering technique for skin lesion border detection is parallelized and redesigned to run very efficiently on the heterogeneous platforms (e.g. tablets, SmartPhones, multi-core CPUs, GPUs, and fully-integrated Accelerated Processing Units) by transforming the technique into a series of independent concurrent operations. Heterogeneous computing is adopted to support accessibility, portability and multi-device use in the clinical settings. For this, we used WebCL, an emerging technology that enables a HTML5 Web browser to execute code in parallel for heterogeneous platforms. We depicted WebCL and our parallel algorithm design. In addition, we tested parallel code on 100 dermoscopy images and showed the execution speedups with respect to the serial version. Results indicate that parallel (WebCL) version and serial version of density based lesion border detection methods generate the same accuracy rates for 100 dermoscopy images, in which mean of border error is 6.94%, mean of recall is 76.66%, and mean of precision is 99.29% respectively. Moreover, WebCL version's speedup factor for 100 dermoscopy images' lesion border detection averages around ~491.2. Conclusions When large amount of high resolution dermoscopy images considered in a usual clinical setting along with the critical importance of early detection and diagnosis of melanoma before metastasis, the importance of fast processing dermoscopy images become obvious. In this paper, we introduce WebCL and the use of it for biomedical image processing applications. WebCL is a javascript binding of OpenCL, which takes advantage of GPU computing from a web browser. Therefore, WebCL parallel version of density based skin lesion border detection introduced in this study can supplement expert dermatologist, and aid them in early diagnosis of skin lesions. While WebCL is currently an emerging technology, a full adoption of WebCL into the HTML5 standard would allow for this implementation to run on a very large set of hardware and software systems. WebCL takes full advantage of parallel computational resources including multi-cores and GPUs on a local machine, and allows for compiled code to run directly from the Web Browser. PMID:26423836

Density-based parallel skin lesion border detection with webCL.

PubMed

Lemon, James; Kockara, Sinan; Halic, Tansel; Mete, Mutlu

2015-01-01

Dermoscopy is a highly effective and noninvasive imaging technique used in diagnosis of melanoma and other pigmented skin lesions. Many aspects of the lesion under consideration are defined in relation to the lesion border. This makes border detection one of the most important steps in dermoscopic image analysis. In current practice, dermatologists often delineate borders through a hand drawn representation based upon visual inspection. Due to the subjective nature of this technique, intra- and inter-observer variations are common. Because of this, the automated assessment of lesion borders in dermoscopic images has become an important area of study. Fast density based skin lesion border detection method has been implemented in parallel with a new parallel technology called WebCL. WebCL utilizes client side computing capabilities to use available hardware resources such as multi cores and GPUs. Developed WebCL-parallel density based skin lesion border detection method runs efficiently from internet browsers. Previous research indicates that one of the highest accuracy rates can be achieved using density based clustering techniques for skin lesion border detection. While these algorithms do have unfavorable time complexities, this effect could be mitigated when implemented in parallel. In this study, density based clustering technique for skin lesion border detection is parallelized and redesigned to run very efficiently on the heterogeneous platforms (e.g. tablets, SmartPhones, multi-core CPUs, GPUs, and fully-integrated Accelerated Processing Units) by transforming the technique into a series of independent concurrent operations. Heterogeneous computing is adopted to support accessibility, portability and multi-device use in the clinical settings. For this, we used WebCL, an emerging technology that enables a HTML5 Web browser to execute code in parallel for heterogeneous platforms. We depicted WebCL and our parallel algorithm design. In addition, we tested parallel code on 100 dermoscopy images and showed the execution speedups with respect to the serial version. Results indicate that parallel (WebCL) version and serial version of density based lesion border detection methods generate the same accuracy rates for 100 dermoscopy images, in which mean of border error is 6.94%, mean of recall is 76.66%, and mean of precision is 99.29% respectively. Moreover, WebCL version's speedup factor for 100 dermoscopy images' lesion border detection averages around ~491.2. When large amount of high resolution dermoscopy images considered in a usual clinical setting along with the critical importance of early detection and diagnosis of melanoma before metastasis, the importance of fast processing dermoscopy images become obvious. In this paper, we introduce WebCL and the use of it for biomedical image processing applications. WebCL is a javascript binding of OpenCL, which takes advantage of GPU computing from a web browser. Therefore, WebCL parallel version of density based skin lesion border detection introduced in this study can supplement expert dermatologist, and aid them in early diagnosis of skin lesions. While WebCL is currently an emerging technology, a full adoption of WebCL into the HTML5 standard would allow for this implementation to run on a very large set of hardware and software systems. WebCL takes full advantage of parallel computational resources including multi-cores and GPUs on a local machine, and allows for compiled code to run directly from the Web Browser.

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.

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.

[A solution for display and processing of DICOM images in web PACS].

PubMed

Xue, Wei-jing; Lu, Wen; Wang, Hai-yang; Meng, Jian

2009-03-01

Use the technique of Java Applet to realize the supporting of DICOM image in ordinary Web browser, thereby to expand the processing function of medical image. First analyze the format of DICOM file and design a class which can acquire the pixels, then design two Applet classes, of which one is used to disposal the DICOM image, the other is used to display DICOM image that have been disposaled in the first Applet. They all embedded in the View page, and they communicate by Applet Context object. The method designed in this paper can make users display and process DICOM images directly by using ordinary Web browser, which makes Web PACS not only have the advantages of B/S model, but also have the advantages of the C/S model. Java Applet is the key for expanding the Web browser's function in Web PACS, which provides a guideline to sharing of medical images.

New Interfaces to Web Documents and Services

NASA Technical Reports Server (NTRS)

Carlisle, W. H.

1996-01-01

This paper reports on investigations into how to extend capabilities of the Virtual Research Center (VRC) for NASA's Advanced Concepts Office. The work was performed as part of NASA's 1996 Summer Faculty Fellowship program, and involved research into and prototype development of software components that provide documents and services for the World Wide Web (WWW). The WWW has become a de-facto standard for sharing resources over the internet, primarily because web browsers are freely available for the most common hardware platforms and their operating systems. As a consequence of the popularity of the internet, tools, and techniques associated with web browsers are changing rapidly. New capabilities are offered by companies that support web browsers in order to achieve or remain a dominant participant in internet services. Because a goal of the VRC is to build an environment for NASA centers, universities, and industrial partners to share information associated with Advanced Concepts Office activities, the VRC tracks new techniques and services associated with the web in order to determine the their usefulness for distributed and collaborative engineering research activities. Most recently, Java has emerged as a new tool for providing internet services. Because the major web browser providers have decided to include Java in their software, investigations into Java were conducted this summer.

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

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

D3GB: An Interactive Genome Browser for R, Python, and WordPress.

PubMed

Barrios, David; Prieto, Carlos

2017-05-01

Genome browsers are useful not only for showing final results but also for improving analysis protocols, testing data quality, and generating result drafts. Its integration in analysis pipelines allows the optimization of parameters, which leads to better results. New developments that facilitate the creation and utilization of genome browsers could contribute to improving analysis results and supporting the quick visualization of genomic data. D3 Genome Browser is an interactive genome browser that can be easily integrated in analysis protocols and shared on the Web. It is distributed as an R package, a Python module, and a WordPress plugin to facilitate its integration in pipelines and the utilization of platform capabilities. It is compatible with popular data formats such as GenBank, GFF, BED, FASTA, and VCF, and enables the exploration of genomic data with a Web browser.

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.

An Autonomous Learning System of Bengali Characters Using Web-Based Intelligent Handwriting Recognition

ERIC Educational Resources Information Center

Khatun, Nazma; Miwa, Jouji

2016-01-01

This research project was aimed to develop an intelligent Bengali handwriting education system to improve the literacy level in Bangladesh. Due to the socio-economical limitation, all of the population does not have the chance to go to school. Here, we developed a prototype of web-based (iPhone/smartphone or computer browser) intelligent…

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...

The biodigital human: a web-based 3D platform for medical visualization and education.

PubMed

Qualter, John; Sculli, Frank; Oliker, Aaron; Napier, Zachary; Lee, Sabrina; Garcia, Julio; Frenkel, Sally; Harnik, Victoria; Triola, Marc

2012-01-01

NYU School of Medicine's Division of Educational Informatics in collaboration with BioDigital Systems LLC (New York, NY) has created a virtual human body dataset that is being used for visualization, education and training and is accessible over modern web browsers.

Using GBrowse 2.0 to visualize and share next-generation sequence data

PubMed Central

2013-01-01

GBrowse is a mature web-based genome browser that is suitable for deployment on both public and private web sites. It supports most of genome browser features, including qualitative and quantitative (wiggle) tracks, track uploading, track sharing, interactive track configuration, semantic zooming and limited smooth track panning. As of version 2.0, GBrowse supports next-generation sequencing (NGS) data by providing for the direct display of SAM and BAM sequence alignment files. SAM/BAM tracks provide semantic zooming and support both local and remote data sources. This article provides step-by-step instructions for configuring GBrowse to display NGS data. PMID:23376193

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 .

Eco-Health Relationship Browser

EPA Science Inventory

The Eco-Health Relationship Browser (Browser) is a web tool designed to portray, in an engaging and intuitive way, the linkages between ecosystems, their services, and potential health outcomes that have been associated with those services in the literature. It functions an inte...

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.

78 FR 44603 - Byron Nuclear Station, Units 1 and 2, and Braidwood Nuclear Station, Units 1 and 2; Exelon...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-24

... rule, the participant must file the document using the NRC's online, Web-based submission form. In... form, including the installation of the Web browser plug-in, is available on the NRC's public Web site... 61010, and near Braidwood at the Fossil Ridge (Braidwood) Public Library, 386 W. Kennedy Road, Braidwood...

JSXGraph--Dynamic Mathematics with JavaScript

ERIC Educational Resources Information Center

Gerhauser, Michael; Valentin, Bianca; Wassermann, Alfred

2010-01-01

Since Java applets seem to be on the retreat in web application, other approaches for displaying interactive mathematics in the web browser are needed. One such alternative could be our open-source project JSXGraph. It is a cross-browser library for displaying interactive geometry, function plotting, graphs, and data visualization in a web…

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.

World Wide Web Page Design: A Structured Approach.

ERIC Educational Resources Information Center

Gregory, Gwen; Brown, M. Marlo

1997-01-01

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

The rendering context for stereoscopic 3D web

NASA Astrophysics Data System (ADS)

Chen, Qinshui; Wang, Wenmin; Wang, Ronggang

2014-03-01

3D technologies on the Web has been studied for many years, but they are basically monoscopic 3D. With the stereoscopic technology gradually maturing, we are researching to integrate the binocular 3D technology into the Web, creating a stereoscopic 3D browser that will provide users with a brand new experience of human-computer interaction. In this paper, we propose a novel approach to apply stereoscopy technologies to the CSS3 3D Transforms. Under our model, each element can create or participate in a stereoscopic 3D rendering context, in which 3D Transforms such as scaling, translation and rotation, can be applied and be perceived in a truly 3D space. We first discuss the underlying principles of stereoscopy. After that we discuss how these principles can be applied to the Web. A stereoscopic 3D browser with backward compatibility is also created for demonstration purposes. We take advantage of the open-source WebKit project, integrating the 3D display ability into the rendering engine of the web browser. For each 3D web page, our 3D browser will create two slightly different images, each representing the left-eye view and right-eye view, both to be combined on the 3D display to generate the illusion of depth. And as the result turns out, elements can be manipulated in a truly 3D space.

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

Using a Web Browser for Environmental and Climate Change Studies

NASA Technical Reports Server (NTRS)

Bess, T. Dale; Stackhouse, Paul; Mangosing, Daniel; Smith, G. Louis

2002-01-01

A new web browser for viewing and manipulating meteorological data sets is located on a web server at NASA, Langley Research Center. The browser uses a live access server (LAS) developed by the Thermal Modeling and Analysis Project at NOAA's Pacific Marine Environmental Laboratory. LAS allows researchers to interact directly with the data to view, select, and subset the data in terms of location (latitude, longitude) and time such as day, month, or year. In addition, LAS can compare two data sets and can perform averages and variances, LAS is used here to show how it functions as an internet/web browser for use by the scientific and educational community. In particular its versatility in displaying and manipulating data sets of atmospheric measurements in the earth s radiation budget (ERB) or energy balance, which includes measurements of absorbed solar radiation, reflected shortwave radiation (RSW), thermal outgoing longwave radiation (OLR), and net radiation is demonstrated. These measurements are from the Clouds and the Earth s Radiant Energy System (CERES) experiment and the surface radiation budget (SRB) experiment.

Using a Web Browser for Environmental and Climate Change Studies

NASA Technical Reports Server (NTRS)

Bess, T. Dale; Stackhouse, Paul; Mangosing, Daniel; Smith, G. Louis

2005-01-01

A new web browser for viewing and manipulating meteorological data sets is located on a web server at NASA, Langley Research Center. The browser uses a live access server (LAS) developed by the Thermal Modeling and Analysis Project at NOAA's Pacific Marine Environmental Laboratory. LAS allows researchers to interact directly with the data to view, select, and subset the data in terms of location (latitude, longitude) and time such as day, month, or year. In addition, LAS can compare two data sets and can perform averages and variances, LAS is used here to show how it functions as an internet/web browser for use by the scientific and educational community. In particular its versatility in displaying and manipulating data sets of atmospheric measurements in the earth's radiation budget (ERB) or energy balance, which includes measurements of absorbed solar radiation, reflected shortwave radiation (RSW), thermal outgoing longwave radiation (OLR), and net radiation is demonstrated. These measurements are from the Clouds and the Earth's Radiant Energy System (CERES) experiment and the surface radiation budget (SRB) experiment.

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

DTIC Science & Technology

2017-06-01

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

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

DTIC Science & Technology

2016-03-01

distribution is unlimited. 13. SUPPLEMENTARY NOTES 14. ABSTRACT This document serves as the quick-start guide for GIFT Cloud, the web -based...to users with a GIFT Account at no cost. GIFT Cloud is a new implementation of GIFT. This web -based application allows learners, authors, and...distribution is unlimited. 3 3. Requirements for GIFT Cloud GIFT Cloud is accessed via a web browser. Officially, GIFT Cloud has been tested to work on

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.

Interactive metagenomic visualization in a Web browser.

PubMed

Ondov, Brian D; Bergman, Nicholas H; Phillippy, Adam M

2011-09-30

A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in assignments to these groups makes it important to consider both their hierarchical contexts and their prediction confidence. The current tools for visualizing metagenomic data, however, omit or distort quantitative hierarchical relationships and lack the facility for displaying secondary variables. Here we present Krona, a new visualization tool that allows intuitive exploration of relative abundances and confidences within the complex hierarchies of metagenomic classifications. Krona combines a variant of radial, space-filling displays with parametric coloring and interactive polar-coordinate zooming. The HTML5 and JavaScript implementation enables fully interactive charts that can be explored with any modern Web browser, without the need for installed software or plug-ins. This Web-based architecture also allows each chart to be an independent document, making them easy to share via e-mail or post to a standard Web server. To illustrate Krona's utility, we describe its application to various metagenomic data sets and its compatibility with popular metagenomic analysis tools. Krona is both a powerful metagenomic visualization tool and a demonstration of the potential of HTML5 for highly accessible bioinformatic visualizations. Its rich and interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages. Both the Krona rendering code and conversion tools are freely available under a BSD open-source license, and available from: http://krona.sourceforge.net.

Network Analysis of Reconnaissance and Intrusion of an Industrial Control System

DTIC Science & Technology

2016-09-01

simulated a plant engineer using the engineering workstation web browser to authenticate to the vegetable cooker HMI. While the engineer established the...observed the vegetable cooker HMI web display, the attacker stopped capturing network traffic. Acting as the attacker, we searched the attacker’s pcap...manually controlled by human activity. In this testbed network, only web browser traffic (HTTP) is created by an operator to view an HMI status

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.

SU-E-J-114: Web-Browser Medical Physics Applications Using HTML5 and Javascript.

PubMed

Bakhtiari, M

2012-06-01

Since 2010, there has been a great attention about HTML5. Application developers and browser makers fully embrace and support the web of the future. Consumers have started to embrace HTML5, especially as more users understand the benefits and potential that HTML5 can mean for the future.Modern browsers such as Firefox, Google Chrome, and Safari are offering better and more robust support for HTML5, CSS3, and JavaScript. The idea is to introduce the HTML5 to medical physics community for open source software developments. The benefit of using HTML5 is developing portable software systems. The HTML5, CSS, and JavaScript programming languages were used to develop several applications for Quality Assurance in radiation therapy. The canvas element of HTML5 was used for handling and displaying the images, and JavaScript was used to manipulate the data. Sample application were developed to: 1. analyze the flatness and symmetry of the radiotherapy fields in a web browser, 2.analyze the Dynalog files from Varian machines, 3. visualize the animated Dynamic MLC files, 4. Simulation via Monte Carlo, and 5. interactive image manipulation. The programs showed great performance and speed in uploading the data and displaying the results. The flatness and symmetry program and Dynalog file analyzer ran in a fraction of second. The reason behind this performance is using JavaScript language which is a lower level programming language in comparison to the most of the scientific programming packages such as Matlab. The second reason is that JavaScript runs locally on client side computers not on the web-servers. HTML5 and JavaScript can be used to develop useful applications that can be run online or offline on different modern web-browsers. The programming platform can be also one of the modern web-browsers which are mostly open source (such as Firefox). © 2012 American Association of Physicists in Medicine.

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.

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.

Phased development of a web-based PACS viewer

NASA Astrophysics Data System (ADS)

Gidron, Yoad; Shani, Uri; Shifrin, Mark

2000-05-01

The Web browser is an excellent environment for the rapid development of an effective and inexpensive PACS viewer. In this paper we will share our experience in developing a browser-based viewer, from the inception and prototype stages to its current state of maturity. There are many operational advantages to a browser-based viewer, even when native viewers already exist in the system (with multiple and/or high resolution screens): (1) It can be used on existing personal workstations throughout the hospital. (2) It is easy to make the service available from physician's homes. (3) The viewer is extremely portable and platform independent. There is a wide variety of means available for implementing the browser- based viewer. Each file sent to the client by the server can perform some end-user or client/server interaction. These means range from HTML (for HyperText Markup Language) files, through Java Script, to Java applets. Some data types may also invoke plug-in code in the client, although this would reduce the portability of the viewer, it would provide the needed efficiency in critical places. On the server side the range of means is also very rich: (1) A set of files: html, Java Script, Java applets, etc. (2) Extensions of the server via cgi-bin programs, (3) Extensions of the server via servlets, (4) Any other helper application residing and working with the server to access the DICOM archive. The viewer architecture consists of two basic parts: The first part performs query and navigation through the DICOM archive image folders. The second part does the image access and display. While the first part deals with low data traffic, it involves many database transactions. The second part is simple as far as access transactions are concerned, but requires much more data traffic and display functions. Our web-based viewer has gone through three development stages characterized by the complexity of the means and tools employed on both client and server sides.

Gobe: an interactive, web-based tool for comparative genomic visualization.

PubMed

Pedersen, Brent S; Tang, Haibao; Freeling, Michael

2011-04-01

Gobe is a web-based tool for viewing comparative genomic data. It supports viewing multiple genomic regions simultaneously. Its simple text format and flash-based rendering make it an interactive, exploratory research tool. Gobe can be used without installation through our web service, or downloaded and customized with stylesheets and javascript callback functions. Gobe is a flash application that runs in all modern web-browsers. The full source-code, including that for the online web application is available under the MIT license at: http://github.com/brentp/gobe. Sample applications are hosted at http://try-gobe.appspot.com/ and http://synteny.cnr.berkeley.edu/gobe-app/.

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.…

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…

A topological framework for interactive queries on 3D models in the Web.

PubMed

Figueiredo, Mauro; Rodrigues, José I; Silvestre, Ivo; Veiga-Pires, Cristina

2014-01-01

Several technologies exist to create 3D content for the web. With X3D, WebGL, and X3DOM, it is possible to visualize and interact with 3D models in a web browser. Frequently, three-dimensional objects are stored using the X3D file format for the web. However, there is no explicit topological information, which makes it difficult to design fast algorithms for applications that require adjacency and incidence data. This paper presents a new open source toolkit TopTri (Topological model for Triangle meshes) for Web3D servers that builds the topological model for triangular meshes of manifold or nonmanifold models. Web3D client applications using this toolkit make queries to the web server to get adjacent and incidence information of vertices, edges, and faces. This paper shows the application of the topological information to get minimal local points and iso-lines in a 3D mesh in a web browser. As an application, we present also the interactive identification of stalactites in a cave chamber in a 3D web browser. Several tests show that even for large triangular meshes with millions of triangles, the adjacency and incidence information is returned in real time making the presented toolkit appropriate for interactive Web3D applications.

A Topological Framework for Interactive Queries on 3D Models in the Web

PubMed Central

Figueiredo, Mauro; Rodrigues, José I.; Silvestre, Ivo; Veiga-Pires, Cristina

2014-01-01

Several technologies exist to create 3D content for the web. With X3D, WebGL, and X3DOM, it is possible to visualize and interact with 3D models in a web browser. Frequently, three-dimensional objects are stored using the X3D file format for the web. However, there is no explicit topological information, which makes it difficult to design fast algorithms for applications that require adjacency and incidence data. This paper presents a new open source toolkit TopTri (Topological model for Triangle meshes) for Web3D servers that builds the topological model for triangular meshes of manifold or nonmanifold models. Web3D client applications using this toolkit make queries to the web server to get adjacent and incidence information of vertices, edges, and faces. This paper shows the application of the topological information to get minimal local points and iso-lines in a 3D mesh in a web browser. As an application, we present also the interactive identification of stalactites in a cave chamber in a 3D web browser. Several tests show that even for large triangular meshes with millions of triangles, the adjacency and incidence information is returned in real time making the presented toolkit appropriate for interactive Web3D applications. PMID:24977236

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.

Auditory presentation and synchronization in Adobe Flash and HTML5/JavaScript Web experiments.

PubMed

Reimers, Stian; Stewart, Neil

2016-09-01

Substantial recent research has examined the accuracy of presentation durations and response time measurements for visually presented stimuli in Web-based experiments, with a general conclusion that accuracy is acceptable for most kinds of experiments. However, many areas of behavioral research use auditory stimuli instead of, or in addition to, visual stimuli. Much less is known about auditory accuracy using standard Web-based testing procedures. We used a millisecond-accurate Black Box Toolkit to measure the actual durations of auditory stimuli and the synchronization of auditory and visual presentation onsets. We examined the distribution of timings for 100 presentations of auditory and visual stimuli across two computers with difference specs, three commonly used browsers, and code written in either Adobe Flash or JavaScript. We also examined different coding options for attempting to synchronize the auditory and visual onsets. Overall, we found that auditory durations were very consistent, but that the lags between visual and auditory onsets varied substantially across browsers and computer systems.

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

Association of Small Computer Users in Education: Proceedings of the ASCUE Summer Conference (31st, North Myrtle Beach, South Carolina, June 7-11, 1998).

ERIC Educational Resources Information Center

Smith, Peter, Ed.

Topics addressed by the papers including in this proceedings include: multimedia in the classroom; World Wide Web site development; the evolution of academic library services; a Web-based literature course; development of a real-time intelligent network environment; serving grades over the Internet; e-mail over a Web browser; using technology to…

WebScope: A New Tool for Fusion Data Analysis and Visualization

NASA Astrophysics Data System (ADS)

Yang, Fei; Dang, Ningning; Xiao, Bingjia

2010-04-01

A visualization tool was developed through a web browser based on Java applets embedded into HTML pages, in order to provide a world access to the EAST experimental data. It can display data from various trees in different servers in a single panel. With WebScope, it is easier to make a comparison between different data sources and perform a simple calculation over different data sources.

EntrezAJAX: direct web browser access to the Entrez Programming Utilities.

PubMed

Loman, Nicholas J; Pallen, Mark J

2010-06-21

Web applications for biology and medicine often need to integrate data from Entrez services provided by the National Center for Biotechnology Information. However, direct access to Entrez from a web browser is not possible due to 'same-origin' security restrictions. The use of "Asynchronous JavaScript and XML" (AJAX) to create rich, interactive web applications is now commonplace. The ability to access Entrez via AJAX would be advantageous in the creation of integrated biomedical web resources. We describe EntrezAJAX, which provides access to Entrez eUtils and is able to circumvent same-origin browser restrictions. EntrezAJAX is easily implemented by JavaScript developers and provides identical functionality as Entrez eUtils as well as enhanced functionality to ease development. We provide easy-to-understand developer examples written in JavaScript to illustrate potential uses of this service. For the purposes of speed, reliability and scalability, EntrezAJAX has been deployed on Google App Engine, a freely available cloud service. The EntrezAJAX webpage is located at http://entrezajax.appspot.com/

Interactive Web Graphs with Fewer Restrictions

NASA Technical Reports Server (NTRS)

Fiedler, James

2012-01-01

There is growing popularity for interactive, statistical web graphs and programs to generate them. However, it seems that these programs tend to be somewhat restricted in which web browsers and statistical software are supported. For example, the software might use SVG (e.g., Protovis, gridSVG) or HTML canvas, both of which exclude most versions of Internet Explorer, or the software might be made specifically for R (gridSVG, CRanvas), thus excluding users of other stats software. There are more general tools (d3, Rapha lJS) which are compatible with most browsers, but using one of these to make statistical graphs requires more coding than is probably desired, and requires learning a new tool. This talk will present a method for making interactive web graphs, which, by design, attempts to support as many browsers and as many statistical programs as possible, while also aiming to be relatively easy to use and relatively easy to extend.

phiGENOME: an integrative navigation throughout bacteriophage genomes.

PubMed

Stano, Matej; Klucar, Lubos

2011-11-01

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

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.

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.

IMAGE EXPLORER: Astronomical Image Analysis on an HTML5-based Web Application

NASA Astrophysics Data System (ADS)

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

2014-05-01

Large datasets produced by recent astronomical imagers cause the traditional paradigm for basic visual analysis - typically downloading one's entire image dataset and using desktop clients like DS9, Aladin, etc. - to not scale, despite advances in desktop computing power and storage. This paper describes Image Explorer, a web framework that offers several of the basic visualization and analysis functionality commonly provided by tools like DS9, on any HTML5 capable web browser on various platforms. It uses a combination of the modern HTML5 canvas, JavaScript, and several layers of lossless PNG tiles producted from the FITS image data. Astronomers are able to rapidly and simultaneously open up several images on their web-browser, adjust the intensity min/max cutoff or its scaling function, and zoom level, apply color-maps, view position and FITS header information, execute typically used data reduction codes on the corresponding FITS data using the FRIAA framework, and overlay tiles for source catalog objects, etc.

Firefox add-ons for medical reference.

PubMed

Hoy, Matthew B

2010-07-01

Firefox is a Web browser created by the Mozilla project, an open-source software group. Features of the browser include automated updates, advanced security and standards compliance, and the ability to add functionality through add-ons and extensions. First introduced in 2004, Firefox now accounts for roughly 30% of the browser market. This article will focus primarily on add-ons and extensions available for the browser that are useful to medical researchers.

Interactive 3d Landscapes on Line

NASA Astrophysics Data System (ADS)

Fanini, B.; Calori, L.; Ferdani, D.; Pescarin, S.

2011-09-01

The paper describes challenges identified while developing browser embedded 3D landscape rendering applications, our current approach and work-flow and how recent development in browser technologies could affect. All the data, even if processed by optimization and decimation tools, result in very huge databases that require paging, streaming and Level-of-Detail techniques to be implemented to allow remote web based real time fruition. Our approach has been to select an open source scene-graph based visual simulation library with sufficient performance and flexibility and adapt it to the web by providing a browser plug-in. Within the current Montegrotto VR Project, content produced with new pipelines has been integrated. The whole Montegrotto Town has been generated procedurally by CityEngine. We used this procedural approach, based on algorithms and procedures because it is particularly functional to create extensive and credible urban reconstructions. To create the archaeological sites we used optimized mesh acquired with laser scanning and photogrammetry techniques whereas to realize the 3D reconstructions of the main historical buildings we adopted computer-graphic software like blender and 3ds Max. At the final stage, semi-automatic tools have been developed and used up to prepare and clusterise 3D models and scene graph routes for web publishing. Vegetation generators have also been used with the goal of populating the virtual scene to enhance the user perceived realism during the navigation experience. After the description of 3D modelling and optimization techniques, the paper will focus and discuss its results and expectations.

New Perspectives on Popular Culture, Science and Technology: Web Browsers and the New Illiteracy

ERIC Educational Resources Information Center

Charters, Elizabeth

2004-01-01

Analysts predict that the knowledge economy of the near future will require people to be both computer literate and print literate. However, some of the reading and thinking habits of current college students suggest that electronic media such as web browsers may be limiting the new generation's ability to absorb and process what they read. Their…

Interactive metagenomic visualization in a Web browser

PubMed Central

2011-01-01

Background A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in assignments to these groups makes it important to consider both their hierarchical contexts and their prediction confidence. The current tools for visualizing metagenomic data, however, omit or distort quantitative hierarchical relationships and lack the facility for displaying secondary variables. Results Here we present Krona, a new visualization tool that allows intuitive exploration of relative abundances and confidences within the complex hierarchies of metagenomic classifications. Krona combines a variant of radial, space-filling displays with parametric coloring and interactive polar-coordinate zooming. The HTML5 and JavaScript implementation enables fully interactive charts that can be explored with any modern Web browser, without the need for installed software or plug-ins. This Web-based architecture also allows each chart to be an independent document, making them easy to share via e-mail or post to a standard Web server. To illustrate Krona's utility, we describe its application to various metagenomic data sets and its compatibility with popular metagenomic analysis tools. Conclusions Krona is both a powerful metagenomic visualization tool and a demonstration of the potential of HTML5 for highly accessible bioinformatic visualizations. Its rich and interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages. Both the Krona rendering code and conversion tools are freely available under a BSD open-source license, and available from: http://krona.sourceforge.net. PMID:21961884

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

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.

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.

The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications

PubMed Central

Bare, J Christopher; Shannon, Paul T; Schmid, Amy K; Baliga, Nitin S

2007-01-01

Background Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoing maintenance of local copies of public databases. Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data. Results The Firegoose, an extension to the Mozilla Firefox web browser, enables data transfer between web sites and desktop tools. As a component of the Gaggle integration framework, Firegoose can also exchange data with Cytoscape, the R statistical package, Multiexperiment Viewer (MeV), and several other popular desktop software tools. Firegoose adds the capability to easily use local data to query KEGG, EMBL STRING, DAVID, and other widely-used bioinformatics web sites. Query results from these web sites can be transferred to desktop tools for further analysis with a few clicks. Firegoose acquires data from the web by screen scraping, microformats, embedded XML, or web services. We define a microformat, which allows structured information compatible with the Gaggle to be embedded in HTML documents. We demonstrate the capabilities of this software by performing an analysis of the genes activated in the microbe Halobacterium salinarum NRC-1 in response to anaerobic environments. Starting with microarray data, we explore functions of differentially expressed genes by combining data from several public web resources and construct an integrated view of the cellular processes involved. Conclusion The Firegoose incorporates Mozilla Firefox into the Gaggle environment and enables interactive sharing of data between diverse web resources and desktop software tools without maintaining local copies. Additional web sites can be incorporated easily into the framework using the scripting platform of the Firefox browser. Performing data integration in the browser allows the excellent search and navigation capabilities of the browser to be used in combination with powerful desktop tools. PMID:18021453

The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications.

PubMed

Bare, J Christopher; Shannon, Paul T; Schmid, Amy K; Baliga, Nitin S

2007-11-19

Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoing maintenance of local copies of public databases. Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data. The Firegoose, an extension to the Mozilla Firefox web browser, enables data transfer between web sites and desktop tools. As a component of the Gaggle integration framework, Firegoose can also exchange data with Cytoscape, the R statistical package, Multiexperiment Viewer (MeV), and several other popular desktop software tools. Firegoose adds the capability to easily use local data to query KEGG, EMBL STRING, DAVID, and other widely-used bioinformatics web sites. Query results from these web sites can be transferred to desktop tools for further analysis with a few clicks. Firegoose acquires data from the web by screen scraping, microformats, embedded XML, or web services. We define a microformat, which allows structured information compatible with the Gaggle to be embedded in HTML documents. We demonstrate the capabilities of this software by performing an analysis of the genes activated in the microbe Halobacterium salinarum NRC-1 in response to anaerobic environments. Starting with microarray data, we explore functions of differentially expressed genes by combining data from several public web resources and construct an integrated view of the cellular processes involved. The Firegoose incorporates Mozilla Firefox into the Gaggle environment and enables interactive sharing of data between diverse web resources and desktop software tools without maintaining local copies. Additional web sites can be incorporated easily into the framework using the scripting platform of the Firefox browser. Performing data integration in the browser allows the excellent search and navigation capabilities of the browser to be used in combination with powerful desktop tools.

Phylowood: interactive web-based animations of biogeographic and phylogeographic histories.

PubMed

Landis, Michael J; Bedford, Trevor

2014-01-01

Phylowood is a web service that uses JavaScript to generate in-browser animations of biogeographic and phylogeographic histories from annotated phylogenetic input. The animations are interactive, allowing the user to adjust spatial and temporal resolution, and highlight phylogenetic lineages of interest. All documentation and source code for Phylowood is freely available at https://github.com/mlandis/phylowood, and a live web application is available at https://mlandis.github.io/phylowood.

An Analysis of the Elements of Collaboration Associated with Top Collaborative Tools

DTIC Science & Technology

2010-03-01

lets you access your e-mail, calendar, and files from any web browser anywhere in the world. Web based www.hotoffice.com Noodle Vialect’s (parent...www.taroby.org Yuuguu Yuuguu is an instant screen sharing, web conferencing, remote support, desktop remote control and messaging tool. Client...Office, Noodle , Novlet, Revizr, Taroby, and Yuuguu) received all seven NS ratings (see Table 20 below). The overall ratings for the major elements

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.

QMachine: commodity supercomputing in web browsers.

PubMed

Wilkinson, Sean R; Almeida, Jonas S

2014-06-09

Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for querying, processing, and visualizing genomics' "Big Data" from sources like The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) without local software installation or configuration. The design of QMachine (QM) was driven by the opportunity to use this pervasive computing model in the context of the Web of Linked Data in Biomedicine. QM is an open-sourced, publicly available web service that acts as a messaging system for posting tasks and retrieving results over HTTP. The illustrative application described here distributes the analyses of 20 Streptococcus pneumoniae genomes for shared suffixes. Because all analytical and data retrieval tasks are executed by volunteer machines, few server resources are required. Any modern web browser can submit those tasks and/or volunteer to execute them without installing any extra plugins or programs. A client library provides high-level distribution templates including MapReduce. This stark departure from the current reliance on expensive server hardware running "download and install" software has already gathered substantial community interest, as QM received more than 2.2 million API calls from 87 countries in 12 months. QM was found adequate to deliver the sort of scalable bioinformatics solutions that computation- and data-intensive workflows require. Paradoxically, the sandboxed execution of code by web browsers was also found to enable them, as compute nodes, to address critical privacy concerns that characterize biomedical environments.

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

NASA Astrophysics Data System (ADS)

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

2011-03-01

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

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.

IRIS Earthquake Browser with Integration to the GEON IDV for 3-D Visualization of Hypocenters.

NASA Astrophysics Data System (ADS)

Weertman, B. R.

2007-12-01

We present a new generation of web based earthquake query tool - the IRIS Earthquake Browser (IEB). The IEB combines the DMC's large set of earthquake catalogs (provided by USGS/NEIC, ISC and the ANF) with the popular Google Maps web interface. With the IEB you can quickly and easily find earthquakes in any region of the globe. Using Google's detailed satellite images, earthquakes can be easily co-located with natural geographic features such as volcanoes as well as man made features such as commercial mines. A set of controls allow earthquakes to be filtered by time, magnitude, and depth range as well as catalog name, contributor name and magnitude type. Displayed events can be easily exported in NetCDF format into the GEON Integrated Data Viewer (IDV) where hypocenters may be visualized in three dimensions. Looking "under the hood", the IEB is based on AJAX technology and utilizes REST style web services hosted at the IRIS DMC. The IEB is part of a broader effort at the DMC aimed at making our data holdings available via web services. The IEB is useful both educationally and as a research tool.

Display gamma is an important factor in Web image viewing

NASA Astrophysics Data System (ADS)

Zhang, Xuemei; Lavin, Yingmei; Silverstein, D. Amnon

2001-06-01

We conducted a perceptual image preference experiment over the web to find our (1) if typical computer users have significant variations in their display gamma settings, and (2) if so, do the gamma settings have significant perceptual effect on the appearance of images in their web browsers. The digital image renderings used were found to have preferred tone characteristics from a previous lab- controlled experiment. They were rendered with 4 different gamma settings. The subjects were asked to view the images over the web, with their own computer equipment and web browsers. The subjects werewe asked to view the images over the web, with their own computer equipment and web browsers. The subjects made pair-wise subjective preference judgements on which rendering they liked bets for each image. Each subject's display gamma setting was estimated using a 'gamma estimator' tool, implemented as a Java applet. The results indicated that (1) the user's gamma settings, as estimated in the experiment, span a wide range from about 1.8 to about 3.0; (2) the subjects preferred images that werewe rendered with a 'correct' gamma value matching their display setting. Subjects disliked images rendered with a gamma value not matching their displays'. This indicates that display gamma estimation is a perceptually significant factor in web image optimization.

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

Interoperative fundus image and report sharing in compliance with integrating the healthcare enterprise conformance and web access to digital imaging and communication in medicine persistent object protocol.

PubMed

Wu, Hui-Qun; Lv, Zheng-Min; Geng, Xing-Yun; Jiang, Kui; Tang, Le-Min; Zhou, Guo-Min; Dong, Jian-Cheng

2013-01-01

To address issues in interoperability between different fundus image systems, we proposed a web eye-picture archiving and communication system (PACS) framework in conformance with digital imaging and communication in medicine (DICOM) and health level 7 (HL7) protocol to realize fundus images and reports sharing and communication through internet. Firstly, a telemedicine-based eye care work flow was established based on integrating the healthcare enterprise (IHE) Eye Care technical framework. Then, a browser/server architecture eye-PACS system was established in conformance with the web access to DICOM persistent object (WADO) protocol, which contains three tiers. In any client system installed with web browser, clinicians could log in the eye-PACS to observe fundus images and reports. Multipurpose internet mail extensions (MIME) type of a structured report is saved as pdf/html with reference link to relevant fundus image using the WADO syntax could provide enough information for clinicians. Some functions provided by open-source Oviyam could be used to query, zoom, move, measure, view DICOM fundus images. Such web eye-PACS in compliance to WADO protocol could be used to store and communicate fundus images and reports, therefore is of great significance for teleophthalmology.

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

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.

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

vMon-mobile provides wireless connection to the electronic patient record

NASA Astrophysics Data System (ADS)

Oliveira, Pedro P., Jr.; Rebelo, Marina; Pilon, Paulo E.; Gutierrez, Marco A.; Tachinardi, Umberto

2002-05-01

This work presents the development of a set of tools to help doctors to continuously monitor critical patients. Real-time monitoring signals are displayed via a Web Based Electronic Patient Record (Web-EPR) developed at the Heart Institute. Any computer on the Hospital's Intranet can access the Web-EPR that will open a browser plug-in called vMon. Recently vMon was adapted to wireless mobile devices providing the same real-time visualization of vital signals of its desktop counterpart. The monitoring network communicates with the hospital network through a gateway using HL7 messages and has the ability to export waveforms in real time using the multicast protocol through an API library. A dedicated ActiveX component was built that establishes the streaming of the biomedical signals under monitoring and displays them on an Internet Explorer 5.x browser. The mobile version - called vMon-mobile - will parse the browser window and deliver it to a PDA device connected to a local area network. The result is a virtual monitor presenting real-time data on a mobile device. All parameters and signals acquired from the moment the patient is connected to the monitors are stored for a few days. The most clinically relevant information is added to patient's EPR.

EntrezAJAX: direct web browser access to the Entrez Programming Utilities

PubMed Central

2010-01-01

Web applications for biology and medicine often need to integrate data from Entrez services provided by the National Center for Biotechnology Information. However, direct access to Entrez from a web browser is not possible due to 'same-origin' security restrictions. The use of "Asynchronous JavaScript and XML" (AJAX) to create rich, interactive web applications is now commonplace. The ability to access Entrez via AJAX would be advantageous in the creation of integrated biomedical web resources. We describe EntrezAJAX, which provides access to Entrez eUtils and is able to circumvent same-origin browser restrictions. EntrezAJAX is easily implemented by JavaScript developers and provides identical functionality as Entrez eUtils as well as enhanced functionality to ease development. We provide easy-to-understand developer examples written in JavaScript to illustrate potential uses of this service. For the purposes of speed, reliability and scalability, EntrezAJAX has been deployed on Google App Engine, a freely available cloud service. The EntrezAJAX webpage is located at http://entrezajax.appspot.com/ PMID:20565938

Web Extensible Display Manager

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

Slominski, Ryan; Larrieu, Theodore L.

Jefferson Lab's Web Extensible Display Manager (WEDM) allows staff to access EDM control system screens from a web browser in remote offices and from mobile devices. Native browser technologies are leveraged to avoid installing and managing software on remote clients such as browser plugins, tunnel applications, or an EDM environment. Since standard network ports are used firewall exceptions are minimized. To avoid security concerns from remote users modifying a control system, WEDM exposes read-only access and basic web authentication can be used to further restrict access. Updates of monitored EPICS channels are delivered via a Web Socket using a webmore » gateway. The software translates EDM description files (denoted with the edl suffix) to HTML with Scalable Vector Graphics (SVG) following the EDM's edl file vector drawing rules to create faithful screen renderings. The WEDM server parses edl files and creates the HTML equivalent in real-time allowing existing screens to work without modification. Alternatively, the familiar drag and drop EDM screen creation tool can be used to create optimized screens sized specifically for smart phones and then rendered by WEDM.« less

Detecting Heap-Spraying Code Injection Attacks in Malicious Web Pages Using Runtime Execution

NASA Astrophysics Data System (ADS)

Choi, Younghan; Kim, Hyoungchun; Lee, Donghoon

The growing use of web services is increasing web browser attacks exponentially. Most attacks use a technique called heap spraying because of its high success rate. Heap spraying executes a malicious code without indicating the exact address of the code by copying it into many heap objects. For this reason, the attack has a high potential to succeed if only the vulnerability is exploited. Thus, attackers have recently begun using this technique because it is easy to use JavaScript to allocate the heap memory area. This paper proposes a novel technique that detects heap spraying attacks by executing a heap object in a real environment, irrespective of the version and patch status of the web browser. This runtime execution is used to detect various forms of heap spraying attacks, such as encoding and polymorphism. Heap objects are executed after being filtered on the basis of patterns of heap spraying attacks in order to reduce the overhead of the runtime execution. Patterns of heap spraying attacks are based on analysis of how an web browser accesses benign web sites. The heap objects are executed forcibly by changing the instruction register into the address of them after being loaded into memory. Thus, we can execute the malicious code without having to consider the version and patch status of the browser. An object is considered to contain a malicious code if the execution reaches a call instruction and then the instruction accesses the API of system libraries, such as kernel32.dll and ws_32.dll. To change registers and monitor execution flow, we used a debugger engine. A prototype, named HERAD(HEap spRAying Detector), is implemented and evaluated. In experiments, HERAD detects various forms of exploit code that an emulation cannot detect, and some heap spraying attacks that NOZZLE cannot detect. Although it has an execution overhead, HERAD produces a low number of false alarms. The processing time of several minutes is negligible because our research focuses on detecting heap spraying. This research can be applied to existing systems that collect malicious codes, such as Honeypot.

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

Empowering radiologic education on the Internet: a new virtual website technology for hosting interactive educational content on the World Wide Web.

PubMed

Frank, M S; Dreyer, K

2001-06-01

We describe a virtual web site hosting technology that enables educators in radiology to emblazon and make available for delivery on the world wide web their own interactive educational content, free from dependencies on in-house resources and policies. This suite of technologies includes a graphically oriented software application, designed for the computer novice, to facilitate the input, storage, and management of domain expertise within a database system. The database stores this expertise as choreographed and interlinked multimedia entities including text, imagery, interactive questions, and audio. Case-based presentations or thematic lectures can be authored locally, previewed locally within a web browser, then uploaded at will as packaged knowledge objects to an educator's (or department's) personal web site housed within a virtual server architecture. This architecture can host an unlimited number of unique educational web sites for individuals or departments in need of such service. Each virtual site's content is stored within that site's protected back-end database connected to Internet Information Server (Microsoft Corp, Redmond WA) using a suite of Active Server Page (ASP) modules that incorporate Microsoft's Active Data Objects (ADO) technology. Each person's or department's electronic teaching material appears as an independent web site with different levels of access--controlled by a username-password strategy--for teachers and students. There is essentially no static hypertext markup language (HTML). Rather, all pages displayed for a given site are rendered dynamically from case-based or thematic content that is fetched from that virtual site's database. The dynamically rendered HTML is displayed within a web browser in a Socratic fashion that can assess the recipient's current fund of knowledge while providing instantaneous user-specific feedback. Each site is emblazoned with the logo and identification of the participating institution. Individuals with teacher-level access can use a web browser to upload new content as well as manage content already stored on their virtual site. Each virtual site stores, collates, and scores participants' responses to the interactive questions posed on line. This virtual web site strategy empowers the educator with an end-to-end solution for creating interactive educational content and hosting that content within the educator's personalized and protected educational site on the world wide web, thus providing a valuable outlet that can magnify the impact of his or her talents and contributions.

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,…

Comparing Commercial WWW Browsers.

ERIC Educational Resources Information Center

Notess, Greg R.

1995-01-01

Four commercial World Wide Web browsers are evaluated for features such as handling of WWW protocols and different URLs: FTP, Telnet, Gopher and WAIS, and e-mail and news; bookmark capabilities; navigation features; file management; and security support. (JKP)

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.

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

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

PubMed

Eng, J

1997-01-01

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

QMachine: commodity supercomputing in web browsers

PubMed Central

2014-01-01

Background Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for querying, processing, and visualizing genomics’ “Big Data” from sources like The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) without local software installation or configuration. The design of QMachine (QM) was driven by the opportunity to use this pervasive computing model in the context of the Web of Linked Data in Biomedicine. Results QM is an open-sourced, publicly available web service that acts as a messaging system for posting tasks and retrieving results over HTTP. The illustrative application described here distributes the analyses of 20 Streptococcus pneumoniae genomes for shared suffixes. Because all analytical and data retrieval tasks are executed by volunteer machines, few server resources are required. Any modern web browser can submit those tasks and/or volunteer to execute them without installing any extra plugins or programs. A client library provides high-level distribution templates including MapReduce. This stark departure from the current reliance on expensive server hardware running “download and install” software has already gathered substantial community interest, as QM received more than 2.2 million API calls from 87 countries in 12 months. Conclusions QM was found adequate to deliver the sort of scalable bioinformatics solutions that computation- and data-intensive workflows require. Paradoxically, the sandboxed execution of code by web browsers was also found to enable them, as compute nodes, to address critical privacy concerns that characterize biomedical environments. PMID:24913605

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.

Formats and Network Protocols for Browser Access to 2D Raster Data

NASA Astrophysics Data System (ADS)

Plesea, L.

2015-12-01

Tiled web maps in browsers are a major success story, forming the foundation of many current web applications. Enabling tiled data access is the next logical step, and is likely to meet with similar success. Many ad-hoc approaches have already started to appear, and something similar is explored within the Open Geospatial Consortium. One of the main obstacles in making browser data access a reality is the lack of a well-known data format. This obstacle also represents an opportunity to analyze the requirements and possible candidates, applying lessons learned from web tiled image services and protocols. Similar to the image counterpart, a web tile raster data format needs to have good intrinsic compression and be able to handle high byte count data types including floating point. An overview of a possible solution to the format problem, a 2D data raster compression algorithm called Limited Error Raster Compression (LERC) will be presented. In addition to the format, best practices for high request rate HTTP services also need to be followed. In particular, content delivery network (CDN) caching suitability needs to be part of any design, not an after-thought. Last but not least, HTML 5 browsers will certainly be part of any solution since they provide improved access to binary data, as well as more powerful ways to view and interact with the data in the browser. In a simple but relevant application, digital elevation model (DEM) raster data is served as LERC compressed data tiles which are used to generate terrain by a HTML5 scene viewer.

Web Apollo: a web-based genomic annotation editing platform.

PubMed

Lee, Eduardo; Helt, Gregg A; Reese, Justin T; Munoz-Torres, Monica C; Childers, Chris P; Buels, Robert M; Stein, Lincoln; Holmes, Ian H; Elsik, Christine G; Lewis, Suzanna E

2013-08-30

Web Apollo is the first instantaneous, collaborative genomic annotation editor available on the web. One of the natural consequences following from current advances in sequencing technology is that there are more and more researchers sequencing new genomes. These researchers require tools to describe the functional features of their newly sequenced genomes. With Web Apollo researchers can use any of the common browsers (for example, Chrome or Firefox) to jointly analyze and precisely describe the features of a genome in real time, whether they are in the same room or working from opposite sides of the world.

Web Apollo: a web-based genomic annotation editing platform

PubMed Central

2013-01-01

Web Apollo is the first instantaneous, collaborative genomic annotation editor available on the web. One of the natural consequences following from current advances in sequencing technology is that there are more and more researchers sequencing new genomes. These researchers require tools to describe the functional features of their newly sequenced genomes. With Web Apollo researchers can use any of the common browsers (for example, Chrome or Firefox) to jointly analyze and precisely describe the features of a genome in real time, whether they are in the same room or working from opposite sides of the world. PMID:24000942

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.

Extracting Related Words from Anchor Text Clusters by Focusing on the Page Designer's Intention

NASA Astrophysics Data System (ADS)

Liu, Jianquan; Chen, Hanxiong; Furuse, Kazutaka; Ohbo, Nobuo

Approaches for extracting related words (terms) by co-occurrence work poorly sometimes. Two words frequently co-occurring in the same documents are considered related. However, they may not relate at all because they would have no common meanings nor similar semantics. We address this problem by considering the page designer’s intention and propose a new model to extract related words. Our approach is based on the idea that the web page designers usually make the correlative hyperlinks appear in close zone on the browser. We developed a browser-based crawler to collect “geographically” near hyperlinks, then by clustering these hyperlinks based on their pixel coordinates, we extract related words which can well reflect the designer’s intention. Experimental results show that our method can represent the intention of the web page designer in extremely high precision. Moreover, the experiments indicate that our extracting method can obtain related words in a high average precision.

Integrating Socioeconomic and Earth Science Data Using Geobrowsers and Web Services: A Demonstration

NASA Astrophysics Data System (ADS)

Schumacher, J. A.; Yetman, G. G.

2007-12-01

The societal benefit areas identified as the focus for the Global Earth Observing System of Systems (GEOSS) 10- year implementation plan are an indicator of the importance of integrating socioeconomic data with earth science data to support decision makers. To aid this integration, CIESIN is delivering its global and U.S. demographic data to commercial and open source Geobrowsers and providing open standards based services for data access. Currently, data on population distribution, poverty, and detailed census data for the U.S. are available for visualization and access in Google Earth, NASA World Wind, and a browser-based 2-dimensional mapping client. The mapping client allows for the creation of web map documents that pull together layers from distributed servers and can be saved and shared. Visualization tools with Geobrowsers, user-driven map creation and sharing via browser-based clients, and a prototype for characterizing populations at risk to predicted precipitation deficits will be demonstrated.

Use of mobile devices to answer online surveys: implications for research.

PubMed

Cunningham, John A; Neighbors, Clayton; Bertholet, Nicolas; Hendershot, Christian S

2013-07-08

There is a growing use of mobile devices to access the Internet. We examined whether participants who used a mobile device to access a brief online survey were quicker to respond to the survey but also, less likely to complete it than participants using a traditional web browser. Using data from a recently completed online intervention trial, we found that participants using mobile devices were quicker to access the survey but less likely to complete it compared to participants using a traditional web browser. More concerning, mobile device users were also less likely to respond to a request to complete a six week follow-up survey compared to those using traditional web browsers. With roughly a third of participants using mobile devices to answer an online survey in this study, the impact of mobile device usage on survey completion rates is a concern. ClinicalTrials.gov: NCT01521078.

pileup.js: a JavaScript library for interactive and in-browser visualization of genomic data.

PubMed

Vanderkam, Dan; Aksoy, B Arman; Hodes, Isaac; Perrone, Jaclyn; Hammerbacher, Jeff

2016-08-01

P: ileup.js is a new browser-based genome viewer. It is designed to facilitate the investigation of evidence for genomic variants within larger web applications. It takes advantage of recent developments in the JavaScript ecosystem to provide a modular, reliable and easily embedded library. The code and documentation for pileup.js is publicly available at https://github.com/hammerlab/pileup.js under the Apache 2.0 license. correspondence@hammerlab.org. © The Author 2016. Published by Oxford University Press.

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.

Distributing medical images with internet technologies: a DICOM web server and a DICOM java viewer.

PubMed

Fernàndez-Bayó, J; Barbero, O; Rubies, C; Sentís, M; Donoso, L

2000-01-01

With the advent of filmless radiology, it becomes important to be able to distribute radiologic images digitally throughout an entire hospital. A new approach based on World Wide Web technologies was developed to accomplish this objective. This approach involves a Web server that allows the query and retrieval of images stored in a Digital Imaging and Communications in Medicine (DICOM) archive. The images can be viewed inside a Web browser with use of a small Java program known as the DICOM Java Viewer, which is executed inside the browser. The system offers several advantages over more traditional picture archiving and communication systems (PACS): It is easy to install and maintain, is platform independent, allows images to be manipulated and displayed efficiently, and is easy to integrate with existing systems that are already making use of Web technologies. The system is user-friendly and can easily be used from outside the hospital if a security policy is in place. The simplicity and flexibility of Internet technologies makes them highly preferable to the more complex PACS workstations. The system works well, especially with magnetic resonance and computed tomographic images, and can help improve and simplify interdepartmental relationships in a filmless hospital environment.

Web-Based Distributed Simulation of Aeronautical Propulsion System

NASA Technical Reports Server (NTRS)

Zheng, Desheng; Follen, Gregory J.; Pavlik, William R.; Kim, Chan M.; Liu, Xianyou; Blaser, Tammy M.; Lopez, Isaac

2001-01-01

An application was developed to allow users to run and view the Numerical Propulsion System Simulation (NPSS) engine simulations from web browsers. Simulations were performed on multiple INFORMATION POWER GRID (IPG) test beds. The Common Object Request Broker Architecture (CORBA) was used for brokering data exchange among machines and IPG/Globus for job scheduling and remote process invocation. Web server scripting was performed by JavaServer Pages (JSP). This application has proven to be an effective and efficient way to couple heterogeneous distributed components.

An innovative browser-based data exploration tool with simultaneous scrolling in time and wavelength domains

NASA Astrophysics Data System (ADS)

Slater, Gregory L.; Schiff, David; De Pontieu, Bart; Tarbell, Theodore D.; Freeland, Samuel L.

2017-08-01

We present Cruiser, a new web tool for the precision interactive blending of image series across time and wavelength domains. Scrolling in two dimensions enables discovery and investigation of similarities and differences in structure and evolution across multiple wavelengths. Cruiser works in the latest versions of standards compliant browsers on both desktop and IOS platforms. Co-aligned data cubes have been generated for AIA, IRIS, and Hinode SOT FG, and image data from additional instruments, both space-based and ground-based, can be data sources. The tool has several movie playing and image adjustment controls which will be described in the poster and demonstrated on a MacOS notebook and iPad.

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.

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.

X3DOM as Carrier of the Virtual Heritage

NASA Astrophysics Data System (ADS)

Jung, Y.; Behr, J.; Graf, H.

2011-09-01

Virtual Museums (VM) are a new model of communication that aims at creating a personalized, immersive, and interactive way to enhance our understanding of the world around us. The term "VM" is a short-cut that comprehends various types of digital creations. One of the carriers for the communication of the virtual heritage at future internet level as de-facto standard is browser front-ends presenting the content and assets of museums. A major driving technology for the documentation and presentation of heritage driven media is real-time 3D content, thus imposing new strategies for a web inclusion. 3D content must become a first class web media that can be created, modified, and shared in the same way as text, images, audio and video are handled on the web right now. A new integration model based on a DOM integration into the web browsers' architecture opens up new possibilities for declarative 3 D content on the web and paves the way for new application scenarios for the virtual heritage at future internet level. With special regards to the X3DOM project as enabling technology for declarative 3D in HTML, this paper describes application scenarios and analyses its technological requirements for an efficient presentation and manipulation of virtual heritage assets on the web.

jsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web.

PubMed

Smits, Samuel A; Ouverney, Cleber C

2010-08-18

Many software packages have been developed to address the need for generating phylogenetic trees intended for print. With an increased use of the web to disseminate scientific literature, there is a need for phylogenetic trees to be viewable across many types of devices and feature some of the interactive elements that are integral to the browsing experience. We propose a novel approach for publishing interactive phylogenetic trees. We present a javascript library, jsPhyloSVG, which facilitates constructing interactive phylogenetic trees from raw Newick or phyloXML formats directly within the browser in Scalable Vector Graphics (SVG) format. It is designed to work across all major browsers and renders an alternative format for those browsers that do not support SVG. The library provides tools for building rectangular and circular phylograms with integrated charting. Interactive features may be integrated and made to respond to events such as clicks on any element of the tree, including labels. jsPhyloSVG is an open-source solution for rendering dynamic phylogenetic trees. It is capable of generating complex and interactive phylogenetic trees across all major browsers without the need for plugins. It is novel in supporting the ability to interpret the tree inference formats directly, exposing the underlying markup to data-mining services. The library source code, extensive documentation and live examples are freely accessible at www.jsphylosvg.com.

A tool for improving the Web accessibility of visually handicapped persons.

PubMed

Fujiki, Tadayoshi; Hanada, Eisuke; Yamada, Tomomi; Noda, Yoshihiro; Antoku, Yasuaki; Nakashima, Naoki; Nose, Yoshiaki

2006-04-01

Abstract Much has been written concerning the difficulties faced by visually handicapped persons when they access the internet. To solve some of the problems and to make web pages more accessible, we developed a tool we call the "Easy Bar," which works as a toolbar on the web browser. The functions of the Easy Bar are to change the size of web texts and images, to adjust the color, and to clear cached data that is automatically saved by the web browser. These functions are executed with ease by clicking buttons and operating a pull-down list. Since the icons built into Easy Bar are quite large, it is not necessary for the user to deal with delicate operations. The functions of Easy Bar run on any web page without increasing the processing time. For the visually handicapped, Easy Bar would contribute greatly to improved web accessibility to medical information.

NASA-Langley Web-Based Operational Real-time Cloud Retrieval Products from Geostationary Satellites

NASA Technical Reports Server (NTRS)

Palikonda, Rabindra; Minnis, Patrick; Spangenberg, Douglas A.; Khaiyer, Mandana M.; Nordeen, Michele L.; Ayers, Jeffrey K.; Nguyen, Louis; Yi, Yuhong; Chan, P. K.; Trepte, Qing Z.;

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.

Database Reports Over the Internet

NASA Technical Reports Server (NTRS)

Smith, Dean Lance

2002-01-01

Most of the summer was spent developing software that would permit existing test report forms to be printed over the web on a printer that is supported by Adobe Acrobat Reader. The data is stored in a DBMS (Data Base Management System). The client asks for the information from the database using an HTML (Hyper Text Markup Language) form in a web browser. JavaScript is used with the forms to assist the user and verify the integrity of the entered data. Queries to a database are made in SQL (Sequential Query Language), a widely supported standard for making queries to databases. Java servlets, programs written in the Java programming language running under the control of network server software, interrogate the database and complete a PDF form template kept in a file. The completed report is sent to the browser requesting the report. Some errors are sent to the browser in an HTML web page, others are reported to the server. Access to the databases was restricted since the data are being transported to new DBMS software that will run on new hardware. However, the SQL queries were made to Microsoft Access, a DBMS that is available on most PCs (Personal Computers). Access does support the SQL commands that were used, and a database was created with Access that contained typical data for the report forms. Some of the problems and features are discussed below.

EPA's EnviroAtlas Educational Curriculum

EPA Science Inventory

U.S. EPA’s EnviroAtlas provides a collection of web-based, interactive tools for exploring ecosystem services: an Interactive Map, which provides access to 300+ maps at multiple extents for the U.S., and an Eco-Health Relationship Browser, which displays the linkages betwee...

A demanding web-based PACS supported by web services technology

NASA Astrophysics Data System (ADS)

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

2006-03-01

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

Web-based visual analysis for high-throughput genomics

PubMed Central

2013-01-01

Background Visualization plays an essential role in genomics research by making it possible to observe correlations and trends in large datasets as well as communicate findings to others. Visual analysis, which combines visualization with analysis tools to enable seamless use of both approaches for scientific investigation, offers a powerful method for performing complex genomic analyses. However, there are numerous challenges that arise when creating rich, interactive Web-based visualizations/visual analysis applications for high-throughput genomics. These challenges include managing data flow from Web server to Web browser, integrating analysis tools and visualizations, and sharing visualizations with colleagues. Results We have created a platform simplifies the creation of Web-based visualization/visual analysis applications for high-throughput genomics. This platform provides components that make it simple to efficiently query very large datasets, draw common representations of genomic data, integrate with analysis tools, and share or publish fully interactive visualizations. Using this platform, we have created a Circos-style genome-wide viewer, a generic scatter plot for correlation analysis, an interactive phylogenetic tree, a scalable genome browser for next-generation sequencing data, and an application for systematically exploring tool parameter spaces to find good parameter values. All visualizations are interactive and fully customizable. The platform is integrated with the Galaxy (http://galaxyproject.org) genomics workbench, making it easy to integrate new visual applications into Galaxy. Conclusions Visualization and visual analysis play an important role in high-throughput genomics experiments, and approaches are needed to make it easier to create applications for these activities. Our framework provides a foundation for creating Web-based visualizations and integrating them into Galaxy. Finally, the visualizations we have created using the framework are useful tools for high-throughput genomics experiments. PMID:23758618

Virtual Earth System Laboratory (VESL): A Virtual Research Environment for The Visualization of Earth System Data and Process Simulations

NASA Astrophysics Data System (ADS)

Cheng, D. L. C.; Quinn, J. D.; Larour, E. Y.; Halkides, D. J.

2017-12-01

The Virtual Earth System Laboratory (VESL) is a Web application, under continued development at the Jet Propulsion Laboratory and UC Irvine, for the visualization of Earth System data and process simulations. As with any project of its size, we have encountered both successes and challenges during the course of development. Our principal point of success is the fact that VESL users can interact seamlessly with our earth science simulations within their own Web browser. Some of the challenges we have faced include retrofitting the VESL Web application to respond to touch gestures, reducing page load time (especially as the application has grown), and accounting for the differences between the various Web browsers and computing platforms.

PAVA: Physiological and Anatomical Visual Analytics for Mapping of Tissue-Specific Concentration and Time-Course Data

EPA Science Inventory

We describe the development and implementation of a Physiological and Anatomical Visual Analytics tool (PAVA), a web browser-based application, used to visualize experimental/simulated chemical time-course data (dosimetry), epidemiological data and Physiologically-Annotated Data ...

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.

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.

Handle with care: the impact of using Java applets in Web-based studies on dropout and sample composition.

PubMed

Stieger, Stefan; Göritz, Anja S; Voracek, Martin

2011-05-01

In Web-based studies, Web browsers are used to display online questionnaires. If an online questionnaire relies on non-standard technologies (e.g., Java applets), it is often necessary to install a particular browser plug-in. This can lead to technically induced dropout because some participants lack the technological know-how or the willingness to install the plug-in. In two thematically identical online studies conducted across two time points in two different participant pools (N = 1,527 and 805), we analyzed whether using a Java applet produces dropout and distortion of demographics in the final sample. Dropout was significantly higher on the Java applet questionnaire page than on the preceding and subsequent questionnaire pages. Age-specific effects were found only in one sample (i.e., dropouts were older), whereas sex-specific effects were found in both samples (i.e., women dropped out more frequently than men on the Java applet page). These results additionally support the recommendation that using additional technologies (e.g., Java applets) can be dangerous in producing a sample that is biased toward both younger and male respondents.

JANIS 4: An Improved Version of the NEA Java-based Nuclear Data Information System

NASA Astrophysics Data System (ADS)

Soppera, N.; Bossant, M.; Dupont, E.

2014-06-01

JANIS is software developed to facilitate the visualization and manipulation of nuclear data, giving access to evaluated data libraries, and to the EXFOR and CINDA databases. It is stand-alone Java software, downloadable from the web and distributed on DVD. Used offline, the system also makes use of an internet connection to access the NEA Data Bank database. It is now also offered as a full web application, only requiring a browser. The features added in the latest version of the software and this new web interface are described.

Application of Microsoft's ActiveX and DirectX technologies to the visulization of physical system dynamics

NASA Astrophysics Data System (ADS)

Mann, Christopher; Narasimhamurthi, Natarajan

1998-08-01

This paper discusses a specific implementation of a web and complement based simulation systems. The overall simulation container is implemented within a web page viewed with Microsoft's Internet Explorer 4.0 web browser. Microsoft's ActiveX/Distributed Component Object Model object interfaces are used in conjunction with the Microsoft DirectX graphics APIs to provide visualization functionality for the simulation. The MathWorks' Matlab computer aided control system design program is used as an ActiveX automation server to provide the compute engine for the simulations.

JANIS 4: An Improved Version of the NEA Java-based Nuclear Data Information System

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

Soppera, N., E-mail: nicolas.soppera@oecd.org; Bossant, M.; Dupont, E.

JANIS is software developed to facilitate the visualization and manipulation of nuclear data, giving access to evaluated data libraries, and to the EXFOR and CINDA databases. It is stand-alone Java software, downloadable from the web and distributed on DVD. Used offline, the system also makes use of an internet connection to access the NEA Data Bank database. It is now also offered as a full web application, only requiring a browser. The features added in the latest version of the software and this new web interface are described.

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

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.

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.

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

PubMed

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

2012-01-01

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

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

PubMed

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

2008-01-01

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

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

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.

Surfing the World Wide Web to Education Hot-Spots.

ERIC Educational Resources Information Center

Dyrli, Odvard Egil

1995-01-01

Provides a brief explanation of Web browsers and their use, as well as technical information for those considering access to the WWW (World Wide Web). Curriculum resources and addresses to useful Web sites are included. Sidebars show sample searches using Yahoo and Lycos search engines, and a list of recommended Web resources. (JKP)

Development of a Browser-Based Mobile Audience Response System for Large Classrooms

ERIC Educational Resources Information Center

Andergassen, Monika; Guerra, Victor; Ledermüller, Karl; Neumann, Gustaf

2013-01-01

Didactical advantages of audience response systems (ARS) have been discussed extensively ever since they have been used in classes. However, conventional ARS bear some drawbacks, such as requiring specific hardware, generating costs (text messaging based and web service fees) and creating a dependency on external hosts. In this paper we present a…

Using NetCloak to develop server-side Web-based experiments without writing CGI programs.

PubMed

Wolfe, Christopher R; Reyna, Valerie F

2002-05-01

Server-side experiments use the Web server, rather than the participant's browser, to handle tasks such as random assignment, eliminating inconsistencies with JAVA and other client-side applications. Heretofore, experimenters wishing to create server-side experiments have had to write programs to create common gateway interface (CGI) scripts in programming languages such as Perl and C++. NetCloak uses simple, HTML-like commands to create CGIs. We used NetCloak to implement an experiment on probability estimation. Measurements of time on task and participants' IP addresses assisted quality control. Without prior training, in less than 1 month, we were able to use NetCloak to design and create a Web-based experiment and to help graduate students create three Web-based experiments of their own.

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

Airborne Hazards and Open Burn Pit Registry

MedlinePlus

... Burn Pit Registry requires a common web browser technology to guide you through the registry questionnaire. You may try a different browser, or you may try from a different computer. You may also see this problem if you are in a high security environment where this is disabled by a network policy. ...

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.

The design and implementation of stereoscopic 3D scalable vector graphics based on WebKit

NASA Astrophysics Data System (ADS)

Liu, Zhongxin; Wang, Wenmin; Wang, Ronggang

2014-03-01

Scalable Vector Graphics (SVG), which is a language designed based on eXtensible Markup Language (XML), is used to describe basic shapes embedded in webpages, such as circles and rectangles. However, it can only depict 2D shapes. As a consequence, web pages using classical SVG can only display 2D shapes on a screen. With the increasing development of stereoscopic 3D (S3D) technology, binocular 3D devices have been widely used. Under this circumstance, we intend to extend the widely used web rendering engine WebKit to support the description and display of S3D webpages. Therefore, the extension of SVG is of necessity. In this paper, we will describe how to design and implement SVG shapes with stereoscopic 3D mode. Two attributes representing the depth and thickness are added to support S3D shapes. The elimination of hidden lines and hidden surfaces, which is an important process in this project, is described as well. The modification of WebKit is also discussed, which is made to support the generation of both left view and right view at the same time. As is shown in the result, in contrast to the 2D shapes generated by the Google Chrome web browser, the shapes got from our modified browser are in S3D mode. With the feeling of depth and thickness, the shapes seem to be real 3D objects away from the screen, rather than simple curves and lines as before.

A Browser-Based Multi-User Working Environment for Physicists

NASA Astrophysics Data System (ADS)

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

2014-06-01

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

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.

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

A web-based genome browser for 'SNP-aware' assay design

USDA-ARS?s Scientific Manuscript database

Human and animal genomes contain an abundance of single nucleotide polymorphisms (SNPs) that are useful for genetic testing. However, the relatively large number of SNPs present in diverse populations can pose serious problems when designing assays. It is important to “mask” some SNP positions so ...

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…

Sharing the Knowledge: Browser Based Writing Business Applications.

ERIC Educational Resources Information Center

Evans, Nancy R.; Tuzi, Frank

The focus of this paper is the combination of oral and written response and technology, the components that form electronic feedback, and their possible benefits to business. The paper proposes that Web writing applications can provide numerous benefits to businesses and increase the communication and management of that communication. With the…

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...

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 .

SensA: web-based sensitivity analysis of SBML models.

PubMed

Floettmann, Max; Uhlendorf, Jannis; Scharp, Till; Klipp, Edda; Spiesser, Thomas W

2014-10-01

SensA is a web-based application for sensitivity analysis of mathematical models. The sensitivity analysis is based on metabolic control analysis, computing the local, global and time-dependent properties of model components. Interactive visualization facilitates interpretation of usually complex results. SensA can contribute to the analysis, adjustment and understanding of mathematical models for dynamic systems. SensA is available at http://gofid.biologie.hu-berlin.de/ and can be used with any modern browser. The source code can be found at https://bitbucket.org/floettma/sensa/ (MIT license) © The Author 2014. Published by Oxford University Press.

Value of Information Web Application

DTIC Science & Technology

2015-04-01

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

Technical Services and the World Wide Web.

ERIC Educational Resources Information Center

Scheschy, Virginia M.

The World Wide Web and browsers such as Netscape and Mosaic have simplified access to electronic resources. Today, technical services librarians can share in the wealth of information available on the Web. One of the premier Web sites for acquisitions librarians is AcqWeb, a cousin of the AcqNet listserv. In addition to interesting news items,…

The Genomic HyperBrowser: an analysis web server for genome-scale data

PubMed Central

Sandve, Geir K.; Gundersen, Sveinung; Johansen, Morten; Glad, Ingrid K.; Gunathasan, Krishanthi; Holden, Lars; Holden, Marit; Liestøl, Knut; Nygård, Ståle; Nygaard, Vegard; Paulsen, Jonas; Rydbeck, Halfdan; Trengereid, Kai; Clancy, Trevor; Drabløs, Finn; Ferkingstad, Egil; Kalaš, Matúš; Lien, Tonje; Rye, Morten B.; Frigessi, Arnoldo; Hovig, Eivind

2013-01-01

The immense increase in availability of genomic scale datasets, such as those provided by the ENCODE and Roadmap Epigenomics projects, presents unprecedented opportunities for individual researchers to pose novel falsifiable biological questions. With this opportunity, however, researchers are faced with the challenge of how to best analyze and interpret their genome-scale datasets. A powerful way of representing genome-scale data is as feature-specific coordinates relative to reference genome assemblies, i.e. as genomic tracks. The Genomic HyperBrowser (http://hyperbrowser.uio.no) is an open-ended web server for the analysis of genomic track data. Through the provision of several highly customizable components for processing and statistical analysis of genomic tracks, the HyperBrowser opens for a range of genomic investigations, related to, e.g., gene regulation, disease association or epigenetic modifications of the genome. PMID:23632163

The Genomic HyperBrowser: an analysis web server for genome-scale data.

PubMed

Sandve, Geir K; Gundersen, Sveinung; Johansen, Morten; Glad, Ingrid K; Gunathasan, Krishanthi; Holden, Lars; Holden, Marit; Liestøl, Knut; Nygård, Ståle; Nygaard, Vegard; Paulsen, Jonas; Rydbeck, Halfdan; Trengereid, Kai; Clancy, Trevor; Drabløs, Finn; Ferkingstad, Egil; Kalas, Matús; Lien, Tonje; Rye, Morten B; Frigessi, Arnoldo; Hovig, Eivind

2013-07-01

The immense increase in availability of genomic scale datasets, such as those provided by the ENCODE and Roadmap Epigenomics projects, presents unprecedented opportunities for individual researchers to pose novel falsifiable biological questions. With this opportunity, however, researchers are faced with the challenge of how to best analyze and interpret their genome-scale datasets. A powerful way of representing genome-scale data is as feature-specific coordinates relative to reference genome assemblies, i.e. as genomic tracks. The Genomic HyperBrowser (http://hyperbrowser.uio.no) is an open-ended web server for the analysis of genomic track data. Through the provision of several highly customizable components for processing and statistical analysis of genomic tracks, the HyperBrowser opens for a range of genomic investigations, related to, e.g., gene regulation, disease association or epigenetic modifications of the genome.

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

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

NASA Astrophysics Data System (ADS)

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

2014-06-01

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

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

PubMed

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

2013-02-01

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

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.

Specification and Verification of Web Applications in Rewriting Logic

NASA Astrophysics Data System (ADS)

Alpuente, María; Ballis, Demis; Romero, Daniel

This paper presents a Rewriting Logic framework that formalizes the interactions between Web servers and Web browsers through a communicating protocol abstracting HTTP. The proposed framework includes a scripting language that is powerful enough to model the dynamics of complex Web applications by encompassing the main features of the most popular Web scripting languages (e.g. PHP, ASP, Java Servlets). We also provide a detailed characterization of browser actions (e.g. forward/backward navigation, page refresh, and new window/tab openings) via rewrite rules, and show how our models can be naturally model-checked by using the Linear Temporal Logic of Rewriting (LTLR), which is a Linear Temporal Logic specifically designed for model-checking rewrite theories. Our formalization is particularly suitable for verification purposes, since it allows one to perform in-depth analyses of many subtle aspects related to Web interaction. Finally, the framework has been completely implemented in Maude, and we report on some successful experiments that we conducted by using the Maude LTLR model-checker.

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.

A Study and Taxonomy of Vulnerabilities in Web Based Animation and Interactivity Software

DTIC Science & Technology

2010-12-01

Flash Player is available as a plugin for most common Web browsers (Firefox, Mozilla, Netscape, Opera) and as an ActiveX control for Internet...script or HTML via (1) a swf file that uses the asfunction: protocol or (2) the navigateToURL function when used with the Flash Player ActiveX ...malicious page or open a malicious file. 2. Coding an Exploit The specific flaw exists in the Flash Player ActiveX Control’s handling of the

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.

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.

Eyes on the Earth 3D

NASA Technical Reports Server (NTRS)

Kulikov, anton I.; Doronila, Paul R.; Nguyen, Viet T.; Jackson, Randal K.; Greene, William M.; Hussey, Kevin J.; Garcia, Christopher M.; Lopez, Christian A.

2013-01-01

Eyes on the Earth 3D software gives scientists, and the general public, a realtime, 3D interactive means of accurately viewing the real-time locations, speed, and values of recently collected data from several of NASA's Earth Observing Satellites using a standard Web browser (climate.nasa.gov/eyes). Anyone with Web access can use this software to see where the NASA fleet of these satellites is now, or where they will be up to a year in the future. The software also displays several Earth Science Data sets that have been collected on a daily basis. This application uses a third-party, 3D, realtime, interactive game engine called Unity 3D to visualize the satellites and is accessible from a Web browser.

Web-based X-ray quality control documentation.

PubMed

David, George; Burnett, Lou Ann; Schenkel, Robert

2003-01-01

The department of radiology at the Medical College of Georgia Hospital and Clinics has developed an equipment quality control web site. Our goal is to provide immediate access to virtually all medical physics survey data. The web site is designed to assist equipment engineers, department management and technologists. By improving communications and access to equipment documentation, we believe productivity is enhanced. The creation of the quality control web site was accomplished in three distinct steps. First, survey data had to be placed in a computer format. The second step was to convert these various computer files to a format supported by commercial web browsers. Third, a comprehensive home page had to be designed to provide convenient access to the multitude of surveys done in the various x-ray rooms. Because we had spent years previously fine-tuning the computerization of the medical physics quality control program, most survey documentation was already in spreadsheet or database format. A major technical decision was the method of conversion of survey spreadsheet and database files into documentation appropriate for the web. After an unsatisfactory experience with a HyperText Markup Language (HTML) converter (packaged with spreadsheet and database software), we tried creating Portable Document Format (PDF) files using Adobe Acrobat software. This process preserves the original formatting of the document and takes no longer than conventional printing; therefore, it has been very successful. Although the PDF file generated by Adobe Acrobat is a proprietary format, it can be displayed through a conventional web browser using the freely distributed Adobe Acrobat Reader program that is available for virtually all platforms. Once a user installs the software, it is automatically invoked by the web browser whenever the user follows a link to a file with a PDF extension. Although no confidential patient information is available on the web site, our legal department recommended that we secure the site in order to keep out those wishing to make mischief. Our interim solution has not been to password protect the page, which we feared would hinder access for occasional legitimate users, but also not to provide links to it from other hospital and department pages. Utility and productivity were improved and time and money were saved by making radiological equipment quality control documentation instantly available on-line.

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…

Benefits of Using Online Student Response Systems in Japanese EFL Classrooms

ERIC Educational Resources Information Center

Mork, Cathrine-Mette

2014-01-01

Online student response systems (OSRSs) are fast replacing classroom response systems (CRSs), also known as personal or audience response systems or "clickers". OSRSs can more easily be implemented in the classroom because they are web-based and allow students to use any browser and device to do the "clicking" required to…

Usability of Browser-Based Tools for Web-Search Privacy

DTIC Science & Technology

2010-03-01

What might Italians call maize? — Polenta From which country do french fries originate? — Belgium In Peru, which color potatoes are grown, in addition...What is kartofflen? — Potato Dumplings What is the name of the flatbread eaten with most Indian cuisine ? — Naan What type of cuisine offers Dim Sum

Augmenting Research, Education, and Outreach with Client-Side Web Programming.

PubMed

Abriata, Luciano A; Rodrigues, João P G L M; Salathé, Marcel; Patiny, Luc

2018-05-01

The evolution of computing and web technologies over the past decade has enabled the development of fully fledged scientific applications that run directly on web browsers. Powered by JavaScript, the lingua franca of web programming, these 'web apps' are starting to revolutionize and democratize scientific research, education, and outreach. Copyright © 2017 Elsevier Ltd. All rights reserved.

XML Content Finally Arrives on the Web!

ERIC Educational Resources Information Center

Funke, Susan

1998-01-01

Explains extensible markup language (XML) and how it differs from hypertext markup language (HTML) and standard generalized markup language (SGML). Highlights include features of XML, including better formatting of documents, better searching capabilities, multiple uses for hyperlinking, and an increase in Web applications; Web browsers; and what…

Dynamic alarm response procedures

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

Martin, J.; Gordon, P.; Fitch, K.

2006-07-01

The Dynamic Alarm Response Procedure (DARP) system provides a robust, Web-based alternative to existing hard-copy alarm response procedures. This paperless system improves performance by eliminating time wasted looking up paper procedures by number, looking up plant process values and equipment and component status at graphical display or panels, and maintenance of the procedures. Because it is a Web-based system, it is platform independent. DARP's can be served from any Web server that supports CGI scripting, such as Apache{sup R}, IIS{sup R}, TclHTTPD, and others. DARP pages can be viewed in any Web browser that supports Javascript and Scalable Vector Graphicsmore » (SVG), such as Netscape{sup R}, Microsoft Internet Explorer{sup R}, Mozilla Firefox{sup R}, Opera{sup R}, and others. (authors)« less

Comparative analysis and visualization of multiple collinear genomes

PubMed Central

2012-01-01

Background Genome browsers are a common tool used by biologists to visualize genomic features including genes, polymorphisms, and many others. However, existing genome browsers and visualization tools are not well-suited to perform meaningful comparative analysis among a large number of genomes. With the increasing quantity and availability of genomic data, there is an increased burden to provide useful visualization and analysis tools for comparison of multiple collinear genomes such as the large panels of model organisms which are the basis for much of the current genetic research. Results We have developed a novel web-based tool for visualizing and analyzing multiple collinear genomes. Our tool illustrates genome-sequence similarity through a mosaic of intervals representing local phylogeny, subspecific origin, and haplotype identity. Comparative analysis is facilitated through reordering and clustering of tracks, which can vary throughout the genome. In addition, we provide local phylogenetic trees as an alternate visualization to assess local variations. Conclusions Unlike previous genome browsers and viewers, ours allows for simultaneous and comparative analysis. Our browser provides intuitive selection and interactive navigation about features of interest. Dynamic visualizations adjust to scale and data content making analysis at variable resolutions and of multiple data sets more informative. We demonstrate our genome browser for an extensive set of genomic data sets composed of almost 200 distinct mouse laboratory strains. PMID:22536897

XML — an opportunity for data standards in the geosciences

NASA Astrophysics Data System (ADS)

Houlding, Simon W.

2001-08-01

Extensible markup language (XML) is a recently introduced meta-language standard on the Web. It provides the rules for development of metadata (markup) standards for information transfer in specific fields. XML allows development of markup languages that describe what information is rather than how it should be presented. This allows computer applications to process the information in intelligent ways. In contrast hypertext markup language (HTML), which fuelled the initial growth of the Web, is a metadata standard concerned exclusively with presentation of information. Besides its potential for revolutionizing Web activities, XML provides an opportunity for development of meaningful data standards in specific application fields. The rapid endorsement of XML by science, industry and e-commerce has already spawned new metadata standards in such fields as mathematics, chemistry, astronomy, multi-media and Web micro-payments. Development of XML-based data standards in the geosciences would significantly reduce the effort currently wasted on manipulating and reformatting data between different computer platforms and applications and would ensure compatibility with the new generation of Web browsers. This paper explores the evolution, benefits and status of XML and related standards in the more general context of Web activities and uses this as a platform for discussion of its potential for development of data standards in the geosciences. Some of the advantages of XML are illustrated by a simple, browser-compatible demonstration of XML functionality applied to a borehole log dataset. The XML dataset and the associated stylesheet and schema declarations are available for FTP download.

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.

Rational analyses of information foraging on the web.

PubMed

Pirolli, Peter

2005-05-06

This article describes rational analyses and cognitive models of Web users developed within information foraging theory. This is done by following the rational analysis methodology of (a) characterizing the problems posed by the environment, (b) developing rational analyses of behavioral solutions to those problems, and (c) developing cognitive models that approach the realization of those solutions. Navigation choice is modeled as a random utility model that uses spreading activation mechanisms that link proximal cues (information scent) that occur in Web browsers to internal user goals. Web-site leaving is modeled as an ongoing assessment by the Web user of the expected benefits of continuing at a Web site as opposed to going elsewhere. These cost-benefit assessments are also based on spreading activation models of information scent. Evaluations include a computational model of Web user behavior called Scent-Based Navigation and Information Foraging in the ACT Architecture, and the Law of Surfing, which characterizes the empirical distribution of the length of paths of visitors at a Web site. 2005 Lawrence Erlbaum Associates, Inc.

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.

Semantic Body Browser: graphical exploration of an organism and spatially resolved expression data visualization.

PubMed

Lekschas, Fritz; Stachelscheid, Harald; Seltmann, Stefanie; Kurtz, Andreas

2015-03-01

Advancing technologies generate large amounts of molecular and phenotypic data on cells, tissues and organisms, leading to an ever-growing detail and complexity while information retrieval and analysis becomes increasingly time-consuming. The Semantic Body Browser is a web application for intuitively exploring the body of an organism from the organ to the subcellular level and visualising expression profiles by means of semantically annotated anatomical illustrations. It is used to comprehend biological and medical data related to the different body structures while relying on the strong pattern recognition capabilities of human users. The Semantic Body Browser is a JavaScript web application that is freely available at http://sbb.cellfinder.org. The source code is provided on https://github.com/flekschas/sbb. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Online interactive analysis of protein structure ensembles with Bio3D-web.

PubMed

Skjærven, Lars; Jariwala, Shashank; Yao, Xin-Qiu; Grant, Barry J

2016-11-15

Bio3D-web is an online application for analyzing the sequence, structure and conformational heterogeneity of protein families. Major functionality is provided for identifying protein structure sets for analysis, their alignment and refined structure superposition, sequence and structure conservation analysis, mapping and clustering of conformations and the quantitative comparison of their predicted structural dynamics. Bio3D-web is based on the Bio3D and Shiny R packages. All major browsers are supported and full source code is available under a GPL2 license from http://thegrantlab.org/bio3d-web CONTACT: bjgrant@umich.edu or lars.skjarven@uib.no. © The Author 2016. Published by Oxford University Press.

Finding, Browsing and Getting Data Easily Using SPDF Web Services

NASA Technical Reports Server (NTRS)

Candey, R.; Chimiak, R.; Harris, B.; Johnson, R.; Kovalick, T.; Lal, N.; Leckner, H.; Liu, M.; McGuire, R.; Papitashvili, N.;

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

Streamlining Data for Cross-Platform Web Delivery

ERIC Educational Resources Information Center

Watkins, Sean; Battles, Jason; Vacek, Rachel

2013-01-01

Smartphone users expect the presentation of Web sites on their mobile browsers to look and feel like native applications. With the pressure on library Web developers to produce app-like mobile sites, there is often a rush to get a site up without considering the importance of reusing or even restructuring the data driving the Web sites. An…

WebTag: Web browsing into sensor tags over NFC.

PubMed

Echevarria, Juan Jose; Ruiz-de-Garibay, Jonathan; Legarda, Jon; Alvarez, Maite; Ayerbe, Ana; Vazquez, Juan Ignacio

2012-01-01

Information and Communication Technologies (ICTs) continue to overcome many of the challenges related to wireless sensor monitoring, such as for example the design of smarter embedded processors, the improvement of the network architectures, the development of efficient communication protocols or the maximization of the life cycle autonomy. This work tries to improve the communication link of the data transmission in wireless sensor monitoring. The upstream communication link is usually based on standard IP technologies, but the downstream side is always masked with the proprietary protocols used for the wireless link (like ZigBee, Bluetooth, RFID, etc.). This work presents a novel solution (WebTag) for a direct IP based access to a sensor tag over the Near Field Communication (NFC) technology for secure applications. WebTag allows a direct web access to the sensor tag by means of a standard web browser, it reads the sensor data, configures the sampling rate and implements IP based security policies. It is, definitely, a new step towards the evolution of the Internet of Things paradigm.

WebTag: Web Browsing into Sensor Tags over NFC

PubMed Central

Echevarria, Juan Jose; Ruiz-de-Garibay, Jonathan; Legarda, Jon; Álvarez, Maite; Ayerbe, Ana; Vazquez, Juan Ignacio

2012-01-01

Information and Communication Technologies (ICTs) continue to overcome many of the challenges related to wireless sensor monitoring, such as for example the design of smarter embedded processors, the improvement of the network architectures, the development of efficient communication protocols or the maximization of the life cycle autonomy. This work tries to improve the communication link of the data transmission in wireless sensor monitoring. The upstream communication link is usually based on standard IP technologies, but the downstream side is always masked with the proprietary protocols used for the wireless link (like ZigBee, Bluetooth, RFID, etc.). This work presents a novel solution (WebTag) for a direct IP based access to a sensor tag over the Near Field Communication (NFC) technology for secure applications. WebTag allows a direct web access to the sensor tag by means of a standard web browser, it reads the sensor data, configures the sampling rate and implements IP based security policies. It is, definitely, a new step towards the evolution of the Internet of Things paradigm. PMID:23012511

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

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

DTIC Science & Technology

2015-01-01

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

A Course Evolves-Physical Anthropology.

ERIC Educational Resources Information Center

O'Neil, Dennis

2001-01-01

Describes the development of an online physical anthropology course at Palomar College (California) that evolved from online tutorials. Discusses the ability to update materials on the Web more quickly than in traditional textbooks; creating Web pages that are readable by most Web browsers; test security issues; and clarifying ownership of online…

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/.

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.

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.

Accident/Mishap Investigation System

NASA Technical Reports Server (NTRS)

Keller, Richard; Wolfe, Shawn; Gawdiak, Yuri; Carvalho, Robert; Panontin, Tina; Williams, James; Sturken, Ian

2007-01-01

InvestigationOrganizer (IO) is a Web-based collaborative information system that integrates the generic functionality of a database, a document repository, a semantic hypermedia browser, and a rule-based inference system with specialized modeling and visualization functionality to support accident/mishap investigation teams. This accessible, online structure is designed to support investigators by allowing them to make explicit, shared, and meaningful links among evidence, causal models, findings, and recommendations.

Reusable Client-Side JavaScript Modules for Immersive Web-Based Real-Time Collaborative Neuroimage Visualization.

PubMed

Bernal-Rusiel, Jorge L; Rannou, Nicolas; Gollub, Randy L; Pieper, Steve; Murphy, Shawn; Robertson, Richard; Grant, Patricia E; Pienaar, Rudolph

2017-01-01

In this paper we present a web-based software solution to the problem of implementing real-time collaborative neuroimage visualization. In both clinical and research settings, simple and powerful access to imaging technologies across multiple devices is becoming increasingly useful. Prior technical solutions have used a server-side rendering and push-to-client model wherein only the server has the full image dataset. We propose a rich client solution in which each client has all the data and uses the Google Drive Realtime API for state synchronization. We have developed a small set of reusable client-side object-oriented JavaScript modules that make use of the XTK toolkit, a popular open-source JavaScript library also developed by our team, for the in-browser rendering and visualization of brain image volumes. Efficient realtime communication among the remote instances is achieved by using just a small JSON object, comprising a representation of the XTK image renderers' state, as the Google Drive Realtime collaborative data model. The developed open-source JavaScript modules have already been instantiated in a web-app called MedView , a distributed collaborative neuroimage visualization application that is delivered to the users over the web without requiring the installation of any extra software or browser plugin. This responsive application allows multiple physically distant physicians or researchers to cooperate in real time to reach a diagnosis or scientific conclusion. It also serves as a proof of concept for the capabilities of the presented technological solution.

Proposal and Implementation of SSH Client System Using Ajax

NASA Astrophysics Data System (ADS)

Kosuda, Yusuke; Sasaki, Ryoichi

Technology called Ajax gives web applications the functionality and operability of desktop applications. In this study, we propose and implement a Secure Shell (SSH) client system using Ajax, independent of the OS or Java execution environment. In this system, SSH packets are generated on a web browser by using JavaScript and a web server works as a proxy in communication with an SSH server to realize end-to-end SSH communication. We implemented a prototype program and confirmed by experiment that it runs on several web browsers and mobile phones. This system has enabled secure SSH communication from a PC at an Internet cafe or any mobile phone. By measuring the processing performance, we verified satisfactory performance for emergency use, although the speed was unsatisfactory in some cases with mobile phone. The system proposed in this study will be effective in various fields of E-Business.

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.

Chemical Space: Big Data Challenge for Molecular Diversity.

PubMed

Awale, Mahendra; Visini, Ricardo; Probst, Daniel; Arús-Pous, Josep; Reymond, Jean-Louis

2017-10-25

Chemical space describes all possible molecules as well as multi-dimensional conceptual spaces representing the structural diversity of these molecules. Part of this chemical space is available in public databases ranging from thousands to billions of compounds. Exploiting these databases for drug discovery represents a typical big data problem limited by computational power, data storage and data access capacity. Here we review recent developments of our laboratory, including progress in the chemical universe databases (GDB) and the fragment subset FDB-17, tools for ligand-based virtual screening by nearest neighbor searches, such as our multi-fingerprint browser for the ZINC database to select purchasable screening compounds, and their application to discover potent and selective inhibitors for calcium channel TRPV6 and Aurora A kinase, the polypharmacology browser (PPB) for predicting off-target effects, and finally interactive 3D-chemical space visualization using our online tools WebDrugCS and WebMolCS. All resources described in this paper are available for public use at www.gdb.unibe.ch.

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.

FloorspaceJS - A New, Open Source, Web-Based Geometry Editor for Building Energy Modeling (BEM): Preprint

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

Macumber, Daniel L; Horowitz, Scott G; Schott, Marjorie

Across most industries, desktop applications are being rapidly migrated to web applications for a variety of reasons. Web applications are inherently cross platform, mobile, and easier to distribute than desktop applications. Fueling this trend are a wide range of free, open source libraries and frameworks that make it incredibly easy to develop powerful web applications. The building energy modeling community is just beginning to pick up on these larger trends, with a small but growing number of building energy modeling applications starting on or moving to the web. This paper presents a new, open source, web based geometry editor formore » Building Energy Modeling (BEM). The editor is written completely in JavaScript and runs in a modern web browser. The editor works on a custom JSON file format and is designed to be integrated into a variety of web and desktop applications. The web based editor is available to use as a standalone web application at: https://nrel.github.io/openstudio-geometry-editor/. An example integration is demonstrated with the OpenStudio desktop application. Finally, the editor can be easily integrated with a wide range of possible building energy modeling web applications.« less

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.

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.

Mobile Monitoring Stations and Web Visualization of Biotelemetric System - Guardian II

NASA Astrophysics Data System (ADS)

Krejcar, Ondrej; Janckulik, Dalibor; Motalova, Leona; Kufel, Jan

The main area of interest of our project is to provide solution which can be used in different areas of health care and which will be available through PDAs (Personal Digital Assistants), web browsers or desktop clients. The realized system deals with an ECG sensor connected to mobile equipment, such as PDA/Embedded, based on Microsoft Windows Mobile operating system. The whole system is based on the architecture of .NET Compact Framework, and Microsoft SQL Server. Visualization possibilities of web interface and ECG data are also discussed and final suggestion is made to Microsoft Silverlight solution along with current screenshot representation of implemented solution. The project was successfully tested in real environment in cryogenic room (-136OC).

EPA MED-DULUTH'S ECOTOX AND ECO-SSL WEB APPLICATIONS

EPA Science Inventory

The ECOTOX (ECOTOXicology Database) system developed by the USEPA, National Health and Environmental Effects Research Laboratory (NHEERL), Mid-Continent Ecology Division in Duluth, MN (MED-Duluth), provides a web browser search interface for locating aquatic and terrestrial toxic...

Navigating protected genomics data with UCSC Genome Browser in a Box.

PubMed

Haeussler, Maximilian; Raney, Brian J; Hinrichs, Angie S; Clawson, Hiram; Zweig, Ann S; Karolchik, Donna; Casper, Jonathan; Speir, Matthew L; Haussler, David; Kent, W James

2015-03-01

Genome Browser in a Box (GBiB) is a small virtual machine version of the popular University of California Santa Cruz (UCSC) Genome Browser that can be run on a researcher's own computer. Once GBiB is installed, a standard web browser is used to access the virtual server and add personal data files from the local hard disk. Annotation data are loaded on demand through the Internet from UCSC or can be downloaded to the local computer for faster access. Software downloads and installation instructions are freely available for non-commercial use at https://genome-store.ucsc.edu/. GBiB requires the installation of open-source software VirtualBox, available for all major operating systems, and the UCSC Genome Browser, which is open source and free for non-commercial use. Commercial use of GBiB and the Genome Browser requires a license (http://genome.ucsc.edu/license/). © The Author 2014. Published by Oxford University Press.

Resource Management Scheme Based on Ubiquitous Data Analysis

PubMed Central

Lee, Heung Ki; Jung, Jaehee

2014-01-01

Resource management of the main memory and process handler is critical to enhancing the system performance of a web server. Owing to the transaction delay time that affects incoming requests from web clients, web server systems utilize several web processes to anticipate future requests. This procedure is able to decrease the web generation time because there are enough processes to handle the incoming requests from web browsers. However, inefficient process management results in low service quality for the web server system. Proper pregenerated process mechanisms are required for dealing with the clients' requests. Unfortunately, it is difficult to predict how many requests a web server system is going to receive. If a web server system builds too many web processes, it wastes a considerable amount of memory space, and thus performance is reduced. We propose an adaptive web process manager scheme based on the analysis of web log mining. In the proposed scheme, the number of web processes is controlled through prediction of incoming requests, and accordingly, the web process management scheme consumes the least possible web transaction resources. In experiments, real web trace data were used to prove the improved performance of the proposed scheme. PMID:25197692

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

PubMed

Basu, M K

2001-06-01

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

Learning To Use the World Wide Web. Academic Edition.

ERIC Educational Resources Information Center

Ackerman, Ernest

This book emphasizes how to use Netscape Navigator to access the World Wide Web and associated resources and services in a step-by-step, organized manner. Chapters include -- Chapter 1: Introduction to the World Wide Web and the Internet; Chapter 2: Using a Web Browser; Chapter 3: The Basics of Electronic Mail and Using Netscape Email; Chapter 4:…

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

PubMed Central

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

2013-01-01

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

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.

Google Wave: Collaboration Reworked

ERIC Educational Resources Information Center

Rethlefsen, Melissa L.

2010-01-01

Over the past several years, Internet users have become accustomed to Web 2.0 and cloud computing-style applications. It's commonplace and even intuitive to drag and drop gadgets on personalized start pages, to comment on a Facebook post without reloading the page, and to compose and save documents through a web browser. The web paradigm has…

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…

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.

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.

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.

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.

Creating Web-Based Scientific Applications Using Java Servlets

NASA Technical Reports Server (NTRS)

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

2001-01-01

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

Worldwide telemedicine services based on distributed multimedia electronic patient records by using the second generation Web server hyperwave.

PubMed

Quade, G; Novotny, J; Burde, B; May, F; Beck, L E; Goldschmidt, A

1999-01-01

A distributed multimedia electronic patient record (EPR) is a central component of a medicine-telematics application that supports physicians working in rural areas of South America, and offers medical services to scientists in Antarctica. A Hyperwave server is used to maintain the patient record. As opposed to common web servers--and as a second generation web server--Hyperwave provides the capability of holding documents in a distributed web space without the problem of broken links. This enables physicians to browse through a patient's record by using a standard browser even if the patient's record is distributed over several servers. The patient record is basically implemented on the "Good European Health Record" (GEHR) architecture.

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/.

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.

BigWig and BigBed: enabling browsing of large distributed datasets.

PubMed

Kent, W J; Zweig, A S; Barber, G; Hinrichs, A S; Karolchik, D

2010-09-01

BigWig and BigBed files are compressed binary indexed files containing data at several resolutions that allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser. The visualization is implemented using a multi-layered software approach that takes advantage of specific capabilities of web-based protocols and Linux and UNIX operating systems files, R trees and various indexing and compression tricks. As a result, only the data needed to support the current browser view is transmitted rather than the entire file, enabling fast remote access to large distributed data sets. Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/. Source code for the creation and visualization software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. The UCSC Genome Browser is available at http://genome.ucsc.edu.

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).

Introduction to the world wide web.

PubMed

Downes, P K

2007-05-12

The World Wide Web used to be nicknamed the 'World Wide Wait'. Now, thanks to high speed broadband connections, browsing the web has become a much more enjoyable and productive activity. Computers need to know where web pages are stored on the Internet, in just the same way as we need to know where someone lives in order to post them a letter. This section explains how the World Wide Web works and how web pages can be viewed using a web browser.

Security and Efficiency Concerns With Distributed Collaborative Networking Environments

DTIC Science & Technology

2003-09-01

have the ability to access Web communications services of the WebEx MediaTone Network from a single login. [24] WebEx provides a range of secure...Web. WebEx services enable secure data, voice and video communications through the browser and are supported by the WebEx MediaTone Network, a global...designed to host large-scale, structured events and conferences, featuring a Q&A Manager that allows multiple moderators to handle questions while

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.

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.

Using the Internet in Secondary Schools.

ERIC Educational Resources Information Center

De Cicco, Eta; Farmer, Mike; Hargrave, James

This book provides practical information for secondary school teachers on using the Internet to enhance learning. The first chapter looks at how to make the best use of a World Wide Web browser, gives some general tips for using the Web, and examines more advanced topics such as downloading, plug-ins, and using the Web "offline." Tips on…

Enhanced interfaces for web-based enterprise-wide image distribution.

PubMed

Jost, R Gilbert; Blaine, G James; Fritz, Kevin; Blume, Hartwig; Sadhra, Sarbjit

2002-01-01

Modern Web browsers support image distribution with two shortcomings: (1) image grayscale presentation at client workstations is often sub-optimal and generally inconsistent with the presentation state on diagnostic workstations and (2) an Electronic Patient Record (EPR) application usually cannot directly access images with an integrated viewer. We have modified our EPR and our Web-based image-distribution system to allow access to images from within the EPR. In addition, at the client workstation, a grayscale transformation is performed that consists of two components: a client-display-specific component based on the characteristic display function of the class of display system, and a modality-specific transformation that is downloaded with every image. The described techniques have been implemented in our institution and currently support enterprise-wide clinical image distribution. The effectiveness of the techniques is reviewed.

Engineering the ATLAS TAG Browser

NASA Astrophysics Data System (ADS)

Zhang, Qizhi; ATLAS Collaboration

2011-12-01

ELSSI is a web-based event metadata (TAG) browser and event-level selection service for ATLAS. In this paper, we describe some of the challenges encountered in the process of developing ELSSI, and the software engineering strategies adopted to address those challenges. Approaches to management of access to data, browsing, data rendering, query building, query validation, execution, connection management, and communication with auxiliary services are discussed. We also describe strategies for dealing with data that may vary over time, such as run-dependent trigger decision decoding. Along with examples, we illustrate how programming techniques in multiple languages (PHP, JAVASCRIPT, XML, AJAX, and PL/SQL) have been blended to achieve the required results. Finally, we evaluate features of the ELSSI service in terms of functionality, scalability, and performance.

Reusable Client-Side JavaScript Modules for Immersive Web-Based Real-Time Collaborative Neuroimage Visualization

PubMed Central

Bernal-Rusiel, Jorge L.; Rannou, Nicolas; Gollub, Randy L.; Pieper, Steve; Murphy, Shawn; Robertson, Richard; Grant, Patricia E.; Pienaar, Rudolph

2017-01-01

In this paper we present a web-based software solution to the problem of implementing real-time collaborative neuroimage visualization. In both clinical and research settings, simple and powerful access to imaging technologies across multiple devices is becoming increasingly useful. Prior technical solutions have used a server-side rendering and push-to-client model wherein only the server has the full image dataset. We propose a rich client solution in which each client has all the data and uses the Google Drive Realtime API for state synchronization. We have developed a small set of reusable client-side object-oriented JavaScript modules that make use of the XTK toolkit, a popular open-source JavaScript library also developed by our team, for the in-browser rendering and visualization of brain image volumes. Efficient realtime communication among the remote instances is achieved by using just a small JSON object, comprising a representation of the XTK image renderers' state, as the Google Drive Realtime collaborative data model. The developed open-source JavaScript modules have already been instantiated in a web-app called MedView, a distributed collaborative neuroimage visualization application that is delivered to the users over the web without requiring the installation of any extra software or browser plugin. This responsive application allows multiple physically distant physicians or researchers to cooperate in real time to reach a diagnosis or scientific conclusion. It also serves as a proof of concept for the capabilities of the presented technological solution. PMID:28507515

Web surveillance system using platform-based design

NASA Astrophysics Data System (ADS)

Lin, Shin-Yo; Tsai, Tsung-Han

2004-04-01

A revolutionary methodology of SOPC platform-based design environment for multimedia communications will be developed. We embed a softcore processor to perform the image compression in FPGA. Then, we plug-in an Ethernet daughter board in the SOPC development platform system. Afterward, a web surveillance platform system is presented. The web surveillance system consists of three parts: image capture, web server and JPEG compression. In this architecture, user can control the surveillance system by remote. By the IP address configures to Ethernet daughter board, the user can access the surveillance system via browser. When user access the surveillance system, the CMOS sensor presently capture the remote image. After that, it will feed the captured image with the embedded processor. The embedded processor immediately performs the JPEG compression. Afterward, the user receives the compressed data via Ethernet. To sum up of the above mentioned, the all system will be implemented on APEX20K200E484-2X device.

First Operational Experience With a High-Energy Physics Run Control System Based on Web Technologies

NASA Astrophysics Data System (ADS)

Bauer, Gerry; Beccati, Barbara; Behrens, Ulf; Biery, Kurt; Branson, James; Bukowiec, Sebastian; Cano, Eric; Cheung, Harry; Ciganek, Marek; Cittolin, Sergio; Coarasa Perez, Jose Antonio; Deldicque, Christian; Erhan, Samim; Gigi, Dominique; Glege, Frank; Gomez-Reino, Robert; Gulmini, Michele; Hatton, Derek; Hwong, Yi Ling; Loizides, Constantin; Ma, Frank; Masetti, Lorenzo; Meijers, Frans; Meschi, Emilio; Meyer, Andreas; Mommsen, Remigius K.; Moser, Roland; O'Dell, Vivian; Oh, Alexander; Orsini, Luciano; Paus, Christoph; Petrucci, Andrea; Pieri, Marco; Racz, Attila; Raginel, Olivier; Sakulin, Hannes; Sani, Matteo; Schieferdecker, Philipp; Schwick, Christoph; Shpakov, Dennis; Simon, Michal; Sumorok, Konstanty; Yoon, Andre Sungho

2012-08-01

Run control systems of modern high-energy particle physics experiments have requirements similar to those of today's Internet applications. The Compact Muon Solenoid (CMS) collaboration at CERN's Large Hadron Collider (LHC) therefore decided to build the run control system for its detector based on web technologies. The system is composed of Java Web Applications distributed over a set of Apache Tomcat servlet containers that connect to a database back-end. Users interact with the system through a web browser. The present paper reports on the successful scaling of the system from a small test setup to the production data acquisition system that comprises around 10.000 applications running on a cluster of about 1600 hosts. We report on operational aspects during the first phase of operation with colliding beams including performance, stability, integration with the CMS Detector Control System and tools to guide the operator.

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters

PubMed Central

Ono, Keiichiro; Demchak, Barry; Ideker, Trey

2014-01-01

In this paper we present new data export modules for Cytoscape 3 that can generate network files for Cytoscape.js and D3.js. Cytoscape.js exporter is implemented as a core feature of Cytoscape 3, and D3.js exporter is available as a Cytoscape 3 app. These modules enable users to seamlessly export network and table data sets generated in Cytoscape to popular JavaScript library readable formats. In addition, we implemented template web applications for browser-based interactive network visualization that can be used as basis for complex data visualization applications for bioinformatics research. Example web applications created with these tools demonstrate how Cytoscape works in modern data visualization workflows built with traditional desktop tools and emerging web-based technologies. This interactivity enables researchers more flexibility than with static images, thereby greatly improving the quality of insights researchers can gain from them. PMID:25520778

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters.

PubMed

Ono, Keiichiro; Demchak, Barry; Ideker, Trey

2014-01-01

In this paper we present new data export modules for Cytoscape 3 that can generate network files for Cytoscape.js and D3.js. Cytoscape.js exporter is implemented as a core feature of Cytoscape 3, and D3.js exporter is available as a Cytoscape 3 app. These modules enable users to seamlessly export network and table data sets generated in Cytoscape to popular JavaScript library readable formats. In addition, we implemented template web applications for browser-based interactive network visualization that can be used as basis for complex data visualization applications for bioinformatics research. Example web applications created with these tools demonstrate how Cytoscape works in modern data visualization workflows built with traditional desktop tools and emerging web-based technologies. This interactivity enables researchers more flexibility than with static images, thereby greatly improving the quality of insights researchers can gain from them.

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.

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.

Technical Considerations in Remote LIMS Access via the World Wide Web

PubMed Central

Schlabach, David M.

2005-01-01

The increased dependency on the World Wide Web by both laboratories and their customers has led LIMS developers to take advantage of thin-client web applications that provide both remote data entry and manipulation, along with remote reporting functionality. Use of an LIMS through a web browser allows a person to interact with a distant application, providing both remote administration and real-time analytical result delivery from virtually anywhere in the world. While there are many benefits of web-based LIMS applications, some concern must be given to these new methods of system architecture before justifying them as a suitable replacement for their traditional client-server systems. Developers and consumers alike must consider the security aspects of introducing a wide area network capable system into a production environment, as well as the concerns of data integrity and usability. PMID:18924736

Aladin Lite: Lightweight sky atlas for browsers

NASA Astrophysics Data System (ADS)

Boch, Thomas

2014-02-01

Aladin Lite is a lightweight version of the Aladin tool, running in the browser and geared towards simple visualization of a sky region. It allows visualization of image surveys (JPEG multi-resolution HEALPix all-sky surveys) and permits superimposing tabular (VOTable) and footprints (STC-S) data. Aladin Lite is powered by HTML5 canvas technology and is easily embeddable on any web page and can also be controlled through a Javacript API.

JNSViewer—A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures

PubMed Central

Dong, Min; Graham, Mitchell; Yadav, Nehul

2017-01-01

Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome) were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html. PMID:28582416

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.

Nurses' Internet self-efficacy and attitudes toward web-based continuing learning.

PubMed

Liang, Jyh-Chong; Wu, Szu-Hsien; Tsai, Chin-Chung

2011-11-01

There are increasing opportunities for nurses to engage in continuing learning via the Internet; hence, it is important to explore nurses' attitudes toward web-based continuing learning. This paper explores 267 Taiwanese clinical nurses' attitudes toward web-based continuing learning. In addition, the role of the nurses' Internet self-efficacy in their attitudes is investigated. This study utilizes two questionnaires to respectively survey the nurses' Internet self-efficacy and their attitudes toward web-based continuing learning. In particular, the Internet Self-efficacy Survey includes two scales: 'Basic self-efficacy' (the perceived confidence of using basic Internet functions, such as the confidence in using a web browser or searching for online information) and 'Advanced self-efficacy' (the perceived confidence of using advanced Internet functions, such as the confidence in online discussion or making online payments). Exploratory factor analyses indicated adequate reliability and validity of the two questionnaires. The regression analyses revealed that both nurses' basic and advanced Internet self-efficacy can positively explain the perceived usefulness, ease of use and friendly feeling when using web-based continuing learning environments, whereas nurses' advanced Internet self-efficacy was the only predictor to explain how they intend to use web-based continuing learning environments more. Copyright © 2010 Elsevier Ltd. All rights reserved.

Understanding Web Activity Patterns among Teachers, Students and Teacher Candidates

ERIC Educational Resources Information Center

Kimmons, Royce; Clark, B.; Lim, M.

2017-01-01

This study sought to understand generational and role differences in web usage of teachers, teacher candidates and K-12 students in a state in the USA (n = 2261). The researchers employed unique methods, which included using a custom-built persistent web browser to track user behaviours free of self-report, self-selection and perception bias.…

THE ECOTOX DATABASE AND ECOLOGICAL SOIL SCREENING LEVEL (ECO-SSL) WEB SITES

EPA Science Inventory

The EPA's ECOTOX database (http://www.epa.gov/ecotox/) provides a web browser search interface for locating aquatic and terrestrial toxic effects information. Data on more than 8100 chemicals and 5700 terrestrial and aquatic species are included in the database. Information is ...

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.

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

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.

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.

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.

Embedding the shapes of regions of interest into a Clinical Document Architecture document.

PubMed

Minh, Nguyen Hai; Yi, Byoung-Kee; Kim, Il Kon; Song, Joon Hyun; Binh, Pham Viet

2015-03-01

Sharing a medical image visually annotated by a region of interest with a remotely located specialist for consultation is a good practice. It may, however, require a special-purpose (and most likely expensive) system to send and view them, which is an unfeasible solution in developing countries such as Vietnam. In this study, we design and implement interoperable methods based on the HL7 Clinical Document Architecture and the eXtensible Markup Language Stylesheet Language for Transformation standards to seamlessly exchange and visually present the shapes of regions of interest using web browsers. We also propose a new integration architecture for a Clinical Document Architecture generator that enables embedding of regions of interest and simultaneous auto-generation of corresponding style sheets. Using the Clinical Document Architecture document and style sheet, a sender can transmit clinical documents and medical images together with coordinate values of regions of interest to recipients. Recipients can easily view the documents and display embedded regions of interest by rendering them in their web browser of choice. © The Author(s) 2014.

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.

Interpolate with DIVA and view the products in OceanBrowser : what's up ?

NASA Astrophysics Data System (ADS)

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

2017-04-01

The Data-Interpolating Variational Analysis (DIVA) software is a statistical tool designed to reconstruct a continuous field from discrete measurements. This method is based on the numerical implementation of the Variational Inverse Model (VIM), which consists of a minimization of a cost function, allowing the choice of the analyzed field fitting at best the data sets without presenting unrealistic strong variations. The problem is solved efficiently using a finite-element method. This method, equivalent to the Optimal Interpolation, is particularly suited to deal with irregularly-spaced observations and produces outputs on a regular grid (2D, 3D or 4D). The results are stored in NetCDF files, the most widespread format in the earth sciences community. OceanBrowser is a web-service that allows one to visualize gridded fields on-line. Within the SeaDataNet and EMODNET (Chemical lot) projects, several national ocean data centers have created gridded climatologies of different ocean properties using the data analysis software DIVA. In order to give a common viewing service to those interpolated products, the GHER has developed OceanBrowser which is based on open standards from the Open Geospatial Consortium (OGC), in particular Web Map Service (WMS) and Web Feature Service (WFS). These standards define a protocol for describing, requesting and querying two-dimensional maps at a given depth and time. DIVA and OceanBrowser are both softwares tools which are continuously upgraded and distributed for free through frequent version releases. The development is funded by the EMODnet and SeaDataNet projects and include many discussions and feedback from the users community. Here, we present two recent major upgrades. First, we have implemented a "customization" of DIVA analyses following the sea bottom, using the bottom depth gradient as a new source of information. The weaker the slope of the bottom ocean, the higher the correlation length. This correlation length being associated with the propagation of the information, it is therefore harder to interpolate through bottom topographic "barriers" such as the continental slope and easier to do it in the perpendicular direction. Although realistic for most applications, this behaviour can always be disabled by the user. Second, we have added some combined products in OceanBrowser, covering all European seas at once. Based on the analyses performed by the other EMODnet partners using DIVA on five zones (Atlantic, North Sea, Baltic Sea, Black Sea, Mediterranean Sea), we have computed a single European product for five variables : ammonium, chlorophyll-a, dissolved oxygen concentration, phosphate and silicate. At boundaries, a smooth filter was used to remove possible discrepancies between regional analyses. Our European combined product is available for all seasons and several depths. This is the first step towards the use of a common reference field for all European seas when running DIVA.

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

PubMed

Vali, Faisal; Hong, Robert

2007-10-11

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

Services for Emodnet-Chemistry Data Products

NASA Astrophysics Data System (ADS)

Santinelli, Giorgio; Hendriksen, Gerrit; Barth, Alexander

2016-04-01

In the framework of Emodnet Chemistry lot, data products from regional leaders were made available in order to transform information into a database. This has been done by using functions and scripts, reading so-called enriched ODV files and inserting data directly into a cloud relational geodatabase. The main table is the one of observations which contains the main data and meta-data associated with the enriched ODV files. A particular implementation in data loading is used in order to improve on-the-fly computational speed. Data from Baltic Sea, North Sea, Mediterrean, Black Sea and part of the Atlantic region has been entered into the geodatabase, and consequently being instantly available from the OceanBrowser Emodnet portal. Furthermore, Deltares has developed an application that provides additional visualisation services for the aggregated and validated data collections. The visualisations are produced by making use of part of the OpenEarthTool stack (http://www.openearth.eu), by the integration of Web Feature Services and by the implementation of Web Processing Services. The goal is the generation of server-side plots of timeseries, profiles, timeprofiles and maps of selected parameters from data sets of selected stations. Regional data collections are retrieved using Emodnet Chemistry cloud relational geo-database. The spatial resolution in time and the intensity of data availability for selected parameters is shown using Web Service requests via the OceanBrowser Emodnet Web portal. OceanBrowser also shows station reference codes, which are used to establish a link for additional metadata, further data shopping and download.

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.

GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions.

PubMed

Gundersen, Gregory W; Jones, Matthew R; Rouillard, Andrew D; Kou, Yan; Monteiro, Caroline D; Feldmann, Axel S; Hu, Kevin S; Ma'ayan, Avi

2015-09-15

Identification of differentially expressed genes is an important step in extracting knowledge from gene expression profiling studies. The raw expression data from microarray and other high-throughput technologies is deposited into the Gene Expression Omnibus (GEO) and served as Simple Omnibus Format in Text (SOFT) files. However, to extract and analyze differentially expressed genes from GEO requires significant computational skills. Here we introduce GEO2Enrichr, a browser extension for extracting differentially expressed gene sets from GEO and analyzing those sets with Enrichr, an independent gene set enrichment analysis tool containing over 70 000 annotated gene sets organized into 75 gene-set libraries. GEO2Enrichr adds JavaScript code to GEO web-pages; this code scrapes user selected accession numbers and metadata, and then, with one click, users can submit this information to a web-server application that downloads the SOFT files, parses, cleans and normalizes the data, identifies the differentially expressed genes, and then pipes the resulting gene lists to Enrichr for downstream functional analysis. GEO2Enrichr opens a new avenue for adding functionality to major bioinformatics resources such GEO by integrating tools and resources without the need for a plug-in architecture. Importantly, GEO2Enrichr helps researchers to quickly explore hypotheses with little technical overhead, lowering the barrier of entry for biologists by automating data processing steps needed for knowledge extraction from the major repository GEO. GEO2Enrichr is an open source tool, freely available for installation as browser extensions at the Chrome Web Store and FireFox Add-ons. Documentation and a browser independent web application can be found at http://amp.pharm.mssm.edu/g2e/. avi.maayan@mssm.edu. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Integration of multiple DICOM Web servers into an enterprise-wide Web-based electronic medical record

NASA Astrophysics Data System (ADS)

Stewart, Brent K.; Langer, Steven G.; Martin, Kelly P.

1999-07-01

The purpose of this paper is to integrate multiple DICOM image webservers into the currently existing enterprises- wide web-browsable electronic medical record. Over the last six years the University of Washington has created a clinical data repository combining in a distributed relational database information from multiple departmental databases (MIND). A character cell-based view of this data called the Mini Medical Record (MMR) has been available for four years, MINDscape, unlike the text-based MMR. provides a platform independent, dynamic, web browser view of the MIND database that can be easily linked with medical knowledge resources on the network, like PubMed and the Federated Drug Reference. There are over 10,000 MINDscape user accounts at the University of Washington Academic Medical Centers. The weekday average number of hits to MINDscape is 35,302 and weekday average number of individual users is 1252. DICOM images from multiple webservers are now being viewed through the MINDscape electronic medical record.

Prokaryotic Contig Annotation Pipeline Server: Web Application for a Prokaryotic Genome Annotation Pipeline Based on the Shiny App Package.

PubMed

Park, Byeonghyeok; Baek, Min-Jeong; Min, Byoungnam; Choi, In-Geol

2017-09-01

Genome annotation is a primary step in genomic research. To establish a light and portable prokaryotic genome annotation pipeline for use in individual laboratories, we developed a Shiny app package designated as "P-CAPS" (Prokaryotic Contig Annotation Pipeline Server). The package is composed of R and Python scripts that integrate publicly available annotation programs into a server application. P-CAPS is not only a browser-based interactive application but also a distributable Shiny app package that can be installed on any personal computer. The final annotation is provided in various standard formats and is summarized in an R markdown document. Annotation can be visualized and examined with a public genome browser. A benchmark test showed that the annotation quality and completeness of P-CAPS were reliable and compatible with those of currently available public pipelines.

Client-side Medical Image Colorization in a Collaborative Environment.

PubMed

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

2015-01-01

The paper presents an application related to collaborative medicine using a browser based medical visualization system with focus on the medical image colorization process and the underlying open source web development technologies involved. Browser based systems allow physicians to share medical data with their remotely located counterparts or medical students, assisting them during patient diagnosis, treatment monitoring, surgery planning or for educational purposes. This approach brings forth the advantage of ubiquity. The system can be accessed from a any device, in order to process the images, assuring the independence towards having a specific proprietary operating system. The current work starts with processing of DICOM (Digital Imaging and Communications in Medicine) files and ends with the rendering of the resulting bitmap images on a HTML5 (fifth revision of the HyperText Markup Language) canvas element. The application improves the image visualization emphasizing different tissue densities.

60. The World-Wide Inaccessible Web, Part 1: Browsing

ERIC Educational Resources Information Center

Baggaley, Jon; Batpurev, Batchuluun

2007-01-01

Two studies are reported, comparing the browser loading times of webpages created using common Web development techniques. The loading speeds were estimated in 12 Asian countries by members of the "PANdora" network, funded by the International Development Research Centre (IDRC) to conduct collaborative research in the development of…

Viewing Files — EDRN Public Portal

Cancer.gov

In addition to standard HTML Web pages, our web site contain other file formats. You may need additional software or browser plug-ins to view some of the information available on our site. This document lists show each format, along with links to the corresponding freely available plug-ins or viewers.

IT Security: Target: The Web

ERIC Educational Resources Information Center

Waters, John K.

2009-01-01

In December, Microsoft announced a major security flaw affecting its Internet Explorer web browser. The flaw allowed hackers to use hidden computer code they had already injected into legitimate websites to steal the passwords of visitors to those sites. Reportedly, more than 10,000 websites were infected with the destructive code by the time…

Regular paths in SparQL: querying the NCI Thesaurus.

PubMed

Detwiler, Landon T; Suciu, Dan; Brinkley, James F

2008-11-06

OWL, the Web Ontology Language, provides syntax and semantics for representing knowledge for the semantic web. Many of the constructs of OWL have a basis in the field of description logics. While the formal underpinnings of description logics have lead to a highly computable language, it has come at a cognitive cost. OWL ontologies are often unintuitive to readers lacking a strong logic background. In this work we describe GLEEN, a regular path expression library, which extends the RDF query language SparQL to support complex path expressions over OWL and other RDF-based ontologies. We illustrate the utility of GLEEN by showing how it can be used in a query-based approach to defining simpler, more intuitive views of OWL ontologies. In particular we show how relatively simple GLEEN-enhanced SparQL queries can create views of the OWL version of the NCI Thesaurus that match the views generated by the web-based NCI browser.

Secure electronic commerce communication system based on CA

NASA Astrophysics Data System (ADS)

Chen, Deyun; Zhang, Junfeng; Pei, Shujun

2001-07-01

In this paper, we introduce the situation of electronic commercial security, then we analyze the working process and security for SSL protocol. At last, we propose a secure electronic commerce communication system based on CA. The system provide secure services such as encryption, integer, peer authentication and non-repudiation for application layer communication software of browser clients' and web server. The system can implement automatic allocation and united management of key through setting up the CA in the network.

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.

Web GIS in practice VIII: HTML5 and the canvas element for interactive online mapping.

PubMed

Boulos, Maged N Kamel; Warren, Jeffrey; Gong, Jianya; Yue, Peng

2010-03-03

HTML5 is being developed as the next major revision of HTML (Hypertext Markup Language), the core markup language of the World Wide Web. It aims at reducing the need for proprietary, plug-in-based rich Internet application (RIA) technologies such as Adobe Flash. The canvas element is part of HTML5 and is used to draw graphics using scripting (e.g., JavaScript). This paper introduces Cartagen, an open-source, vector-based, client-side framework for rendering plug-in-free, offline-capable, interactive maps in native HTML5 on a wide range of Web browsers and mobile phones. Cartagen was developed at MIT Media Lab's Design Ecology group. Potential applications of the technology as an enabler for participatory online mapping include mapping real-time air pollution, citizen reporting, and disaster response, among many other possibilities.

CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets.

PubMed

Schofield, E C; Carver, T; Achuthan, P; Freire-Pritchett, P; Spivakov, M; Todd, J A; Burren, O S

2016-08-15

Promoter capture Hi-C (PCHi-C) allows the genome-wide interrogation of physical interactions between distal DNA regulatory elements and gene promoters in multiple tissue contexts. Visual integration of the resultant chromosome interaction maps with other sources of genomic annotations can provide insight into underlying regulatory mechanisms. We have developed Capture HiC Plotter (CHiCP), a web-based tool that allows interactive exploration of PCHi-C interaction maps and integration with both public and user-defined genomic datasets. CHiCP is freely accessible from www.chicp.org and supports most major HTML5 compliant web browsers. Full source code and installation instructions are available from http://github.com/D-I-L/django-chicp ob219@cam.ac.uk. © The Author 2016. Published by Oxford University Press. All rights reserved.

Building Identification Wizard: Version 1.5.1

DTIC Science & Technology

2018-04-01

35 6.1 Exporting to a web or PDF File...applications. Users also have access to other WCP reports from regions of interest that are formatted as HTML and are viewable in any web browser. The WCP...feature, shown in Figure 23, checks for updates on the WCP web server by comparing a byte count of the contents of the files that are installed on

Tactical Applications (TACAPPS) JavaScript Framework Investigation

DTIC Science & Technology

2017-02-01

frameworks explored were Angular JavaScript (AngularJS), jQuery UI, Meteor, Ember, React JavaScript (ReactJS) and Web Components. The team evaluated the...10 Issues and Risks 11 Web Components 11 Benefits 13 Issues and Risks 13 Conclusions 14 Bibliography 15 Distribution List 19...3 Basic Flux flow 10 4 Shadow DOM tree hierarchy 12 5 Web Components browser support 13 UNCLASSIFIED Approved for

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.

Web-based platform for collaborative medical imaging research

NASA Astrophysics Data System (ADS)

Rittner, Leticia; Bento, Mariana P.; Costa, André L.; Souza, Roberto M.; Machado, Rubens C.; Lotufo, Roberto A.

2015-03-01

Medical imaging research depends basically on the availability of large image collections, image processing and analysis algorithms, hardware and a multidisciplinary research team. It has to be reproducible, free of errors, fast, accessible through a large variety of devices spread around research centers and conducted simultaneously by a multidisciplinary team. Therefore, we propose a collaborative research environment, named Adessowiki, where tools and datasets are integrated and readily available in the Internet through a web browser. Moreover, processing history and all intermediate results are stored and displayed in automatic generated web pages for each object in the research project or clinical study. It requires no installation or configuration from the client side and offers centralized tools and specialized hardware resources, since processing takes place in the cloud.

mORCA: sailing bioinformatics world with mobile devices.

PubMed

Díaz-Del-Pino, Sergio; Falgueras, Juan; Perez-Wohlfeil, Esteban; Trelles, Oswaldo

2018-03-01

Nearly 10 years have passed since the first mobile apps appeared. Given the fact that bioinformatics is a web-based world and that mobile devices are endowed with web-browsers, it seemed natural that bioinformatics would transit from personal computers to mobile devices but nothing could be further from the truth. The transition demands new paradigms, designs and novel implementations. Throughout an in-depth analysis of requirements of existing bioinformatics applications we designed and deployed an easy-to-use web-based lightweight mobile client. Such client is able to browse, select, compose automatically interface parameters, invoke services and monitor the execution of Web Services using the service's metadata stored in catalogs or repositories. mORCA is available at http://bitlab-es.com/morca/app as a web-app. It is also available in the App store by Apple and Play Store by Google. The software will be available for at least 2 years. ortrelles@uma.es. Source code, final web-app, training material and documentation is available at http://bitlab-es.com/morca. © The Author(s) 2017. Published by Oxford University Press.

NRV web knowledge base on low-energy nuclear physics

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

Karpov, V., E-mail: karpov@jinr.ru; Denikin, A. S.; Alekseev, A. P.

Principles underlying the organization and operation of the NRV web knowledge base on low-energy nuclear physics (http://nrv.jinr.ru) are described. This base includes a vast body of digitized experimental data on the properties of nuclei and on cross sections for nuclear reactions that is combined with a wide set of interconnected computer programs for simulating complex nuclear dynamics, which work directly in the browser of a remote user. Also, the current situation in the realms of application of network information technologies in nuclear physics is surveyed. The potential of the NRV knowledge base is illustrated in detail by applying it tomore » the example of an analysis of the fusion of nuclei that is followed by the decay of the excited compound nucleus formed.« less

svviz: a read viewer for validating structural variants.

PubMed

Spies, Noah; Zook, Justin M; Salit, Marc; Sidow, Arend

2015-12-15

Visualizing read alignments is the most effective way to validate candidate structural variants (SVs) with existing data. We present svviz, a sequencing read visualizer for SVs that sorts and displays only reads relevant to a candidate SV. svviz works by searching input bam(s) for potentially relevant reads, realigning them against the inferred sequence of the putative variant allele as well as the reference allele and identifying reads that match one allele better than the other. Separate views of the two alleles are then displayed in a scrollable web browser view, enabling a more intuitive visualization of each allele, compared with the single reference genome-based view common to most current read browsers. The browser view facilitates examining the evidence for or against a putative variant, estimating zygosity, visualizing affected genomic annotations and manual refinement of breakpoints. svviz supports data from most modern sequencing platforms. svviz is implemented in python and freely available from http://svviz.github.io/. Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US.

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.

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/.

Design and Development of a Framework Based on Ogc Web Services for the Visualization of Three Dimensional Large-Scale Geospatial Data Over the Web

NASA Astrophysics Data System (ADS)

Roccatello, E.; Nozzi, A.; Rumor, M.

2013-05-01

This paper illustrates the key concepts behind the design and the development of a framework, based on OGC services, capable to visualize 3D large scale geospatial data streamed over the web. WebGISes are traditionally bounded to a bi-dimensional simplified representation of the reality and though they are successfully addressing the lack of flexibility and simplicity of traditional desktop clients, a lot of effort is still needed to reach desktop GIS features, like 3D visualization. The motivations behind this work lay in the widespread availability of OGC Web Services inside government organizations and in the technology support to HTML 5 and WebGL standard of the web browsers. This delivers an improved user experience, similar to desktop applications, therefore allowing to augment traditional WebGIS features with a 3D visualization framework. This work could be seen as an extension of the Cityvu project, started in 2008 with the aim of a plug-in free OGC CityGML viewer. The resulting framework has also been integrated in existing 3DGIS software products and will be made available in the next months.

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.

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

NASA Astrophysics Data System (ADS)

Johnston, Semay; Renambot, Luc; Sauter, Daniel

2013-03-01

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

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.

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 low-latency, big database system and browser for storage, querying and visualization of 3D genomic data.

PubMed

Butyaev, Alexander; Mavlyutov, Ruslan; Blanchette, Mathieu; Cudré-Mauroux, Philippe; Waldispühl, Jérôme

2015-09-18

Recent releases of genome three-dimensional (3D) structures have the potential to transform our understanding of genomes. Nonetheless, the storage technology and visualization tools need to evolve to offer to the scientific community fast and convenient access to these data. We introduce simultaneously a database system to store and query 3D genomic data (3DBG), and a 3D genome browser to visualize and explore 3D genome structures (3DGB). We benchmark 3DBG against state-of-the-art systems and demonstrate that it is faster than previous solutions, and importantly gracefully scales with the size of data. We also illustrate the usefulness of our 3D genome Web browser to explore human genome structures. The 3D genome browser is available at http://3dgb.cs.mcgill.ca/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data

PubMed Central

Butyaev, Alexander; Mavlyutov, Ruslan; Blanchette, Mathieu; Cudré-Mauroux, Philippe; Waldispühl, Jérôme

2015-01-01

Recent releases of genome three-dimensional (3D) structures have the potential to transform our understanding of genomes. Nonetheless, the storage technology and visualization tools need to evolve to offer to the scientific community fast and convenient access to these data. We introduce simultaneously a database system to store and query 3D genomic data (3DBG), and a 3D genome browser to visualize and explore 3D genome structures (3DGB). We benchmark 3DBG against state-of-the-art systems and demonstrate that it is faster than previous solutions, and importantly gracefully scales with the size of data. We also illustrate the usefulness of our 3D genome Web browser to explore human genome structures. The 3D genome browser is available at http://3dgb.cs.mcgill.ca/. PMID:25990738

Design and Implementation of High Interaction Client Honeypot for Drive-by-Download Attacks

NASA Astrophysics Data System (ADS)

Akiyama, Mitsuaki; Iwamura, Makoto; Kawakoya, Yuhei; Aoki, Kazufumi; Itoh, Mitsutaka

Nowadays, the number of web-browser targeted attacks that lead users to adversaries' web sites and exploit web browser vulnerabilities is increasing, and a clarification of their methods and countermeasures is urgently needed. In this paper, we introduce the design and implementation of a new client honeypot for drive-by-download attacks that has the capacity to detect and investigate a variety of malicious web sites. On the basis of the problems of existing client honeypots, we enumerate the requirements of a client honeypot: 1) detection accuracy and variety, 2) collection variety, 3) performance efficiency, and 4) safety and stability. We improve our system with regard to these requirements. The key features of our developed system are stepwise detection focusing on exploit phases, multiple crawler processing, tracking of malware distribution networks, and malware infection prevention. Our evaluation of our developed system in a laboratory experiment and field experiment indicated that its detection variety and crawling performance are higher than those of existing client honeypots. In addition, our system is able to collect information for countermeasures and is secure and stable for continuous operation. We conclude that our system can investigate malicious web sites comprehensively and support countermeasures.

A WebGIS-based system for analyzing and visualizing air quality data for Shanghai Municipality

NASA Astrophysics Data System (ADS)

Wang, Manyi; Liu, Chaoshun; Gao, Wei

2014-10-01

An online visual analytical system based on Java Web and WebGIS for air quality data for Shanghai Municipality was designed and implemented to quantitatively analyze and qualitatively visualize air quality data. By analyzing the architecture of WebGIS and Java Web, we firstly designed the overall scheme for system architecture, then put forward the software and hardware environment and also determined the main function modules for the system. The visual system was ultimately established with the DIV + CSS layout method combined with JSP, JavaScript, and some other computer programming languages based on the Java programming environment. Moreover, Struts, Spring, and Hibernate frameworks (SSH) were integrated in the system for the purpose of easy maintenance and expansion. To provide mapping service and spatial analysis functions, we selected ArcGIS for Server as the GIS server. We also used Oracle database and ESRI file geodatabase to store spatial data and non-spatial data in order to ensure the data security. In addition, the response data from the Web server are resampled to implement rapid visualization through the browser. The experimental successes indicate that this system can quickly respond to user's requests, and efficiently return the accurate processing results.

The New Frontier: Conquering the World Wide Web by Mule.

ERIC Educational Resources Information Center

Gresham, Morgan

1999-01-01

Examines effects of teaching hypertext markup language on students' perceptions of class goals in a networked composition classroom. Suggests sending documents via file transfer protocol by command line and viewing the Web with a textual browser shifted emphasis from writing to coding. Argues that helping students identify a balance between…

46 CFR 520.9 - Access to tariffs.

Code of Federal Regulations, 2013 CFR

2013-10-01

... networks (“PSTN”); or (2) The Internet (Web) by: (i) Web browser; or (ii) Telnet session. (b) Dial-up...) Internet connection. (1) This connection option requires that systems provide: (i) A universal resource locator (“URL”) Internet address (e.g., http://www.tariffsrus.com or http://1.2.3.4); and/or (ii) A URL...

46 CFR 520.9 - Access to tariffs.

Code of Federal Regulations, 2012 CFR

2012-10-01

... networks (“PSTN”); or (2) The Internet (Web) by: (i) Web browser; or (ii) Telnet session. (b) Dial-up...) Internet connection. (1) This connection option requires that systems provide: (i) A universal resource locator (“URL”) Internet address (e.g., http://www.tariffsrus.com or http://1.2.3.4); and/or (ii) A URL...

46 CFR 520.9 - Access to tariffs.

Code of Federal Regulations, 2014 CFR

2014-10-01

... networks (“PSTN”); or (2) The Internet (Web) by: (i) Web browser; or (ii) Telnet session. (b) Dial-up...) Internet connection. (1) This connection option requires that systems provide: (i) A universal resource locator (“URL”) Internet address (e.g., http://www.tariffsrus.com or http://1.2.3.4); and/or (ii) A URL...

46 CFR 525.3 - Availability of marine terminal operator schedules.

Code of Federal Regulations, 2010 CFR

2010-10-01

...) Availability of terminal schedules—(1) Availability to the Commission. A complete and current set of terminal... computer (PC) by: (1) Dial-up connection via public switched telephone networks (PSTN); or (2) The Internet (Web) by: (i) Web browser; or (ii) Telnet session. (c) Dial-up connection via PSTN. (1) This connection...

46 CFR 525.3 - Availability of marine terminal operator schedules.

Code of Federal Regulations, 2011 CFR

2011-10-01

...) Availability of terminal schedules—(1) Availability to the Commission. A complete and current set of terminal... computer (PC) by: (1) Dial-up connection via public switched telephone networks (PSTN); or (2) The Internet (Web) by: (i) Web browser; or (ii) Telnet session. (c) Dial-up connection via PSTN. (1) This connection...

46 CFR 520.9 - Access to tariffs.

Code of Federal Regulations, 2010 CFR

2010-10-01

... networks (“PSTN”); or (2) The Internet (Web) by: (i) Web browser; or (ii) Telnet session. (b) Dial-up...) Internet connection. (1) This connection option requires that systems provide: (i) A universal resource locator (“URL”) Internet address (e.g., http://www.tariffsrus.com or http://1.2.3.4); and/or (ii) A URL...

46 CFR 520.9 - Access to tariffs.

Code of Federal Regulations, 2011 CFR

2011-10-01

... networks (“PSTN”); or (2) The Internet (Web) by: (i) Web browser; or (ii) Telnet session. (b) Dial-up...) Internet connection. (1) This connection option requires that systems provide: (i) A universal resource locator (“URL”) Internet address (e.g., http://www.tariffsrus.com or http://1.2.3.4); and/or (ii) A URL...

A Structured Approach to Homepage Design.

ERIC Educational Resources Information Center

Gregory, Gwen; Brown, M. Marlo

With no standards governing their creation, a variety of formats are being used for World Wide Web homepages. Some are well organized, present their information clearly, and work with multiple browsers. Others, however, are slow to load, function poorly with some Web browsing software, and are so badly structured that they are very difficult to…

A Conversion Tool for Mathematical Expressions in Web XML Files.

ERIC Educational Resources Information Center

Ohtake, Nobuyuki; Kanahori, Toshihiro

2003-01-01

This article discusses the conversion of mathematical equations into Extensible Markup Language (XML) on the World Wide Web for individuals with visual impairments. A program is described that converts the presentation markup style to the content markup style in MathML to allow browsers to render mathematical expressions without other programs.…

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.

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

KernPaeP - a web-based pediatric palliative documentation system for home care.

PubMed

Hartz, Tobias; Verst, Hendrik; Ueckert, Frank

2009-01-01

KernPaeP is a new web-based on- and offline documentation system, which has been developed for pediatric palliative care-teams supporting patient documentation and communication among health care professionals. It provides a reliable system making fast and secure home care documentation possible. KernPaeP is accessible online by registered users using any web-browser. Home care teams use an offline version of KernPaeP running on a netbook for patient documentation on site. Identifying and medical patient data are strictly separated and stored on two database servers. The system offers a stable, enhanced two-way algorithm for synchronization between the offline component and the central database servers. KernPaeP is implemented meeting highest security standards while still maintaining high usability. The web-based documentation system allows ubiquitous and immediate access to patient data. Sumptuous paper work is replaced by secure and comprehensive electronic documentation. KernPaeP helps saving time and improving the quality of documentation. Due to development in close cooperation with pediatric palliative professionals, KernPaeP fulfils the broad needs of home-care documentation. The technique of web-based online and offline documentation is in general applicable for arbitrary home care scenarios.

An automated image-collection system for crystallization experiments using SBS standard microplates.

PubMed

Brostromer, Erik; Nan, Jie; Su, Xiao Dong

2007-02-01

As part of a structural genomics platform in a university laboratory, a low-cost in-house-developed automated imaging system for SBS microplate experiments has been designed and constructed. The imaging system can scan a microplate in 2-6 min for a 96-well plate depending on the plate layout and scanning options. A web-based crystallization database system has been developed, enabling users to follow their crystallization experiments from a web browser. As the system has been designed and built by students and crystallographers using commercially available parts, this report is aimed to serve as a do-it-yourself example for laboratory robotics.

Spatial data available on the web at http://mrdata.usgs.gov/

USGS Publications Warehouse

Johnson, Bruce

2002-01-01

Earth science information is important to decisionmakers who formulate public policy related to mineral resource sustainability, land stewardship, environmental hazards, the economy, and public health. To meet the growing demand for easily accessible data, the Mineral Resources Program has developed, in cooperation with other Federal and State agencies, an Internet-based, data-delivery system that allows interested customers worldwide to download accurate, up-to-date mineral resource-related data at any time. All data in the system are spatially located and customers with Internet access and a modern Web browser can easily produce maps having user-defined overlays for any region of interest.

Interacting With A Near Real-Time Urban Digital Watershed Using Emerging Geospatial Web Technologies

NASA Astrophysics Data System (ADS)

Liu, Y.; Fazio, D. J.; Abdelzaher, T.; Minsker, B.

2007-12-01

The value of real-time hydrologic data dissemination including river stage, streamflow, and precipitation for operational stormwater management efforts is particularly high for communities where flash flooding is common and costly. Ideally, such data would be presented within a watershed-scale geospatial context to portray a holistic view of the watershed. Local hydrologic sensor networks usually lack comprehensive integration with sensor networks managed by other agencies sharing the same watershed due to administrative, political, but mostly technical barriers. Recent efforts on providing unified access to hydrological data have concentrated on creating new SOAP-based web services and common data format (e.g. WaterML and Observation Data Model) for users to access the data (e.g. HIS and HydroSeek). Geospatial Web technology including OGC sensor web enablement (SWE), GeoRSS, Geo tags, Geospatial browsers such as Google Earth and Microsoft Virtual Earth and other location-based service tools provides possibilities for us to interact with a digital watershed in near-real-time. OGC SWE proposes a revolutionary concept towards a web-connected/controllable sensor networks. However, these efforts have not provided the capability to allow dynamic data integration/fusion among heterogeneous sources, data filtering and support for workflows or domain specific applications where both push and pull mode of retrieving data may be needed. We propose a light weight integration framework by extending SWE with open source Enterprise Service Bus (e.g., mule) as a backbone component to dynamically transform, transport, and integrate both heterogeneous sensor data sources and simulation model outputs. We will report our progress on building such framework where multi-agencies" sensor data and hydro-model outputs (with map layers) will be integrated and disseminated in a geospatial browser (e.g. Microsoft Virtual Earth). This is a collaborative project among NCSA, USGS Illinois Water Science Center, Computer Science Department at UIUC funded by the Adaptive Environmental Infrastructure Sensing and Information Systems initiative at UIUC.

Development and evaluation of a stand-alone web-based CAL program. A case study.

PubMed

Perryer, G; Walmsley, A D; Barclay, C W; Shaw, L; Smith, A J

2000-08-01

The use of web browser technology allows the construction of computer-aided learning programs which will have a familiar interface to dentists. This paper reports on the evaluation of a web-based CAL program which covered the topic of tooth wear with an emphasis on the rôle of erosion in its aetiology. Evaluation of the software was made by 50 dentists contacted by an electronic mailing list. They completed a questionnaire which evaluated aspects of the functionality of the program educational objectives. The average age of the dentists was 39 years (range 24-70) and 82% were male. The average time of use was 1 h 10 min (range 15 min to 3 h). A significant change in their knowledge of tooth wear before and after using the program was recorded. Both the use of patient cases and leaflets scored highly with other aspects such as treatment planning and patient advice receiving high marks. All dentists commented that they had gained greater knowledge with particular reference to treatment and advice of tooth wear problems. 34 dentists (68%) found the web interface easy to use. Negative comments were mainly attributed to the quality of the pictures (4/50) which were corrected in the final release version. Respondents were asked to compare the program to other educational media on the same subject. 80% rated this CAL program as better than video, and 14% claimed it was as good as video. 84% rated it better than books, and 14% said it was as good as books. 98% preferred it to audio tapes and 86% preferred it to journals. The average amount that they would pay for a CAL package such as "tooth wear" would be 42 ECU. It is concluded that web browser software is a suitable medium for the use of a CAL program and this is reflected in its ease of use by dentists.

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.

Framework Development Supporting the Safety Portal

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

Prescott, Steven Ralph; Kvarfordt, Kellie Jean; Vang, Leng

2015-07-01

In a collaborating scientific research arena it is important to have an environment where analysts have access to a shared repository of information, documents, and software tools, and be able to accurately maintain and track historical changes in models. The new Safety Portal cloud-based environment will be accessible remotely from anywhere regardless of computing platforms given that the platform has available Internet access and proper browser capabilities. Information stored at this environment would be restricted based on user assigned credentials. This report discusses current development of a cloud-based web portal for PRA tools.

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

PubMed

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

2017-09-13

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

Web based 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

Web GIS in practice VIII: HTML5 and the canvas element for interactive online mapping

PubMed Central

2010-01-01

HTML5 is being developed as the next major revision of HTML (Hypertext Markup Language), the core markup language of the World Wide Web. It aims at reducing the need for proprietary, plug-in-based rich Internet application (RIA) technologies such as Adobe Flash. The canvas element is part of HTML5 and is used to draw graphics using scripting (e.g., JavaScript). This paper introduces Cartagen, an open-source, vector-based, client-side framework for rendering plug-in-free, offline-capable, interactive maps in native HTML5 on a wide range of Web browsers and mobile phones. Cartagen was developed at MIT Media Lab's Design Ecology group. Potential applications of the technology as an enabler for participatory online mapping include mapping real-time air pollution, citizen reporting, and disaster response, among many other possibilities. PMID:20199681

The internet

PubMed Central

Al-Shahi, R; Sadler, M; Rees, G; Bateman, D

2002-01-01

The growing use of email and the world wide web (WWW), by the public, academics, and clinicians—as well as the increasing availability of high quality information on the WWW—make a working knowledge of the internet important. Although this article aims to enhance readers' existing use of the internet and medical resources on the WWW, it is also intelligible to someone unfamiliar with the internet. A web browser is one of the central pieces of software in modern computing: it is a window on the WWW, file transfer protocol sites, networked newsgroups, and your own computer's files. Effective use of the internet for professional purposes requires an understanding of the best strategies to search the WWW and the mechanisms for ensuring secure data transfer, as well as a compendium of online resources including journals, textbooks, medical portals, and sites providing high quality patient information. This article summarises these resources, available to incorporate into your web browser as downloadable "Favorites" or "Bookmarks" from www.jnnp.com, where there are also freely accessible hypertext links to the recommended sites. PMID:12438460

NASA World Wind: A New Mission

NASA Astrophysics Data System (ADS)

Hogan, P.; Gaskins, T.; Bailey, J. E.

2008-12-01

Virtual Globes are well into their first generation, providing increasingly rich and beautiful visualization of more types and quantities of information. However, they are still mostly single and proprietary programs, akin to a web browser whose content and functionality are controlled and constrained largely by the browser's manufacturer. Today Google and Microsoft determine what we can and cannot see and do in these programs. NASA World Wind started out in nearly the same mode, a single program with limited functionality and information content. But as the possibilities of virtual globes became more apparent, we found that while enabling a new class of information visualization, we were also getting in the way. Many users want to provide World Wind functionality and information in their programs, not ours. They want it in their web pages. They want to include their own features. They told us that only with this kind of flexibility, could their objectives and the potential of the technology be truly realized. World Wind therefore changed its mission: from providing a single information browser to enabling a whole class of 3D geographic applications. Instead of creating one program, we create components to be used in any number of programs. World Wind is NASA open source software. With the source code being fully visible, anyone can readily use it and freely extend it to serve any use. Imagery and other information provided by the World Wind servers is also free and unencumbered, including the server technology to deliver geospatial data. World Wind developers can therefore provide exclusive and custom solutions based on user needs.

The Trouble with Color.

ERIC Educational Resources Information Center

Merchant, David

1999-01-01

Discusses problems with color quality in Web sites. Topics include differences in monitor settings, including contrast; amount of video RAM; user preference settings; browser-safe colors; cross-platform readability; and gamma values. (LRW)

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.

Determining the Navigational Aids Use on the Internet: The Information Technologies Teacher Candidates' Case

ERIC Educational Resources Information Center

Kuzu, Abdullah; Firat, Mehmet

2010-01-01

The Internet users who fail to cope with navigation may generally face various problems such as disorientation, distraction, low motivation and abandonment of information retrieval. Therefore, navigational aids are frequently used in today's Web browsers and Web sites to help users navigate on the Internet. However, it is asserted that…

Bringing Interactivity to the Web: The JAVA Solution.

ERIC Educational Resources Information Center

Knee, Richard H.; Cafolla, Ralph

Java is an object-oriented programming language of the Internet. It's popularity lies in its ability to create interactive Web sites across platforms. The most common Java programs are applications and applets, which adhere to a set of conventions that lets them run within a Java-compatible browser. Java is becoming an essential subject matter and…

Migration of the Three-dimensional Wind Field (3DWF) Model from Linux to Windows and Mobile Platforms

DTIC Science & Technology

2017-11-01

7 Fig. 10 Build executable code ........................................................................... 8 Fig. 11 3DWF GUI’s main web ...can be designed in any Windows operating system with internet access via Microsoft’s Internet Explorer (IE) web browser. For this particular project...Therefore, it is advised to have network security safeguards in place and operate only in a trusted PC. The GUI’s Hypertext Markup Language (HTML) web

bioWeb3D: an online webGL 3D data visualisation tool.

PubMed

Pettit, Jean-Baptiste; Marioni, John C

2013-06-07

Data visualization is critical for interpreting biological data. However, in practice it can prove to be a bottleneck for non trained researchers; this is especially true for three dimensional (3D) data representation. Whilst existing software can provide all necessary functionalities to represent and manipulate biological 3D datasets, very few are easily accessible (browser based), cross platform and accessible to non-expert users. An online HTML5/WebGL based 3D visualisation tool has been developed to allow biologists to quickly and easily view interactive and customizable three dimensional representations of their data along with multiple layers of information. Using the WebGL library Three.js written in Javascript, bioWeb3D allows the simultaneous visualisation of multiple large datasets inputted via a simple JSON, XML or CSV file, which can be read and analysed locally thanks to HTML5 capabilities. Using basic 3D representation techniques in a technologically innovative context, we provide a program that is not intended to compete with professional 3D representation software, but that instead enables a quick and intuitive representation of reasonably large 3D datasets.

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.

Towards the Geospatial Web: Media Platforms for Managing Geotagged Knowledge Repositories

NASA Astrophysics Data System (ADS)

Scharl, Arno

International media have recognized the visual appeal of geo-browsers such as NASA World Wind and Google Earth, for example, when Web and television coverage on Hurricane Katrina used interactive geospatial projections to illustrate its path and the scale of destruction in August 2005. Yet these early applications only hint at the true potential of geospatial technology to build and maintain virtual communities and to revolutionize the production, distribution and consumption of media products. This chapter investigates this potential by reviewing the literature and discussing the integration of geospatial and semantic reference systems, with an emphasis on extracting geospatial context from unstructured text. A content analysis of news coverage based on a suite of text mining tools (webLyzard) sheds light on the popularity and adoption of geospatial platforms.

Payao: a community platform for SBML pathway model curation

PubMed Central

Matsuoka, Yukiko; Ghosh, Samik; Kikuchi, Norihiro; Kitano, Hiroaki

2010-01-01

Summary: Payao is a community-based, collaborative web service platform for gene-regulatory and biochemical pathway model curation. The system combines Web 2.0 technologies and online model visualization functions to enable a collaborative community to annotate and curate biological models. Payao reads the models in Systems Biology Markup Language format, displays them with CellDesigner, a process diagram editor, which complies with the Systems Biology Graphical Notation, and provides an interface for model enrichment (adding tags and comments to the models) for the access-controlled community members. Availability and implementation: Freely available for model curation service at http://www.payaologue.org. Web site implemented in Seaser Framework 2.0 with S2Flex2, MySQL 5.0 and Tomcat 5.5, with all major browsers supported. Contact: kitano@sbi.jp PMID:20371497

A General Purpose Connections type CTI Server Based on SIP Protocol and Its Implementation

NASA Astrophysics Data System (ADS)

Watanabe, Toru; Koizumi, Hisao

In this paper, we propose a general purpose connections type CTI (Computer Telephony Integration) server that provides various CTI services such as voice logging where the CTI server communicates with IP-PBX using the SIP (Session Initiation Protocol), and accumulates voice packets of external line telephone call flowing between an IP telephone for extension and a VoIP gateway connected to outside line networks. The CTI server realizes CTI services such as voice logging, telephone conference, or IVR (interactive voice response) with accumulating and processing voice packets sampled. Furthermore, the CTI server incorporates a web server function which can provide various CTI services such as a Web telephone directory via a Web browser to PCs, cellular telephones or smart-phones in mobile environments.

ViralEpi v1.0: a high-throughput spectrum of viral epigenomic methylation profiles from diverse diseases.

PubMed

Khan, Mohd Shoaib; Gupta, Amit Kumar; Kumar, Manoj

2016-01-01

To develop a computational resource for viral epigenomic methylation profiles from diverse diseases. Methylation patterns of Epstein-Barr virus and hepatitis B virus genomic regions are provided as web platform developed using open source Linux-Apache-MySQL-PHP (LAMP) bundle: programming and scripting languages, that is, HTML, JavaScript and PERL. A comprehensive and integrated web resource ViralEpi v1.0 is developed providing well-organized compendium of methylation events and statistical analysis associated with several diseases. Additionally, it also facilitates 'Viral EpiGenome Browser' for user-affable browsing experience using JavaScript-based JBrowse. This web resource would be helpful for research community engaged in studying epigenetic biomarkers for appropriate prognosis and diagnosis of diseases and its various stages.

Reactome diagram viewer: data structures and strategies to boost performance.

PubMed

Fabregat, Antonio; Sidiropoulos, Konstantinos; Viteri, Guilherme; Marin-Garcia, Pablo; Ping, Peipei; Stein, Lincoln; D'Eustachio, Peter; Hermjakob, Henning

2018-04-01

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. For web-based pathway visualization, Reactome uses a custom pathway diagram viewer that has been evolved over the past years. Here, we present comprehensive enhancements in usability and performance based on extensive usability testing sessions and technology developments, aiming to optimize the viewer towards the needs of the community. The pathway diagram viewer version 3 achieves consistently better performance, loading and rendering of 97% of the diagrams in Reactome in less than 1 s. Combining the multi-layer html5 canvas strategy with a space partitioning data structure minimizes CPU workload, enabling the introduction of new features that further enhance user experience. Through the use of highly optimized data structures and algorithms, Reactome has boosted the performance and usability of the new pathway diagram viewer, providing a robust, scalable and easy-to-integrate solution to pathway visualization. As graph-based visualization of complex data is a frequent challenge in bioinformatics, many of the individual strategies presented here are applicable to a wide range of web-based bioinformatics resources. Reactome is available online at: https://reactome.org. The diagram viewer is part of the Reactome pathway browser (https://reactome.org/PathwayBrowser/) and also available as a stand-alone widget at: https://reactome.org/dev/diagram/. The source code is freely available at: https://github.com/reactome-pwp/diagram. fabregat@ebi.ac.uk or hhe@ebi.ac.uk. Supplementary data are available at Bioinformatics online.

Use of World Wide Web server and browser software to support a first-year medical physiology course.

PubMed

Davis, M J; Wythe, J; Rozum, J S; Gore, R W

1997-06-01

We describe the use of a World Wide Web (Web) server to support a team-taught physiology course for first-year medical students. Our objectives were to reduce the number of formal lecture hours and enhance student enthusiasm by using more multimedia materials and creating opportunities for interactive learning. On-line course materials, consisting of administrative documents, lecture notes, animations, digital movies, practice tests, and grade reports, were placed on a departmental computer with an Internet connection. Students used Web browsers to access on-line materials from a variety of computing platforms on campus, at home, and at remote sites. To assess use of the materials and their effectiveness, we analyzed 1) log files from the server, and 2) the results of a written course evaluation completed by all students. Lecture notes and practice tests were the most-used documents. The students' evaluations indicated that computer use in class made the lecture material more interesting, while the on-line documents helped reinforce lecture materials and the textbook. We conclude that the effectiveness of on-line materials depends on several different factors, including 1) the number of instructors that provide materials; 2) the quantity of other materials handed out; 3) the degree to which computer use is demonstrated in class and integrated into lectures; and 4) the ease with which students can access the materials. Finally, we propose that additional implementation of Internet-based resources beyond what we have described would further enhance a physiology course for first-year medical students.

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.

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.

State Cancer Profiles

MedlinePlus

... the site again. The following web browsers and operating systems are sufficiently secure and advanced. These version numbers ... also acceptable. Microsoft Internet Explorer 7, if your operating system is Windows Vista or later. No version of ...

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.

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

[Study of sharing platform of web-based enhanced extracorporeal counterpulsation hemodynamic waveform data].

PubMed

Huang, Mingbo; Hu, Ding; Yu, Donglan; Zheng, Zhensheng; Wang, Kuijian

2011-12-01

Enhanced extracorporeal counterpulsation (EECP) information consists of both text and hemodynamic waveform data. At present EECP text information has been successfully managed through Web browser, while the management and sharing of hemodynamic waveform data through Internet has not been solved yet. In order to manage EECP information completely, based on the in-depth analysis of EECP hemodynamic waveform file of digital imaging and communications in medicine (DICOM) format and its disadvantages in Internet sharing, we proposed the use of the extensible markup language (XML), which is currently the Internet popular data exchange standard, as the storage specification for the sharing of EECP waveform data. Then we designed a web-based sharing system of EECP hemodynamic waveform data via ASP. NET 2.0 platform. Meanwhile, we specifically introduced the four main system function modules and their implement methods, including DICOM to XML conversion module, EECP waveform data management module, retrieval and display of EECP waveform module and the security mechanism of the system.

Web-based system for surgical planning and simulation

NASA Astrophysics Data System (ADS)

Eldeib, Ayman M.; Ahmed, Mohamed N.; Farag, Aly A.; Sites, C. B.

1998-10-01

The growing scientific knowledge and rapid progress in medical imaging techniques has led to an increasing demand for better and more efficient methods of remote access to high-performance computer facilities. This paper introduces a web-based telemedicine project that provides interactive tools for surgical simulation and planning. The presented approach makes use of client-server architecture based on new internet technology where clients use an ordinary web browser to view, send, receive and manipulate patients' medical records while the server uses the supercomputer facility to generate online semi-automatic segmentation, 3D visualization, surgical simulation/planning and neuroendoscopic procedures navigation. The supercomputer (SGI ONYX 1000) is located at the Computer Vision and Image Processing Lab, University of Louisville, Kentucky. This system is under development in cooperation with the Department of Neurological Surgery, Alliant Health Systems, Louisville, Kentucky. The server is connected via a network to the Picture Archiving and Communication System at Alliant Health Systems through a DICOM standard interface that enables authorized clients to access patients' images from different medical modalities.

Available, intuitive and free! Building e-learning modules using web 2.0 services.

PubMed

Tam, Chun Wah Michael; Eastwood, Anne

2012-01-01

E-learning is part of the mainstream in medical education and often provides the most efficient and effective means of engaging learners in a particular topic. However, translating design and content ideas into a useable product can be technically challenging, especially in the absence of information technology (IT) support. There is little published literature on the use of web 2.0 services to build e-learning activities. To describe the web 2.0 tools and solutions employed to build the GP Synergy evidence-based medicine and critical appraisal online course. We used and integrated a number of free web 2.0 services including: Prezi, a web-based presentation platform; YouTube, a video sharing service; Google Docs, a online document platform; Tiny.cc, a URL shortening service; and Wordpress, a blogging platform. The course consisting of five multimedia-rich, tutorial-like modules was built without IT specialist assistance or specialised software. The web 2.0 services used were free. The course can be accessed with a modern web browser. Modern web 2.0 services remove many of the technical barriers for creating and sharing content on the internet. When used synergistically, these services can be a flexible and low-cost platform for building e-learning activities. They were a pragmatic solution in our context.

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

NASA Astrophysics Data System (ADS)

Delipetrev, Blagoj

2016-04-01

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

Integration of a Zero-footprint Cloud-based Picture Archiving and Communication System with Customizable Forms for Radiology Research and Education.

PubMed

Hostetter, Jason; Khanna, Nishanth; Mandell, Jacob C

2018-06-01

The purpose of this study was to integrate web-based forms with a zero-footprint cloud-based Picture Archiving and Communication Systems (PACS) to create a tool of potential benefit to radiology research and education. Web-based forms were created with a front-end and back-end architecture utilizing common programming languages including Vue.js, Node.js and MongoDB, and integrated into an existing zero-footprint cloud-based PACS. The web-based forms application can be accessed in any modern internet browser on desktop or mobile devices and allows the creation of customizable forms consisting of a variety of questions types. Each form can be linked to an individual DICOM examination or a collection of DICOM examinations. Several uses are demonstrated through a series of case studies, including implementation of a research platform for multi-reader multi-case (MRMC) studies and other imaging research, and creation of an online Objective Structure Clinical Examination (OSCE) and an educational case file. Copyright © 2018 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

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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.

Transforming Clinical Imaging and 3D Data for Virtual Reality Learning Objects: HTML5 and Mobile Devices Implementation

ERIC Educational Resources Information Center

Trelease, Robert B.; Nieder, Gary L.

2013-01-01

Web deployable anatomical simulations or "virtual reality learning objects" can easily be produced with QuickTime VR software, but their use for online and mobile learning is being limited by the declining support for web browser plug-ins for personal computers and unavailability on popular mobile devices like Apple iPad and Android…

Use of World Wide Web Server and Browser Software To Support a First-Year Medical Physiology Course.

ERIC Educational Resources Information Center

Davis, Michael J.; And Others

1997-01-01

Describes the use of a World Wide Web server to support a team-taught physiology course for first-year medical students. The students' evaluations indicate that computer use in class made lecture material more interesting, while the online documents helped reinforce lecture materials and textbooks. Lists factors which contribute to the…

61. The World-Wide Inaccessible Web, Part 2: Internet Routes

ERIC Educational Resources Information Center

Baggaley, Jon; Batpurev, Batchuluun; Klaas, Jim

2007-01-01

In the previous report in this series, Web browser loading times were measured in 12 Asian countries, and were found to be up to four times slower than commonly prescribed as acceptable. Failure of webpages to load at all was frequent. The current follow-up study compares these loading times with the complexity of the Internet routes linking the…

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.

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

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

Prototype of Multifunctional Full-text Library in the Architecture Web-browser / Web-server / SQL-server

NASA Astrophysics Data System (ADS)

Lyapin, Sergey; Kukovyakin, Alexey

Within the framework of the research program "Textaurus" an operational prototype of multifunctional library T-Libra v.4.1. has been created which makes it possible to carry out flexible parametrizable search within a full-text database. The information system is realized in the architecture Web-browser / Web-server / SQL-server. This allows to achieve an optimal combination of universality and efficiency of text processing, on the one hand, and convenience and minimization of expenses for an end user (due to applying of a standard Web-browser as a client application), on the other one. The following principles underlie the information system: a) multifunctionality, b) intelligence, c) multilingual primary texts and full-text searching, d) development of digital library (DL) by a user ("administrative client"), e) multi-platform working. A "library of concepts", i.e. a block of functional models of semantic (concept-oriented) searching, as well as a subsystem of parametrizable queries to a full-text database, which is closely connected with the "library", serve as a conceptual basis of multifunctionality and "intelligence" of the DL T-Libra v.4.1. An author's paragraph is a unit of full-text searching in the suggested technology. At that, the "logic" of an educational / scientific topic or a problem can be built in a multilevel flexible structure of a query and the "library of concepts", replenishable by the developers and experts. About 10 queries of various level of complexity and conceptuality are realized in the suggested version of the information system: from simple terminological searching (taking into account lexical and grammatical paradigms of Russian) to several kinds of explication of terminological fields and adjustable two-parameter thematic searching (a [set of terms] and a [distance between terms] within the limits of an author's paragraph are such parameters correspondingly).

BIRD: Bio-Image Referral Database. Design and implementation of a new web based and patient multimedia data focused system for effective medical diagnosis and therapy.

PubMed

Pinciroli, Francesco; Masseroli, Marco; Acerbo, Livio A; Bonacina, Stefano; Ferrari, Roberto; Marchente, Mario

2004-01-01

This paper presents a low cost software platform prototype supporting health care personnel in retrieving patient referral multimedia data. These information are centralized in a server machine and structured by using a flexible eXtensible Markup Language (XML) Bio-Image Referral Database (BIRD). Data are distributed on demand to requesting client in an Intranet network and transformed via eXtensible Stylesheet Language (XSL) to be visualized in an uniform way on market browsers. The core server operation software has been developed in PHP Hypertext Preprocessor scripting language, which is very versatile and useful for crafting a dynamic Web environment.

An overview of the web-based Google Earth coincident imaging tool

USGS Publications Warehouse

Chander, Gyanesh; Kilough, B.; Gowda, S.

2010-01-01

The Committee on Earth Observing Satellites (CEOS) Visualization Environment (COVE) tool is a browser-based application that leverages Google Earth web to display satellite sensor coverage areas. The analysis tool can also be used to identify near simultaneous surface observation locations for two or more satellites. The National Aeronautics and Space Administration (NASA) CEOS System Engineering Office (SEO) worked with the CEOS Working Group on Calibration and Validation (WGCV) to develop the COVE tool. The CEOS member organizations are currently operating and planning hundreds of Earth Observation (EO) satellites. Standard cross-comparison exercises between multiple sensors to compare near-simultaneous surface observations and to identify corresponding image pairs are time-consuming and labor-intensive. COVE is a suite of tools that have been developed to make such tasks easier.

VEDA: a web-based virtual environment for dynamic atomic force microscopy.

PubMed

Melcher, John; Hu, Shuiqing; Raman, Arvind

2008-06-01

We describe here the theory and applications of virtual environment dynamic atomic force microscopy (VEDA), a suite of state-of-the-art simulation tools deployed on nanoHUB (www.nanohub.org) for the accurate simulation of tip motion in dynamic atomic force microscopy (dAFM) over organic and inorganic samples. VEDA takes advantage of nanoHUB's cyberinfrastructure to run high-fidelity dAFM tip dynamics computations on local clusters and the teragrid. Consequently, these tools are freely accessible and the dAFM simulations are run using standard web-based browsers without requiring additional software. A wide range of issues in dAFM ranging from optimal probe choice, probe stability, and tip-sample interaction forces, power dissipation, to material property extraction and scanning dynamics over hetereogeneous samples can be addressed.

Invited Article: VEDA: A web-based virtual environment for dynamic atomic force microscopy

NASA Astrophysics Data System (ADS)

Melcher, John; Hu, Shuiqing; Raman, Arvind

2008-06-01

We describe here the theory and applications of virtual environment dynamic atomic force microscopy (VEDA), a suite of state-of-the-art simulation tools deployed on nanoHUB (www.nanohub.org) for the accurate simulation of tip motion in dynamic atomic force microscopy (dAFM) over organic and inorganic samples. VEDA takes advantage of nanoHUB's cyberinfrastructure to run high-fidelity dAFM tip dynamics computations on local clusters and the teragrid. Consequently, these tools are freely accessible and the dAFM simulations are run using standard web-based browsers without requiring additional software. A wide range of issues in dAFM ranging from optimal probe choice, probe stability, and tip-sample interaction forces, power dissipation, to material property extraction and scanning dynamics over hetereogeneous samples can be addressed.

Web-based encyclopedia on physical effects

NASA Astrophysics Data System (ADS)

Papliatseyeu, Andrey; Repich, Maryna; Ilyushonak, Boris; Hurbo, Aliaksandr; Makarava, Katerina; Lutkovski, Vladimir M.

2004-07-01

Web-based learning applications open new horizons for educators. In this work we present the computer encyclopedia designed to overcome drawbacks of traditional paper information sources such as awkward search, low update rate, limited copies count and high cost. Moreover, we intended to improve access and search functions in comparison with some Internet sources in order to make it more convenient. The system is developed using modern Java technologies (Jave Servlets, Java Server Pages) and contains systemized information about most important and explored physical effects. It also may be used in other fields of science. The system is accessible via Intranet/Internet networks by means of any up-to-date Internet browser. It may be used for general learning purposes and as a study guide or tutorial for performing laboratory works.

Using Browser Notebooks to Analyse Big Atmospheric Data-sets in the Cloud

NASA Astrophysics Data System (ADS)

Robinson, N.; Tomlinson, J.; Arribas, A.; Prudden, R.

2016-12-01

We are presenting an account of our experience building an ecosystem for the analysis of big atmospheric data-sets. By using modern technologies we have developed a prototype platform which is scaleable and capable of analysing very large atmospheric datasets. We tested different big-data ecosystems such as Hadoop MapReduce, Spark and Dask, in order to find the one which was best suited for analysis of multidimensional binary data such as NetCDF. We make extensive use of infrastructure-as-code and containerisation to provide a platform which is reusable, and which can scale to accommodate changes in demand. We make this platform readily accessible using browser based notebooks. As a result, analysts with minimal technology experience can, in tens of lines of Python, make interactive data-visualisation web pages, which can analyse very large amounts of data using cutting edge big-data technology

Promises and pitfalls of Web-based experimentation in the advance of replicable psychological science: A reply to Plant (2015).

PubMed

van Steenbergen, Henk; Bocanegra, Bruno R

2016-12-01

In a recent letter, Plant (2015) reminded us that proper calibration of our laboratory experiments is important for the progress of psychological science. Therefore, carefully controlled laboratory studies are argued to be preferred over Web-based experimentation, in which timing is usually more imprecise. Here we argue that there are many situations in which the timing of Web-based experimentation is acceptable and that online experimentation provides a very useful and promising complementary toolbox to available lab-based approaches. We discuss examples in which stimulus calibration or calibration against response criteria is necessary and situations in which this is not critical. We also discuss how online labor markets, such as Amazon's Mechanical Turk, allow researchers to acquire data in more diverse populations and to test theories along more psychological dimensions. Recent methodological advances that have produced more accurate browser-based stimulus presentation are also discussed. In our view, online experimentation is one of the most promising avenues to advance replicable psychological science in the near future.

TermGenie – a web-application for pattern-based ontology class generation

DOE PAGES

Dietze, Heiko; Berardini, Tanya Z.; Foulger, Rebecca E.; ...

2014-01-01

Biological ontologies are continually growing and improving from requests for new classes (terms) by biocurators. These ontology requests can frequently create bottlenecks in the biocuration process, as ontology developers struggle to keep up, while manually processing these requests and create classes. TermGenie allows biocurators to generate new classes based on formally specified design patterns or templates. The system is web-based and can be accessed by any authorized curator through a web browser. Automated rules and reasoning engines are used to ensure validity, uniqueness and relationship to pre-existing classes. In the last 4 years the Gene Ontology TermGenie generated 4715 newmore » classes, about 51.4% of all new classes created. The immediate generation of permanent identifiers proved not to be an issue with only 70 (1.4%) obsoleted classes. Lastly, TermGenie is a web-based class-generation system that complements traditional ontology development tools. All classes added through pre-defined templates are guaranteed to have OWL equivalence axioms that are used for automatic classification and in some cases inter-ontology linkage. At the same time, the system is simple and intuitive and can be used by most biocurators without extensive training.« less

TermGenie – a web-application for pattern-based ontology class generation

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

Dietze, Heiko; Berardini, Tanya Z.; Foulger, Rebecca E.

Biological ontologies are continually growing and improving from requests for new classes (terms) by biocurators. These ontology requests can frequently create bottlenecks in the biocuration process, as ontology developers struggle to keep up, while manually processing these requests and create classes. TermGenie allows biocurators to generate new classes based on formally specified design patterns or templates. The system is web-based and can be accessed by any authorized curator through a web browser. Automated rules and reasoning engines are used to ensure validity, uniqueness and relationship to pre-existing classes. In the last 4 years the Gene Ontology TermGenie generated 4715 newmore » classes, about 51.4% of all new classes created. The immediate generation of permanent identifiers proved not to be an issue with only 70 (1.4%) obsoleted classes. Lastly, TermGenie is a web-based class-generation system that complements traditional ontology development tools. All classes added through pre-defined templates are guaranteed to have OWL equivalence axioms that are used for automatic classification and in some cases inter-ontology linkage. At the same time, the system is simple and intuitive and can be used by most biocurators without extensive training.« less

TermGenie - a web-application for pattern-based ontology class generation.

PubMed

Dietze, Heiko; Berardini, Tanya Z; Foulger, Rebecca E; Hill, David P; Lomax, Jane; Osumi-Sutherland, David; Roncaglia, Paola; Mungall, Christopher J

2014-01-01

Biological ontologies are continually growing and improving from requests for new classes (terms) by biocurators. These ontology requests can frequently create bottlenecks in the biocuration process, as ontology developers struggle to keep up, while manually processing these requests and create classes. TermGenie allows biocurators to generate new classes based on formally specified design patterns or templates. The system is web-based and can be accessed by any authorized curator through a web browser. Automated rules and reasoning engines are used to ensure validity, uniqueness and relationship to pre-existing classes. In the last 4 years the Gene Ontology TermGenie generated 4715 new classes, about 51.4% of all new classes created. The immediate generation of permanent identifiers proved not to be an issue with only 70 (1.4%) obsoleted classes. TermGenie is a web-based class-generation system that complements traditional ontology development tools. All classes added through pre-defined templates are guaranteed to have OWL equivalence axioms that are used for automatic classification and in some cases inter-ontology linkage. At the same time, the system is simple and intuitive and can be used by most biocurators without extensive training.

Qualitative evaluation of a mobile phone and web-based collaborative care intervention for patients with type 2 diabetes.

PubMed

Lyles, Courtney Rees; Harris, Lynne T; Le, Tung; Flowers, Jan; Tufano, James; Britt, Diane; Hoath, James; Hirsch, Irl B; Goldberg, Harold I; Ralston, James D

2011-05-01

Drawing on previous web-based diabetes management programs based on the Chronic Care Model, we expanded an intervention to include care management through mobile phones and a game console web browser. The pilot intervention enrolled eight diabetes patients from the University of Washington in Seattle into a collaborative care program: connecting them to a care provider specializing in diabetes, providing access to their full electronic medical record, allowing wireless glucose uploads and e-mail with providers, and connecting them to the program's web services through a game system. To evaluate the study, we conducted qualitative thematic analysis of semistructured interviews. Participants expressed frustrations with using the cell phones and the game system in their everyday lives, but liked the wireless system for collaborating with a provider on uploaded glucoses and receiving automatic feedback on their blood sugar trends. A majority of participants also expressed that their participation in the trial increased their health awareness. Mobile communication technologies showed promise within a web-based collaborative care program for type 2 diabetes. Future intervention design should focus on integrating easy-to-use applications within mobile technologies already familiar to patients and ensure the system allows for sufficient collaboration with a care provider.

Systematic plan of building Web geographic information system based on ActiveX control

NASA Astrophysics Data System (ADS)

Zhang, Xia; Li, Deren; Zhu, Xinyan; Chen, Nengcheng

2003-03-01

A systematic plan of building Web Geographic Information System (WebGIS) using ActiveX technology is proposed in this paper. In the proposed plan, ActiveX control technology is adopted in building client-side application, and two different schemas are introduced to implement communication between controls in users¡ browser and middle application server. One is based on Distribute Component Object Model (DCOM), the other is based on socket. In the former schema, middle service application is developed as a DCOM object that communicates with ActiveX control through Object Remote Procedure Call (ORPC) and accesses data in GIS Data Server through Open Database Connectivity (ODBC). In the latter, middle service application is developed using Java language. It communicates with ActiveX control through socket based on TCP/IP and accesses data in GIS Data Server through Java Database Connectivity (JDBC). The first one is usually developed using C/C++, and it is difficult to develop and deploy. The second one is relatively easy to develop, but its performance of data transfer relies on Web bandwidth. A sample application is developed using the latter schema. It is proved that the performance of the sample application is better than that of some other WebGIS applications in some degree.

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

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

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.

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.

Usage of Data-Encoded Web Maps with Client Side Color Rendering for Combined Data Access, Visualization and Modeling Purposes

NASA Technical Reports Server (NTRS)

Pliutau, Denis; Prasad, Narashimha S.

2013-01-01

Current approaches to satellite observation data storage and distribution implement separate visualization and data access methodologies which often leads to the need in time consuming data ordering and coding for applications requiring both visual representation as well as data handling and modeling capabilities. We describe an approach we implemented for a data-encoded web map service based on storing numerical data within server map tiles and subsequent client side data manipulation and map color rendering. The approach relies on storing data using the lossless compression Portable Network Graphics (PNG) image data format which is natively supported by web-browsers allowing on-the-fly browser rendering and modification of the map tiles. The method is easy to implement using existing software libraries and has the advantage of easy client side map color modifications, as well as spatial subsetting with physical parameter range filtering. This method is demonstrated for the ASTER-GDEM elevation model and selected MODIS data products and represents an alternative to the currently used storage and data access methods. One additional benefit includes providing multiple levels of averaging due to the need in generating map tiles at varying resolutions for various map magnification levels. We suggest that such merged data and mapping approach may be a viable alternative to existing static storage and data access methods for a wide array of combined simulation, data access and visualization purposes.

Towards 100,000 CPU Cycle-Scavenging by Genetic Algorithms

NASA Technical Reports Server (NTRS)

Globus, Al; Biegel, Bryan A. (Technical Monitor)

2001-01-01

We examine a web-centric design using standard tools such as web servers, web browsers, PHP, and mySQL. We also consider the applicability of Information Power Grid tools such as the Globus (no relation to the author) Toolkit. We intend to implement this architecture with JavaGenes running on at least two cycle-scavengers: Condor and United Devices. JavaGenes, a genetic algorithm code written in Java, will be used to evolve multi-species reactive molecular force field parameters.

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.

Userscripts for the life sciences.

PubMed

Willighagen, Egon L; O'Boyle, Noel M; Gopalakrishnan, Harini; Jiao, Dazhi; Guha, Rajarshi; Steinbeck, Christoph; Wild, David J

2007-12-21

The web has seen an explosion of chemistry and biology related resources in the last 15 years: thousands of scientific journals, databases, wikis, blogs and resources are available with a wide variety of types of information. There is a huge need to aggregate and organise this information. However, the sheer number of resources makes it unrealistic to link them all in a centralised manner. Instead, search engines to find information in those resources flourish, and formal languages like Resource Description Framework and Web Ontology Language are increasingly used to allow linking of resources. A recent development is the use of userscripts to change the appearance of web pages, by on-the-fly modification of the web content. This opens possibilities to aggregate information and computational results from different web resources into the web page of one of those resources. Several userscripts are presented that enrich biology and chemistry related web resources by incorporating or linking to other computational or data sources on the web. The scripts make use of Greasemonkey-like plugins for web browsers and are written in JavaScript. Information from third-party resources are extracted using open Application Programming Interfaces, while common Universal Resource Locator schemes are used to make deep links to related information in that external resource. The userscripts presented here use a variety of techniques and resources, and show the potential of such scripts. This paper discusses a number of userscripts that aggregate information from two or more web resources. Examples are shown that enrich web pages with information from other resources, and show how information from web pages can be used to link to, search, and process information in other resources. Due to the nature of userscripts, scientists are able to select those scripts they find useful on a daily basis, as the scripts run directly in their own web browser rather than on the web server. This flexibility allows the scientists to tune the features of web resources to optimise their productivity.

Userscripts for the Life Sciences

PubMed Central

Willighagen, Egon L; O'Boyle, Noel M; Gopalakrishnan, Harini; Jiao, Dazhi; Guha, Rajarshi; Steinbeck, Christoph; Wild, David J

2007-01-01

Background The web has seen an explosion of chemistry and biology related resources in the last 15 years: thousands of scientific journals, databases, wikis, blogs and resources are available with a wide variety of types of information. There is a huge need to aggregate and organise this information. However, the sheer number of resources makes it unrealistic to link them all in a centralised manner. Instead, search engines to find information in those resources flourish, and formal languages like Resource Description Framework and Web Ontology Language are increasingly used to allow linking of resources. A recent development is the use of userscripts to change the appearance of web pages, by on-the-fly modification of the web content. This opens possibilities to aggregate information and computational results from different web resources into the web page of one of those resources. Results Several userscripts are presented that enrich biology and chemistry related web resources by incorporating or linking to other computational or data sources on the web. The scripts make use of Greasemonkey-like plugins for web browsers and are written in JavaScript. Information from third-party resources are extracted using open Application Programming Interfaces, while common Universal Resource Locator schemes are used to make deep links to related information in that external resource. The userscripts presented here use a variety of techniques and resources, and show the potential of such scripts. Conclusion This paper discusses a number of userscripts that aggregate information from two or more web resources. Examples are shown that enrich web pages with information from other resources, and show how information from web pages can be used to link to, search, and process information in other resources. Due to the nature of userscripts, scientists are able to select those scripts they find useful on a daily basis, as the scripts run directly in their own web browser rather than on the web server. This flexibility allows the scientists to tune the features of web resources to optimise their productivity. PMID:18154664

Introduction to the fathead minnow genome browser and ...

EPA Pesticide Factsheets

Ab initio gene prediction and evidence alignment were used to produce the first annotations for the fathead minnow SOAPdenovo genome assembly. Additionally, a genome browser hosted at genome.setac.org provides simplified access to the annotation data in context with fathead minnow genomic sequence. This work is meant to extend the utility of fathead minnow genome as a resource and enable the continued development of this species as a model organism. The fathead minnow (Pimephales promelas) is a laboratory model organism widely used in regulatory toxicity testing and ecotoxicology research. Despite, the wealth of toxicological data for this organism, until recently genome scale information was lacking for the species, which limited the utility of the species for pathway-based toxicity testing and research. As part of a EPA Pathfinder Innovation Project, next generation sequencing was applied to generate a draft genome assembly, which was published in 2016. However, application of those genome-scale sequencing resources was still limited by the lack of available gene annotations for fathead minnow. Here we report on development of a first generation genome annotation for fathead minnow and the dissemination of that information through a web-based browser that makes it easy to search for genes of interest, extract the corresponding sequence, identify intron and exon boundaries and regulatory regions, and align the computationally predicted genes with other supporti

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.

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.

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).

Computational algorithm to evaluate product disassembly cost index

NASA Astrophysics Data System (ADS)

Zeid, Ibrahim; Gupta, Surendra M.

2002-02-01

Environmentally conscious manufacturing is an important paradigm in today's engineering practice. Disassembly is a crucial factor in implementing this paradigm. Disassembly allows the reuse and recycling of parts and products that reach their death after their life cycle ends. There are many questions that must be answered before a disassembly decision can be reached. The most important question is economical. The cost of disassembly versus the cost of scrapping a product is always considered. This paper develops a computational tool that allows decision-makers to calculate the disassembly cost of a product. The tool makes it simple to perform 'what if' scenarios fairly quickly. The tool is Web based and has two main parts. The front-end part is a Web page and runs on the client side in a Web browser, while the back-end part is a disassembly engine (servlet) that has disassembly knowledge and costing algorithms and runs on the server side. The tool is based on the client/server model that is pervasively utilized throughout the World Wide Web. An example is used to demonstrate the implementation and capabilities of the tool.

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

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.

Desirable attributes of public educational websites.

PubMed

Whitbeck, Caroline

2005-07-01

Certain attributes are particularly desirable for public educational websites, and websites for ethics education in particular. Among the most important of these attributes is wide accessibility through adherence to the World Wide Web Consortium (W3C) standards for HTML code. Adherence to this standard produces webpages that can be rendered by a full range of web browsers, including Braille and speech browsers. Although almost no academic websites, including ethics websites, and even fewer commercial websites are accessible by W3C standards, as illustrated by the Online Ethics Center for Engineering and Science , even websites created on limited budgets and with an undergraduate student staff can fulfill these standards. Other desirable attributes, such as provision of annotation for all links and the use of annotated links to give the user alternate ways of ordering and organizing content, are important for making full use of the educational possibilities of hypermedia for websites.

Saint: a lightweight integration environment for model annotation.

PubMed

Lister, Allyson L; Pocock, Matthew; Taschuk, Morgan; Wipat, Anil

2009-11-15

Saint is a web application which provides a lightweight annotation integration environment for quantitative biological models. The system enables modellers to rapidly mark up models with biological information derived from a range of data sources. Saint is freely available for use on the web at http://www.cisban.ac.uk/saint. The web application is implemented in Google Web Toolkit and Tomcat, with all major browsers supported. The Java source code is freely available for download at http://saint-annotate.sourceforge.net. The Saint web server requires an installation of libSBML and has been tested on Linux (32-bit Ubuntu 8.10 and 9.04).

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.

bioWeb3D: an online webGL 3D data visualisation tool

PubMed Central

2013-01-01

Background Data visualization is critical for interpreting biological data. However, in practice it can prove to be a bottleneck for non trained researchers; this is especially true for three dimensional (3D) data representation. Whilst existing software can provide all necessary functionalities to represent and manipulate biological 3D datasets, very few are easily accessible (browser based), cross platform and accessible to non-expert users. Results An online HTML5/WebGL based 3D visualisation tool has been developed to allow biologists to quickly and easily view interactive and customizable three dimensional representations of their data along with multiple layers of information. Using the WebGL library Three.js written in Javascript, bioWeb3D allows the simultaneous visualisation of multiple large datasets inputted via a simple JSON, XML or CSV file, which can be read and analysed locally thanks to HTML5 capabilities. Conclusions Using basic 3D representation techniques in a technologically innovative context, we provide a program that is not intended to compete with professional 3D representation software, but that instead enables a quick and intuitive representation of reasonably large 3D datasets. PMID:23758781

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.

An Extraction Method of an Informative DOM Node from a Web Page by Using Layout Information

NASA Astrophysics Data System (ADS)

Tsuruta, Masanobu; Masuyama, Shigeru

We propose an informative DOM node extraction method from a Web page for preprocessing of Web content mining. Our proposed method LM uses layout data of DOM nodes generated by a generic Web browser, and the learning set consists of hundreds of Web pages and the annotations of informative DOM nodes of those Web pages. Our method does not require large scale crawling of the whole Web site to which the target Web page belongs. We design LM so that it uses the information of the learning set more efficiently in comparison to the existing method that uses the same learning set. By experiments, we evaluate the methods obtained by combining one that consists of the method for extracting the informative DOM node both the proposed method and the existing methods, and the existing noise elimination methods: Heur removes advertisements and link-lists by some heuristics and CE removes the DOM nodes existing in the Web pages in the same Web site to which the target Web page belongs. Experimental results show that 1) LM outperforms other methods for extracting the informative DOM node, 2) the combination method (LM, {CE(10), Heur}) based on LM (precision: 0.755, recall: 0.826, F-measure: 0.746) outperforms other combination methods.

A Case Study in Web 2.0 Application Development

NASA Astrophysics Data System (ADS)

Marganian, P.; Clark, M.; Shelton, A.; McCarty, M.; Sessoms, E.

2010-12-01

Recent web technologies focusing on languages, frameworks, and tools are discussed, using the Robert C. Byrd Green Bank Telescopes (GBT) new Dynamic Scheduling System as the primary example. Within that example, we use a popular Python web framework, Django, to build the extensive web services for our users. We also use a second complimentary server, written in Haskell, to incorporate the core scheduling algorithms. We provide a desktop-quality experience across all the popular browsers for our users with the Google Web Toolkit and judicious use of JQuery in Django templates. Single sign-on and authentication throughout all NRAO web services is accomplished via the Central Authentication Service protocol, or CAS.

DNATagger, colors for codons.

PubMed

Scherer, N M; Basso, D M

2008-09-16

DNATagger is a web-based tool for coloring and editing DNA, RNA and protein sequences and alignments. It is dedicated to the visualization of protein coding sequences and also protein sequence alignments to facilitate the comprehension of evolutionary processes in sequence analysis. The distinctive feature of DNATagger is the use of codons as informative units for coloring DNA and RNA sequences. The codons are colored according to their corresponding amino acids. It is the first program that colors codons in DNA sequences without being affected by "out-of-frame" gaps of alignments. It can handle single gaps and gaps inside the triplets. The program also provides the possibility to edit the alignments and change color patterns and translation tables. DNATagger is a JavaScript application, following the W3C guidelines, designed to work on standards-compliant web browsers. It therefore requires no installation and is platform independent. The web-based DNATagger is available as free and open source software at http://www.inf.ufrgs.br/~dmbasso/dnatagger/.

Web-based analysis and publication of flow cytometry experiments.

PubMed

Kotecha, Nikesh; Krutzik, Peter O; Irish, Jonathan M

2010-07-01

Cytobank is a Web-based application for storage, analysis, and sharing of flow cytometry experiments. Researchers use a Web browser to log in and use a wide range of tools developed for basic and advanced flow cytometry. In addition to providing access to standard cytometry tools from any computer, Cytobank creates a platform and community for developing new analysis and publication tools. Figure layouts created on Cytobank are designed to allow transparent access to the underlying experiment annotation and data processing steps. Since all flow cytometry files and analysis data are stored on a central server, experiments and figures can be viewed or edited by anyone with the proper permission, from any computer with Internet access. Once a primary researcher has performed the initial analysis of the data, collaborators can engage in experiment analysis and make their own figure layouts using the gated, compensated experiment files. Cytobank is available to the scientific community at http://www.cytobank.org. (c) 2010 by John Wiley & Sons, Inc.

Web-Based Analysis and Publication of Flow Cytometry Experiments

PubMed Central

Kotecha, Nikesh; Krutzik, Peter O.; Irish, Jonathan M.

2014-01-01

Cytobank is a web-based application for storage, analysis, and sharing of flow cytometry experiments. Researchers use a web browser to log in and use a wide range of tools developed for basic and advanced flow cytometry. In addition to providing access to standard cytometry tools from any computer, Cytobank creates a platform and community for developing new analysis and publication tools. Figure layouts created on Cytobank are designed to allow transparent access to the underlying experiment annotation and data processing steps. Since all flow cytometry files and analysis data are stored on a central server, experiments and figures can be viewed or edited by anyone with the proper permissions from any computer with Internet access. Once a primary researcher has performed the initial analysis of the data, collaborators can engage in experiment analysis and make their own figure layouts using the gated, compensated experiment files. Cytobank is available to the scientific community at www.cytobank.org PMID:20578106

Image query and indexing for digital x rays

NASA Astrophysics Data System (ADS)

Long, L. Rodney; Thoma, George R.

1998-12-01

The web-based medical information retrieval system (WebMIRS) allows interned access to databases containing 17,000 digitized x-ray spine images and associated text data from National Health and Nutrition Examination Surveys (NHANES). WebMIRS allows SQL query of the text, and viewing of the returned text records and images using a standard browser. We are now working (1) to determine utility of data directly derived from the images in our databases, and (2) to investigate the feasibility of computer-assisted or automated indexing of the images to support image retrieval of images of interest to biomedical researchers in the field of osteoarthritis. To build an initial database based on image data, we are manually segmenting a subset of the vertebrae, using techniques from vertebral morphometry. From this, we will derive and add to the database vertebral features. This image-derived data will enhance the user's data access capability by enabling the creation of combined SQL/image-content queries.

Delivery of laboratory data with World Wide Web technology.

PubMed

Hahn, A W; Leon, M A; Klein-Leon, S; Allen, G K; Boon, G D; Patrick, T B; Klimczak, J C

1997-01-01

We have developed an experimental World Wide Web (WWW) based system to deliver laboratory results to clinicians in our Veterinary Medical Teaching Hospital. Laboratory results are generated by the clinical pathology section of our Veterinary Medical Diagnostic Laboratory and stored in a legacy information system. This system does not interface directly to the hospital information system, and it cannot be accessed directly by clinicians. Our "meta" system first parses routine print reports and then instantiates the data into a modern, open-architecture relational database using a data model constructed with currently accepted international standards for data representation and communication. The system does not affect either of the existing legacy systems. Location-independent delivery of patient data is via a secure WWW based system which maximizes usability and allows "value-added" graphic representations. The data can be viewed with any web browser. Future extensibility and intra- and inter-institutional compatibility served as key design criteria. The system is in the process of being evaluated using accepted methods of assessment of information technologies.

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

PubMed Central

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

2004-01-01

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

Web-Based 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.

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.

[Design of visualized medical images network and web platform based on MeVisLab].

PubMed

Xiang, Jun; Ye, Qing; Yuan, Xun

2017-04-01

With the trend of the development of "Internet +", some further requirements for the mobility of medical images have been required in the medical field. In view of this demand, this paper presents a web-based visual medical imaging platform. First, the feasibility of medical imaging is analyzed and technical points. CT (Computed Tomography) or MRI (Magnetic Resonance Imaging) images are reconstructed three-dimensionally by MeVisLab and packaged as X3D (Extensible 3D Graphics) files shown in the present paper. Then, the B/S (Browser/Server) system specially designed for 3D image is designed by using the HTML 5 and WebGL rendering engine library, and the X3D image file is parsed and rendered by the system. The results of this study showed that the platform was suitable for multiple operating systems to realize the platform-crossing and mobilization of medical image data. The development of medical imaging platform is also pointed out in this paper. It notes that web application technology will not only promote the sharing of medical image data, but also facilitate image-based medical remote consultations and distance learning.

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.

Informatics in radiology: A prototype Web-based reporting system for onsite-offsite clinician communication.

PubMed

Arnold, Corey W; Bui, Alex A T; Morioka, Craig; El-Saden, Suzie; Kangarloo, Hooshang

2007-01-01

The communication of imaging findings to a referring physician is an important role of the radiologist. However, communication between onsite and offsite physicians is a time-consuming process that can obstruct work flow and frequently involves no exchange of visual information, which is especially problematic given the importance of radiologic images for diagnosis and treatment. A prototype World Wide Web-based image documentation and reporting system was developed for use in supporting a "communication loop" that is based on the concept of a classic "wet-read" system. The proposed system represents an attempt to address many of the problems seen in current communication work flows by implementing a well-documented and easily accessible communication loop that is adaptable to different types of imaging study evaluation. Images are displayed in a native (DICOM) Digital Imaging and Communications in Medicine format with a Java applet, which allows accurate presentation along with use of various image manipulation tools. The Web-based infrastructure consists of a server that stores imaging studies and reports, with Web browsers that download and install necessary client software on demand. Application logic consists of a set of PHP (hypertext preprocessor) modules that are accessible with an application programming interface. The system may be adapted to any clinician-specialist communication loop, and, because it integrates radiologic standards with Web-based technologies, can more effectively communicate and document imaging data. RSNA, 2007

Web-based home telemedicine system for orthopedics

NASA Astrophysics Data System (ADS)

Lau, Christopher; Churchill, Sean; Kim, Janice; Matsen, Frederick A., III; Kim, Yongmin

2001-05-01

Traditionally, telemedicine systems have been designed to improve access to care by allowing physicians to consult a specialist about a case without sending the patient to another location, which may be difficult or time-consuming to reach. The cost of the equipment and network bandwidth needed for this consultation has restricted telemedicine use to contact between physicians instead of between patients and physicians. Recently, however, the wide availability of Internet connectivity and client and server software for e- mail, world wide web, and conferencing has made low-cost telemedicine applications feasible. In this work, we present a web-based system for asynchronous multimedia messaging between shoulder replacement surgery patients at home and their surgeons. A web browser plug-in was developed to simplify the process of capturing video and transferring it to a web site. The video capture plug-in can be used as a template to construct a plug-in that captures and transfers any type of data to a web server. For example, readings from home biosensor instruments (e.g., blood glucose meters and spirometers) that can be connected to a computing platform can be transferred to a home telemedicine web site. Both patients and doctors can access this web site to monitor progress longitudinally. The system has been tested with 3 subjects for the past 7 weeks, and we plan to continue testing in the foreseeable future.

Test Your Knowledge of Internet Vocabulary.

ERIC Educational Resources Information Center

Bigham, Vicki Smith

1998-01-01

Answers common questions about the Internet, i.e., what it is, its components, and the definitions of its various features. Questions include what Web pages and browsers are, and the definitions of URLs, ISPs, home pages, search engines, and hyperlinks. (GR)

A Workshop on UNIX, Workstations, and Internet Connections.

ERIC Educational Resources Information Center

Vierheller, Timothy R.

1997-01-01

Describes a workshop that introduces participants to the UNIX operating system. Provides an overview of how to access information on the Internet and gain familiarity with Web browsers, file transfer programs, telnet sessions, newsreaders, and Gopher services. (DDR)

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").